pubs.Rmd

---
title: "Publications"
---

<a href="http://scholar.google.com/citations?user=5SzRq1oAAAAJ"><img src="images/scholar.png" style="width: 100px;"></a>
<SCRIPT language="JavaScript" SRC='https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js'></SCRIPT>

```{r,results='hide',echo=FALSE}
rxiv=5
img1 <- "images/alert.jpg"
img2 <- "images/alert.jpg"
img3 <- "images/alert.jpg"
result <- ifelse(rxiv>=3,img1,ifelse(rxiv>=2,"b","c"))
cat("![](",result,")")
```

Journal names have been intentionally excluded. Lab member names can be bolded through the publication overrides file. Shared first authors can be marked with a superscript \* and corresponding authors with a superscript &dagger;. Click on a triangle for the article abstract.

<!-- PUBS:BEGIN -->
### Preprints

<details>
<summary> [Bias in diversity estimators and neutrality tests induced by neutral polymorphic structural variants](https://doi.org/10.64898/2026.02.26.708357) [[preprint](https://doi.org/10.64898/2026.02.26.708357)]  
S. E. Ramos-Onsins, **J. Ross-Ibarra**, M. Caceres, L. Ferretti
</summary>
<p style="margin-left: 30px">
Abstract Estimators of genetic diversity and neutrality tests derived from the site frequency spectrum (SFS), such as Watterson’s θ W , nucleotide diversity π , Tajima’s D , and Fay and Wu’s H , are designed to be interpreted relative to a baseline defined by the standard neutral SFS. In genomic regions strongly linked to a polymorphic structural variant (SV), deviations from these baselines occur even under strict neutrality: conditioning on an SV at known frequency partitions samples into SV and non-SV haplotypes and distorts the SFS for linked neutral mutations. These deviations are well understood for genomic inversions under long-term balancing selection. However, not all SVs are under strong selection, and the evolution of some SVs may be better approximated as neutral. Here we derive analytical expectations for the unfolded (and, when necessary, folded) SFS of single nucleotide polymorphisms conditional on neutral linked polymorphic SVs, including inversions, deletions, insertions, and introgressions. We use these expectations to quantify the resulting bias in standard diversity estimators and neutrality tests as a function of SV frequency and type. Finally, we discuss approaches to build corrected estimators of diversity and neutrality tests that are unbiased/centered after accounting for the presence and frequency of the SV.
</p></details><p></p>
<details>
<summary> [Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin](https://doi.org/10.64898/2026.02.02.703385) [[preprint](https://doi.org/10.64898/2026.02.02.703385)]  
**S. Snodgrass<sup>&ast;</sup><sup>&dagger;</sup>**, **F. Li<sup>&ast;</sup><sup>&dagger;</sup>**, **S. Mambakkam**, S. G. Medina-Muñoz, ...[7 authors including **L. Sparreo**, **M. Menon**, **C. Perez**]..., A. Moreno-Estrada, D. Runcie, G. Coop, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Population structure and environmental features often capture major axes of genetic variation in many species. Yet the impacts of human activity often remain unquantified. For domesticated species that rely on human activity for survival and dispersal, human movements and cultural differences may play key roles patterning genetic diversity. Maize is a staple crop of enormous cultural importance to indigenous peoples of the Americas, but cannot survive or disperse without farmers. Using publicly available genotyping and passport data from almost 2,000 traditional maize varieties, more than 500 whole genome sequences of humans from Mexico, and indigenous linguistic maps, we quantify anthropogenic effects on maize genetic diversity in the Americas. Maize shows very little overall structure, highlighting the effectiveness of indigenous farmers in moving and mixing maize populations. While principal components of maize diversity show meaningful correlations to human genetic diversity, our linear modeling suggests little additional impact of human population structure beyond shared geography. Though differences in maize diversity are often patterned by language locally, we find only weak genome-wide effects at larger spatial scales. Despite the relatively weak global signal of anthropogenic effects, linguistic GWAS, outlier F ST analyses, and selection scans identified loci associated with specific languages. Leveraging landscape-level sequencing data, we highlight how anthropogenic factors have shaped patterns of maize genetic diversity across Mesoamerica.
</p></details><p></p>
<details>
<summary> [The MexMAGIC population reveals the genetic architecture of clinal trait variation in Mexican native maize](https://doi.org/10.64898/2026.01.17.700095) [[preprint](https://doi.org/10.64898/2026.01.17.700095)]  
S. Perez-Limón, A. L. Alonso-Nieves, M. R. Ramírez-Flores, G. C. Cintora-Martínez, ...[10 authors including **F. Li**]..., **J. Ross-Ibarra**, C. S. Gillmor, R. Rellán-Álvarez, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
ABSTRACT Defining the genetic basis of local adaptation is fundamental to evolutionary biology and crop improvement. Theory predicts that when selective pressures track differences in the environment, a cline will be established. Such clines might be exploited to uncover adaptive variation by association of alleles with environmental stressors. However, monotonic phenotypic change over a cline is not necessarily mirrored by adaptive genetic variants. Furthermore, population structure can complicate the interpretation of genotype-environment association. To test the assumptions of genotype-environment association in a crop species, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize varieties sourced from distinct agroecological zones. We mapped two clinal traits (tassel branching and flowering time) differing in genetic architecture. Variation in tassel branch number was dominated by a single QTL with allele effects that aligned well with a negative elevational cline. In contrast, we mapped 11 flowering time QTL with allele effects that were not consistently correlated with any one source environmental factor and distinct loci donated by highland and lowland early maturing varieties. Our observations support the theoretical result that genotype-environment association will be strongest under simple genetic architecture, although identification of adaptive alleles may still be confounded by population structure. Plain Language: Nine thousand years of careful selection and cultivation by indigenous farmers has generated a rich diversity of native Mexican maize (corn) varieties, grown from sea level to high mountains, and from jungle to semidesert. By crossing native varieties adapted to different locations, we can uncover important genetic variants conferring tolerance to environmental stressors.
</p></details><p></p>
<details>
<summary> [The origins and adaptive consequences of polyploidy in a dominant prairie grass](https://doi.org/10.1101/2025.11.25.690567) [[preprint](https://doi.org/10.1101/2025.11.25.690567)]  
**A. R. Phillips<sup>&dagger;</sup>**, T. AuBuchon-Elder, K. Barry, M. Stitzer, ...[20 authors including **E. Cryan**, **J. Porter**, **B. Solomon**]..., S. Flint-Garcia, M. C. Romay, E. A. Kellogg, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi , a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C 4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9 x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9 x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9 x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9 x A. gerardi , the establishment of 9 x may lower overall population fitness due to the lower reproductive viability of 9 x individuals. Significance statement Polyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi , the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.
</p></details><p></p>
<details>
<summary> [The dominance of gene expression controlled by trans -eQTL hotspots contributes to phenotypic heterosis in maize](https://doi.org/10.1101/2025.11.03.686376) [[preprint](https://doi.org/10.1101/2025.11.03.686376)]  
G. Xu, X. Yang, M. Zhang, C. Kang, ...[3 authors]..., P. Liu, **J. Ross-Ibarra**, J. Yang, H. Liu
</summary>
<p style="margin-left: 30px">
ABSTRACT Heterosis, or hybrid vigor, is a key phenomenon in genetics research and agricultural production, and has been primarily attributed to non-additive genetic effects such as dominance — a prevailing consensus shaped by decades of empirical research and theoretical debate. Although dominance may arguably arise from distal modifiers, their selective advantage is debated due to presumably small individual effects. To address this long-standing question, particularly how genetic dominance manifests at the transcriptomic level and contributes to phenotypic heterosis, we integrated transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We found that ∼ 30% of the expressed seedling genes in a significant proportion of hybrids exhibited expression patterns deviating from the average of the two parents, indicative of non-additivity. Further analysis suggests that while hybrid gene expression per se is primarily regulated by cis -eQTLs, expression dominance (or non-additivity) is disproportionately controlled by trans -eQTLs. These trans -eQTLs cluster into hotspots that regulate the non-additivity of hundreds of target genes, mostly within co-expression networks, and are notably enriched for transcription factors (TFs). Focusing on one such hotspot, we functionally validated a classical maize gene ZmR1 , a basic helix-loop-helix (bHLH) TF associated with multiple seedling trait heterosis, as a candidate regulator of expression dominance across hundreds of genes. Overexpression of ZmR1 enhances expression dominance of downstream genes and increases phenotypic heterosis in both seedling and adult traits. Further experiments confirmed its direct regulatory role in modulating genes involved in anthocyanin biosynthesis and lignin metabolism, driving transcriptome-level dominance. These results provide empirical support for the modifier hypothesis under an omnigenic model, suggesting that heterosis arises not from the modification of a single gene’s inheritance but through the coordinated regulation of hundreds of phenotype-associated genes, thereby helping to reconcile the long-standing debate over the genetic basis of dominance in heterosis.
</p></details><p></p>
<details>
<summary> [Genome-wide selection on transposable elements in maize](https://doi.org/10.1101/2025.09.16.676665) [[preprint](https://doi.org/10.1101/2025.09.16.676665)]  
**B. Liu<sup>&dagger;</sup>**, M. Munasinghe, R. A. Fairbanks, C. N. Hirsch, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
ABSTRACT While most evolutionary research has focused on single nucleotide polymorphisms (SNPs), transposable elements (TEs) represent a major but understudied source of mutations that can influence organismal fitness. Previous studies on TEs often overlook the mechanisms and rates of transposition, rely on short-read sequencing that limits TE detection, or focus on small genomes such as Arabidopsis or Drosophila . In this study, we leveraged high-quality, long-read genome assemblies from 26 maize inbreds to investigate natural selection on TEs. We developed a novel and interpretable method, Φ SFS , which incorporates TE age and improves resolution for detecting selection. Using this approach, we identified key factors influencing selection on TEs: (1) the distance to the nearest gene, (2) the pre-insertion DNA methylation level at the insertion site, and (3) intrinsic TE characteristics, including copy number and expression level. This work represents the first application of long-read genome assemblies to study TE selection in a major crop species with a typical plant genome size. Our Φ SFS method offers a broadly applicable framework for detecting selection on TEs, and the factors uncovered provide new insights into the evolutionary dynamics and trade-offs between TEs and host genes.
</p></details><p></p>
<details>
<summary> [Heritability and QTL mapping of aerial roots and other yield component traits with implications for N2 fixation in Zea mays](https://doi.org/10.1101/2025.09.10.675198)  
D. A. O’Donnell, **J. Yang**, P. Zamora, **A. Lorant**, C. Miao, A. Van Deynze, A. Bennett, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
ABSTRACT Zea mays L. spp. mays (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of Zea entries spanning pre-domestication, post-domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits ( i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana . Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties. ARTICLE SUMMARY Zea mays aerial roots (AR) and mucilage have been implicated in diazotrophic recruitment. This study estimates heritability and identifies QTL for AR and yield components via a diverse panel of Zea entries and F2:F3 mapping populations. Genetic mapping reveals three QTL for AR and several QTL for other yield traits, both novel and previously reported. This study also compares QTL and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into a native cultivar. For AR QTL, enrichment for mexicana -derived haplotypes is greater than expected under a uniform genomic distribution, suggesting adaptive introgression from mexicana .
</p></details><p></p>
<details>
<summary> [Extensive genome evolution distinguishes maize within a stable tribe of grasses](https://doi.org/10.1101/2025.01.22.633974)  
M. C. Stitzer, A. S. Seetharam, A. Scheben, S. K. Hsu, ...[35 authors including **A. R. Phillips**, **J. Ross-Ibarra**]..., M. C. Romay, E. A. Kellogg, E. S. Buckler, M. B. Hufford
</summary>
<p style="margin-left: 30px">
Abstract Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy – a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum . In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea , 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.
</p></details><p></p>

