Biology subjects

Szpiech, Z.

Publications and source records attributed to Szpiech, Z..

2 recordsLinked to original sources

bioRxiv2022

Genomes of the extinct Bachman's Warbler shows high divergence and no evidence of admixture with other extant Vermivora Warblers

Bachmans Warbler (Vermivora bachmanii) - last sighted in 1988 - is one of the few North American passerines that have gone extinct. Given the extensive ongoing hybridization of its two extant congeners - the Blue-Winged Warbler (V. cyanoptera) and Golden-Winged Warbler (V. chrysoptera) - and shared patterns of plumage variation between Bachmans Warbler and hybrids between those extant species, it has been suggested that Bachmans Warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genome sequencing of Bachmans Warblers collected at the turn of the 20th century to address this possibility. We combine these data with genomes of the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii being a highly divergent, reproductively isolated species, with no evidence of introgression. We show that both V. bachmanii and V. chrysoptera have elevated runs of homozygosity compared to V. cyanoptera, consistent with the effects of a small effective population size or population bottlenecks in the former two species. We also found--using population branch statistic estimates of all three species--previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a novel pigmentation gene candidate for warblers, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species. SignificanceFew common North American passerines have gone extinct. Bachmans Warbler is, unfortunately, one that has--the last sighting was in 1988. Here we use whole genome historical DNA from museum specimens of Bachmans warblers collected at the turn of the 20th century to learn about the evolution of this species and test whether there was evidence for hybridization and gene flow between it and two extant members of the same genus which, today, hybridize extensively. We find Bachmans warbler was highly divergent with no evidence of gene flow. We also find evidence of elevated "runs of homozygosity" in both Bachmans warbler and one of the two extant Vermivora species, suggesting the effects of a small population size or population bottlenecks.

evolutionary biology↗

bioRxiv2017

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data

BackgroundGenomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to detect ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns.\n\nResultsWe report a weighted likelihood approach for identifying ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to detect ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies.\n\nConclusionsThis weighted likelihood ROA detection approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease.

genomics↗