Biology subjects

Brandvain, Y. J.

Publications and source records attributed to Brandvain, Y. J..

12 recordsLinked to original sources

bioRxiv2026

Promoter Structural Variants are Drivers of Genome-Wide Differential Expression in Maize

BackgroundStructural variants (SVs) are large insertions or deletions of DNA sequences. While less numerous than single nucleotide polymorphisms, SVs often account for a greater proportion of nucleotide differences between genomes. Their size and frequent association with repetitive sequences has historically hindered their detection, which has limited the ability to associate this variation with molecular and phenotypic trait variation. While some SVs have been linked to observable traits, it remains unclear whether such effects are rare or broadly distributed across the genome. ResultsTo test for genome-wide relationships between SVs and gene expression, we analyzed genome assemblies and transcriptomic data from 10 tissues across 26 diverse maize inbred lines. We identified SVs amongst these lines and examined variants located within the 1kb promoter region upstream of genes. Thousands of genes showed expression differences associated with promoter SVs, often in a tissue-specific manner. One common feature of these SVs was the presence of transposable element sequences. LTR retrotransposons were enriched amongst promoter SVs associated with differential expression and often reduced expression of the nearby gene. Despite widespread expression changes, we found no enrichment for specific biological functions or pathways among affected genes. ConclusionsOur findings indicate that extant TE-mediated promoter SVs play a significant role in shaping gene expression patterns across the maize genome. However, their phenotypic effects appear limited or context-dependent, suggesting that many variants may have minimal impact outside specific developmental stages or environmental conditions.

genomics↗

bioRxiv2023

Mating system and environment predict the direction and extent of introgression between incipient Clarkia species

Introgression is pervasive across the tree of life, varying across taxa, geography, and genomes. However, we are only beginning to understand the factors that modulate this variation and how they may be affected by global change. Here, we used 200 genomes and a 15-year site-specific environmental dataset to investigate the effect of mating system divergence and environmental variation on the magnitude of introgression between two recently diverged annual plants. Two subspecies of Clarkia xantiana diverged ca. 65k years ago and subsequently came into secondary sympatry where they form replicated contact zones. We found that introgression is asymmetric between taxa, with substantially more introgression from the self-fertilizing taxon to the outcrossing taxon. This asymmetry is caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrossers admixture proportion among contact zones, which is predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation result in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.

evolutionary biology↗

bioRxiv2023

Together Inbreeding and Reproductive Compensation Favor Lethal t-Haplotypes

Male mice who are heterozygous for distorting and non-distorting alleles at the t-haplotype transmit the driving t-haplotype around 90% of the time - a drastic departure from Mendelian expectations. This selfish act comes at a cost. The mechanism underlying transmission distortion in this system causes severe sterility in males homozygous for the drive alleles, ultimately preventing its fixation. Curiously, many driving t-haplotypes also induce embryonic lethality in both sexes when homozygous, however, this is neither universal nor a necessity for this distortion mechanism. Charlesworth provided an adaptive explanation for the evolution of lethal t-haplotypes in a population segregating for distorting and non-distorting t alleles - namely, if mothers compensate by replacing dead embryos with new offspring (or by transferring energy to surviving offspring), a recessive lethal can be favored because it effectively allows mothers the opportunity to trade in infertile males for potentially fertile offspring. However, this model requires near complete reproductive compensation for the invasion of the lethal t-haplotype and produces an equilibrium frequency of lethal drivers well below what is observed in nature. We show that even low levels of systemic inbreeding, which we model as brother-sister mating, allows lethal t-haplotypes to invade with much lower levels of reproductive compensation. Furthermore, inbreeding allows these lethal haplotypes to largely displace the ancestral male-sterile haplotypes. Our results show that together inbreeding and reproductive compensation move expected equilibria closer to observed haplotype frequencies in natural populations and occur under more reasonable parameter combinations.

evolutionary biology↗

bioRxiv2023

Early acting inbreeding depression can evolve as an inbreeding avoidance mechanism

