Biology subjects

Howell, E. K.

Publications and source records attributed to Howell, E. K..

6 recordsLinked to original sources

bioRxiv2026

Evolution of mutational fitness effects in island populations

The distribution of fitness effects (DFE) quantifies the selective consequences of newly arising mutations. Theoretical and empirical investigations of the DFE suggest that it is highly context-specific, shaped by both intrinsic properties of an organism (e.g., biological complexity) and extrinsic properties of a population (e.g., environment). Despite recent comparisons of the DFE between populations and species, little is known about how this distribution changes over shorter evolutionary timescales. Islands provide a powerful framework for understanding the impact of recent shifts in selection on the DFE, as founding populations often experience abrupt environmental changes. Using whole-genome, population-level sequence data, we investigate how such extreme transitions shape the DFE in two island radiations of Peromyscus mice: white-footed mice (P. leucopus) in Massachusettss Boston Harbor and deer mice (P. maniculatus) in the Gulf Islands of British Columbia. To measure the extent to which the selective effects of mutations have diverged between island and mainland populations, we leverage recent advances that extend DFE inference to multiple populations. By reconstructing the "joint DFE", we estimate both the strength of selection acting on distinct mutational classes and the correlation in mutational fitness effects between populations. We find that mutational fitness effects have diverged between island and mainland populations, despite the relative recency of these radiations. Comparisons between island populations, which reveal higher fitness effect correlations, suggest that this feature of the joint DFE captures broad-scale divergence in the environment populations inhabit. Together, our discoveries provide a rare empirical example of divergent environments shaping genome-wide patterns of fitness-affecting genetic variation in natural populations.

evolutionary biology↗

bioRxiv2025

The genomic imprint of chromosomal inversions and demographic history in island populations of deer mice

Populations that colonize islands experience novel selective pressures, fluctuations in size, and changes to their connectivity. Owing to their unique geographic setting, islands can function as natural laboratories in which to examine the interactions between demographic history and natural selection replicated across isolated populations. We used whole genome sequences of wild-caught deer mice (Peromyscus maniculatus) from two islands (Saturna and Pender) and one mainland location (Maple Ridge) in the Gulf Islands region of coastal British Columbia to investigate two primary determinants of genome-wide diversity: chromosomal inversions and non-equilibrium demographic history. We found that segregating inversions produce characteristic, large-scale distortions in allele frequencies and linkage disequilibrium that make it possible to identify and characterize them from short-read sequence data. Patterns of variation within and between karyotypes indicate that six inversion polymorphisms have been maintained by a shared history of balancing selection in both island and mainland populations. Whereas the estimated timing of contemporary population splits is consistent with the isolation of island populations from each other following the Last Glacial Maximum, ancestral island and mainland lineages are inferred to have diverged much earlier. These aspects of demographic history suggest that shared inversions existed long ago in a common ancestor or spread via limited gene flow between ancestral island and mainland lineages. Our results raise the possibility that inversions segregating among Gulf Islands populations are on similar evolutionary trajectories, providing a contrast to previous findings in mainland P. maniculatus and contributing to the emerging portrait of inversion evolution in this species.

evolutionary biology↗

bioRxiv2025

Population history across timescales in an urban archipelago

Contemporary patterns of genetic variation reflect the cumulative history of a population. Population splitting, migration, and changes in population size leave genomic signals that enable their characterization. Existing methods aimed at reconstructing these features of demographic history are often restricted in their temporal resolution, leaving gaps about how basic evolutionary parameters change over time. To illustrate the prospects for extracting insights about dynamic population histories, we turn to a system that has undergone dramatic changes on both geological and contemporary timescales - an urbanized, near-shore archipelago. Using whole genome sequences, we employed both common and novel summaries of variation to infer the demographic history of three populations of endemic white-footed mice (Peromyscus leucopus) in Massachusetts Boston Harbor. We find informative contrasts among the inferences drawn from these distinct patterns of diversity. While demographic models that fit the joint site frequency spectrum (jSFS) coincide with the known geological history of the Boston Harbor, patterns of linkage disequilibrium reveal collapses in population size on contemporary timescales that are not recovered by our candidate models. Historical migration between populations is also absent from best-fitting models for the jSFS, but rare variants show unusual clustering along the genome within individual mice, a pattern that is reproduced by simulations of recent migration. Together, our findings indicate that these urban archipelago populations have been shaped by both ancient geological processes and recent human influence. More broadly, our study demonstrates that the temporal resolution of demographic history can be extended by examining multiple facets of genomic variation. Significance StatementDetailed information about a populations history can be obtained by studying patterns of genomic variation, but these insights can be limited in their temporal scope. Our investigation of white-footed mice in the urban Boston Harbor archipelago demonstrates how combining multiple summaries of genomic variation enables a more complete reconstruction of population history over both the recent and distant past.

evolutionary biology↗

bioRxiv2025

Population Genomics of Giant Mice from the Faroe Islands: Hybridization, Colonization, and a Novel Challenge to Identifying Genomic Targets of Selection

Populations that colonize islands provide unique insights into demography, adaptation, and the spread of invasive species. House mice on the Faroe Islands evolved exceptionally large bodies after colonization, generating interest from biologists since Darwin. To reconstruct the evolutionary history of these mice, we sequenced genomes of population samples from three Faroe Islands (Sandoy, Nolsoy, and Mykines) and Norway as a mainland comparison. Mice from the Faroe Islands are hybrids between the subspecies Mus musculus domesticus and M. m. musculus, with ancestry alternating along the genome. Analyses based on the site frequency spectrum of single nucleotide polymorphisms and the ancestral recombination graph (ARG) indicate that mice arrived on the Faroe Islands on a timescale consistent with transport by Norwegian Vikings, with colonization of Sandoy likely preceding colonization of Nolsoy. Substantial reductions in nucleotide diversity and effective population size associated with colonization suggest that mice on the Faroe Islands evolved large body size during periods of heightened genetic drift. Genomic scans for positive selection uncover windows with unusual site frequency spectra, but this pattern is mostly generated by clusters of singletons in individual mice. Variants showing evidence of selection in both Nolsoy and Sandoy based on the ARG are enriched for genes with neurological functions. Our findings reveal a dynamic evolutionary history for the enigmatic mice from Faroe Island and emphasize the challenges that accompany population genomic inferences in island populations. Significance StatementPopulations that colonize islands are expected to have unusual histories compared to their mainland counterparts. Using population genomic data, we conclude that giant mice living on the Faroe Islands originated from hybrids, invaded the islands on a timescale consistent with transport by Vikings, and persisted despite drastic reductions in population size. We also uncover a novel challenge to scanning genomes for genes involved in adaptation.

evolutionary biology↗

bioRxiv2021

Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations

ObjectivesThe aim of this study was to characterize the genetic relationships within and among four neighboring populations in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. Materials and MethodsWe collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. ResultsHere we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. DiscussionOverall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.

genetics↗

bioRxiv2020

Revisiting the notion of deleterious sweeps

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites - both in the presence and absence of interference amongst deleterious mutations - and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of FST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.

evolutionary biology↗