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. 2019 Oct 18;10:4769. doi: 10.1038/s41467-019-12741-1

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — Demographic history of pumas. a Mitochondrial maximum likelihood phylogeny of the ten pumas in this study plus an additional puma from Big Cypress (KP202261.1) and the African cheetah (KP202271.1) as the outgroup. We calculated divergence times by determining the number of pairwise divergences between sequences and used a mitochondrial divergence rate of 1.15% bp per Myr^7,⁵⁷. We estimate a common maternal ancestor of these pumas 278,000 ± 5,639 years ago (star; 100% bootstrap support), divergence between North American and South American mitochondrial lineages 201,000 ± 1952 years ago (pentagon; 63% bootstrap support), and a common maternal ancestor of North American pumas 21,000 ± 10,412 years ago (circle; 100% bootstrap support). b Inferred changes in effective population size (N_e) over time using the pairwise sequentially Markovian coalescent (PSMC) model²⁹ for the ten pumas. We assume a generation time of 5 years and a per generation mutation rate of 0.5e-8 per bp per generation⁶¹. The PSMC model for EVG21 shows a sharp increase in inferred N_e that is probably attributable to its hybrid ancestry³¹.