Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1

BackgroundMost genetic studies on modern cattle have established a common origin for all taurine breeds in the Near East, during the Neolithic transition about 10 thousand years (ka) ago. Yet, the possibility of independent and/or secondary domestication events is still debated and is fostered by the finding of rare mitochondrial DNA (mtDNA) haplogroups like P, Q and R. Haplogroup T1, because of its geographic distribution, has been the subject of several investigations pointing to a possible independent domestication event in Africa and suggesting a genetic contribution of African cattle to the formation of Iberian and Creole cattle. Whole mitochondrial genome sequence analysis, with its proven effectiveness in improving the resolution of phylogeographic studies, is the most appropriate tool to investigate the origin and structure of haplogroup T1. MethodologyA survey of >2200 bovine mtDNA control regions representing 28 breeds (15 European, 10 African, 3 American) identified 281 subjects belonging to haplogroup T1. Fifty-four were selected for whole mtDNA genome sequencing, and combined with ten T1 complete sequences from previous studies into the most detailed T1 phylogenetic tree available to date. ConclusionsPhylogenetic analysis of the 64 T1 mitochondrial complete genomes revealed six distinct sub-haplogroups (T1a–T1f). Our data support the overall scenario of a Near Eastern origin of the T1 sub-haplogroups from as much as eight founding T1 haplotypes. However, the possibility that one sub-haplogroup (T1d) arose in North Africa, in domesticated stocks, shortly after their arrival from the Near East, can not be ruled out. Finally, the previously identified “African-derived American" (AA) haplotype turned out to be a sub-clade of T1c (T1c1a1). This haplotype was found here for the first time in Africa (Egypt), indicating that it probably originated in North Africa, reached the Iberian Peninsula and sailed to America, with the first European settlers.背景 现有针对现代家牛的多数遗传学研究已确认，所有普通牛（taurine）品种的共同起源地为近东地区，时间可追溯至约1万年前（以ka表示千年前）的新石器时代转型期。然而，独立驯化或二次驯化的可能性仍存在争议，而P、Q、R这类罕见的线粒体DNA（mtDNA）单倍群的发现进一步推动了相关讨论。单倍群T1因其地理分布特征，成为多项研究的关注对象，相关研究提出非洲地区可能存在独立的家牛驯化事件，并暗示非洲家牛的遗传物质对伊比利亚与克里奥尔家牛的种群形成具有贡献。完整线粒体基因组序列分析已被证实可有效提升系统地理学研究的分辨率，是探究单倍群T1起源与内部结构的最优工具。 研究方法 本研究对覆盖28个品种（15个欧洲品种、10个非洲品种、3个美洲品种）的超过2200条牛线粒体DNA控制区序列进行筛查，共鉴定出281个属于单倍群T1的样本。从中选取54个样本进行完整线粒体基因组测序，并结合此前研究中获取的10条T1完整序列，构建了当前最为详尽的T1系统发育树。 结论 对64条T1完整线粒体基因组的系统发育分析共识别出6个独立的亚单倍群（T1a至T1f）。研究结果整体支持T1亚单倍群起源于近东地区、且由至少8个奠基性T1单倍型演化而来的假说。不过，其中一个亚单倍群（T1d）可能在从近东传入北非后，于驯化种群中独立出现，这一可能性仍无法排除。此外，此前被认定为"非洲起源美洲型"（AA）的单倍型被证实为T1c的一个亚分支（T1c1a1）。本研究首次在非洲（埃及）检测到该单倍型，表明其可能起源于北非，随后传入伊比利亚半岛，并随首批欧洲殖民者跨洋抵达美洲。