Biology subjects

Sendrowski, J.

Publications and source records attributed to Sendrowski, J..

6 recordsLinked to original sources

bioRxiv2026

Ancestree: unified likelihood inference of ancestral alleles under supplied or inferred genealogies

Inferring ancestral states--determining, at each polymorphic site, which allele is ancestral and which derived--underpins many downstream population-genetic analyses, from selection scans and the unfolded site-frequency spectrum to demographic inference. However, no existing tool uniformly supports the full range of relevant inputs: plain variant data or ancestral recombination graphs (ARGs), with or without outgroups, while accommodating poly-allelic and recurrently-mutated sites. Here we present Ancestree, a likelihood-based engine that unifies these inputs within a single framework and returns full posteriors over the four nucleotide states at every site. It runs in three modes: a fixed-tree mode that assumes a single topology across sites and co-infers the per-branch substitution rates by maximum likelihood; an ARG mode that reads a different local tree at each site directly from a supplied ancestral recombination graph; and a local-tree mode that instead samples those local trees from the genotype data via a pairwise-coalescent HMM, needing no pre-existing ARG. On simulated data, the genealogy-based modes (ARG and local-tree) are more accurate and scale better, and remain robust under outgroup configurations that violate the fixed-tree assumption. Outgroups themselves remain difficult to replace: per-site inference accuracy on ingroup-polymorphic sites is markedly limited without them, and improves substantially with a single outgroup. The hardest sites are those fixed for the derived allele within the ingroup, which carry no within-ingroup signal and so need several sufficiently deep outgroups to recover, yet these are also highly informative downstream, carrying the high-frequency divergence signal on which selection and adaptation analyses often depend. Ancestree is available at github.com/Sendrowski/Ancestree.

evolutionary biology↗

bioRxiv2026

Comparison of the Distribution of Fitness Effects Across Primates

The distribution of fitness effects (DFE) of mutations is a key determinant of both the efficacy of natural selection and the genetic load of populations. It also provides an indirect summary of the underlying fitness landscape, so the extent to which the DFE is conserved across species is informative about the invariance of those landscapes. Here, we infer the DFE of amino-acid-changing mutations in 38 catarrhine subspecies using site-frequency spectrum (SFS)-based methods. We find that effective population size (Ne) is the dominant axis of cross-species variation in the population-scaled DFE for deleterious mutations, with the apparent clade-level clustering of estimates explained mainly by shared Ne rather than by clade-specific effects. A quantile-based test further shows that the underlying unscaled DFE does not vary significantly across species, so differences are consistent with Ne-rescaling of a single conserved DFE. Consistent with this, the deleterious (non-adaptive) substitution rate {omega}na declines significantly with Ne, reflecting more efficient purging of slightly deleterious mutations in larger populations. Turning to adaptive substitution, we find weaker, suggestive evidence that the adaptive rate {omega}a increases with Ne. These conclusions are robust to the choice of DFE parametrization, phylogenetic regression framework, the effect of GC-biased gene conversion, and ancestral misidentification. We also extend the DFE estimation procedure to relax the assumption of additive fitness effects, finding that dominance is only weakly identifiable from the SFS but has minimal impact on comparative DFE inference.

evolutionary biology↗

bioRxiv2025

The genomic basis of local adaptation in the white x Engelmann spruce hybrid zone

Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migration and selection, and identifying loci involved in adaptation and reproductive isolation. However, interpreting how evolutionary processes shape genomic patterns can be challenging: repeatability of genotype-environment association alone is not strong evidence for selection, as hybrid zones derived from the same parental species are not evolutionarily independent. Conversely, processes that operate within the middle of each hybrid zone, such as selection driving directional introgression, may be more evolutionarily independent, and therefore provide stronger evidence of selection. Here we compared hybridization and local adaptation patterns between two replicated regions within the western Canada interior spruce hybrid zone: a broad latitudinal transect with gradual environmental variation and a narrow elevational transect with substantial topographical and environmental variation. We discovered a complex pattern of introgression, with strong differences in ancestry maintained even across small spatial scales at several locations along the elevational transect. Despite differences in their spatial scales, the elevational and latitudinal transects revealed strikingly similar genome-wide patterns of differentiation and adaptation, and consistent patterns of directional introgression. We explore the extent to which the evolutionary non-independence of these hybrid zones allows inferences about the role of natural selection and drift in shaping these patterns. Consistent with theory, we found longer genomic tracts in the elevational transect, likely because the steeper environmental gradients over shorter distances limit the rate of mixing by migration and recombination relative to drift and selection.

evolutionary biology↗

bioRxiv2025

PhaseGen: Exact Solutions for Time-Inhomogenous Multivariate Coalescent Distributions under Diverse Demographies

Phase-type theory is emerging as a powerful framework for modeling coalescent processes, allowing for the exact computation of quantities of interest. This includes moments of tree height, total branch length, the site-frequency spectrum (SFS), and the full distribution of the time to the most recent common ancestor (TMRCA). However, prior applications have largely been limited to time-homogeneous settings, with constant population sizes and migration rates, restricting the range of demographic scenarios that can be modeled. In this study, we apply time-inhomogeneous phase-type theory to enable the exact computation of (cross-)moments of arbitrary order and reward structure under piecewise-constant demographies. This extension enables the modeling of significantly more complex demographic scenarios, including population expansions, contractions, bottlenecks, and splits. It furthermore supports the fitting of demo-graphic models to data through gradient-based optimization. To support these advancements, we introduce PhaseGen--a software package designed for the numerically stable computation of exact moments under diverse demographic scenarios, with support for gradient-based parameter estimation.

genetics↗

bioRxiv2023

fastDFE: fast and flexible joint inference of the distribution of fitness effects

Estimating the distribution of fitness effects (DFE) of new mutations is of fundamental importance in evolutionary biology, ecology, and conservation. However, existing methods for DFE estimation suffer from limitations, such as slow computation speed and limited scalability. To address these issues, we introduce fastDFE, a Python-based software package, offering fast and flexible DFE inference from site-frequency spectrum (SFS) data. Apart from providing efficient joint inference of multiple DFEs that share parameters, it offers the feature of introducing genomic covariates that influence the DFEs, and testing their significance. To further simplify usage, fastDFE is equipped with comprehensive VCF-to-SFS parsing utilities. These include options for site filtering and stratification, as well as site-degeneracy annotation and probabilistic 11 ancestral-allele inference. fastDFE thereby covers the entire workflow of DFE inference from the moment of acquiring a raw VCF file. Despite its Python foundation, fastDFE comprises a full R interface, including native R visualization capabilities. The package is comprehensively tested, and documented at fastdfe.readthedocs.io.

evolutionary biology↗

bioRxiv2022

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones. Significance StatementUnderstanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.

evolutionary biology↗