Despite the potential for mechanical, developmental and/or chemical mechanisms to prevent self-fertilization, incidental self-fertilization is inevitable in many predominantly outcrossing species. In such cases, inbreeding can compromise individual fitness. Unquestionably, much of this inbreeding depression is maladaptive. However, we show that when reproductive compensation allows for the replacement of inviable embryos lost early in development, selection can favor deleterious recessive variants that induce "self-sacrificial" death of inbred embryos. Our theoretical results provide numerous testable predictions which could challenge the assumption that inbreeding depression is always maladaptive. Our work is applicable any species that cannot fully avoid inbreeding, exhibits substantial inbreeding depression, and has the potential to compensate embryos lost early in development. In addition to its general applicability our theory suggests that self-sacrificial variants might be responsible for the remarkably low realized selfing rates of gymnosperms with high primary selfing rates, as gymnosperms exhibit strong inbreeding depression, have effective reproductive compensation mechanisms, and cannot evolve chemical self-incompatibility.

evolutionary biology↗

bioRxiv2022

Linked selection and the evolution of altruism in a family-structured population

Much research on the evolution of altruism via kin selection, group selection, and reciprocity focuses on the role of a single locus or quantitative trait. Very few studies have explored how linked selection, or selection at loci neighboring an altruism locus, impacts the evolution of altruism. While linked selection can decrease the efficacy of selection at neighboring loci, it might have other effects including promoting selection for altruism by increasing relatedness in regions of low recombination. Here, we used population genetic simulations to study how negative selection at linked loci, or background selection, affects the evolution of altruism. When altruism occurs between full siblings, we found that background selection interfered with selection on the altruistic allele, increasing its fixation probability when the altruistic allele was disfavored and reducing its fixation when the allele was favored. In other words, background selection has the same effect on altruistic genes in family-structured populations as it does on other, nonsocial, genes. This contrasts with prior research showing that linked selective sweeps can favor the evolution of cooperation, and we discuss possibilities for resolving these contrasting results.

evolutionary biology↗

bioRxiv2022

Critical Role of Insertion Preference for Invasion Trajectory of Transposons

Transposable elements (TEs) are mobile DNA sequences that have been highly successful at invading eukaryotic genomes. It is unclear how TE families reach high copy number given the expectation that some novel insertions will be deleterious. It has been hypothesized that TE families may evolve to target and insert into specific DNA sequences to adjust the underlying distribution of fitness effects for new insertions. Preferentially inserting into neutral sites could minimize the cumulative deleterious load of a TE family, allowing the mean TE copy number to increase with less risk for host population extinction. To test this hypothesis, we constructed simulations to explore how the transposition probability and insertion preference of a TE family influence the evolution of mean TE copy number and host population size, allowing for extinction. We find that extinction is most common in our simulations under high transposition probabilities, but, as we reduce transposition rates, the risk of extinction persists while the preference for neutral insertion sites is high. In the absence of mechanisms that regulate TE transposition, a preference for neutral insertion sites is not protective and, in fact, actively accelerates both an increase in TE copy number and the time to population extinction.

evolutionary biology↗

bioRxiv2020

Reproductive compensation and embryo competition drive the evolution of polyembryony

Simple polyembryony - where one gametophyte produces multiple embryos with different sires but the same maternal haplotype - is common among vascular plants. We show that together polyembryonys two benefits - "reproductive compensation" achieved by providing a backup for inviable embryos, and the opportunity to favor the fitter of surviving embryos, can favor the evolution of polyembryony. To do so, we develop an infinite-site, forward population genetics model to test how these factors can favor the evolution of polyembryony, and how these underlying benefits of polyembryony shape the genetic load under a range of biological parameters. While these two benefits are difficult to disentangle in nature, we construct variant models of polyembryony that either only include or only exclude the opportunity for reproductive compensation. We find that reproductive compensation strongly favors the evolution of polyembryony, and that polyembryony is favored much more weekly in its absence, suggesting that the benefit of a backup embryo is the force favoring polyembryony. Remarkably we find nearly identical results in cases in which mutations impact either embryo or post-embryonic fitness (no pleiotropy), and in cases in which mutations have identical fitness effects embryo or post-embryonic fitness (extreme pleiotropy). Finally, we find that the consequences of polyembryony depends on its function - polyembryony results in a decrease in mean embryonic fitness when acting as a mechanism of embryo compensation, and ultimately increases mean embryonic fitness when we exclude this potential benefit. Nature is, above all, profligate. Dont believe them when they tell you how economical and thrifty nature is. - Annie Dillard 1974.

evolutionary biology↗

bioRxiv2020

Conflict over fertilization underlies the transient evolution of reinforcement

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 LD between trait and preference 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 in light of 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.

evolutionary biology↗

bioRxiv2020

Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and untapped variation available for improved breeding.

