Biology subjects

Veller, C.

Publications and source records attributed to Veller, C..

17 recordsLinked to original sources

bioRxiv2026

Sexually antagonistic environments and the stability of environmental sex determination

Just as sexually antagonistic genetic variants have different effects on male and female fitness, environmental conditions too can have sexually antagonistic fitness effects. Such Charnov-Bull effects have been invoked to explain the origin and persistence of environmental sex determination (ESD), which allows development of each sex in the environments in which it has a comparative advantage. Here, we study different forms of Charnov-Bull effects to characterize how they shape the evolution and stability of ESD. We show that the precise functional form of Charnov-Bull effects can generate large differences in the vulnerability of ESD systems to the invasion of sex-biasing alleles, as well as in the fate of those alleles if they invade. For some configurations of Charnov-Bull effects, strong sex-biasing alleles are likely to spread to intermediate frequencies, rather than to fixation, resulting in mixed ESD systems in which large genetic effects segregate. Overall, our results indicate that the precise nature of Charnov-Bull effects can play a crucial role in the evolutionary dynamics of ESD.

evolutionary biology↗

bioRxiv2025

Quantitative system drift

We consider a biological system composed of multiple genetically variable components, the combined result of which is a quantitative trait under stabilizing selection for an optimal value. We show mathematically that, while the mean value of the system is ultimately constrained to remain near its optimum, the values of individual components are free to drift far from their initial values. Each components drift, though qualitatively similar to neutral drift, is slower by a factor that depends on the fraction of the systems genetic variance contributed by the component. Our results provide a population-genetic basis for system drift, the concept that individual components of a biological system can evolve despite selective constraint on their combined product. A special case is a single polygenic trait under stabilizing selection, where our results predict that the mean genetic contributions to the trait of different subregions of the genome, such as the chromosomes, can drift despite constraint on the genome-wide genetic value. We explore the implications of this latter result for selection against interspecific hybrids and selection against turnovers of sex-determining systems. We further apply our general results to a continuous public goods game played between two species, where they predict that individual species contributions to a costly public good can drift freely. Finally, we show that symmetric mutation between alleles that increase and decrease components contributions to the system provides a weak long-term brake on components drift.

evolutionary biology↗

bioRxiv2024

Stabilizing selection generates selection against introgressed DNA

DNA introgressed from one population into another is often deleterious to the recipient population if the two populations have diverged genetically from one another. Previous explanations of this phenomenon have posited negative interactions between donor-population alleles and the recipient populations genome or environment, or higher genetic load in the donor population. Here, we show that stabilizing selection on quantitative traits--even around the same optimal trait values in the two populations and when the populations are demographically identical--generates selection against the minor-parent ancestry in a population formed via unequal admixture of the two populations. We calculate the rate at which minor-parent ancestry is purged under this mechanism, both in the early generations after admixture and in the long term, and we verify these calculations with whole-genome simulations. Because of its ubiquity, stabilizing selection offers a general mechanism for the deleterious effect of introgressed ancestry.

evolutionary biology↗

bioRxiv2024

The effect of long-range linkage disequilibrium on allele-frequency dynamics under stabilizing selection

Stabilizing selection on a polygenic trait reduces the traits genetic variance by (i) generating correlations (linkage disequilibria) between opposite-effect alleles throughout the genome, and (ii) selecting against rare alleles at loci that affect the trait, eroding heterozygosity at these loci. Here, we show that the linkage disequilibria, which stabilizing selection generates on a rapid timescale, slow down the subsequent allele-frequency dynamics at individual loci, which proceed on a much longer timescale. Exploiting this separation of timescales, we obtain expressions for the expected per-generation change in minor-allele frequency at individual loci, as functions of the effect sizes at these loci, the strength of selection on the trait, its variance and heritability, and the linkage relations among loci. Using whole-genome simulations, we show that our expressions predict allele-frequency dynamics under stabilizing selection more accurately than the formulae that have previously been used for this purpose. Our results have implications for understanding the genetic architecture of complex traits.