### 2026

<details>
<summary> [Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution](https://doi.org/10.1016/j.isci.2025.114062)  
**Y. Cao**, J. Yan, **J. Ross-Ibarra<sup>&dagger;</sup>**, N. Yang<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2025

<details>
<summary> [Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize](https://doi.org/10.1038/s41588-025-02246-7) [[preprint](https://doi.org/10.1101/2023.08.08.551183)]  
J. Engelhorn, S. J. Snodgrass, A. Kok, A. S. Seetharam, ...[17 authors]..., B. Stich, W. B. Frommer, **J. Ross-Ibarra**, T. Hartwig
</summary>
<p style="margin-left: 30px">
Abstract Comprehensive maps of functional variation at transcription factor (TF) binding sites ( cis -elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis -element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1 , ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis -variation accessible at scale for genetic studies and targeted engineering of complex traits.
</p></details><p></p>
<details>
<summary> [An ancient origin of the naked grains of maize](https://doi.org/10.1073/pnas.2503748122) [[preprint](https://doi.org/10.1101/2024.12.02.626434)]  
R. A. Fairbanks, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Adaptation to novel environments requires genetic variation, but whether adaptation typically acts upon preexisting genetic variation or must wait for new mutations remains a fundamental question in evolutionary biology. Selection during domestication has been long used as a model to understand evolutionary processes, providing information not only on the phenotypes selected but also, in many cases, an understanding of the causal loci. For each of the causal loci that have been identified in maize, the selected allele can be found segregating in natural populations, consistent with their origin as standing genetic variation. The sole exception to this pattern is the well-characterized domestication locus tga1 ( teosinte glume architecture1 ), which has long been thought to be an example of selection on a de novo mutation. Here, we use a large dataset of maize and teosinte genomes to reconstruct the origin and evolutionary history of tga1 . We first estimated the age of tga1-maize using a genealogy-based method, finding that the allele arose approximately 42,000 to 49,000 y ago, predating the beginning of maize domestication. We also identify tga1-maize in teosinte populations, indicating that the allele can survive in the wild. Finally, we compare observed patterns of haplotype structure and mutational age distributions near tga1 with simulations, finding that patterns near tga1 in maize better resemble those generated under simulated selective sweeps on standing variation. These multiple lines of evidence suggest that maize domestication likely drew upon standing genetic variation at tga1 and cement the importance of standing variation in driving adaptation during domestication.
</p></details><p></p>
<details>
<summary> [Environmental data provide marginal benefit for predicting climate adaptation](https://doi.org/10.1371/journal.pgen.1011714)  
**F. Li<sup>&dagger;</sup>**, **D. J. Gates**, E. S. Buckler, M. B. Hufford, ...[7 authors]..., M. C. Willcox, S. J. Hearne, **J. Ross-Ibarra<sup>&dagger;</sup>**, D. E. Runcie<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Climate change poses a major challenge for both natural and cultivated species. Genomic tools are increasingly used in both conservation and breeding to identify adaptive loci that can be used to guide management in future climates. Here, we study the utility of climate and genomic data for identifying promising alleles using common gardens of a large, geographically diverse sample of traditional maize varieties to evaluate multiple approaches. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be pre-adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify loci associated with historical divergence along climatic gradients. Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genome-wide relatedness and population structure, and that incorporating envGWAS-identified variants or environment-of-origin data provide little additional predictive information. While our results suggest that environmental data provide limited benefit in predicting fitness-related phenotypes, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci associated with adaptation, especially when coupled with high density genotyping.
</p></details><p></p>
<details>
<summary> [The population genetics of convergent adaptation in maize and teosinte is not locally restricted](https://doi.org/10.7554/eLife.92405) [[preprint](https://doi.org/10.1101/2021.09.09.459637)]  
**S. Tittes<sup>&dagger;</sup>**, **A. Lorant**, **S. P. McGinty**, J. B. Holland, J. de Jesus Sánchez-González, A. Seetharam, M. Tenaillon, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte ( Zea mays subsp. parviglumis ). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.
</p></details><p></p>
<details>
<summary> [Molecular evolution of a reproductive barrier in maize and related species](https://doi.org/10.1093/genetics/iyaf085)  
**E. Cryan<sup>&dagger;</sup>**, **G. Phinney**, A. S. Seetharam, M. M. S. Evans, E. A. Kellogg, J. Zhan, B. Meyers, D. J. Kliebenstein, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (Zea mays ssp. mays) and its wild teosinte relatives. These 3 loci, Teosinte crossing barrier1 (Tcb1), Gametophytic factor1 (Ga1), and Ga2, each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes both a silk-active and a matching pollen-active pectin methylesterase (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly of maize line P8860 that contains active versions of all 3 loci. We then examined 52 assembled genomes from 17 species to classify haplotype diversity and identify sites under diversifying selection during the evolution of these genes. We show that Ga2, the oldest of these 3 loci, was duplicated to form Ga1 at least 12 million years ago. Tcb1, the youngest locus, arose as a duplicate of Ga1 before or around the time of diversification of the Zea genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the Ga1 locus is a conserved ga1 allele (ga1-Off), which is specific haplotype containing 3 full-length PME gene copies, all of which are noncoding due to conserved stop codons and are between 610 thousand and 1.5 million years old. We show that the ga1-Off allele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional Ga1 alleles. In previously published crosses, the ga1-Off allele was associated with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of an allele at a reproductive barrier locus being associated with an as yet undetermined mechanism capable of silencing the reproductive barrier.
</p></details><p></p>

