Abstract
BackgroundThe Bovinae subfamily incorporates an array of antelope, buffalo and cattle species. All of the members of this subfamily have diverged recently. Not surprisingly, a number of phylogenetic studies from molecular and morphological data have resulted in ambiguous trees and relationships amongst species, especially for Yak and Bison species. A partial phylogenetic reconstruction of 13 extant members of the Bovini tribe (Bovidae, Bovinae) from 15 complete or partially sequenced autosomal genes is presented.ResultsWe identified 3 distinct lineages after the Bovini split from the Boselaphini and Tragelaphini tribes, which has lead to the (1) Buffalo clade (Bubalus and Syncerus species) and a more recent divergence leading to the (2) Banteng, Gaur and Mithan and (3) Domestic cattle clades. A fourth lineage may also exist that leads to Bison and Yak. However, there was some ambiguity as to whether this was a divergence from the Banteng/Gaur/Mithan or the Domestic cattle clade. From an analysis of approximately 30,000 sites that were amplified in all species 133 sites were identified with ambiguous inheritance, in that all trees implied more than one mutation at the same site. Closer examination of these sites has identified that they are the result of ancient polymorphisms that have subsequently undergone lineage sorting in the Bovini tribe, of which 53 have remained polymorphic since Bos and Bison species last shared a common ancestor with Bubalus between 5–8 million years ago (MYA).ConclusionUncertainty arises in our phylogenetic reconstructions because many species in the Bovini diverged over a short period of time. It appears that a number of sites with ambiguous inheritance have been maintained in subsequent populations by chance (lineage sorting) and that they have contributed to an association between Yak and Domestic cattle and an unreliable phylogenetic reconstruction for the Bison/Yak clade. Interestingly, a number of these aberrant sites are in coding sections of the genome and their identification may have important implications for studying the neutral rate of mutation at nonsynonymous sites. The presence of these sites could help account for the apparent contradiction between levels of polymorphism and effective population size in domesticated cattle.
Highlights
The Bovinae subfamily incorporates an array of antelope, buffalo and cattle species
In addition early Bovini fossils do not exist in nearby regions like Afghanistan and Iran suggesting that these early Bovini were restricted to the open forests of India and Pakistan until < 7 million years ago (MYA) when the earliest Bovini fossils begin to appear in Africa, Asia and Europe, respectively
Sequencing In total 84 amplicons from 15 genes were sequenced across 14 representatives of the Bovinae subfamily, including members of the Bovini and Tragelaphini tribes, which we used to infer the sequence from the most recent common ancestor
Summary
The Bovinae subfamily incorporates an array of antelope, buffalo and cattle species. All of the members of this subfamily have diverged recently. The first divergence within the Bovini occurred between 5–10 million years ago (MYA) with the splitting of the buffalo or the subtribe Bubalina (Bubalus and Syncerus spp.) from the nonbuffalo or the subtribe Bovina (Bos and Bison spp.) [1,7,8,9,10,11,12]. These two subtribes consistently resolve themselves as dichotomous groups, and show no evidence of producing viable hybrid offspring [1,6,9,13,14]. The dramatic range expansion of domestic cattle has resulted in an increased threat of introgression by domestic cattle DNA into the genomes of many wild populations, either intentionally or accidentally [11,20], all of which may confuse phylogenetic relationships
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
