Biology subjects

Brandvain, Y.

Publications and source records attributed to Brandvain, Y..

13 recordsLinked to original sources

bioRxiv2025

Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids

How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interactions between variants in the genomes of diverged lineages, known as hybrid incompatibilities, will reduce viability or fertility in hybrids. The genetic architecture of these interactions and the evolutionary paths through which they arise have profound implications for the efficacy of hybrid incompatibilities as barriers to gene flow between species. While these questions have been studied using theoretical approaches for several decades, only recently has it become possible to genetically map larger numbers of hybrid incompatibilities. Here, we use admixture mapping in natural hybrid populations of swordtail fish (Xiphophorus) to identify hybrid incompatibilities involving genetic interactions between the mitochondrial and nuclear genomes. We find that at least nine regions of the genome are involved in mitonuclear incompatibilities. These incompatibilities involve interactions between the nuclear genome and the X. malinche mitochondria, the X. birchmanni mitochondria, or both. Moreover, they vary in the strength of selection they experience, and the degree to which they limit gene flow in natural hybrid populations. Our results build a deeper understanding of the complex architecture of selection against incompatibilities in naturally hybridizing species and highlight an important role of mitonuclear interactions in the evolution of reproductive barriers between closely related species.

evolutionary biology↗

bioRxiv2023

RenSeq of Silphium integrifolium Reveals a Biotic Gradient for Disease Resistance

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plants source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

evolutionary biology↗

bioRxiv2023

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

BackgroundStructural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de-novo genome assemblies of 26 diverse inbred maize lines. ResultsWe generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both putative insertion and deletion events. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that, genome-wide, deletions of transposable elements account for more structural variation than insertions. These deletions are often large structural variants containing multiple transposable elements. ConclusionsCombined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.

genomics↗

bioRxiv2021

Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback

Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are intrinsic, meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (semi-natural experimental ponds) or the laboratory (aquaria). We tested for differences in excess heterozygosity between these two environments at ancestry informative loci--a genetic signature of selection against incompatibilities. We found that excess ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Previous results from F1 hybrids in the field suggest that pond-specific (single-locus) heterosis is unlikely to explain this finding. Our study suggests that, in stickleback, a coarse signal of environment-dependent hybrid incompatibilities is reliably detectable and that extrinsic incompatibilities have evolved before intrinsic incompatibilities.

evolutionary biology↗

bioRxiv2021

Genetic load may increase or decrease with selfing depending upon the recombination environment

The ability of natural selection to remove deleterious mutations from a population is a function of the effective population size. Increases in selfing rate, and concomitant increases in population-level homozygosity, can increase or decrease the efficacy of selection, depending on the dominance and selection coefficients of the deleterious mutations. Most theory has focused on how (partial) selfing affects the efficacy of selection for mutations of a given dominance and fitness effect in isolation. It remains unclear how selfing affects the purging of deleterious mutations in a genome-wide context where mutations with different selection and dominance coefficients co-segregate. Here, we use computer simulations to investigate how mutation, selection and recombination interact with selfing rate to shape genome-wide patterns of genetic load. We recover various mechanisms previously described for how (partial) selfing affects the efficacy of selection against mutations of a given dominance class. However, we find that the interaction of purifying selection against mutations of different dominance classes changes with selfing rate. In particular, as outcrossing populations transition from purifying selection to pseudo-overdominance they experience a dramatic increase in the genetic load caused by additive, mildly deleterious mutations. We describe the threshold selfing rate that prevents pseudo-overdominance and decreases genetic load.

genetics↗

bioRxiv2021

Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

O_LISilphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and has a sporophytic self-incompatibility system--the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. C_LIO_LIWe used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we identified potential gene candidates using synteny analysis with the annual sunflower (Helianthus annuus) genome. C_LIO_LIOur linkage map contains 198 SNP markers and resolved into the correct number of linkage groups. We were able to successfully map the S-locus and identify several potential gene candidates in the sunflower syntenic region. C_LIO_LIOur method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than previous studies, and could be readily be applied to other species. Our best gene candidate appears to be worthy of future work in S. integrifolium and other Asteraceae species. C_LI

plant biology↗

bioRxiv2020

Nonself-recognition-based self-incompatibility canalternatively promote or prevent introgression

1O_LITraditionally, we expect that self-incompatibility alleles (S-alleles), which prevent self-fertilization, should benefit from negative-frequency dependent selection and rise to high frequency when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through nonself-recognition, which drastically alters the process of S-allele diversification. C_LIO_LIWe analyze a model of S-allele evolution in two populations connected by migration, focusing on comparisons among the fates of S-alleles originally unique to each population and those shared among populations. C_LIO_LIWe find that both shared and unique S-alleles originating from the population with more unique S-alleles were usually fitter than S-alleles from the population with fewer. Resident S-alleles were often driven extinct and replaced by migrant S-alleles, though this outcome could be averted by pollen limitation or biased migration. C_LIO_LINonself-recognition-based self-incompatibility will usually either disfavor introgression of S-alleles or result in the whole-sale replacement of S-alleles from one population with those from another. C_LI

evolutionary biology↗

bioRxiv2020

Reconstructing the history and biological consequences of a plant invasion on the Galapagos islands

