Biology subjects

Barker, M. S.

Publications and source records attributed to Barker, M. S..

At least 19 recordsLinked to original sources

bioRxiv2026

The Genomic Legacy of Ancient Polyploidy in Crop Domestication

Species that have an ancestry of whole-genome duplications (WGDs) are more likely to be domesticated, but the underlying mechanisms remain unclear. We tested whether paleologs--genes duplicated during ancient WGDs--are enriched in candidate domestication lists across 22 crop species spanning 17 genera. Paleologs were significantly enriched in 14 species, with single-copy paleologs showing the most consistent overrepresentation. In contrast, genes from small-scale duplications were consistently underrepresented among domestication candidates. This enrichment was independent of WGD age and degree of gene loss, indicating that constraint on copy number does not preclude selection on gene function. Several non-mutually exclusive processes could explain this pattern, including accumulated genetic diversity becoming available upon return to single-copy, selection to maintain essential functions, and greater selection efficiency on unmasked loci. Ancient WGDs thus provide a persistent genomic substrate for crop evolution millions of years later.

bioinformatics↗

bioRxiv2025

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics

Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of life, population genetics theory for polyploids is not well developed. The lack of theoretical models limits our understanding of polyploid evolution and restricts our ability to harness polyploidy for crop improvement amidst increasing environmental stress. To address this gap, we developed and analyzed deterministic models of mutation-selection balance for tetraploids under polysomic (autotetraploid) and disomic (allote-traploid) inheritance patterns and arbitrary dominance relationships. We also introduced a new mathematical framework based on ordinary differential equations and nonlinear dynamics for analyzing the models. We find that autotetraploids approach Hardy-Weinberg Equilibrium 33% faster than allotetraploids, but the different tetraploid inheritance models show little differences in mutation load and allele frequency at mutation-selection balance. Our model also reveals two bistable points of mutation-selection balance for dominant alleles with biased mutation rates over a wide range of selection coefficients in the tetraploid models compared to bistability in only a narrow range for diploids. Finally, using discrete time simulations, we explore the temporal dynamics of allele frequency and fitness change and compare these dynamics to the predictions of Fishers Fundamental Theorem of Natural Selection. While Fishers predictions generally hold, we show that the bistable dynamics for dominant mutations fundamentally alter the associated temporal dynamics. Overall, this work develops foundational theoretical models that will facilitate the development of population genetic models and methodologies to study evolution in empirical tetraploid populations.

evolutionary biology↗

bioRxiv2024

Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns

A longstanding question in plant evolution is why ferns have many more chromosomes than angiosperms. The leading hypothesis proposes that ferns have ancient polyploidy without chromosome loss or gene deletion to explain the high chromosome numbers of ferns. Here, we test this hypothesis by estimating ancient polyploidy frequency, chromosome evolution, protein evolution in meiosis genes, and patterns of gene retention in ferns. We found similar rates of paleopolyploidy in ferns and angiosperms from independent phylogenomic and chromosome number evolution analyses, but lower rates of chromosome loss in ferns. We found elevated evolutionary rates in meiosis genes in angiosperms, but not in ferns. Finally, we found some evidence of parallel and biased gene retention in ferns, but this was comparatively weak to patterns in angiosperms. This work provides genomic evidence supporting a decades-old hypothesis on fern genome evolution and provides a foundation for future work on plant genome structure.

evolutionary biology↗

bioRxiv2024

A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions

Whole genome duplications (WGDs) can be a key event in evolution, playing a role in both adaptation and speciation. While WGDs are common throughout the history of plants, only a few examples have been proposed in metazoans. Among these, recent proposals of WGD events in Chelicerates, the group of Arthropods that includes horseshoe crabs, ticks, scorpions, and spiders, include several rounds in the history of horseshoe crabs, with an additional WGD proposed in the ancestor of spiders and scorpions. However, many of these inferences are based on evidence from only a small portion of the genome (in particular, the Hox gene cluster); therefore, genome-wide inferences with broader species sampling may give a clearer picture of WGDs in this clade. Here, we investigate signals of WGD in Chelicerates using whole genomes from 17 species. We employ multiple methods to look for these signals, including gene tree analysis of thousands of gene families, comparisons of synteny, and signals of divergence among within-species paralogs. We test several scenarios of WGD in Chelicerates using multiple species trees as a backbone for all hypotheses. While we do find support for at least one WGD in the ancestral horseshoe crab lineage, we find no evidence for a WGD in the history of spiders and scorpions using any genome-scale method. This study not only sheds light on genome evolution and phylogenetics within Chelicerates, but also demonstrates how a combination of comparative methods can be used to investigate signals of ancient WGDs.

