International Journal of Molecular Zoology, 2025, Vol.15, No.1, 1-9 http://animalscipublisher.com/index.php/ijmz 1 Research Insights Open Access The Hidden Complexity of Capra Evolution: A Multi-Layered Phylogenomic Reconstruction Using Chromosome-Level Assemblies Xiaofang Lin 1 , XumingLü2 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 Corresponding author: xiaofang.lin@hitar.org 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 Copyright © 2025 Lin and Lü, 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. Preferred citation for this article: 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) Abstract 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. Keywords Genus Capra; Phylogeny; Chromosomal rearrangement; Gene introgression; Chromosome-level genome assembly 1 Introduction The genus Capra includes mountainous animals in the Bovidae family and Caprinae subfamily. It contains wild and domesticated animals. They are known for their survival in harsh environments, different horn shapes in males and females, and well-developed ruminant digestive systems. Because of their success in harsh, low-resource environments, Capra species are ideal examples from which to learn about animal adaptation to mountains, the domestication process, and new species formation. It contains nine or more known species, including the Alpine ibex (Capra ibex), the wild goat (Capra aegagrus), the markhor (Capra falconeri), and the domestic goat (Capra hircus). They are found in parts of Europe, North Africa, the Middle East, and across Asia (Zhou et al., 2019). The wild species have limited, fragmented populations due to geography and specialized habitat needs. At the same time, domestic goats—originating from C. aegagrus-exist almost everywhere now because of human spread. These ecological and geographical differences together render it interesting and complicated to look into how all these species are related (Gippoliti and Robovský, 2018). Previous studies to investigate the evolution of Capra were not straightforward. They were largely based on fragmented genetic data, tiny samples, and mostly mitochondrial or low-resolution nuclear DNA. As such, the resulting evolutionary trees naturally tended to disagree with each other. These disagreements were then further exacerbated by events including past hybridization, incomplete lineage sorting, and gene flow between species. Their interbreeding has also gone on unabated with the wild goats, thereby obliterating species lines and also complicating their evolutionary history (Lin et al., 2023; Wang et al., 2023). To address these concerns, the current research employs well-constructed assembled chromosome-level genomes of different Capra species. Whole genomes account for a better understanding of how the species had evolved.
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