genetics↗

bioRxiv2023

Causal interpretations of family GWAS in the presence of heterogeneous effects

Family-based genome-wide association studies (GWAS) have emerged as a gold standard for assessing causal effects of alleles and polygenic scores. Notably, family studies are often claimed to provide an unbiased estimate of the average causal effect (or average treatment effect; ATE) of an allele, on the basis of an analogy between the random transmission of alleles from parents to children and a randomized controlled trial. Here, we show that this interpretation does not hold in general. Because Mendelian segregation only randomizes alleles among children of heterozygotes, the effects of alleles in the children of homozygotes are not observable. Consequently, if an allele has different average effects in the children of homozygotes and heterozygotes, as can arise in the presence of gene-by-environment interactions, gene-by-gene interactions, or differences in LD patterns, family studies provide a biased estimate of the average effect in the sample. At a single locus, family-based association studies can be thought of as providing an unbiased estimate of the average effect in the children of heterozygotes (i.e., a local average treatment effect; LATE). This interpretation does not extend to polygenic scores, however, because different sets of SNPs are heterozygous in each family. Therefore, other than under specific conditions, the within-family regression slope of a PGS cannot be assumed to provide an un-biased estimate for any subset or weighted average of families. Instead, family-based studies can be reinterpreted as enabling an unbiased estimate of the extent to which Mendelian segregation at loci in the PGS contributes to the population-level variance in the trait. Because this estimate does not include the between-family variance, however, this interpretation applies to only (roughly) half of the sample PGS variance. In practice, the potential biases of a family-based GWAS are likely smaller than those arising from confounding in a standard, population-based GWAS, and so family studies remain important for the dissection of genetic contributions to phenotypic variation. Nonetheless, the causal interpretation of family-based GWAS estimates is less straightforward than has been widely appreciated.

genetics↗

bioRxiv2023

Interpreting population and family-based genome-wide association studies in the presence of confounding

A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individuals phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding, and can also absorb the indirect genetic effects of relatives genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of Mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect size estimates are used in polygenic scores. We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. In addition to known biases that can arise in family-based GWASs when interactions between family members are ignored, we show that biases can also arise from gene-by-environment (GxE) interactions when parental genotypes are not distributed identically across interacting environmental and genetic backgrounds. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding and interactions.

genetics↗

bioRxiv2023

Two teosintes made modern maize

Despite its global importance as a crop with broad economic, dietary, and cultural importance, the origins of maize and its closest wild relatives remained the topic of vigorous debate for nearly a century. Molecular analyses ultimately concluded that maize was domesticated once from a common ancestor with its closest extant relative, the lowland wild grass Zea mays ssp. parviglumis. But neither the current genetic model nor earlier models based on archaeological data account for the totality of available data, and recent work has highlighted the potential contribution of a second wild relative, the highland Zea mays ssp. mexicana. Here we present a detailed population genetic analysis of the contributions of both wild taxa to modern maize diversity using the largest sample of traditional maize varieties sequenced to date. We show that all modern maize can trace its origin to an ancient admixture event between domesticated ancient maize and Zea mays ssp. mexicana in the highlands of Mexico ca 5300 cal BP, some 4,000 years after domestication began. We show that variation in admixture is a key component of modern maize genetic and phenotypic diversity, both at the level of individual loci and as a factor driving a substantial component of additive genetic variation across a number of agronomic traits. Our results clarify the long-debated origin of modern maize, highlight the potential contributions of crop wild relatives to agronomic improvement, and raise new questions about the anthropogenic mechanisms underlying multiple waves of dispersal throughout the Americas. One-Sentence SummaryOur results clarify the long-debated origin of modern maize and highlight the contributions of crop wild relatives to the agronomic improvement of modern varieties.

evolutionary biology↗

bioRxiv2021

Mate choice enhances post-zygotic barriers to gene flow via ancestry bundling

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, selection often purges introgressed DNA genome-wide. While mate choice can prevent hybridization in the first place, it is also known to play an important role in post-zygotic selection against hybrids, and thus the purging of introgressed DNA. However, this role is usually thought of as a direct one: a mating preference for conspecifics reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of mate choice as a barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which post-zygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choices overall effect as a post-zygotic barrier to gene flow, and that it is driven by ancestry covariances between and within maternally and paternally inherited genomes. We derive a simple method for estimating the impact of the bundling effect from standard measures of assortative mating. Applying this method to data from a diverse set of hybrid zones, we find that the bundling effect increases the purging of introgressed DNA by between 1.2-fold (in a baboon system with weak assortative mating) and 14-fold (in a swordtail system with strong assortative mating). Thus, the bundling effect of mate choice contributes substantially to the genetic isolation of species.

