Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.
Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.
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DOI：
10.1186/s12864-015-2342-2
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发表时间：
2015-12-29
期刊：
影响因子：
4.4
通讯作者：
Achilli A
中科院分区：
文献类型：
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作者：
Colli L;Lancioni H;Cardinali I;Olivieri A;Capodiferro MR;Pellecchia M;Rzepus M;Zamani W;Naderi S;Gandini F;Vahidi SM;Agha S;Randi E;Battaglia V;Sardina MT;Portolano B;Rezaei HR;Lymberakis P;Boyer F;Coissac E;Pompanon F;Taberlet P;Ajmone Marsan P;Achilli A
目前广泛使用的国内山羊（山羊）是由于其中等大小和高适应性的多品种。它的遗传变异在多大程度上受到早期驯化做法的影响在很大程度上是未知的。分析牲畜物种母系遗传变异性的常用标准是通过对整个有丝分裂基因组（线粒体DNA、线粒体DNA）进行完整测序。我们提出了第一个广泛的调查山羊有丝分裂基因组的变异性的基础上84个完整的序列，从最初收集的758个样本，代表60个不同品种的C。hircus及其野生姊妹种，来自伊朗的牛黄（Capra aegagrus）。我们的系统发育分析确定了C. hircus到~ 460，000年（ka）前，并确定了五个独特的家庭单倍型群（A，B1，C1 a，D1和G）。90%以上的被检山羊属于单倍群A.这些家庭谱系主要嵌套在C。Aegagrus分支，在Epipaleolithic和新石器时代早期之间的界面处同时分叉，并从约12-10 ka前开始经历了急剧的扩张。国内山羊有丝分裂基因组下降，从一个小数目的成立单倍型，经历驯化后生存的最后一次冰期在近东避难所。所有现代单倍型A可能起源于一个单一的（或最多几个密切相关的）女性C。山羊。动物考古学数据表明驯化首先发生在安纳托利亚东南部。伴随着新石器时代第一波移民浪潮进入地中海的山羊已经具有两种祖先A和C变体的特征。C分支的古老分离（~130 ka前）表明一个遗传上不同的种群可能参与了第二次驯化事件。这里定义的新的诊断突变基序，区分野生和国内单倍群，可用于了解现代品种和古代遗骸之间的系统发育关系，并评估是否选择差异影响线粒体基因组变异在经济上重要的品种的发展。本文的在线版本（doi：10.1186/s12864-015-2342-2）包含补充材料，可供授权用户使用。
The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.