### 2024

<details>
<summary> [Teosinte Pollen Drive guides maize diversification and domestication by RNAi](https://doi.org/10.1038/s41586-024-07788-0) [[preprint](https://doi.org/10.1101/2023.07.12.548689)]  
B. Berube, E. Ernst, J. Cahn, B. Roche, ...[4 authors]..., A. Siepel, **J. Ross-Ibarra**, J. Kermicle, R. A. Martienssen
</summary>
<p style="margin-left: 30px">
Abstract Selfish genetic elements contribute to hybrid incompatibility and bias or ‘drive’ their own transmission 1,2 . Chromosomal drive typically functions in asymmetric female meiosis, whereas gene drive is normally post-meiotic and typically found in males. Here, using single-molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive , an instance of gene drive in hybrids between maize ( Zea mays ssp. mays ) and teosinte mexicana ( Z. mays ssp. mexicana ) that depends on RNA interference (RNAi). 22-nucleotide small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-like 2 ( Dcl2 ) and target Teosinte Drive Responder 1 ( Tdr1 ), which encodes a lipase required for pollen viability. Dcl2 , Tdr1 and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas 3 , and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize 4 . A survey of maize traditional varieties and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least four chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive probably had a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of ‘self’ small RNAs in the germ lines of plants and animals.
</p></details><p></p>
<details>
<summary> [Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits](https://doi.org/10.1093/evolut/qpae130) [[preprint](https://doi.org/10.1101/2021.04.20.440703)]  
A. M. O’Brien, R. J. H. Sawers, J. Gasca-Pineda, I. Baxter, L. E. Eguiarte, **J. Ross-Ibarra**, S. Y. Strauss
</summary>
<p style="margin-left: 30px">
Abstract While biotic interactions often impose selection, species and populations vary in whether they are locally adapted to biotic interactions. Evolutionary theory predicts that environmental conditions drive this variable local adaptation by altering the fitness impacts of species interactions. To investigate the influence of an environmental gradient on adaptation between a plant and its associated rhizosphere biota, we cross-combined teosinte (Zea mays ssp. mexicana) and rhizosphere biota collected across a gradient of decreasing temperature, precipitation, and nutrients in a greenhouse common garden experiment. We measured both fitness and phenotypes expected to be influenced by biota, including concentrations of nutrients in leaves. Independent, main effects of teosinte and biota source explained most variation in teosinte fitness and traits. For example, biota from warmer sites provided population-independent fitness benefits across teosinte hosts. Effects of biota that depended on teosinte genotype were often not specific to their local hosts, and most traits had similar relationships to fitness across biota treatments. However, we found weak patterns of local adaptation between teosinte and biota from colder sites, suggesting environmental gradients may alter the importance of local adaptation in teosinte–biota interactions, as evolutionary theory predicts.
</p></details><p></p>
<details>
<summary> [A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize](https://doi.org/10.1093/g3journal/jkae281)  
C. M. Andorf, **J. Ross-Ibarra**, A. S. Seetharam, M. B. Hufford, M. R. Woodhouse
</summary>
<p style="margin-left: 30px">
Abstract Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
</p></details><p></p>

### 2023

<details>
<summary> [Two teosintes made modern maize](https://doi.org/10.1126/science.adg8940) [[preprint](https://doi.org/10.1101/2023.01.31.526540)]  
**N. Yang<sup>&ast;</sup><sup>&dagger;</sup>**, Y. Wang<sup>&ast;</sup>, X. Liu<sup>&ast;</sup>, M. Jin, ...[22 authors including **S. Mambakkam**, **M. Menon**, **S. Snodgrass**]..., M. C. Stitzer, D. Runcie, J. Yan<sup>&dagger;</sup>, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana . Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
</p></details><p></p>
<details>
<summary> [A happy accident: a novel turfgrass reference genome](https://doi.org/10.1093/g3journal/jkad073) [[preprint](https://doi.org/10.1101/2022.03.08.483531)]  
**A. R. Phillips<sup>&dagger;</sup>**, A. S. Seetharam, P. S. Albert, T. AuBuchon-Elder, ...[5 authors]..., M. C. Romay, R. J. Soreng, E. A. Kellogg, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
</p></details><p></p>
<details>
<summary> [Genetic modification can improve crop yields — but stop overselling it](https://doi.org/10.1038/d41586-023-02895-w)  
M. Khaipho-Burch, M. Cooper, J. Crossa, N. de Leon, ...[5 authors]..., P. Ronald, **J. Ross-Ibarra**, D. Weigel, E. S. Buckler
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes](https://doi.org/10.1371/journal.pbio.3002235)  
S. Flint-Garcia, M. J. Feldmann, H. Dempewolf, P. L. Morrell, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.
</p></details><p></p>
<details>
<summary> [Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding](https://doi.org/10.1093/molbev/msad170)  
S. Sun, B. Wang, C. Li, G. Xu, J. Yang, M. B. Hufford, **J. Ross-Ibarra<sup>&dagger;</sup>**, H. Wang<sup>&dagger;</sup>, L. Wang<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
</p></details><p></p>

### 2022

<details>
<summary> [Analysis of genotype-by-environment interactions in a maize mapping population](https://doi.org/10.1093/g3journal/jkac013) [[preprint](https://doi.org/10.1101/2021.07.21.453280)]  
**A. I. Hudson<sup>&dagger;</sup>**, **S. G. Odell**, P. Dubreuil, M. H. Tixier, S. Praud, D. E. Runcie, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance–covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population.
</p></details><p></p>
<details>
<summary> [Genome sequencing reveals evidence of adaptive variation in the genus Zea](https://doi.org/10.1038/s41588-022-01184-y) [[preprint](https://doi.org/10.1101/2022.06.03.494450)]  
L. Chen, J. Luo, M. Jin, N. Yang<sup>&dagger;</sup>, ...[27 authors]..., A. R. Fernie, M. L. Warburton, **J. Ross-Ibarra<sup>&dagger;</sup>**, J. Yan<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize](https://doi.org/10.1093/molbev/msac239) [[preprint](https://doi.org/10.1101/2022.07.15.500250)]  
H. Hu, T. Crow, S. Nojoomi, A. J. Schulz, ...[3 authors]..., R. Sawers, R. Rellán-Álvarez, **J. Ross-Ibarra**, D. E. Runcie
</summary>
<p style="margin-left: 30px">
Abstract Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize's adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele–specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.
</p></details><p></p>
<details>
<summary> [Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum](https://doi.org/10.1093/gbe/evac016) [[preprint](https://doi.org/10.1101/2021.08.16.456262)]  
**R. Horvath<sup>&dagger;</sup>**, **M. Menon**, M. Stitzer, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs. But TE evolution differs from standard models in a number of ways that can impact the power and interpretation of the SFS. For example, rather than mutating under a clock-like model, transposition often occurs in bursts which can inflate particular frequency categories compared with expectations under a standard neutral model. If a TE burst has been recent, the excess of low-frequency polymorphisms can mimic the effect of purifying selection. Here, we investigate how transposition bursts affect the frequency distribution of TEs and the correlation between age and allele frequency. Using information on the TE age distribution, we propose an age-adjusted SFS to compare TEs and neutral polymorphisms to more effectively evaluate whether TEs are under selective constraints. We show that our approach can minimize instances of false inference of selective constraint, remains robust to simple demographic changes, and allows for a correct identification of even weak selection affecting TEs which experienced a transposition burst. The results presented here will help researchers working on TEs to more reliably identify the effects of selection on TEs without having to rely on the assumption of a constant transposition rate.
</p></details><p></p>
<details>
<summary> [A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize](https://doi.org/10.1093/g3journal/jkab447) [[preprint](https://doi.org/10.1101/2021.09.15.460568)]  
S. Perez-Limón, M. Li, G. C. Cintora-Martinez, M. R. Aguilar-Rangel, ...[12 authors including **J. Ross-Ibarra**]..., S. Flint-Garcia, L. Diaz-Garcia, R. Rellán-Álvarez, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
Abstract Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
</p></details><p></p>
<details>
<summary> [Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci](https://doi.org/10.1093/g3journal/jkac011) [[preprint](https://doi.org/10.1101/2021.07.14.452335)]  
**S. G. Odell<sup>&dagger;</sup>**, **A. I. Hudson**, S. Praud, P. Dubreuil, M. H. Tixier, **J. Ross-Ibarra**, D. E. Runcie
</summary>
<p style="margin-left: 30px">
Abstract The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations. Here, we discuss the results of using a multiparent advanced generation intercross population of doubled haploid maize lines created from 16 diverse founders to perform quantitative trait loci mapping. We compare 3 models that assume bi-allelic, founder, and ancestral haplotype allelic states for quantitative trait loci. The 3 methods have differing power to detect quantitative trait loci for a variety of agronomic traits. Although the founder approach finds the most quantitative trait loci, all methods are able to find unique quantitative trait loci, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time quantitative trait loci, qDTA8, which contains vgt1, highlights the strengths and weaknesses of each method and suggests a potential epistatic interaction. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and shows the limitations of binary SNP data for identifying multiallelic quantitative trait loci.
</p></details><p></p>
<details>
<summary> [An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time](https://doi.org/10.1073/pnas.2100036119) [[preprint](https://doi.org/10.1101/2021.01.25.426574)]  
A. C. Barnes, F. Rodríguez-Zapata, K. A. Juárez-Núñez, D. J. Gates, ...[22 authors]..., **J. Ross-Ibarra**, M. B. Hufford, R. J. H. Sawers, R. Rellán-Álvarez
</summary>
<p style="margin-left: 30px">
Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
</p></details><p></p>
<details>
<summary> [Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding](https://doi.org/10.1038/s41477-022-01190-2)  
C. Li, H. Guan, X. Jing, Y. Li<sup>&dagger;</sup>, ...[18 authors]..., **J. Ross-Ibarra<sup>&dagger;</sup>**, Y. Li<sup>&dagger;</sup>, T. Wang<sup>&dagger;</sup>, H. Wang<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Conflict over fertilization underlies the transient evolution of reinforcement](https://doi.org/10.1371/journal.pbio.3001814) [[preprint](https://doi.org/10.1101/2020.11.10.377481)]  
**C. A. Rushworth**, A. M. Wardlaw, **J. Ross-Ibarra**, Y. Brandvain
</summary>
<p style="margin-left: 30px">
When two species meet in secondary contact, the production of low fitness hybrids may be prevented by the adaptive evolution of increased prezygotic isolation, a process known as reinforcement. Theoretical challenges to the evolution of reinforcement are generally cast as a coordination problem, i.e., “how can statistical associations between traits and preferences be maintained in the face of recombination?” However, the evolution of reinforcement also poses a potential conflict between mates. For example, the opportunity costs to hybridization may differ between the sexes or species. This is particularly likely for reinforcement based on postmating prezygotic (PMPZ) incompatibilities, as the ability to fertilize both conspecific and heterospecific eggs is beneficial to male gametes, but heterospecific mating may incur a cost for female gametes. We develop a population genetic model of interspecific conflict over reinforcement inspired by “gametophytic factors”, which act as PMPZ barriers among Zea mays subspecies. We demonstrate that this conflict results in the transient evolution of reinforcement—after females adaptively evolve to reject gametes lacking a signal common in conspecific gametes, this gamete signal adaptively introgresses into the other population. Ultimately, the male gamete signal fixes in both species, and isolation returns to pre-reinforcement levels. We interpret geographic patterns of isolation among Z . mays subspecies considering these findings and suggest when and how this conflict can be resolved. Our results suggest that sexual conflict over fertilization may pose an understudied obstacle to the evolution of reinforcement.
</p></details><p></p>
<details>
<summary> [The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean ( Phaseolus coccineus L.)](https://doi.org/10.1002/evl3.285) [[preprint](https://doi.org/10.1101/2021.02.03.429668)]  
A. Guerra-García, I. C. Rojas-Barrera, **J. Ross-Ibarra**, R. Papa, D. Piñero
</summary>
<p style="margin-left: 30px">
Abstract The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
</p></details><p></p>

