Reduced representation approaches produce similar results to whole genome sequencing for some common phylogeographic analyses.

Autor: Duckett DJ; Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America., Calder K; College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States of America., Sullivan J; Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America., Tank DC; Department of Botany, University of Wyoming, Laramie, WY, United States of America., Carstens BC; Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2023 Nov 30; Vol. 18 (11), pp. e0291941. Date of Electronic Publication: 2023 Nov 30 (Print Publication: 2023).
DOI: 10.1371/journal.pone.0291941
Abstrakt: When designing phylogeographic investigations researchers can choose to collect many different types of molecular markers, including mitochondrial genes or genomes, SNPs from reduced representation protocols, large sequence capture data sets, and even whole genomes. Given that the statistical power and accuracy of various analyses are expected to differ depending on both the type of marker and the amount of data collected, an exploration of the variance across methodological results as a function of marker type should provide valuable information to researchers. Here we collect mitochondrial Cytochrome b sequences, whole mitochondrial genomes, single nucleotide polymorphisms (SNP)s isolated using a genotype by sequencing (GBS) protocol, sequences from ultraconserved elements, and low-coverage nuclear genomes from the North American water vole (Microtus richardsoni). We estimate genetic distances, population genetic structure, and historical demography using data from each of these datasets and compare the results across markers. As anticipated, the results exhibit differences across marker types, particularly in terms of the resolution offered by different analyses. A cost-benefit analysis indicates that SNPs collected using a GBS protocol are the most cost-effective molecular marker, with inferences that mirror those collected from the whole genome data at a fraction of the cost per sample.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Duckett et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje