Biology subjects

Samuk, K.

Publications and source records attributed to Samuk, K..

14 recordsLinked to original sources

bioRxiv2026

Recombination accelerates adaptation across genetic architectures and demographic histories

According to classic population genetics theory, recombination shapes the efficacy of natural selection. However, whether variation in recombination rate itself translates into meaningful differences in adaptive capacity remains poorly understood. Here, we used forward-time simulations to examine polygenic adaptation in populations colonizing novel environments. We varied recombination rate eightfold, modeled QTL effect size distributions using three gamma distributions, and compared constant and contracted population sizes. Across all conditions, higher recombination rates modestly accelerated adaptation, reducing the time to reach a new phenotypic optimum by 2-15%. The benefit was substantially greater in constant-size populations than in those that had experienced a contraction, but did not differ across genetic architectures. To understand the mechanism of this acceleration, we tracked linkage disequilibrium among adaptation-related QTL throughout adaptation. We found that across simulations, beneficial alleles were consistently in repulsion phase with one another and in coupling phase with deleterious alleles, both signatures of Hill-Robertson interference. Higher recombination attenuated both forms of interference, indicating that the benefit of recombination operated primarily through relieving interference among QTL. These results implicate interference among linked loci as the primary constraint on polygenic adaptation in this context, and demographic history as a critical modulator of the benefit of recombination.

evolutionary biology↗

bioRxiv2026

Expanded unbiased population-genomic summary statistics in pixy

Estimates of population-genetic summary statistics are often computed from variant-only VCFs, which commonly omit invariant sites (i.e. sites with only homozygous reference genotypes across all samples). However, these sites are critical for correctly estimating per site statistics such as nucleotide diversity ({pi}) and between population divergence (dxy). Our software pixy addressed this issue by providing support for computing statistics directly from "all-sites" VCFs that encode invariant positions explicitly (Korunes and Samuk 2021). pixy has since been widely adopted and used in a large variety of population genetic studies. Here we present a major update to pixy, which expands the original tool in four major areas. First, we provide implementations of new estimators of Wattersons {theta} and Tajimas D that are unbiased with respect to missing data. Secondly, we provide support for arbitrary ploidy and multiallelic sites. Third, we introduce a variety of optimizations, including multicore execution and a roughly order-of-magnitude reduction in per-worker memory footprint. Finally, we have broadly modernized our code base, test suite, and community contribution pathway. We validate these new features on simulated polyploid and multiallelic datasets, as well as two empirical datasets (one diploid and one autotetraploid), and benchmark the new multicore scaling. We position pixy relative to contemporary tools and discuss shared limitations of VCF-based estimators. By integrating support for diverse ploidies, allelic complexity, and genome-wide scale in one workflow, pixy provides the population genetics community with a straightforward tool for estimates of key summary statistics that are unbiased with respect to missing data. pixy remains completely open-source (MIT-licensed) and easily installable with the conda package management system.

bioinformatics↗

bioRxiv2026

The gonad as a mediator of life history tradeoffs: Antagonistic hormonal pleiotropy facilitates evolutionary divergence in reproductive strategies

High investment in current reproduction can limit future reproductive opportunities, but how selection shapes these hormone-mediated traits remains poorly understood. Androgens can mediate male reproductive investment, and in three-spined stickleback (Gasterosteus aculeatus), exert antagonistic effects on breeding effort versus spermatogenesis. To understand how shifts in reproductive strategy shape this tradeoff, we compared testes transcriptomes and androgen production between two recently diverged stickleback ecotypes that differ in reproductive strategy: the ancestral "common" ecotype, which provides paternal care, and the non-parental "white" ecotype, which has lost paternal care and prioritizes mating effort. During typical breeding, testes gene expression differed little between ecotypes. However, under prolonged summer-like conditions, testes gene expression diverged substantially. Common-biased genes were enriched for meiotic functions and spermatogenic cell type markers, suggesting commons had initiated spermatogenesis while whites had not. Instead, whites expressed higher levels of steroidogenic candidate genes and released significantly more 11-ketotestosterone than commons, indicating sustained investment in current reproduction. F1 hybrids released 11-ketosterone at intermediate rates, suggesting a genetic basis for this divergence. Sustained androgen production in whites may possibly delay the transition into spermatogenesis, limiting investment in future reproduction. These results illustrate how selection on hormonally-integrated traits can drive rapid divergence in life history strategy.

evolutionary biology↗

bioRxiv2025

Genetic divergence in the absence of strong ecological differences between coexisting white and common Atlantic marine sticklebacks