The introduction of non-native species into new habitats is one of the foremost risks to global biodiversity. Here, we evaluate a recent invasion of wild tomato (Solanum pimpinellifolium) onto the Galapagos islands from a population genomic perspective, using a large panel of novel collections from the archipelago as well as historical accessions from mainland Ecuador and Peru. We infer a recent invasion of S. pimpinellifolium on the islands, largely the result of a single event from central Ecuador which, despite its recency, has rapidly spread onto several islands in the Galapagos. By reconstructing patterns of local ancestry throughout the genomes of invasive plants, we uncover evidence for recent hybridization and introgression between S. pimpinellifolium and the closely related endemic species Solanum cheesmaniae. Two large introgressed regions overlap with known fruit color loci involved in carotenoid biosynthesis. Instead of red fruits, admixed individuals with endemic haplotypes at these loci have orange fruit colors that are typically characteristic of the endemic species. We therefore infer that introgression explains the observed trait convergence. Moreover, we infer roles for two independent loci in driving this pattern, and a likely history of selection favoring the repeated phenotypic transition from red to orange fruits. Together, our data reconstruct a complex history of invasion, expansion, and gene flow among wild tomatoes on the Galapagos islands. These findings provide critical data on the evolutionary importance of hybridization during colonization and its role in influencing conservation outcomes. Significance StatementThe isolation and unique diversity of the Galapagos Islands provide numerous natural experiments that have enriched our understanding of evolutionary biology. Here we use population genomic sequencing to reconstruct the timing, path, and consequences of a biological invasion by wild tomato onto the Galapagos. We infer that invasive populations originated from a recent human-mediated migration event from central Ecuador. Our data also indicate that invasive populations are hybridizing with endemic populations, and that this has led to some invasive individuals adopting both fruit color genes and the fruit color characteristic of the endemic island species. Our results demonstrate how hybridization can shape patterns of trait evolution over very short time scales, and characterize genetic factors underlying invasive success.

evolutionary biology↗

bioRxiv2020

Widespread imprinting of transposable elements and young genes in the maize endosperm

Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding the rate of turnover for gain or loss of imprinted expression has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene. Read alignments over maternal TE-gene pairs indicate fused transcripts, suggesting that variable TEs contribute imprinted expression of nearby genes.

plant biology↗

bioRxiv2020

Diversification or collapse of self-incompatibility haplotypes as a rescue process

In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges limit the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. First, there is no obvious selective benefit for pollen compatible with non-existent stylar incompatibilities, which themselves cannot spread if no pollen can fertilize them. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. Second, we show that novel haplotypes can drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10-40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.

evolutionary biology↗

bioRxiv2019

The effect of autopolyploidy on population genetic signals of hard sweeps

Searching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the signal of selection by separating the effects of polyploidy on rates of fixation versus rates of diversity (i.e. mutation and recombination) with a set of coalescent simulations. We explore what the major consequences of polyploidy, such as a more localized signal, greater dependence on dominance, and longer persistence of the signal following fixation, mean for within- and across-ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, studies such as this aid our ability to anticipate, interpret, and compare data across ploidy levels.

evolutionary biology↗

bioRxiv2019

Diversification or collapse of self-incompatibility haplotypes as outcomes of evolutionary rescue

Self-incompatibility systems in angiosperms are exemplars of extreme allelic polymorphism maintained by long-term balancing selection. Pollen that shares an allele with the pollen recipient at the self-incompatibility locus is rejected, and this rejection favors rare alleles as well as preventing self-fertilization. Advances in molecular genetics reveal that an ancient, deeply conserved, and well-studied incompatibility system functions through multiple tightly linked genes encoding separate pollen-expressed F-box proteins and pistil-expressed ribonucleases. We show that certain recombinant haplotypes at the incompatibility locus can drive collapse in the number of incompatibility types. We use a modified evolutionary rescue model to calculate the relative probabilities of increase and collapse in number of incompatibility types given the initial collection of incompatibility haplotypes and the population rate of gene conversion. We find that expansion in haplotype number is possible when population size or the rate of gene conversion is large, but large contractions are likely otherwise. By iterating a Markov chain model derived from these expansion and collapse probabilities, we find that a stable haplotype number distribution in the realistic range of 10-40 is possible under plausible parameters. However, small or moderate-sized populations should be susceptible to substantial additional loss of haplotypes beyond those lost by chance during bottlenecks. The same processes that can generate many incompatibility haplotypes in large populations may therefore be crushing haplotype diversity in smaller populations.

evolutionary biology↗

bioRxiv2018

The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus

Understanding the molecular basis of repeated evolved phenotypes can yield key insights into the evolutionary process. Quantifying the amount of gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture is more common between diverging lineages than previously thought. In this study, we resequenced and analyzed nearly 50 whole genomes of the Mexican tetra from three blind cave populations, two surface populations, and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our dataset. The two lineages likely diverged [~]257k generations ago, which, assuming 1 generation per year, is substantially younger than previous mitochondrial estimates of 5-7mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between [~]161k - 191k generations ago. The favored demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified abundant gene flow between cave and surface fish, between caves, and between separate lineages of cave and surface fish. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite substantial gene flow with surface populations. After incorporating these new demographic estimates, our models support that selection may drive the evolution of cave-derived traits, as opposed to the classic hypothesis of disuse and drift. Finally, we show that a key QTL is enriched for genomic regions with very low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. In sum, our study shows that shared evolutionary history via gene flow must be considered in studies of independent, repeated trait evolution.

evolutionary biology↗