Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.
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DOI：
10.1186/s12864-018-4749-z
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发表时间：
2018-05-10
期刊：
影响因子：
4.4
通讯作者：
Kidd JM
中科院分区：
文献类型：
--
作者：
Oetjens MT;Martin A;Veeramah KR;Kidd JM
对古代和现代狗的大多数遗传分析都集中在常染色体或线粒体的变异上。从古代样本中获得线粒体DNA比从核DNA中更容易获得，线粒体分析揭示了对犬科动物进化史的重要见解。利用最近发表的狗Y染色体参考文献，我们分析了不同犬科动物的Y染色体序列，并确定了三只古老的欧洲狗的Y单倍群。我们使用118只犬的全基因组序列鉴定了1121个双等位Y染色体SNV，并定义了对不同的狗Y单倍群进行诊断的变体。类似于线粒体和以前对Y多样性的更有限的研究，我们在Y染色体树上观察到几个深分裂，这可能是在狗驯养或驯养后与狼混合之前保留Y染色体多样性的结果。我们发现，三只古代欧洲犬(4700-7000岁)的Y染色体属于不同的支系。我们估计，狗Y单倍群的最新评论祖先的时间是68-151千年前。对新石器时代的三条Y染色体的分析证实了欧洲狗的长期搁浅的种群结构。本文的在线版本(10.1186/s12864-0184749-z)包含向授权用户提供的补充材料。
Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs. We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades. We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs. The online version of this article (10.1186/s12864-018-4749-z) contains supplementary material, which is available to authorized users.
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影响因子：
56.9
作者：
Frantz, Laurent A. F.;Mullin, Victoria E.;Larson, Greger
通讯作者：
Larson, Greger
影响因子：
16.6
作者：
Botigué LR;Song S;Scheu A;Gopalan S;Pendleton AL;Oetjens M;Taravella AM;Seregély T;Zeeb-Lanz A;Arbogast RM;Bobo D;Daly K;Unterländer M;Burger J;Kidd JM;Veeramah KR
通讯作者：
Veeramah KR
影响因子：
7
作者：
Decker B;Davis BW;Rimbault M;Long AH;Karlins E;Jagannathan V;Reiman R;Parker HG;Drögemüller C;Corneveaux JJ;Chapman ES;Trent JM;Leeb T;Huentelman MJ;Wayne RK;Karyadi DM;Ostrander EA
通讯作者：
Ostrander EA
影响因子：
4.5
作者：
Auton A;Rui Li Y;Kidd J;Oliveira K;Nadel J;Holloway JK;Hayward JJ;Cohen PE;Greally JM;Wang J;Bustamante CD;Boyko AR
通讯作者：
Boyko AR
影响因子：
4.5
作者：
Larson G;Bradley DG
通讯作者：
Bradley DG