Origins of shared genetic variation in African cichlids.
Origins of shared genetic variation in African cichlids.
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DOI：
10.1093/molbev/mss326
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发表时间：
2013-04
影响因子：
10.7
通讯作者：
Streelman JT
中科院分区：
文献类型：
--
作者：
Loh YH;Bezault E;Muenzel FM;Roberts RB;Swofford R;Barluenga M;Kidd CE;Howe AE;Di Palma F;Lindblad-Toh K;Hey J;Seehausen O;Salzburger W;Kocher TD;Streelman JT
慈鲷鱼在东非沃茨进化出了巨大的形态和行为多样性。在每一个五大湖坦噶尼喀，马拉维，和维多利亚，杂交和保留祖先多态性的现象解释了物种之间的等位基因共享。在这里，我们探讨共享的主要东非慈鲷组合之间的单核苷酸多态性（SNP）。一组约200个基因和非基因SNPs被确定在马拉维湖的五个物种和基因型在一个不同的集合来自非洲各地的160个物种。我们观察到超过50%的这些位点的马拉维血统以外的分离多态性，这同样适用于基因与非基因SNP，以及在假定的CpG与非CpG位点的SNP。贝叶斯和主成分分析的遗传结构的数据表明，马拉维湖特有的羊群是不是单系的，河流物种可能有显着贡献马拉维基因组。聚结模拟支持这一假设，河流慈鲷运输湖泊组合之间的多态性。我们观察到强大的遗传分化之间的马拉维血统约8%的基因座，基因和非基因SNP的贡献。值得注意的是，超过一半的马拉维群体之间的这些离群位点是多态的湖外。慈鲷鱼在马拉维湖进化出多样性，因为新的突变与东非共享的遗传变异相结合。
Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ∼160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
9.8
作者：
Hodgkinson A;Ladoukakis E;Eyre-Walker A
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Eyre-Walker A
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3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar
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作者：
Johansson AM;Pettersson ME;Siegel PB;Carlborg O
通讯作者：
Carlborg O
影响因子：
7.7
作者：
Excoffier, Laurent;Lischer, Heidi E. L.
通讯作者：
Lischer, Heidi E. L.