### 2021

<details>
<summary> [De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes](https://doi.org/10.1126/science.abg5289) [[preprint](https://doi.org/10.1101/2021.01.14.426684)]  
M. B. Hufford, A. S. Seetharam, M. R. Woodhouse, K. M. Chougule, ...[38 authors including **S. Tittes**, **A. I. Hudson**, **J. Ross-Ibarra**]..., J. I. Gent, C. N. Hirsch, D. Ware, R. K. Dawe
</summary>
<p style="margin-left: 30px">
An a-maize-ing set of genomes Maize is an important crop cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping panel, Hufford et al . map important traits and demonstrate the diversity of maize. Examining RNA and methylation of genes across accessions, the authors identified a core set of maize genes. Beyond this core set, comparative analysis across lines identified high levels of variation in the total set of genes, the maize pan-genome. The value of this resource was further exemplified by mapping quantitative traits of interest, including those related to pathogen resistance. —LMZ
</p></details><p></p>
<details>
<summary> [The genomic ecosystem of transposable elements in maize](https://doi.org/10.1371/journal.pgen.1009768) [[preprint](https://doi.org/10.1101/559922)]  
**M. C. Stitzer<sup>&dagger;</sup>**, S. N. Anderson, N. M. Springer, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
</p></details><p></p>
<details>
<summary> [Comparative evolutionary genetics of deleterious load in sorghum and maize](https://doi.org/10.1038/s41477-020-00834-5) [[preprint](https://doi.org/10.1101/777623)]  
R. Lozano, E. Gazave, J. P. R. dos Santos, **M. G. Stetter**, ...[7 authors]..., M. Taylor Perkins, E. S. Buckler, **J. Ross-Ibarra<sup>&dagger;</sup>**, M. A. Gore<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Selective sorting of ancestral introgression in maize and teosinte along an elevational cline](https://doi.org/10.1371/journal.pgen.1009810) [[preprint](https://doi.org/10.1101/2021.03.05.434040)]  
E. Calfee<sup>&dagger;</sup>, **D. Gates**, **A. Lorant**, **M. T. Perkins**, G. Coop<sup>&dagger;</sup>, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize ( Zea mays ssp. mays ) and its wild teosinte relative, mexicana ( Zea mays ssp. mexicana ). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (&gt; 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana , a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low F ST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana , especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.
</p></details><p></p>
<details>
<summary> [Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces](https://doi.org/10.1093/molbev/msab119) [[preprint](https://doi.org/10.1101/2020.07.31.227629)]  
**L. Wang<sup>&dagger;</sup>**, **E. B. Josephs**, K. M. Lee, L. M. Roberts, R. Rellán-Álvarez, **J. Ross-Ibarra<sup>&dagger;</sup>**, M. B. Hufford<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
</p></details><p></p>
<details>
<summary> [Gene body methylation is under selection in Arabidopsis thaliana](https://doi.org/10.1093/genetics/iyab061) [[preprint](https://doi.org/10.1101/2020.09.04.283333)]  
A. Muyle, **J. Ross-Ibarra**, D. K. Seymour, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.
</p></details><p></p>
<details>
<summary> [Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize](https://doi.org/10.1101/gr.266528.120)  
B. Song, E. S. Buckler, H. Wang, Y. Wu, ...[4 authors]..., P. J. Bradbury, **J. Ross-Ibarra**, M. B. Hufford, M. C. Romay
</summary>
<p style="margin-left: 30px">
Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis -regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis -regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.
</p></details><p></p>
<details>
<summary> [Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte](https://doi.org/10.1371/journal.pgen.1009797) [[preprint](https://doi.org/10.1101/2021.09.01.458502)]  
L. F. Samayoa, B. A. Olukolu, C. J. Yang, Q. Chen, ...[8 authors including **M. G. Stetter**, **J. Yang**]..., **J. Ross-Ibarra**, E. S. Buckler, J. F. Doebley, J. B. Holland
</summary>
<p style="margin-left: 30px">
Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.
</p></details><p></p>

### 2020

<details>
<summary> [Evolutionary insights into plant breeding](https://doi.org/10.1016/j.pbi.2020.03.003)  
**S. D. Turner-Hissong<sup>&dagger;</sup>**, M. E. Mabry, T. M. Beissinger, **J. Ross-Ibarra**, J. C. Pires
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genomics of Long- and Short-Term Adaptation in Maize and Teosintes](https://doi.org/10.1007/978-1-0716-0199-0_12)  
**A. Lorant**, **J. Ross-Ibarra**, M. Tenaillon
</summary>
<p style="margin-left: 30px">
Abstract Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize—the teosintes Zea mays ssp. parviglumis and ssp. mexicana —as excellent models for dissecting long-term local adaptation. Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
</p></details><p></p>
<details>
<summary> [Genome-wide selection and genetic improvement during modern maize breeding](https://doi.org/10.1038/s41588-020-0616-3)  
B. Wang, Z. Lin, X. Li, Y. Zhao, ...[19 authors]..., M. B. Hufford, **J. Ross-Ibarra**, H. He, H. Wang
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The Temporal Dynamics of Background Selection in Nonequilibrium Populations](https://doi.org/10.1534/genetics.119.302892) [[preprint](https://doi.org/10.1101/618389)]  
R. Torres<sup>&ast;</sup>, M. G. Stetter<sup>&ast;</sup>, R. D. Hernandez<sup>&dagger;</sup>, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.
</p></details><p></p>
<details>
<summary> [Evolutionary and functional genomics of DNA methylation in maize domestication and improvement](https://doi.org/10.1038/s41467-020-19333-4) [[preprint](https://doi.org/10.1101/2020.03.13.991117)]  
G. Xu, J. Lyu, Q. Li, H. Liu, D. Wang, M. Zhang, N. M. Springer, **J. Ross-Ibarra**, J. Yang
</summary>
<p style="margin-left: 30px">
Abstract DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte ( Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1 -DMR and tb1 -DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
</p></details><p></p>
<details>
<summary> [The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication](https://doi.org/10.1371/journal.pgen.1008791)  
Q. Chen, L. F. Samayoa, C. J. Yang, P. J. Bradbury, ...[5 authors including **A. Lorant**]..., E. S. Buckler, **J. Ross-Ibarra**, J. B. Holland, J. F. Doebley
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces](https://doi.org/10.1534/g3.120.401196) [[preprint](https://doi.org/10.1101/817791)]  
**L. Zeitler**, **J. Ross-Ibarra<sup>&dagger;</sup>**, **M. G. Stetter<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.
</p></details><p></p>

