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

## TL;DR

This study explores the evolutionary history and genetic diversity of the Mustelinae subfamily using whole-genome data from 10 species, revealing insights into their chromosomal evolution and demographic patterns.

## Contribution

The paper provides the first comprehensive comparative and phylogenomic analysis of Mustelinae, including novel genome assemblies and insights into chromosomal evolution.

## Key findings

- Marked homozygosity was observed in some Asian Mustelinae lineages, while widespread species showed high genetic diversity.
- Phylogenomic analysis confirmed the split of M. richardsonii from M. erminea but found no speciation within M. nivalis.
- Ancestral karyotypes for Mustela (2n = 44) and Mustelinae (2n = 42) were confirmed through chromosomal rearrangement analysis.

## 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.