evolutionary biology↗

bioRxiv2024

SLEDGe: Inference of ancient whole genome duplications using machine learning

Ancient whole-genome duplication--previous genome duplication events that have since been eroded via diploidization, are increasingly identified throughout eukaryotes. One of the constraints against large-scale studies of ancient eukaryotic WGD is the relatively large, high-quality datasets often needed to definitively establish ancient WGD events; alternatively, the more low-input method interpretation of genome-wide synonymous substitution rates (Ks plots) is prone to bias and inconsistency. We improve upon the shortcomings of the current Ks plot method by building a Ks plot simulator. This data-agnostic approach simulates common distributions found in Ks plots in the presence or absence of ancient WGD signatures. In conjunction with a machine-learning classifier, this approach can quickly assess the likelihood that transcriptomic and genomic data bear WGD signatures. On independently-generated synthetic data and real plant transcriptomic data, SLEDGE is capable of correctly identifying ancient WGD in 93-100% of samples. This approach can serve as a quick classification step in large-scale genomic analyses, identifying putative ancient polyploids for further study.

bioinformatics↗

bioRxiv2024

Post-zygotic reproductive isolation is not correlated with chromosome number in plants.

The evolution of chromosome numbers is an important but not fully understood aspect of eukaryotic evolution. Although we understand the types of karyotypic changes that can lead to chromosome gain and loss, we still do not understand why chromosome numbers in many plants and animals have an average of n = 9. A recent hypothesis proposed that chromosome number reduction following whole genome duplication (WGD) in angiosperms is driven by an interaction between chromosome number and the strength of reproductive isolation among populations. Chromosome number is expected to determine the maximum number of independently assorting Bateson-Dobzhansky-Muller incompatibilities (BDMIs). Selection against restricted gene flow among populations would result in selection for reduced chromosome number. Here we test for an interaction between chromosome number and post-zygotic reproductive isolation across a broad sample of land plants. We additionally tested for the indirect effects of WGD in generating post-zygotic reproductive isolation. Such an effect is expected if reproductive isolation is driven largely by reciprocal gene loss of WGD-derived paralogs. We found no correlation between post-zygotic reproductive isolation and chromosome number, WGD age, or degree of fractionation, suggesting that the accumulation of genic incompatibilities is likely not a major driver of post-WGD chromosome number reduction.

evolutionary biology↗

bioRxiv2024

Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny

PremiseThe history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we use state of the art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both the uncertainty introduced by inference methods and alternative phylogenetic hypotheses. MethodsTranscriptomic and genomic data were used to infer and place WGDs across two hypothesized angiosperm phylogenies. Initial WGD hypotheses were made using rate corrections to the distribution of synonymous divergences (Ks) of paralogs and orthologs. WGD hypotheses were tested using syntenic inferences and Bayesian models of duplicate gene gain and loss across the phylogeny. Key resultsThe number of ancient WGDs in the history of angiosperms ([~]170) is largely similar across different inference methods, but there is often variation in the precise placement of WGDs on the phylogeny. Ks based methods often yield alternative hypothesized WGD placements largely due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation, allowing for post hoc testing of WGD hypotheses. However, errors in species tree inference can still produce spurious WGD hypotheses regardless of method used. ConclusionsHere we show that different WGD inference methods largely agree on an average of 3.5 WGD in the history of angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

evolutionary biology↗

bioRxiv2022

Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits

Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here we develop new genomic resources for C. solstitialis and map the genetic basis of invasiveness traits. We present a chromosome-scale (1N = 8) reference genome using PacBio CLR and Dovetail Omni-C technologies, and functional gene annotation using RNAseq. We find repeat structure typical of the family Asteraceae, with over 25% of gene content derived from ancestral whole genome duplications (paleologs). Using an F2 mapping population derived from a cross between native and invading parents, with a restriction site-associated DNA (RAD)-based genetic map, we validate the assembly and identify 13 QTL underpinning size traits that have evolved during invasion. We find evidence that large effect QTL may be associated with structural variants between native and invading genotypes, including a variant with an overdominant and pleiotropic effect on key invader traits. We also find evidence of significant paleolog enrichment under two QTL. Our results add to growing evidence of the importance of structural variants in evolution, and to understanding of the rapid evolution of invaders. Significance StatementInvasive species often evolve rapidly in new environments, potentially informing our understanding of the genomic basis of adaptation, but genomic studies of these non-model systems are limited. We provide a chromosome-scale reference genome, annotation, and genetic map for the invasive plant yellow starthistle, and we investigate the genetic basis of invader trait evolution in this system. We find regions of the genome with large effects on traits that differ between native and invading genotypes, and evidence suggesting genome structural variants and past genome duplications could play a role in rapid adaptation of invading populations. These genomic resources and evolutionary insights aid in our understanding of the sources of genomic variation for adaptation, and how their evolution facilitates invasion.

