Bioscience Evidence 2025, Vol.15, No.6, 291-302 http://bioscipublisher.com/index.php/be 292 milk yield, reproduction, disease resistance, and the ability to live in different environments (Macciotta et al., 2021; Sikdar et al., 2021; Khan et al., 2022). For wild water buffaloes, keeping their genetic diversity is even more important. It helps the species survive, and it also keeps the original genetic base for domestic buffaloes. In recent years, with the fast development of tools like microsatellites, single nucleotide polymorphisms (SNPs), and whole-genome sequencing, researchers can now check and manage genetic diversity more clearly and more accurately. Although the importance of genetic diversity in water buffaloes has been widely recognized, there is still a significant lack of systematic understanding of the comparative genetic diversity between wild and domesticated water buffaloes, especially at the genomic level. Most previous studies have focused on a single group (wild or domestic) or a specific population, lacking a comprehensive genomic comparison covering wild, riverine and swamp buffalo. This study conducts a comparative analysis of wild and domestic buffalo populations through extensive sampling and advanced genomics methods and provides references for the management of livestock genetic resources and biodiversity conservation. 2 Evolutionary Background of Buffalo Populations 2.1 Evolutionary origin and phylogenetic relationship between wild and domestic buffaloes The history of buffaloes (genus Bubalus) shows that they split early and have complex family links. Wild and domestic buffaloes also differ a lot. Studies based on DNA and body traits say that the two main domestic types, the river buffalo and the swamp buffalo, did not come from the same group. They came from different wild Asian buffalo (Bubalus arnee) groups. These groups separated about 900 000 years ago, and the two types later developed on their own in different regions (Zhong et al., 2020; Sun et al., 2020). The currently critically endangered wild buffalo is generally regarded as the common ancestor of the two domestic types, but the divergence between river and swamp buffalo predates domestication and can be compared to the degree of divergence between major cattle species, such as the common cattle and the zebu. Recent genomic studies even support the classification of river and swamp buffalo as two subspecies or even different species, while the tamarau (Bubalus mindorensis) and the anoa (Bubalus depressicornis) also provide a richer background for the phylogenetic relationships within the genus Bubalus (Curaudeau et al., 2021; Cailipan et al., 2023). 2.2 Domestication history: timeline, centers, and evidence from archaeological and genomic studies River buffaloes were first domesticated in the western part of the Indian subcontinent (present-day India and Pakistan) around 6 300 BP (Zhong et al., 2020; Nagarajan et al., 2015). Both archaeological records (such as buffalo remains from the Indus Valley Civilization) and mitochondrial DNA studies support this time and geographical center, and suggest that the domestication process may have involved multiple gene introgressions from wild buffaloes. River buffaloes spread westward from their domestication center, eventually reaching Egypt, the Balkan Peninsula, and Italy, and formed multiple breeds with high diversity in production performance and phenotype (Sun et al., 2020). The swamp buffalo was independently domesticated in the border regions between southwestern China and northern Indochina, with an estimated domestication period between 3 000~7 000 BP. Studies on mitochondrial and Y-chromosome diversity all support this region as the domestication center of the swamp buffalo, with populations in southern China and northern Indochina exhibiting the highest genetic diversity (Sun et al., 2020). Ancient DNA research from Neolithic sites in China also suggests the possible existence of now-extinct local wild buffalo species in the past. 2.3 Historical geographical distribution and factors influencing population differentiation During the Pleistocene, climate fluctuations profoundly affected the differentiation and distribution of wild buffaloes. Ice age conditions prompted the separation of major lineages and the formation of different genetic pools. Subsequently, river and marsh water buffaloes spread from their respective domestication centers. River water buffaloes migrated westward from the Indian subcontinent, while marsh water buffaloes spread eastward
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