### 2019

<details>
<summary> [Single-gene resolution of locally adaptive genetic variation in Mexican maize](https://doi.org/10.1101/706739) [[preprint](https://doi.org/10.1101/706739)]  
**D. J. Gates**, D. Runcie, G. M. Janzen, A. R. Navarro, ...[6 authors]..., E. S. Buckler, S. Hearne, M. B. Hufford, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.
</p></details><p></p>
<details>
<summary> [Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens](https://doi.org/10.1534/genetics.118.301786) [[preprint](https://doi.org/10.1101/368506)]  
**E. B. Josephs<sup>&dagger;</sup>**, J. J. Berg, **J. Ross-Ibarra**, G. Coop
</summary>
<p style="margin-left: 30px">
Abstract Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci—a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.
</p></details><p></p>
<details>
<summary> [Transposable elements contribute to dynamic genome content in maize](https://doi.org/10.1111/tpj.14489) [[preprint](https://doi.org/10.1101/547398)]  
S. N. Anderson, M. C. Stitzer, A. B. Brohammer, P. Zhou, ...[2 authors]..., C. D. Hirsch, J. Ross‐Ibarra, C. N. Hirsch, N. M. Springer
</summary>
<p style="margin-left: 30px">
Summary Transposable elements ( TE s) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TE s. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH 207) with uniform structural annotations of TE s. Among these genomes we identified approximately 400 000 TE s that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TE s include a combination of recent transposition events as well as deletions of older TE s. There are examples of polymorphic TE s within each of the superfamilies of TE s and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TE s within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TE s, providing evidence for the role of TE s in contributing to the substantial differences in annotated gene content among these genotypes. TE s are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TE s in driving variation in genome organization and gene content. Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation ; https://mcstitzer.github.io/maize_TEs .
</p></details><p></p>
<details>
<summary> [Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize](https://doi.org/10.1534/g3.119.400431) [[preprint](https://doi.org/10.1101/668558)]  
S. N. Anderson<sup>&ast;</sup>, **M. C. Stitzer<sup>&ast;</sup>**, P. Zhou, **J. Ross-Ibarra**, C. D. Hirsch, N. M. Springer
</summary>
<p style="margin-left: 30px">
Abstract Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in &amp;gt;800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.
</p></details><p></p>
<details>
<summary> [Adaptive phenotypic divergence in an annual grass differs across biotic contexts*](https://doi.org/10.1111/evo.13818) [[preprint](https://doi.org/10.1101/382770)]  
**A. M. O'Brien<sup>&dagger;</sup>**, R. J. Sawers, S. Y. Strauss, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize](https://doi.org/10.1534/genetics.119.302378) [[preprint](https://doi.org/10.1101/588715)]  
W. Xue, S. N. Anderson, X. Wang, L. Yang, ...[8 authors including **P. Bilinski**, **M. C. Stitzer**, **J. Ross-Ibarra**]..., S. Flint-Garcia, X. Chen, N. M. Springer, J. F. Doebley
</summary>
<p style="margin-left: 30px">
Abstract Xue et al. describe a phenomenon in maize and its nearest wild relative, teosinte, by which backcross progeny of a specific teosinte and maize exhibit a sickly whole-plant phenotype involving changes in morphology, vigor, and viability... In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.
</p></details><p></p>
<details>
<summary> [Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize](https://doi.org/10.7717/peerj.6815)  
E. Gonzalez-Segovia, S. Pérez-Limon, G. C. Cíntora-Martínez, A. Guerrero-Zavala, G. M. Janzen, M. B. Hufford, **J. Ross-Ibarra**, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana , prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F 2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
</p></details><p></p>

### 2018

<details>
<summary> [Evolution and Adaptation in the Maize Genome](https://doi.org/10.1007/978-3-319-97427-9_19)  
N. Manchanda, S. J. Snodgrass, **J. Ross-Ibarra**, M. B. Hufford
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Harnessing cross-border resources to confront climate change](https://doi.org/10.1016/j.envsci.2018.01.001)  
O. Aburto-Oropeza, A. F. Johnson, M. Agha, E. B. Allen, ...[85 authors including **J. Ross-Ibarra**]..., G. Woolrich-Piña, A. Yunez-Naude, J. A. Zertuche-González, J. E. Taylor
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Maize domestication and gene interaction](https://doi.org/10.1111/nph.15350)  
M. C. Stitzer, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection 404 VII. Conclusions 405 Acknowledgements 405 References 405 Summary Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays , morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis , was transformed into the domesticate Z. mays subsp. mays . Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
</p></details><p></p>
<details>
<summary> [Adaptation in plant genomes: Bigger is different](https://doi.org/10.1002/ajb2.1002) [[preprint](https://doi.org/10.1101/196501)]  
**W. Mei**, M. G. Stetter, D. J. Gates, M. C. Stitzer, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize](https://doi.org/10.1016/j.cell.2018.03.009)  
R. K. Dawe, E. G. Lowry, J. I. Gent, **M. C. Stitzer**, ...[10 authors including **J. Ross-Ibarra**]..., J. A. Birchler, A. E. Harkess, A. L. Hodges, E. N. Hiatt
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima](https://doi.org/10.1371/journal.pgen.1007794) [[preprint](https://doi.org/10.1101/313247)]  
**M. G. Stetter<sup>&dagger;</sup>**, K. Thornton, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays](https://doi.org/10.1371/journal.pgen.1007162) [[preprint](https://doi.org/10.1101/134528)]  
**P. Bilinski**, P. S. Albert, J. J. Berg, J. A. Birchler, ...[2 authors including **A. Lorant**]..., **J. Quezada**, K. Swarts, **J. Yang**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Evolutionary Responses to Conditionality in Species Interactions across Environmental Gradients](https://doi.org/10.1086/700118) [[preprint](https://doi.org/10.1101/031195)]  
A. M. O’Brien, R. J. H. Sawers, **J. Ross-Ibarra**, S. Y. Strauss
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2017

<details>
<summary> [How to make a domesticate](https://doi.org/10.1016/j.cub.2017.06.048)  
M. G. Stetter, D. J. Gates, **W. Mei**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Improved maize reference genome with single-molecule technologies](https://doi.org/10.1038/nature22971)  
Y. Jiao, P. Peluso, J. Shi, T. Liang, ...[20 authors including **M. R. May**, **J. Ross-Ibarra**]..., R. K. Dawe, A. Hastie, D. R. Rank, D. Ware
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Construction of the third-generation Zea mays haplotype map](https://doi.org/10.1093/gigascience/gix134) [[preprint](https://doi.org/10.1101/026963)]  
R. Bukowski, X. Guo, Y. Lu, C. Zou, ...[18 authors including **J. Ross-Ibarra**, **A. Lorant**, **V. Buffalo**]..., D. Ware, J. Lai, Q. Sun, Y. Xu
</summary>
<p style="margin-left: 30px">
Abstract Background Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world. Results A new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 83 million variant sites. Conclusions We identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.
</p></details><p></p>
<details>
<summary> [Gene Fractionation and Function in the Ancient Subgenomes of Maize](https://doi.org/10.1093/molbev/msx121) [[preprint](https://doi.org/10.1101/095547)]  
**S. Renny-Byfield<sup>&dagger;</sup>**, E. Rodgers-Melnick, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The interplay of demography and selection during maize domestication and expansion](https://doi.org/10.1186/s13059-017-1346-4) [[preprint](https://doi.org/10.1101/114579)]  
**L. Wang**, **T. M. Beissinger**, **A. Lorant**, **C. Ross-Ibarra**, **J. Ross-Ibarra<sup>&dagger;</sup>**, M. B. Hufford<sup>&dagger;</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America](https://doi.org/10.1126/science.aam9425)  
K. Swarts, R. M. Gutaker, B. Benz, M. Blake, ...[11 authors including **J. Ross-Ibarra**]..., R. G. Matson, D. Weigel, E. S. Buckler, H. A. Burbano
</summary>
<p style="margin-left: 30px">
Estimating temperate adaptation in ancient maize Maize as a staple food crop in temperate North America required adaptation to a shorter growing season. On its first introduction in the southwestern United States ∼4000 years ago, maize was extensively grown in the lowlands. Cultivation in the temperate uplands did not occur for another 2000 years. Swarts et al. used ancient DNA data from 1900-year-old maize cobs found in a temperate cave in the southwestern United States and mapped the ancient flowering phenotype. The ancient maize samples were marginally adapted to temperate regions as a result of selection on standing variation. Science , this issue p. 512
</p></details><p></p>
<details>
<summary> [Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize](https://doi.org/10.1371/journal.pgen.1007019) [[preprint](https://doi.org/10.1101/086132)]  
**J. Yang<sup>&ast;</sup><sup>&dagger;</sup>**, **S. Mezmouk<sup>&ast;</sup>**, A. Baumgarten, E. S. Buckler, K. E. Guill, M. D. McMullen, R. H. Mumm, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The potential role of genetic assimilation during maize domestication](https://doi.org/10.1371/journal.pone.0184202) [[preprint](https://doi.org/10.1101/105940)]  
**A. Lorant**, S. Pedersen, I. Holst, M. B. Hufford, K. Winter, D. Piperno, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genomic abundance is not predictive of tandem repeat localization in grass genomes](https://doi.org/10.1371/journal.pone.0177896)  
**P. Bilinski<sup>&dagger;</sup>**, Y. Han, **M. B. Hufford**, **A. Lorant**, P. Zhang, M. C. Estep, J. Jiang, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño](https://doi.org/10.7717/peerj.3737)  
M. R. Aguilar-Rangel, R. A. Chávez Montes, E. González-Segovia, **J. Ross-Ibarra**, J. K. Simpson, R. J. Sawers
</summary>
<p style="margin-left: 30px">
Background Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions. Methods Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F 1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments. Results A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates. Discussion Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis -acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.
</p></details><p></p>