genomics↗

bioRxiv2022

Demographic History Inference and the Polyploid Continuum

Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication (WGD) depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherds purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.

evolutionary biology↗

bioRxiv2021

Applying Machine Learning to Classify the Origins of Gene Duplications

Nearly all lineages of land plants have experienced at least one whole genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD--paleologs--can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.

bioinformatics↗

bioRxiv2021

Underwater CAM photosynthesis elucidated by Isoetes genome

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigated the underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identified several key differences. Notably, for carboxylation of PEP, Isoetes recruited the lesser-known "bacterial-type" PEPC, along with the "plant-type" exclusively used in other terrestrial CAM and C4 plants. Furthermore, we found that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.

plant biology↗

bioRxiv2021

Genome size evolution in the diverse insect order Trichoptera

BackgroundGenome size is implicated in form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: Polyploidy (i.e., whole genome duplication: WGD) or smaller duplication events and bursts in the activity of repetitive elements (RE). Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. ResultsWe detect a ~14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element (RE) expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). ConclusionOur findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

evolutionary biology↗

bioRxiv2021

Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification

Changes in chromosome number are considered an important driver of diversification in angiosperms. Single chromosome number changes caused by dysploidy may produce strong reproductive barriers leading to speciation. Polyploidy, or whole genome duplication, yields new species that are often reproductively isolated from progenitors and may exhibit novel morphology or ecology that may further facilitate diversification. Here, we examined the rates of polyploidy, dysploidy, and diversification across the angiosperms. Our analyses of nearly 30,000 taxa representing 46 orders and 147 families found that rates of polyploidy and dysploidy differed by two to three orders of magnitude. The rates of polyploidy and dysploidy were positively correlated with diversification rates, but relative importance analyses indicated that variation in polyploidy was better correlated with diversification rates than dysploidy. Our results provide an overview of angiosperm chromosomal evolution and a roadmap for future research on the complex relationships among polyploidy, dysploidy, and diversification.

evolutionary biology↗

bioRxiv2020

Animal chromosome counts reveal similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants

Understanding the mechanisms that underlie chromosome evolution may provide insights into the processes underpinning the origin, persistence, and evolutionary tempo of lineages. Here we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for [~]18,000 species. We found remarkable similarity in the distribution of chromosome counts between animals and flowering plants. At larger timescales, selection towards a specific range might explain the similar distribution of chromosome counts between these two groups. Nevertheless, changes in chromosome number are still potential drivers of divergence among species at shorter timescales. We also found that while animals and plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. Based on the ACC, our analyses suggest that changes in chromosome number alone could help explain patterns of diversity within animal clades.

zoology↗

bioRxiv2020

The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible

The members of the tribe Brassiceae share a whole genome triplication (WGT), and one proposed model for its formation is a "two-step" pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using POInT (the Polyploidy Orthology Inference Tool). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring prior to the arrival of the third. We also, for the 90,000 individual genes in our study, make parental "subgenome" assignments, inferring, with measured uncertainty, which of the progenitor genomes of the allohexaploidy each gene derives from. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, where subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

genomics↗

bioRxiv2020

Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their non-independence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1, P2), P3), Out) and a matrix of pairwise nucleotide divergence (dXY) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide-breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to a random forest classifier trained on introgression-based statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing, and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.

evolutionary biology↗

bioRxiv2020

TagSeq for gene expression in non-model plants: a pilot study at the Santa Rita Experimental Range NEON core site

Premise of the studyTagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range NEON core site. MethodsTissue for TagSeq was sampled from multiple individuals of four species [Bouteloua aristidoides and Eragrostis lehmanniana (Poaceae); Tidestromia lanuginosa (Amaranthaceae), and Parkinsonia florida (Fabaceae)] at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. ResultsA high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. DiscussionTagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.

plant biology↗

bioRxiv2020

Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

O_LIPremise of the study: Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes. C_LIO_LIMethods: We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content. C_LIO_LIResults: We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated genes between diploid and polyploid transcriptomes. C_LIO_LIDiscussion: Our resource provides new RNA-seq datasets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers clear opportunities for large scale studies at the intersection of ecology and genomics. C_LI

genomics↗