Identifying taxa in the earliest phases of speciation is critical for understanding how reproductive isolation arises. In Nova Scotia, Canada, "white" threespine sticklebacks co-occur with common marine sticklebacks but differ in nuptial coloration, nesting behavior, and parental care, raising the possibility that they represent a nascent species. We combined population genomics, morphometrics, and stable isotope analysis to test whether white sticklebacks represent a distinct lineage and whether they have diverged along ecological axes as in other stickleback populations. Genotyping-by-sequencing revealed that male and female white sticklebacks form a genetic cluster distinct from sympatric common sticklebacks with evidence of ongoing gene flow yet with very low overall genomic divergence (FST {approx} 0.01). Genetic differences were distributed across many loci rather than localized to a single genomic region. Morphological and isotopic analyses revealed no differences in most classic ecological traits (body shape, armor, gill rakers, or trophic niche). Instead, whites are smaller-bodied, paler, and exhibit shorter spines, reduced testes size, and smaller but more numerous eggs compared to common sticklebacks. These results indicate that white sticklebacks are genetically distinct from the common Atlantic threespine stickleback but have not diverged conspicuously in their ecology, suggesting that their differentiation is driven by reproductive and sexual traits rather than trophic specialization. The white stickleback thus represents a promising new system for investigating the interplay of sexual selection, reproductive strategy, and gene flow in the early stages of speciation.

evolutionary biology↗

bioRxiv2025

Strong but diffuse genetic divergence underlies differentiation in an incipient species of marine stickleback

Understanding how lineages proceed along the "speciation continuum" and how species boundaries are maintained over time remain central questions in evolutionary biology. Populations early in the speciation process can give us detailed insight into the reproductive barriers that first initiate speciation. In this study, we explore the nature of genomic divergence between two sympatric marine stickleback ecotypes from Atlantic Canada, "whites" and "commons". Males of each ecotype exhibit distinct nuptial colorations, nesting habits, and parental care strategies. Using population genomic analyses of SNPs and copy number variants (CNVs; deletions and duplications) we show that whites and commons consistently form distinct populations. We uncover genomic differentiation in the white ecotype characteristic of an incipient species, showing extremely low genome-wide differentiation (FST) and very recent divergence ([~]1 kya). Demographic analysis detected very low levels of ongoing gene flow between populations. Our results and prior genomic studies suggest that reproductive isolation is being maintained between ecotypes despite recent evidence that hybridization in nature does occur. Contrary to other systems, we found many small, but dispersed regions of high differentiation throughout the genome rather than explicitly within chromosomal inversions or the sex chromosomes. On chromosomes VII and XVI, we identified CNVs overlapping genes enriched for olfaction, which may play a role in differences in reproductive strategies between ecotypes. Ultimately, our results demonstrate that genome-wide rather than localized differences can underlie the early stages of divergence, and that this pattern is corroborated by both SNPs and CNVs.

evolutionary biology↗

bioRxiv2025

Evidence of parental care as a novel reproductive isolating mechanism

Variation in behavior can contribute to reproductive isolation by preventing gene flow among populations. Here, we tested the novel hypothesis that parental care, when dysregulated, can function as a reproductive isolating mechanism in three-spined stickleback fish (Gasterosteus aculeatus). In the typical "common" stickleback ecotype, males provide care to their offspring by fanning with their pectoral fins and defending their nest. In contrast, a divergent "white" stickleback ecotype has evolutionarily lost care and disperses embryos into the surrounding environment. We examined how paternal care from common, white, and F1 hybrid fathers influenced offspring survival. We detected no intrinsic incompatibilities in embryos, but F1 hybrid fathers exhibited dysregulated parental care that coincided with decreased survival of parented offspring. The increased offspring mortality may be explained by further dysregulation of feeding and parenting circuitry, as F2 hybrids exhibited significantly higher rates of post-fertilization filial cannibalism than common or white fathers. Additionally, despite strong divergence in nesting-building and courtship behavior, F1 hybrids achieved mating success at a similar rate as male commons and whites, suggesting that prezygotic barriers against hybrids may be weak. The observed postzygotic isolation, and potentially weak prezygotic isolation in lab-based studies, suggest that hybridization is likely occurring at low rates in the wild. Population genetic analysis supported this, as low proportions of putative hybrids were detected in sympatric sites. Together, these results may help explain why genetic divergence between these phenotypically distinct ecotypes is low and provide evidence that dysregulated parental behavior can act as a newly discovered postzygotic reproductive isolating barrier.

evolutionary biology↗

bioRxiv2025

vcfsim: flexible simulation of all-sites VCFs with missing data

BackgroundVCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invariant sites") and thus do not differentiate these from sites where data are completely missing. However, missing data are a key feature of biological datasets across all domains of genomics, and many recent studies have shown that missing data can introduce a variety of statistical biases in the estimation of key population genetic parameters. A solution to this limitation is to include invariant sites in a standard VCF, creating an "all-sites VCF", exposing missing and invariant sites explicitly. One hurdle to the wider adoption of all-sites VCFs is a reliable parameterized simulation framework for generating biologically realistic all-sites VCFs. ResultsHere, we introduce an open-source command line tool, vcfsim, that interfaces with the popular coalescent simulation platform msprime and provides convenience functions for simulating all-sites VCFs with variable levels of ploidy and missing data. We show that the post-processed VCFs generated using vcfsim align precisely with population genetic expectations (i.e. are statistically identical to raw msprime output), accurately introduce missing data, and permit the simulation of data with varying ploidy levels, including the simulation of intraindividual ploidy variation (e.g. heterogametic sex chromosomes) and population structures. ConclusionsOur results vcfsim is a useful and easy-to-use tool for the benchmarking of new software tools, performing population genetic inference, training of machine learning models, and the exploration of the effects of missing data in genomics data sets.