### 2016

<details>
<summary> [Evolutionary Genomics of Peach and Almond Domestication](https://doi.org/10.1534/g3.116.032672)  
**D. Velasco<sup>&dagger;</sup>**, **J. Hough**, M. Aradhya, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
</p></details><p></p>
<details>
<summary> [Recent demography drives changes in linked selection across the maize genome](https://doi.org/10.1038/nplants.2016.84)  
**T. M. Beissinger**, **L. Wang**, **K. Crosby**, **A. Durvasula**, M. B. Hufford, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [angsd ‐wrapper: utilities for analysing next‐generation sequencing data](https://doi.org/10.1111/1755-0998.12578)  
**A. Durvasula**, P. J. Hoffman, **T. V. Kent**, C. Liu, **T. J. Y. Kono**, P. L. Morrell<sup>&dagger;</sup>, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract High‐throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high‐throughput sequencing data. angsd uses probabilistic approaches which can directly make use of genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we present angsd ‐wrapper, a set of wrapper scripts that provides a user‐friendly interface for running angsd and visualizing results. angsd ‐wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression. angsd ‐wrapper also provides interactive graphing of angsd results to enhance data exploration. We demonstrate the usefulness of angsd ‐wrapper by analysing resequencing data from populations of wild and domesticated Zea . angsd ‐wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper .
</p></details><p></p>
<details>
<summary> [Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication](https://doi.org/10.1016/j.cub.2016.09.036)  
J. Ramos-Madrigal, B. D. Smith, J. V. Moreno-Mayar, S. Gopalakrishnan, **J. Ross-Ibarra**, M. T. P. Gilbert, N. Wales
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events](https://doi.org/10.3389/fpls.2016.00308)  
T. K. Wolfgruber, M. M. Nakashima, K. L. Schneider, A. Sharma, ...[4 authors including **P. Bilinski**]..., R. K. Dawe, **J. Ross-Ibarra**, J. A. Birchler, G. G. Presting
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Maize diversity associated with social origin and environmental variation in Southern Mexico](https://doi.org/10.1038/hdy.2016.10)  
Q. Orozco-Ramírez, **J. Ross-Ibarra**, A. Santacruz-Varela, S. Brush
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2015

<details>
<summary> [Genetic, evolutionary and plant breeding insights from the domestication of maize](https://doi.org/10.7554/eLife.05861)  
S. Hake, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
The natural history of maize began nine thousand years ago when Mexican farmers started to collect the seeds of the wild grass, teosinte. Invaluable as a food source, maize permeated Mexican culture and religion. Its domestication eventually led to its adoption as a model organism, aided in large part by its large chromosomes, ease of pollination and growing agricultural importance. Genome comparisons between varieties of maize, teosinte and other grasses are beginning to identify the genes responsible for the domestication of modern maize and are also providing ideas for the breeding of more hardy varieties.
</p></details><p></p>
<details>
<summary> [The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend](https://doi.org/10.1111/mec.13380)  
C. Eberlein, J. Leducq, C. R. Landry
</summary>
<p style="margin-left: 30px">
The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long‐term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al . 2013) and teosinte as the closest relative to maize (reviewed in Hake &amp; Ross‐Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro‐organisms. This has been the case for the budding yeast Saccharomyces cerevisiae , whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al . (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.
</p></details><p></p>
<details>
<summary> [Independent Molecular Basis of Convergent Highland Adaptation in Maize](https://doi.org/10.1534/genetics.115.178327)  
**S. Takuno**, P. Ralph, K. Swarts, R. J. Elshire, J. C. Glaubitz, E. S. Buckler, **M. B. Hufford**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.
</p></details><p></p>
<details>
<summary> [Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport](https://doi.org/10.1038/ng.3422)  
D. Sosso, D. Luo, Q. B. Li, J. Sasse, ...[6 authors]..., P. M. Rogowsky, **J. Ross-Ibarra**, B. Yang, W. B. Frommer
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The origin and evolution of maize in the Southwestern United States](https://doi.org/10.1038/nplants.2014.3)  
R. R. da Fonseca, B. D. Smith, N. Wales, E. Cappellini, ...[12 authors]..., M. B. Hufford, A. Albrechtsen, **J. Ross-Ibarra**, M. T. P. Gilbert
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress](https://doi.org/10.1371/journal.pgen.1004915) [[preprint](https://doi.org/10.1101/008052)]  
I. Makarevitch, A. J. Waters, P. T. West, **M. Stitzer**, C. N. Hirsch, **J. Ross-Ibarra**, N. M. Springer
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Natural variation in teosinte at the domestication locus teosinte branched1 ( tb1 )](https://doi.org/10.7717/peerj.900)  
**L. Vann**, **T. Kono**, **T. Pyhäjärvi**, **M. B. Hufford<sup>&dagger;</sup>**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize](https://doi.org/10.1534/genetics.115.182410)  
J. P. Gerke<sup>&dagger;</sup>, J. W. Edwards, K. E. Guill, **J. Ross-Ibarra<sup>&dagger;</sup>**, M. D. McMullen
</summary>
<p style="margin-left: 30px">
Abstract Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture’s reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and &amp;gt;600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome.
</p></details><p></p>

### 2014

<details>
<summary> [Advances and limits of using population genetics to understand local adaptation](https://doi.org/10.1016/j.tree.2014.10.004)  
P. Tiffin, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The Pattern and Distribution of Deleterious Mutations in Maize](https://doi.org/10.1534/g3.113.008870)  
**S. Mezmouk**, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract Most nonsynonymous mutations are thought to be deleterious because of their effect on protein sequence and are expected to be removed or kept at low frequency by the action of natural selection. Nonetheless, the effect of positive selection on linked sites or drift in small or inbred populations may also impact the evolution of deleterious alleles. Despite their potential to affect complex trait phenotypes, deleterious alleles are difficult to study precisely because they are often at low frequency. Here, we made use of genome-wide genotyping data to characterize deleterious variants in a large panel of maize inbred lines. We show that, despite small effective population sizes and inbreeding, most putatively deleterious SNPs are indeed at low frequencies within individual genetic groups. We find that genes associated with a number of complex traits are enriched for deleterious variants. Together, these data are consistent with the dominance model of heterosis, in which complementation of numerous low-frequency, weak deleterious variants contribute to hybrid vigor.
</p></details><p></p>
<details>
<summary> [Diversity and evolution of centromere repeats in the maize genome](https://doi.org/10.1007/s00412-014-0483-8)  
**P. Bilinski**, **K. Distor**, **J. Gutierrez-Lopez**, G. M. Mendoza, J. Shi, R. K. Dawe, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Reply to Brush et al.: Wake-up call for crop conservation science](https://doi.org/10.1073/pnas.1422645112)  
G. A. Dyer, A. López-Feldman, A. Yúnez-Naude, J. E. Taylor, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2013

