Xiaofang Lin¹ , Xuming Lv²

1 Tropical Animal Medicine Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
2 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
International Journal of Molecular Zoology, 2025, Vol. 15, No. 1   doi: 10.5376/ijmz.2025.15.0001
Received: 24 Nov., 2024    Accepted: 30 Dec., 2024    Published: 10 Jan., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Lin X.F., and Lü X.M.., 2025, The hidden complexity of capra evolution: a multi-layered phylogenomic reconstruction using chromosome-level assemblies, International Journal of Molecular Zoology, 15(1): 1-9 (doi: 10.5376/ijmz.2025.15.0001)

Capra species vary extensively in body shape, habitat, and chromosome structure. Yet, their evolutionary histories have been hard to establish. This study uses high-quality chromosome-level genome data of some of the most important Capra species to investigate their evolutionary history. The study combines multiple sources of information. It involves phylogenetic analysis, comparison between gene trees and species trees, testing for gene flow between species, and analysis of chromosome structural changes. The results show that gene trees are not concordant with the species tree in general. It is likely to be a result of incomplete lineage sorting and hybridization among species in the past. Genes transferred between Capra lineages were also found in the research. Several chromosome rearrangements were discovered, as well as gene family changes implicated in basic biological processes. These changes could have been central to the mechanisms by which new species arose. The scientists also compared the formation of key biological pathways-like those for immunity and metabolism-in both species based on multi-omics data. In all, the research more clearly describes the interrelationship among Capra species and introduces new ideas of chromosome evolution and new mammal species emergence.

Genus Capra; Phylogeny; Chromosomal rearrangement; Gene introgression; Chromosome-level genome assembly