The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus.
The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus.
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DOI：
10.1093/molbev/mst136
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发表时间：
2013-11
影响因子：
10.7
通讯作者：
Borowsky RL
中科院分区：
文献类型：
--
作者：
Bradic M;Teotónio H;Borowsky RL
Astyanax mexicanus 洞穴鱼的不同种群在从地表表型到洞穴表型的独立进化中提供了可重复趋同或平行的惊人例子。然而，人们对基因水平上进化的可重复性发生的程度仍然知之甚少。为了解决这个问题，我们首先表征了 518 个单核苷酸多态性 (SNP) 的遗传多样性，这些单核苷酸多态性是通过 RAD 标签测序获得的，分布在七个洞穴和三组地表种群的整个基因组中。洞穴人口代表了两个不同的谱系（旧的和新的）。 31个SNP在地表和老洞穴种群之间存在显着差异，2个SNP在地表和新洞穴种群之间存在显着差异，44个SNP在老和新洞穴种群之间存在显着差异。此外，我们还确定了这些 SNP 是否映射到先前描述的地表种群和洞穴种群之间数量性状基因座 (QTL) 的相同位置。共有 25 个差异化 SNP 与多个 QTL 共同定位，例如含有与眼睛发育和晶状体大小有关的成纤维细胞生长因子基因 (Fgf8) 的 QTL。此外，许多与 QTL 共同定位的 SNP 在独立衍生的洞穴种群中的身份是相同的。这些结论通过 QTL 区域内 SNP 的单倍型分析得到进一步证实。我们的研究结果表明，进化在遗传水平上的可重复性很大，这表明祖先的遗传变异对适应洞穴环境的群体遗传变异有显着贡献。
Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment.
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影响因子：
4.5
作者：
Counterman BA;Araujo-Perez F;Hines HM;Baxter SW;Morrison CM;Lindstrom DP;Papa R;Ferguson L;Joron M;Ffrench-Constant RH;Smith CP;Nielsen DM;Chen R;Jiggins CD;Reed RD;Halder G;Mallet J;McMillan WO
通讯作者：
McMillan WO
影响因子：
4.5
作者：
Baxter SW;Nadeau NJ;Maroja LS;Wilkinson P;Counterman BA;Dawson A;Beltran M;Perez-Espona S;Chamberlain N;Ferguson L;Clark R;Davidson C;Glithero R;Mallet J;McMillan WO;Kronforst M;Joron M;Ffrench-Constant RH;Jiggins CD
通讯作者：
Jiggins CD
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.4
作者：
Bradic M;Beerli P;García-de León FJ;Esquivel-Bobadilla S;Borowsky RL
通讯作者：
Borowsky RL
影响因子：
2.9
作者：
COHAN, FM;HOFFMANN, AA
通讯作者：
HOFFMANN, AA