<details>
<summary> [Population genetics and ethnobotany of cultivated Diospyros riojae Gómez Pompa (Ebenaceae), an endangered fruit crop from Mexico](https://doi.org/10.1007/s10722-013-0015-z)  
**M. C. Provance<sup>&dagger;</sup>**, I. García-Ruiz, C. Thommes, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Feeding the future](https://doi.org/10.1038/499023a)  
S. McCouch, G. J. Baute, J. Bradeen, P. Bramel, ...[36 authors including **J. Ross-Ibarra**]..., J. Ward, R. Waugh, P. Wenzl, D. Zamir
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [The Genomic Signature of Crop-Wild Introgression in Maize](https://doi.org/10.1371/journal.pgen.1003477) [[preprint](https://doi.org/10.48550/arXiv.1208.3894)]  
**M. B. Hufford**, P. Lubinksy, **T. Pyhäjärvi**, **M. T. Devengenzo**, N. C. Ellstrand, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Complex Patterns of Local Adaptation in Teosinte](https://doi.org/10.1093/gbe/evt109)  
**T. Pyhäjärvi**, **M. B. Hufford**, **S. Mezmouk**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [From Many, One: Genetic Control of Prolificacy during Maize Domestication](https://doi.org/10.1371/journal.pgen.1003604) [[preprint](https://doi.org/10.48550/arXiv.1303.0882)]  
D. M. Wills, C. J. Whipple, **S. Takuno**, L. E. Kursel, L. M. Shannon, **J. Ross-Ibarra**, J. F. Doebley
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution](https://doi.org/10.1186/gb-2013-14-1-r10) [[preprint](https://doi.org/10.48550/arXiv.1209.4967)]  
D. P. Melters, K. R. Bradnam, H. A. Young, N. Telis, ...[9 authors]..., C. Tobias, **J. Ross-Ibarra<sup>&dagger;</sup>**, I. Korf<sup>&dagger;</sup>, S. W. Chan
</summary>
<p style="margin-left: 30px">
Abstract Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.
</p></details><p></p>
<details>
<summary> [Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species](https://doi.org/10.1073/pnas.1309182110)  
A. J. Waters, **P. Bilinski**, S. R. Eichten, M. W. Vaughn, **J. Ross-Ibarra**, M. Gehring, N. M. Springer
</summary>
<p style="margin-left: 30px">
Significance In many eukaryotes, reproduction involves contributions of genetic material from two parents. At some genes there are parent-of-origin differences in the expression of the maternal and paternal alleles of a gene and this is referred to as imprinting. The analysis of allele-specific expression in several maize hybrids allowed the comprehensive detection of imprinted genes. By comparing allelic expression patterns in multiple crosses, it was possible to observe allelic variation for imprinting in maize. The comparison of genes subject to imprinting in multiple plant species reveals limited conservation for imprinting. The subset of genes that exhibit conserved imprinting in maize and rice may play important, dosage-dependent roles in regulation of seed development.
</p></details><p></p>
<details>
<summary> [Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays](https://doi.org/10.1038/hdy.2013.2)  
L. B. Kanizay, **T. Pyhäjärvi**, E. G. Lowry, **M. B. Hufford**, D. G. Peterson, **J. Ross-Ibarra**, R. K. Dawe
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2012

<details>
<summary> [Teosinte as a model system for population and ecological genomics](https://doi.org/10.1016/j.tig.2012.08.004)  
**M. B. Hufford**, **P. Bilinski**, **T. Pyhäjärvi**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Historical genomics of North American maize](https://doi.org/10.1073/pnas.1209275109)  
**J. van Heerwaarden<sup>&dagger;</sup>**, **M. B. Hufford**, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Since the advent of modern plant breeding in the 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite the importance of genetic contributions to historical yield increases, little is known about the underlying genomic changes. Here we use high-density SNP genotyping to characterize a set of North American maize lines spanning the history of modern breeding. We provide a unique analysis of genome-wide developments in genetic diversity, ancestry, and selection. The genomic history of maize is marked by a steady increase in genetic differentiation and linkage disequilibrium, whereas allele frequencies in the total population have remained relatively constant. These changes are associated with increasing genetic separation of breeding pools and decreased diversity in the ancestry of individual lines. We confirm that modern heterotic groups are the product of ongoing divergence from a relatively homogeneous landrace population, but show that differential landrace ancestry remains evident. Using a recent association approach, we characterize signals of directional selection throughout the genome, identifying a number of candidate genes of potential agronomic relevance. However, overall we find that selection has had limited impact on genome-wide patterns of diversity and ancestry, with little evidence for individual lines contributing disproportionately to the accumulation of favorable alleles in today's elite germplasm. Our data suggest breeding progress has mainly involved selection and recombination of relatively common alleles, contributed by a representative but limited set of ancestral lines.
</p></details><p></p>
<details>
<summary> [Reshaping of the maize transcriptome by domestication](https://doi.org/10.1073/pnas.1201961109)  
R. Swanson-Wagner, R. Briskine, R. Schaefer, **M. B. Hufford**, **J. Ross-Ibarra**, C. L. Myers, P. Tiffin, N. M. Springer
</summary>
<p style="margin-left: 30px">
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
</p></details><p></p>
<details>
<summary> [Comparative population genomics of maize domestication and improvement](https://doi.org/10.1038/ng.2309)  
**M. B. Hufford<sup>&ast;</sup>**, X. Xu<sup>&ast;</sup>, **J. van Heerwaarden<sup>&ast;</sup>**, **T. Pyhäjärvi<sup>&ast;</sup>**, ...[17 authors]..., D. Ware, E. S. Buckler, S. Yang<sup>&dagger;</sup>, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Maize HapMap2 identifies extant variation from a genome in flux](https://doi.org/10.1038/ng.2313)  
J. M. Chia, C. Song, P. J. Bradbury, D. Costich, ...[30 authors including **M. B. Hufford**, **T. Pyhäjärvi**, **J. Ross-Ibarra**]..., E. S. Buckler, G. Zhang, Y. Xu, D. Ware
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize](https://doi.org/10.1534/genetics.112.138578)  
Z. Fang, **T. Pyhäjärvi**, A. L. Weber, R. K. Dawe, ...[2 authors]..., **C. Ross-Ibarra**, J. Doebley, P. L. Morrell<sup>&dagger;</sup>, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ∼50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures &amp;gt;700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.
</p></details><p></p>

### 2011

<details>
<summary> [Crop genomics: advances and applications](https://doi.org/10.1038/nrg3097)  
P. L. Morrell, E. S. Buckler, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Identification of a functional transposon insertion in the maize domestication gene tb1](https://doi.org/10.1038/ng.942)  
A. Studer, Q. Zhao, **J. Ross-Ibarra**, J. Doebley
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels  ](https://doi.org/10.1104/pp.111.185033)  
J. P. Cook, M. D. McMullen, J. B. Holland, F. Tian, P. Bradbury, **J. Ross-Ibarra**, E. S. Buckler, S. A. Flint-Garcia
</summary>
<p style="margin-left: 30px">
Abstract The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.
</p></details><p></p>
<details>
<summary> [Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians](https://doi.org/10.1093/gbe/evr008)  
M. I. Tenaillon, **M. B. Hufford**, B. S. Gaut, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2010

<details>
<summary> [Reproductive biology of Macleania rupestris (Ericaceae), a pollen-limited Neotropical cloud-forest species in Costa Rica](https://doi.org/10.1017/S0266467410000064)  
E. J. Fuchs, **J. Ross-Ibarra<sup>&dagger;</sup>**, G. Barrantes
</summary>
<p style="margin-left: 30px">
The reproductive success of hummingbird-pollinated plants often depends on complex interactions between environmental conditions and pollinator biology (Navarro 1999, Stiles 1985, Wolf et al . 1976). The effect of environment on reproductive success of hummingbird-pollinated plants is particularly pronounced at high altitudes, where large daily fluctuations in temperature, relative humidity and solar radiation limit the effective time for photosynthesis (Cavieres et al . 2000) and affect foraging activity (Navarro 1999) and abundance of pollinators (Rahbek 1997). At high altitudes in the tropical cloud forests of Costa Rica these factors may have serious impacts on fruit production.
</p></details><p></p>
<details>
<summary> [Widespread Gene Conversion in Centromere Cores](https://doi.org/10.1371/journal.pbio.1000327)  
J. Shi, S. E. Wolf, J. M. Burke, G. G. Presting, **J. Ross-Ibarra**, R. K. Dawe
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis)](https://doi.org/10.1111/j.1365-294X.2010.04924.x)  
M. B. HUFFORD, P. GEPTS, J. ROSS-IBARRA
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine ( Pinus taeda L., Pinaceae)](https://doi.org/10.1534/genetics.110.115543)  
A. J. Eckert, **J. van Heerwaarden**, J. L. Wegrzyn, C. D. Nelson, **J. Ross-Ibarra**, S. C. González-Martínez, D. B. Neale
</summary>
<p style="margin-left: 30px">
Abstract Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as FST outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.
</p></details><p></p>
<details>
<summary> [A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?](https://doi.org/10.1111/j.1558-5646.2010.00967.x)  
K. D. Whitney, E. J. Baack, J. L. Hamrick, M. J. W. Godt, ...[3 authors]..., C. Goodwillie, S. Kalisz, I. J. Leitch, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genetic signals of origin, spread, and introgression in a large sample of maize landraces](https://doi.org/10.1073/pnas.1013011108)  
**J. van Heerwaarden<sup>&dagger;</sup>**, J. Doebley, W. H. Briggs, J. C. Glaubitz, M. M. Goodman, J. de Jesus Sanchez Gonzalez, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte ( Zea mays subspecies parviglumis ), a wild relative that is endemic to the mid- to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.
</p></details><p></p>
<details>
<summary> [Fine scale genetic structure in the wild ancestor of maize ( Zea mays ssp. parviglumis )](https://doi.org/10.1111/j.1365-294X.2010.04559.x)  
J. VAN HEERWAARDEN, J. ROSS-IBARRA, J. DOEBLEY, J. C. GLAUBITZ, J. DE JESÚS SÁNCHEZ GONZÁLEZ, B. S. GAUT, L. E. EGUIARTE
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2009

