Biology subjects

Eldon, B.

Publications and source records attributed to Eldon, B..

7 recordsLinked to original sources

bioRxiv2026

Gene genealogies in diploid populations evolving according to sweepstakes reproduction

Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for understanding the ecology and evolution of highly fecund natural populations. Sweepstakes reproduction can induce jumps in type frequencies and multiple mergers in gene genealogies of sampled gene copies. We take sweepstakes reproduction to be skewed offspring number distribution due to mechanisms not involving natural selection, such as in chance matching of broadcast spawning with favourable environmental conditions. Here, we consider population genetic models of sweepstakes reproduction in a diploid panmictic populations absent selfing and evolving in a random environment. Our main results are (i) continuous-time Beta and Poisson-Dirichlet coalescents, when combining the results the skewness parameter of the Beta-coalescent ranges from 0 to 2, and the Beta-coalescents may be incomplete due to an upper bound on the number of potential offspring produced by any pair of parents; (ii) in large populations time is measured in units proportional to either N/ log N or N generations (where 2N is the population size when constant); (iii) it follows that incorporating population size changes leads to time-changed coalescents with the time-change independent of ; (iv) using simulations we show that the ancestral process is not well approximated by the corresponding coalescent (as measured through certain functionals of the processes); (v) whenever the skewness of the offspring number distribution is increased the conditional (conditioned on the population ancestry) and the unconditional ancestral processes are not in good agreement.

evolutionary biology↗

bioRxiv2026

Gene genealogies in haploid populations evolving according to sweepstakes reproduction

Recruitment dynamics, or the distribution of the number of offspring among individuals, is fundamental to ecology and evolution. We take sweepstakes reproduction to mean a skewed (heavy right-tailed) offspring number distribution without natural selection being involved. Sweepstakes may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents where a random number of lineages merges at such times. We consider population genetic models of sweepstakes reproduction for haploid panmictic populations of both constant (N), and varying population size, and evolving in a random environment. We construct our models so that we can recover the observed number of new mutations in a given sample without requiring strong assumptions regarding the population size or the mutation rate. Our main results are (i) continuous-time coalescents that are either the Kingman coalescent or specific families of Beta- or Poisson-Dirichlet coalescents; when combining the results the parameter of the Beta-coalescent ranges from 0 to 2, and the Beta-coalescents may be incomplete due to an upper bound on the number of potential offspring an arbitrary individual may produce; (ii) in large populations we measure time in units proportional to either N/ log N or N generations; (iii) incorporating fluctuations in population size leads to time-changed multiple-merger coalescents where the time-change does not depend on ; (iv) using simulations we show that in some cases approximations of functionals of a given coalescent do not match the ones of the ancestral process in the domain of attraction of the given coalescent; (v) approximations of functionals obtained by conditioning on the population ancestry (the ancestral relations of all gene copies at all times) are broadly similar (for the models considered here) to the approximations obtained without conditioning on the population ancestry.

evolutionary biology↗

bioRxiv2026

Beta-coalescents when sample size is large

Individual recruitment success, or the offspring number distribution of a given population, is a fundamental element in ecology and evolution. Sweepstakes reproduction refers to a highly skewed individual recruitment success without involving natural selection and may apply to individuals in broadcast spawning populations characterised by Type III survivorship. We consider an extension of the Schweinsberg (2003) model of sweepstakes reproduction for a haploid panmictic population of constant size N; the extension also works as an alternative to the Wright-Fisher model. Our model incorporates an upper bound on the random number of potential offspring (juveniles) produced by a given individual. Depending on how the bound behaves relative to the total population size, we obtain the Kingman (1982a,c,b) coalescent, an incomplete Beta-coalescent, or the (complete) Beta-coalescent of Schweinsberg (2003). We argue that applying such an upper bound is biologically reasonable. Moreover, we estimate the error of the coalescent approximation. The error estimates reveal that convergence can be slow, and small sample size can be sufficient to invalidate convergence, for example if the stated bound is of the form N/ log N. We use simulations to investigate the effect of increasing sample size on the site-frequency spectrum. When the limit is a Beta-coalescent, the site frequency spectrum will be as predicted by the limiting tree even though the full coalescent tree may deviate from the limiting one. When in the domain of attraction of the Kingman coalescent the effect of increasing sample size depends on the effective population size as has been noted in the case of the Wright-Fisher model. Conditioning on the population ancestry (the random ancestral relations of the entire population at all times) may have little effect on the site-frequency spectrum for the models considered here (as evidenced by simulation results).

evolutionary biology↗

bioRxiv2022

Genome-wide fixation under viability selection

We investigate through simulations the effect of random sweepstakes, recurrent bottlenecks, dominance, and epistasis on selection a diploid population when the phenotype is determined by the genotype at a number of unlinked sites. We assume there are two types at each site, the wild type and a type conferring selective advantage. The focus is on identifying main trends in how the stated elements impact selection when selection acts on at least two unlinked site. We give examples of fixation trajectories under an array of scenarios, and record corresponding numerical estimates of the probability of fixation of the fit type at all the sites in question each time, and the time to fixation conditional on fixation. The results suggest that joint fixation of the fit type at the sites can occur in a number of scenarios, despite starting with the fit type in a single copy at each site. Random sweepstakes generally reduce both the probability and the time to fixation (conditional on fixation). Recurrent strong bottlenecks generally reduce the probability of fixation, but the effect of bottlenecks on the time to fixation (conditional on fixation), depends on the dominance mechanism in question. We identify an example of epistasis where fixation can occur, when in the absence of epistasis fixation does not occur at all or with much lower probability. Our results, coupled with an extensive analysis of genomic data of Atlantic cod(4), is further evidence for pervasive strong positive selection as being a key driving force in the evolution at least of highly fecund populations.

evolutionary biology↗

bioRxiv2022

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.

evolutionary biology↗

bioRxiv2021

Efficient ancestry and mutation simulation with msprime 1.0

Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and tskit library. We summarise msprimes many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

genetics↗

bioRxiv2017

Genealogical properties of subsamples in highly fecund populations

We consider some genealogical properties of nested samples. The complete sample is assumed to have been drawn from a natural population characterised by high fecundity and sweepstakes reproduction (abbreviated HFSR). The random gene genealogies of the samples are -- due to our assumption of HFSR -- modelled by coalescent processes which admit multiple mergers of ancestral lineages looking back in time. Among the genealogical properties we consider are the probability that the most recent common ancestor is shared between the complete sample and the subsample nested within the complete sample; we also compare the lengths of internal branches of nested genealogies between different coalescent processes. The results indicate how informative a subsample is about the properties of the larger complete sample, how much information is gained by increasing the sample size, and how the informativeness of the subsample varies between different coalescent processes.

evolutionary biology↗