Parameterizing Pantherinae: De Novo Mutation Rate Estimates from <i>Panthera</i> and <i>Neofelis</i> Pedigrees

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rates for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate, but these can be largely ameliorated through extensive manual curation. Despite these stochastic effects, manual validation of de novo mutation candidates permitted the reliable inference of pantherine mutation rates. We inferred that base pair mutation rates for all species fell between 3.6 × 10-9 and 7.6 × 10-9 per generation per base pair (mean 5.5 × 10-9 ± 1.7 × 10-9 across Pantherinae at a mean parental age of 5.5 years). Similar to other studies, we show a positive trend of mean parental age with mutation rate and our inferred rates are well within the expected range for other mammals.

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Publication Details

Journal
Genome Biology and Evolution
Published
2025-04-01
DOI
https://doi.org/10.1093/gbe/evaf060
Citations
4
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
3.22

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article

Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees

Klaus‐Peter Koepfli, Gabriele Zenato Lazzari, Ellie E. Armstrong, Jesús E. Maldonado et al.
4 citations
Genome Biology and Evolution
Genomics and Phylogenetic Studies
3.22
article

Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees

Klaus‐Peter Koepfli, Gabriele Zenato Lazzari, Ellie E. Armstrong, Jesús E. Maldonado, Sarah B. Carey, Robert C. Fleischer, P. Sean Walsh, Alex Harkess, Eduardo Eizirik, Dmitri A. Petrov, Michael G. Campana, Katherine A. Solari, Neel Aziz
article en
4 citations

Abstract

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rates for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate, but these can be largely ameliorated through extensive manual curation. Despite these stochastic effects, manual validation of de novo mutation candidates permitted the reliable inference of pantherine mutation rates. We inferred that base pair mutation rates for all species fell between 3.6 × 10-9 and 7.6 × 10-9 per generation per base pair (mean 5.5 × 10-9 ± 1.7 × 10-9 across Pantherinae at a mean parental age of 5.5 years). Similar to other studies, we show a positive trend of mean parental age with mutation rate and our inferred rates are well within the expected range for other mammals.

Genome Biology and EvolutionVol. 17(4)
University of California, Riverside (US), George Mason University (US), Smithsonian Conservation Biology Institute (US), National Zoological Park (US), HudsonAlpha Institute for Biotechnology (US), Conservation Biology Institute, Pontifícia Universidade Católica do Rio Grande do Sul (BR), Washington State University (US), Stanford University (US)
National Science Foundation, Smithsonian Institution, U.S. Department of Agriculture, Washington Research Foundation, Panthera, Conselho Nacional de Desenvolvimento Científico e Tecnológico, National Institutes of Health, National Institute of Food and Agriculture, Smithsonian Conservation Biology Institute, Stanford Research Computing Center, Stanford University, National Institute of General Medical Sciences, Division of Integrative Organismal Systems
Life in Land
Openalex Percentile: Top 9%
Genomics and Phylogenetic Studies
3.22
DOIOpen Access PDFOpenAlex
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