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremiseC_ST_ABSUnderstanding the relationship between genetic structure and geography provides information about a species evolutionary history and can be useful to breeders interested in de novo domestication. The North American prairie is especially interesting because of its relatively recent origin and subsequent dramatic fragmentation and degradation. Silphium integrifolium is an iconic perennial American prairie wildflower targeted for domestication as an oilseed crop. Germplasm in the existing breeding program is derived from accessions collected in restricted geographic regions. We present the first application of population genetic data in this species to address the following goals (1) improve breeding programs by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion. MethodsWe developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe the distribution of genetic variation and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection. Key resultsGenetic variation partitions samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American southeast. Breeding program accessions are from the region with lowest observed genetic variation. ConclusionsThis iconic prairie species did not originate within the modern prairie. Breeding programs can be improved by including accessions from outside of the germplasm founding region, which has relatively little variation. The geographic structuring coupled with the identified targets and drivers of adaptation can guide collecting efforts towards populations with beneficial agronomic traits.

evolutionary biology↗

bioRxiv2019

Identifying the fitness consequences of sex in complex natural environments

In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. Here we use a large-scale transplant experiment of a North American wildflower to show that sex is associated with reduced lifetime fitness, despite lower herbivory. We separate the effects of sex from hybridity, finding that over-winter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped by complex natural environments, correlated traits, and the identity of mates, rather than sex itself.

ecology↗

bioRxiv2018

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

Population-scale genomic datasets have given researchers incredible amounts of information from which to infer evolutionary histories. Concomitant with this flood of data, theoretical and methodological advances have sought to extract information from genomic sequences to infer demographic events such as population size changes and gene flow among closely related populations/species, construct recombination maps, and uncover loci underlying recent adaptation. To date most methods make use of only one or a few summaries of the input sequences and therefore ignore potentially useful information encoded in the data. The most sophisticated of these approaches involve likelihood calculations, which require theoretical advances for each new problem, and often focus on a single aspect of the data (e.g. only allele frequency information) in the interest of mathematical and computational tractability. Directly interrogating the entirety of the input sequence data in a likelihood-free manner would thus offer a fruitful alternative. Here we accomplish this by representing DNA sequence alignments as images and using a class of deep learning methods called convolutional neural networks (CNNs) to make population genetic inferences from these images. We apply CNNs to a number of evolutionary questions and find that they frequently match or exceed the accuracy of current methods. Importantly, we show that CNNs perform accurate evolutionary model selection and parameter estimation, even on problems that have not received detailed theoretical treatments. Thus, when applied to population genetic alignments, CNN are capable of outperforming expert-derived statistical methods, and offer a new path forward in cases where no likelihood approach exists.

evolutionary biology↗

bioRxiv2018

Heterosis from local drift load is likely insufficient to favor reversions to outcrossing

The evolutionary trajectory from cross-to self-fertilization is widely documented in nature, but results from several taxa also suggest that outcrossing may evolve in a formerly selfing population. Population genetic theory explains that selfing can evolve when its advantages overcome its immediate cost of inbreeding depression, but that this process will not run in reverse because a self-fertilizing population purges itself of inbreeding depression. That is, the primary short-term advantage of cross-fertilization over self-fertilization depends on the existence of deleterious alleles exposed upon inbreeding. Here, we explore whether outcrossing can evolve in selfing populations if allelic variation exists as divergence among populations. We consider two monomorphic populations of entirely self-fertilizing individuals, introduce a modifier allele that increases the rate of cross-fertilization, and investigate whether the heterosis among populations is sufficient for the modifier to invade and fix. We find that, despite an initial increase in the frequency of the outcrossing modifier, its fixation is possible only when populations harbor extremely large unique fixed genetic loads. These rare reversions to outcrossing become more likely as the load becomes more polygenic, or when the modifier appears on a rare background, such as by dispersal of an outcrossing genotype into a selfing population.

evolutionary biology↗