Biology subjects

Wooldridge, B.

Publications and source records attributed to Wooldridge, B..

4 recordsLinked to original sources

bioRxiv2026

Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes

A central question in evolutionary biology is whether local adaptation is predictable when a species repeatedly encounters similar environments. The deer mouse, Peromyscus maniculatus, has a range of over 13 million km2 in North America and may be found in nearly every terrestrial habitat. Because of their abundance and wide habitat preference, deer mice and closely related Peromyscus, which we refer to as the P. maniculatus species complex, are at the forefront of studies of biogeography and local adaptation. Here, we undertake a comprehensive survey of genome-wide and phenotypic diversity to characterize the recent evolutionary history of this group. We sequenced whole genomes from 232 individuals across their range, representing the most thorough genetic sampling of the P. maniculatus species complex to date. We identify six geographically delineated clades, several of which encompass both classically recognized P. maniculatus subspecies as well as other recognized species. Ecological niche modelling suggests that this geographic structure resulted from rapid post-LGM range expansion and adaptation to emerging habitats. Our morphological measurements of 979 specimens and field data compiled from over 28,000 museum records show that deer mice in forests across the range consistently have longer tails, larger feet, bigger ears, and elongated whiskers. These traits constitute an arboreal ecotype that has evolved at least three times independently, and was likely lost in other parts of the range as populations moved out of forested habitat. Altogether, these results suggest that post-LGM increases in forested habitat drove the parallel evolution of arboreal ecotypes across the deer mouse range.

evolutionary biology↗

bioRxiv2025

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

Predicting the genetic consequences of population decline is a major problem in conservation genomics. Time lags following demographic bottlenecks can delay genomic erosion and make it difficult to determine a populations current and future risk, especially when pre-bottleneck genomic baselines are unavailable. Black abalone (Haliotis cracherodii) suffered a severe disease bottleneck in the 1980s, resulting in an estimated 99% population decline. However, recent work found surprisingly high genetic diversity and little population structure in current black abalone populations, raising questions of whether genomic erosion has been delayed. To investigate this, we applied ancient DNA methods to pre-bottleneck abalone shells, generating 59 whole genomes including one 34-fold coverage genome from a 1,500-year-old specimen. These data show that heterozygosity, runs of homozygosity, genetic load and population structure remained stable up to and following the bottleneck. Simulations reveal that this stability is consistent with even severe bottleneck scenarios because too few generations have lapsed since the decline. Projections suggest that future genomic erosion may be avoided even in limited recovery scenarios. Following the bottleneck we observe widespread balancing selection at genes with immune function, along with parallel increases of two inversions on separate chromosomes that are in linkage disequilibrium, where the disease bottleneck was most severe. Altogether, these findings explain why genomic change has thus far been limited, outline recovery scenarios that minimize genomic erosion, and identify loci likely that may harbor adaptive variation key to the success of future black abalone populations.

evolutionary biology↗

bioRxiv2024

Direct measurement of the mutation rate and its evolutionary consequences in a critically endangered mollusk

The rate at which mutations arise is a fundamental parameter of biology. Despite recent progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earths biodiversity. We present the first estimate of a germline mutation rate from the phylum Mollusca, which is diverged by more than 1200 Ma years from the closest relative for which a mutation rate estimate exists. We sequenced three pedigreed families of the white abalone Haliotis sorenseni, a long-lived, large-bodied, and critically endangered mollusk, and estimated a de novo mutation rate of 8.60e-09 single nucleotide mutations per site per generation. This mutation rate is similar to rates measured in vertebrates with similar generation times and longevity to abalone, and higher than mutation rates measured in faster-reproducing invertebrates. We use our estimated rate to infer baseline effective population sizes (Ne) across multiple Pacific abalone and find that abalone persisted over most of their evolutionary history as large and stable populations, in contrast to extreme fluctuations over recent history and small census sizes in the present day. We then use our mutation rate to infer the timing and pattern of evolution of the abalone genus Haliotis, which was previously unknown due to few fossil calibrations. Our results are an important step toward understanding mutation rate evolution and establish a key parameter for conservation and evolutionary genomics research in mollusks.

evolutionary biology↗

bioRxiv2024

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species recovery.

evolutionary biology↗