<details>
<summary> [A First-Generation Haplotype Map of Maize](https://doi.org/10.1126/science.1177837)  
M. A. Gore, J. M. Chia, R. J. Elshire, Q. Sun, ...[4 authors]..., G. S. Grills, **J. Ross-Ibarra**, D. H. Ware, E. S. Buckler
</summary>
<p style="margin-left: 30px">
A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).
</p></details><p></p>
<details>
<summary> [Genetic diversity in a crop metapopulation](https://doi.org/10.1038/hdy.2009.110)  
**J. van Heerwaarden<sup>&dagger;</sup>**, F. A. van Eeuwijk, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Selection on grain shattering genes and rates of rice domestication](https://doi.org/10.1111/j.1469-8137.2009.02984.x)  
L. Zhang, Q. Zhu, Z. Wu, J. Ross‐Ibarra, B. S. Gaut, S. Ge, T. Sang
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants](https://doi.org/10.1093/molbev/msp249)  
J. D. Hollister, **J. Ross-Ibarra**, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Historical Divergence and Gene Flow in the Genus Zea](https://doi.org/10.1534/genetics.108.097238)  
**J. Ross-Ibarra**, M. Tenaillon, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ∼150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.
</p></details><p></p>
<details>
<summary> [A Pleistocene Clone of Palmer's Oak Persisting in Southern California](https://doi.org/10.1371/journal.pone.0008346)  
**M. R. May**, **M. C. Provance**, A. C. Sanders, N. C. Ellstrand, **J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2008

<details>
<summary> [Selection on Major Components of Angiosperm Genomes](https://doi.org/10.1126/science.1153586)  
B. S. Gaut, **J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Angiosperms are a relatively recent evolutionary innovation, but their genome sizes have diversified remarkably since their origin, at a rate beyond that of most other taxa. Genome size is often correlated with plant growth and ecology, and extremely large genomes may be limited both ecologically and evolutionarily. Yet the relationship between genome size and natural selection remains poorly understood. The manifold cellular and physiological effects of large genomes may be a function of selection on the major components that contribute to genome size, such as transposable elements and gene duplication. To understand the nature of selection on these genomic components, both population-genetic and comparative approaches are needed.
</p></details><p></p>
<details>
<summary> [Multiple domestications do not appear monophyletic](https://doi.org/10.1073/pnas.0809042105)  
**J. Ross-Ibarra<sup>&dagger;</sup>**, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata](https://doi.org/10.1073/pnas.0804671105)  
S. Lockton, **J. Ross-Ibarra**, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata . The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.
</p></details><p></p>
<details>
<summary> [Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata](https://doi.org/10.1371/journal.pone.0002411)  
**J. Ross-Ibarra**, S. I. Wright, J. P. Foxe, A. Kawabe, L. DeRose-Wilson, G. Gos, D. Charlesworth, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2007

<details>
<summary> [Plant domestication, a unique opportunity to identify the genetic basis of adaptation](https://doi.org/10.1073/pnas.0700643104)  
**J. Ross-Ibarra**, P. L. Morrell, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype–genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.
</p></details><p></p>

### 2006

<details>
<summary> [Mitochondrial DNA and Population Size](https://doi.org/10.1126/science.314.5804.1388)  
O. F. Berry
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>
<details>
<summary> [Genome size and recombination in angiosperms: a second look](https://doi.org/10.1111/j.1420-9101.2006.01275.x)  
J. ROSS‐IBARRA
</summary>
<p style="margin-left: 30px">
Abstract Despite dramatic differences in genome size – and thus space for recombination to occur – previous workers found no correlation between recombination rate and genome size in flowering plants. Here I re‐investigate these claims using phylogenetic comparative methods to test a large data set of recombination data in angiosperms. I show that genome size is significantly correlated with recombination rate across a wide sampling of species and that change in genome size explains a meaningful proportion (∼20%) of variation in recombination rate. I show that the strength of this correlation is comparable with that of several characters previously linked to evolutionary change in recombination rate, but argue that consideration of processes of genome size change likely make the observed correlation a conservative estimate. And finally, although I find that recombination rate increases less than proportionally to change in genome size, several mechanistic and theoretical arguments suggest that this result is not unexpected.
</p></details><p></p>

### 2005

<details>
<summary> [Quantitative trait loci and the study of plant domestication](https://doi.org/10.1007/s10709-004-2744-6)  
**J. Ross-Ibarra<sup>&dagger;</sup>**
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2004

<details>
<summary> [The Evolution of Recombination under Domestication: A Test of Two Hypotheses](https://doi.org/10.1086/380606)  
J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2003

<details>
<summary> [Origen y domesticación de la chaya ( Cnidoscolus aconitifolius Mill I. M. Johnst): La espinaca Maya](https://doi.org/10.1525/msem.2003.19.2.287)  
**J. Ross-Ibarra**
</summary>
<p style="margin-left: 30px">
Mesoamerica has been one of the most active centers of plant domestication worldwide. Along with the many well-known and economically important plants that originated in Mesoamerica exist a variety of other lesser known domesticated plants many of which remain important on a local or regional scale. One of these lesser known plants is chaya (Cnidoscolus aconitifolius, Euphorbiaceae), a shrub cultivated for its highly nutritious leaves. The article presents evidence bearing on the domestication and place of origin of the cultivated varieties of chaya and proposes a model describing the process of their domestication. Mesoamérica ha sido uno de los centros de domesticación más activos a nivel mundial. Junto con las muchas plantas económicas y conocidas de origen Mesoamericana, existen varias plantas domesticadas no tan conocidas, que sin embargo siguen siendo importantes a un nivel local o regional. Una de estas últimas es la chaya (Cnidoscolus aconitifolius,Euphorbiaceae), un arbusto cultivado por sus hojas nutritivas. Se presenta aquí evidencia de la domesticación y lugar de origen de las variedades cultivadas de la chaya, y se propone un modelo para describir su processo de domesticación.
</p></details><p></p>

### 2002

<details>
<summary> [The Ethnobotany of Chaya (Cnidoscolus Aconitifolius ssp. Aconitifolius Breckon): A Nutritious Maya Vegetable1](https://doi.org/10.1663/0013-0001(2002)056[0350:TEOCCA]2.0.CO;2)  
**J. Ross-Ibarra**, A. Molina-Cruz
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p></details><p></p>

### 2001

<details>
<summary> [Implications of mating patterns for conservation of the endangered plant Eriogonum ovalifolium var. vineum (Polygonaceae)](https://doi.org/10.2307/3558332)  
M. C. Neel, J. Ross‐Ibarra, N. C. Ellstrand
</summary>
<p style="margin-left: 30px">
Mating patterns have direct application to conservation because of their influence on structuring genetic diversity within and among populations and on maintaining that diversity over time. We measured population and family outcrossing rates, biparental inbreeding, correlation of outcrossed paternity, and inbreeding coefficients in six populations from throughout the ecological range of the endangered plant Eriogonum ovalifolium var. vineum using naturally pollinated families. The taxon was primarily outcrossed: population outcrossing rates averaged 0.80 (SE 0.03) and family outcrossing rates averaged 0.88 (SE 0.03); neither rate varied among populations. Five population rates were significantly different from 1 while family rates differed from 1 in only one population. We found high correlated outcrossed paternity and evidence for biparental inbreeding in five populations each. As expected from the predominantly outcrossed mating system, levels of diversity were high and inbreeding coefficients among maternal individuals were low (averaging −0.05, SE 0.12). Differences between inbreeding coefficients of progeny (average 0.21, SE 0.06) and mothers indicated selection against homozygous offspring. These results indicate that it is important to maintain large populations to prevent increases in inbreeding and to maintain pollinator communities to facilitate outcrossing.
</p></details><p></p>
<!-- PUBS:END -->