Advances in human sequencing technologies, coupled with statistical and computational tools, have fostered the development of methods for dating admixture events. These methods have merits and drawbacks in estimating admixture events in multi-way admixed populations. Here, we first provide a comprehensive review and comparison of current methods pertinent to dating admixture events. Second, we assess various admixture dating tools. We do so by performing various simulations. Third, we apply the top two assessed methods to real data of a uniquely admixed population from South Africa. Results reveal that current dating admixture models are not sufficiently equipped to estimate ancient admixtures events and to identify multi-faceted admixture events in complex multi-way admixed populations. We conclude with a discussion of research areas where further work on dating admixture-based methods is needed.
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http://dx.doi.org/10.1093/bib/bby112 | DOI Listing |
Ecol Evol
January 2025
United States Fish and Wildlife Service, Texas Fish and Wildlife Conservation Office San Marcos Texas USA.
Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain.
View Article and Find Full Text PDFMol Ecol
January 2025
Estación Biológica de Doñana (EBD-CSIC), Seville, Spain.
Invading species along with increased anthropogenization may lead to hybridization events between wild species and closely related domesticates. As a consequence, wild species may carry introgressed alleles from domestic species, which is generally assumed to yield adverse effects in wild populations. The opposite evolutionary consequence, adaptive introgression, where introgressed genes are positively selected in the wild species, is possible but has rarely been documented.
View Article and Find Full Text PDFMol Ecol
January 2025
Department of Biology and Wildlife, University of Alaska Museum, Fairbanks, Alaska, USA.
The application of high-throughput sequencing to phylogenetic analyses is allowing authors to reconstruct the true evolutionary history of species. This work can illuminate specific mechanisms underlying divergence when combined with analyses of gene flow, recombination and selection. We conducted a phylogenomic analysis of Catharus, a songbird genus with considerable potential for gene flow, variation in migratory behaviour and genomic resources.
View Article and Find Full Text PDFNature
January 2025
Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
Many known and unknown historical events have remained below detection thresholds of genetic studies because subtle ancestry changes are challenging to reconstruct. Methods based on shared haplotypes and rare variants improve power but are not explicitly temporal and have not been possible to adopt in unbiased ancestry models. Here we develop Twigstats, an approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift.
View Article and Find Full Text PDFCurr Issues Mol Biol
December 2024
College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China.
Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot () varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the "" apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software.
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