Biology subjects

Nigenda-Morales, S.

Publications and source records attributed to Nigenda-Morales, S..

2 recordsLinked to original sources

bioRxiv2026

Long-term isolation and introgression shape the genomic distinctiveness of Rice's Whale

Species complex demographic history, including population size changes, isolation and gene flow, shapes patterns of genetic variation and deleterious load. In small and declining populations, understanding these processes is critical for predicting inbreeding depression and extinction risk. The Rices whale (Balaenoptera ricei) is a newly described baleen whale species resident to the heavily industrialized Gulf of Mexico, with a current abundance estimate of 51 (95 % CI: 20-130) individuals, making it one of the most endangered baleen whales globally. Using whole-genome sequences from 25 individuals, we reconstructed the evolutionary and demographic history of Rices whale and assessed its genomic health. Our analyses reinforce its distinctiveness from Brydes whales, and suggest that Rices whale has persisted as a small and isolated population in the Gulf of Mexico for tens of thousands of years. Despite its long-term small effective population size, genomes show modest impacts of inbreeding, including few long runs of homozygosity. We detected a distinct pulse of introgression [~]350 years ago from a Brydes whale-like lineage that resulted in windows of elevated heterozygosity in Rices whale, though it did not alter the burden of deleterious variation. Forward simulations indicate that a recent population collapse to [~]100 breeding individuals places the species at high risk of future inbreeding and genomic erosion unless population growth occurs. These findings highlight that while gene flow can increase genetic diversity, demographic recovery is essential to mitigate long-term genomic risks, underscoring the importance of management actions that promote sustained population growth.

genomics↗

bioRxiv2023

Evolution of the mutation spectrum across a mammalian phylogeny

Little is known about how the spectrum and etiology of germline mutagenesis might vary among mammalian species. To shed light on this mystery, we quantify variation in mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clocklike mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these clocklike signatures to fit each species 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the mutation spectrums phylogenetic signal when fit to non-context-dependent mutation spectrum data in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.

evolutionary biology↗