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. 2022 Nov 2;289(1986):20221561. doi: 10.1098/rspb.2022.1561

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© 2022 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Figure 2. — Population structure and evolutionary relationships among desert pupfishes. (a) Principal component analysis of desert pupfishes revealing substantial population structure among species and populations. (b) Species tree estimated by SVDquartets; nonparametric bootstrap support values indicate the percentage of bootstrap replicates supporting monophyly for each clade. (c) Maximum-likelihood tree of all 30 samples estimated by IQ-TREE. Two internal branches were collapsed due to low support (ultrafast bootstrap < 95%, SH-aLRT < 80%); all other branch support was unequivocal (UFboot = 100%, SH-aLRT = 100%). (d) Ancestry proportions across individuals in Death Valley NP, Ash Meadows NWR and outgroup desert pupfishes (C. albivelis, C. eremus, C. fontinalis, C. macularius, C. radiosus) estimated from a LD-pruned SNP dataset in ADMIXTURE with k = 4. Colours in PCA, trees and ADMIXTURE designate individuals from different species or populations and correspond to the shared figure legend in (a). (Online version in colour.)