evolutionary biology↗

bioRxiv2021

Dominance shifts increase the likelihood of soft selective sweeps

Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from the standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.

evolutionary biology↗

bioRxiv2020

Variation in genetic relatedness is determined by the aggregate recombination process

The genomic proportion that two relatives share identically by descent--their genetic relatedness-- can vary depending on the history of recombination and segregation in their pedigree. This variation is important in many applications of genetics, including pedigree-based estimation of the genetic variance and heritability of traits, and estimation of pedigree relationships from sequence data. Here, we calculate the variance of genetic relatedness for general pedigree relationships, making no assumptions about the recombination process. For the specific relationships of grandparent-grandoffspring and siblings, the variance of genetic relatedness is a simple decreasing function of [Formula], the average proportion of locus pairs that recombine in meiosis. For general pedigree relationships, the variance of genetic relatedness is likewise the average of some function of pairwise recombination rates. Therefore, features of the aggregate recombination process that affect [Formula] and analogs also affect variance in genetic relatedness. Such features include the number of chromosomes and heterogeneity in their size, and the number of crossovers and their location along chromosomes. Our calculations help to explain several recent observations about variance in genetic relatedness, including that it is reduced by crossover interference (which is known to increase [Formula]). Our methods further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling precise statistical inference in F2-based tests for various kinds of selection.

genetics↗

bioRxiv2020

Invasion and maintenance of spore killing in ascomycete fungi

Meiotic drivers are selfish genetic elements that are able to become over-represented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether a meiotic driver can invade a population, and subsequently reach fixation or coexist in a stable polymorphism, depends on the one hand on the biology of the host organism, including its life-cycle, mating system, and population structure, and on the other hand on the specific fitness effects of the driving allele on the host. Here, we present a population genetic model for spore killing, a type of drive specific to fungi. We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here to two well-studied genera of filamentous ascomycetes known to harbor spore killing elements, Neurospora and Podospora. We discuss our results in the light of recent empirical findings for these two systems.

evolutionary biology↗

bioRxiv2019

Recombination, variance in genetic relatedness, and selection against introgressed DNA

DNA introgressed from one species into another is typically deleterious at many genomic loci in the recipient species. It is therefore purged by selection over time. Here, we use mathematical modeling and whole-genome simulations to study the influence of recombination on the purging of introgressed DNA. We find that aggregate recombination controls the genome-wide rate of purging in the first few generations after admixture, when purging is most rapid. Aggregate recombination is quantified by [Formula], the average recombination rate across all locus pairs, and analogous metrics. It is influenced by the number of crossovers (i.e., the map length) and their locations along chromosomes, and by the number of chromosomes and heterogeneity in their size. A comparative prediction of our analysis is that species with fewer chromosomes should purge introgressed DNA more profoundly, and therefore should exhibit a weaker genomic signal of historical introgression. With regard to patterns across the genome, we show that, in heterogametic species with autosomal recombination in both sexes, more purging is expected on sex chromosomes than on autosomes, all else equal. The opposite prediction holds for species without autosomal recombination in the heterogametic sex. Finally, we show that positive genomic correlations between local recombination rate and introgressed ancestry, as recently observed in several taxa, are likely driven not by recombinations effect in unlinking neutral from deleterious introgressed alleles, but rather by its effect on the rate of purging of the deleterious alleles themselves. Note on this versionAn earlier version of this manuscript had two parts: (1) Calculations of the variance of genetic relatedness between individuals with particular pedigree relationships, taking into account the randomness of recombination and segregation in their pedigree. (2) An investigation of the rate of purging of introgressed DNA following admixture, based in part on results from part (1). Part (1) has since been published as Veller et al. (2020). The present manuscript has been reconfigured to focus on part (2).

evolutionary biology↗

bioRxiv2019

On the logic of Fisherian sexual selection

In Fishers model of sexual selection, a female preference for a male trait spreads together with the trait because their genetic bases become correlated. This can be interpreted as a greenbeard system: a preference gene, by inducing a female to mate with a trait-bearing male, favors itself because the male is disproportionately likely also to carry the preference gene. Here, we use this logic to argue that Fisherian sexual selection in diploids proceeds via two channels, corresponding to two reasons that trait-bearing males disproportionately carry preference genes: (i) trait-bearing males are disproportionately the product of matings between preference-bearing mothers and trait-bearing fathers, and thus trait and preference genes are correlated in trans; (ii) trait and preference genes come into gametic phase disequilibrium, and thus are correlated in cis. Gametic phase disequilibrium is generated by three distinct mechanisms: a recombination mechanism, a dominance mechanism, and a sexual admixture mechanism. The trans channel does not operate when sexual selection is restricted to the haploid phase, and therefore represents a fundamental difference between haploid and diploid models of sexual selection. We use simulation experiments to artificially eliminate the cis channel, and show that a preference gene can spread in its absence in the diploid model, but not in the haploid model. We further show that the cis and trans channels contribute equally to the spread of the preference when recombination between the preference and trait loci is free, but that the trans channel becomes substantially more important when linkage is tight.

evolutionary biology↗

bioRxiv2018

Selection for synchronized cell division in simple multicellular organisms

The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a simple population model in which there compete simple multicellular organisms that grow either by synchronous or asynchronous cell divisions. We demonstrate that natural selection can act differently on synchronous and asynchronous cell division, and we offer intuition for why these phenotypes are generally not neutral variants of each other.

evolutionary biology↗

bioRxiv2017

The distribution of crossovers, and the measure of total recombination

Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. However, such studies have been ham-pered by the fact that there has been no direct measure of this quantity. Existing measures consider crossing over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate because the positions of crossovers along a chromosome are also critical: a crossover towards the middle of a chromosome causes more shuffling than a crossover towards the tip. More-over, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendels second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter[r] as the probability that the alleles at two randomly chosen loci will be shuffled in the production of a gamete. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that[r] is larger when crossovers are more evenly spaced, which suggests a novel selective advantage of crossover interference. Utilization of[r] is enabled by powerful emergent methods for determining crossover positions, either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that: (i)[r] in humans is close to its maximum possible value of 1/2, (ii) this high level of shuffling is due almost entirely to independent assortment, whose contribution is ~30 times greater than that of crossovers.

genetics↗

bioRxiv2017

Drift-Induced Selection Between Male And Female Heterogamety

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes and in those creating a new pair. In fact, substitution rates are strongly biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of drift-induced selection operating at every point along the equilibrium paths: stochastic jumps off the paths return, on average, with a directional bias in favor of the dominant segregating sex chromosome. Our results offer novel explanations for the ubiquity of transitions between male and female heterogamety and the preponderance of dominant major sex determining genes.

evolutionary biology↗

bioRxiv2017

The evolution of queen control over worker reproduction in the social Hymenoptera

A trademark of eusocial insect species is reproductive division of labor, in which workers forego their own reproduction while the queen produces almost all offspring. The presence of the queen is key for maintaining social harmony, but the specific role of the queen in the evolution of eusociality remains unclear. A long-discussed scenario is that a queen either behaviorally or chemically sterilizes her workers. However, the demographic and ecological conditions that enable such manipulation are unknown. Accordingly, we propose a simple model of evolutionary dynamics that is based on haplodiploid genetics. We consider a mutation that acts in a queen, causing her to control the reproductive behavior of her workers. Our mathematical analysis yields precise conditions for the evolutionary emergence and stability of queen-induced worker sterility. These conditions do not depend on the queen's mating frequency. Moreover, we find that queen control is always established if it increases colony reproductive efficiency and can evolve even if it decreases colony efficiency. We further outline the conditions under which queen control is evolutionarily stable against invasion by mutant, reproductive workers.

evolutionary biology↗