bioinformatics↗

bioRxiv2022

Chromosomal inversions can limit adaptation to new environments

Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But, what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may also provide one possible explanation for why inversions are often maintained as polymorphisms within species.

evolutionary biology↗

bioRxiv2021

Gene flow biases population genetic inference of recombination rate

Accurate estimates of the rate of recombination are key to understanding a host of evolutionary processes as well as the evolution of recombination rate itself. Model-based population genetic methods that infer recombination rates from patterns of linkage disequilibrium (LD) in the genome have become a popular method to estimate rates of recombination. However, these LD-based methods make a variety of simplifying assumptions about the populations of interest that are often not met in natural populations. One such assumption is the absence of gene flow from other populations. Here, we use forward-time population genetic simulations of isolation-with-migration scenarios to explore how gene flow affects the accuracy of LD-based estimators of recombination rate. We find that moderate levels of gene flow can result in either the overestimation or underestimation of recombination rates by up to 20-50% depending on the timing of divergence. We also find that these biases can affect the detection of interpopulation differences in recombination rate, causing both false positive and false negatives depending on the scenario. We discuss future possibilities for mitigating these biases and recommend that investigators exercise caution and confirm that their study populations meet assumptions before deploying these methods.

evolutionary biology↗

bioRxiv2020

pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the most fundamental of these summary statistics are{pi} and dXY, which are used to describe genetic diversity within and between populations, respectively. Here, we address a widespread issue in{pi} and dXY calculation: systematic bias generated by missing data of various types. Many popular methods for calculating{pi} and dXY operate on data encoded in the Variant Call Format (VCF), which condenses genetic data by omitting invariant sites. When calculating{pi} and dXY using a VCF, it is often implicitly assumed that missing genotypes (including those at sites not represented in the VCF) are homozygous for the reference allele. Here, we show how this assumption can result in substantial downward bias in estimates of{pi} and dXY that is directly proportional to the amount of missing data. We discuss the pervasive nature and importance of this problem in population genetics, and introduce a user-friendly UNIX command line utility, pixy, that solves this problem via an algorithm that generates unbiased estimates of{pi} and dXY in the face of missing data. We compare pixy to existing methods using both simulated and empirical data, and show that pixy alone produces unbiased estimates of{pi} and dXY regardless of the form or amount of missing data. In sum, our software solves a long-standing problem in applied population genetics and highlights the importance of properly accounting for missing data in population genetic analyses.

genetics↗

bioRxiv2019

Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura

While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.

genetics↗

bioRxiv2019

Ancestral reconstruction of sunflower karyotypes reveals dramatic chromosomal evolution

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous ad-hoc methods while being systematic, repeatable, and is applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax. Using syntR, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years - a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.

evolutionary biology↗

bioRxiv2019

Adaptive introgression during environmental change can weaken reproductive isolation

Anthropogenic climate change is an urgent threat to species diversity. One aspect of this threat is the collapse of species reproductive barriers through increased hybridization. The primary mechanism for this collapse is thought to be the weakening of ecologically-mediated reproductive barriers, as demonstrated in many cases of "reverse speciation" . Here, we expand on this idea and show that adaptive introgression between species adapting to a shared, moving climatic optimum can readily weaken any reproductive barrier, including those that are completely independent of the climatic variable. Using genetically explicit forward-time simulations, we show that genetic linkage between alleles conferring adaptation to a changing climate and alleles conferring reproductive isolation can lead to adaptive introgression facilitating the homogenization of reproductive isolation alleles. This effect causes the decay of species boundaries across a broad and biologically-realistic parameter space. We explore how the magnitude of this effect depends upon the rate of climate change, the genetic architecture of adaptation, the initial degree of reproductive isolation and the mutation rate. These results highlight a previously unexplored effect of rapid climate change on species diversity.

evolutionary biology↗

bioRxiv2018

Evolutionary dynamics of recent selection for enhanced social cognition

Cognitive abilities can vary dramatically among species though little is known about the dynamics of cognitive evolution. Here we demonstrate that recent evolution of visual individual recognition in the paper wasp Polistes fuscatus is the target of arguably the strongest positive selective pressure in the species recent history. The most extreme selective sweeps in P. fuscatus are associated with genes known to be involved in long-term memory formation, mushroom body development and visual processing - all traits that have recently evolved in association with individual recognition. Cognitive evolution appears to have been driven initially by selection on standing variation in perceptual traits followed by both hard and soft sweeps on learning and memory. Evolutionary modeling reveals that intense selection as observed in P. fuscatus is likely the norm during the early stages of cognitive evolution. These data provide insight into the dynamics of cognition evolution demonstrating that social selection for increased intelligence can lead to rapid multi-genic adaptation of enhanced recognition abilities.

animal behavior and cognition↗