Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)

Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from 10 species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter- and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the suggested ancestral karyotypes of Mustela (2n = 44) and Mustelinae (2n = 42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.

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Publication Details

Journal
Genome Biology and Evolution
Published
2026-01-22
DOI
https://doi.org/10.1093/gbe/evag014
Primary Topic
Evolution and Paleontology Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)

José Melo‐Ferreira, Klaus‐Peter Koepfli, Andrey Tomarovsky, Anna S. Mukhacheva et al.
Genome Biology and Evolution
Evolution and Paleontology Studies
article

Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)

José Melo‐Ferreira, Klaus‐Peter Koepfli, Andrey Tomarovsky, Anna S. Mukhacheva, Tatiana Bulyonkova, Aliya Yakupova, Violetta R. Beklemisheva, Anna S. Zhuk, Nikolay Cherkasov, Alexei V. Abramov, Alan Scott, Liliana Farelo, Inês Miranda, David W. Mohr, Jürke Grau, Azamat Totikov, Zub Karol, Natalia A. Serdyukova, Victor V. Panov, Daniel W. G. Foerster, M. M. Sidorov, I. M. Okhlopkov, Elena Balanovska, Polina L Perelman, Ksenia Krasheninnikova, Sergei Kliver
article en

Abstract

Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from 10 species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter- and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the suggested ancestral karyotypes of Mustela (2n = 44) and Mustelinae (2n = 42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.

Genome Biology and EvolutionVol. 18(3)
University of Copenhagen (DK), Johns Hopkins University (US), St Petersburg University (RU), ITMO University (RU), Universidade do Porto (PT), Novosibirsk State University (RU), Peter the Great St. Petersburg Polytechnic University (RU), Johns Hopkins Medicine (US), Smithsonian Conservation Biology Institute (US), Zoological Institute (RU), Mammal Research Institute (PL), Max Planck Institute for Ornithology (DE), Yugra State University (RU), Institute of Systematics and Ecology of Animals (RU), Sikhote-Alin Nature Reserve (RU), Saffron Walden Museum (GB), Institute of Molecular and Cell Biology (RU), Institut thématique Génétique, génomique et bioinformatique (FR), Research Centre for Medical Genetics (RU), Leibniz Institute for Zoo and Wildlife Research (DE), Institute of Oil and Gas Problems of the Siberian Branch of the RAS (RU), Ludwig-Maximilians-Universität München (DE)
National Research Foundation, Danmarks Grundforskningsfond, Carlsbergfondet, Siberian Branch, Russian Academy of Sciences, Saint Petersburg State University, Ministério da Ciência, Tecnologia e Ensino Superior, ITMO University, Fundação para a Ciência e a Tecnologia, European Social Fund
Life in Land
Openalex Percentile: Top 53%
Evolution and Paleontology Studies
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