Abstract
The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2nd Pleistocene Glacial Period (~200–130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1′2 and SB) that lived around the Last Glacial Maximum (~26–19 Kya). During the late Holocene optimum (11–6 Kya) lineages differentiated further, and at least eight matrilines (SA1, SA2, SB1a, SB1b, SB2a, SB2b, SB3 and SB4) were domesticated around 7–3 Kya. Haplotype distributions support an initial domestication process in Southeast Asia, while subsequent captures of wild females probably introduced some additional rare lineages (SA3, SC, SD and SE). Dispersal of domestic buffaloes created local population bottlenecks and founder events that further differentiated haplogroup distributions. A lack of maternal gene flow between neighboring populations apparently maintained the strong phylogeography of the swamp buffalo matrilines, which is the more remarkable because of an almost complete absence of phenotypic differentiation.
Highlights
The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya
We report the mitogenomes from an additional 107 Southeast-Asian swamp buffaloes, covering most of its current geographic distribution with as outgroup one mitogenome from a Chinese river buffalo in order to establish the haplogroup phylogeny and reconstruct the demographic history of the swamp buffalo
The 109 swamp buffalo mitogenomes with a length of 16340 to 16363 bps belong to 87 different haplotypes (Ht.s) and are divided into 21 haplogroups or subhaplogroups (Supplementary Dataset S1)
Summary
The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. South Asia and the Mediterranean area (Italy, Egypt and the Balkans), and sporadically in Australia and South America, whereas the swamp buffalo is kept in Northeast India, China (southern regions and Yangtze valley) and Southeast Asia[1, 3] Both types of water buffalo descend from the wild Asian buffalo (Bubalus arnee)[4], which had a widely distribution range in eastern Indian, Sri Lanka and Southeast Asia until the beginning of XIX century[5,6,7,8]. Lau et al.[7] hypothesized that the wild Asian buffalo originated in mainland of Southeast Asia and spread north toward China and west toward the Indian subcontinent, where the river type was probably domesticated. We report the mitogenomes from an additional 107 Southeast-Asian swamp buffaloes, covering most of its current geographic distribution with as outgroup one mitogenome from a Chinese river buffalo in order to establish the haplogroup phylogeny and reconstruct the demographic history of the swamp buffalo
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