Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes.
Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes.
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DOI：
10.1093/molbev/msac251
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发表时间：
2022-11-03
影响因子：
10.7
通讯作者：
Genner MJ
中科院分区：
文献类型：
--
作者：
Carruthers M;Edgley DE;Saxon AD;Gabagambi NP;Shechonge A;Miska EA;Durbin R;Bridle JR;Turner GF;Genner MJ
快速生态物种形成沿着深度梯度已反复发生在淡水鱼类，但分子机制，促进这种多样化通常是不清楚的。在非洲火山口湖Masoko湖，丽鱼Astatotilapia calliptera在过去的1,000年里已经分化成浅水沿岸和深海底栖生态形态，具有惊人的不同颌骨结构。利用全基因组转录组数据，我们探索了两种主要的转录调节机制，即表达和剪接QTL变体，并研究了它们对支撑功能表型的差异基因表达的贡献。共鉴定出7,550个基因，其中5.4%受顺式调控表达QTL的调控，9.2%受顺式调控剪接QTL的调控。我们还发现了与颅面发育相关的差异表达基因上的强烈趋异选择信号。这些结果表明，大规模的转录组修饰在早期物种形成过程中起着重要作用。我们的结论是，调节变体是选择的重要目标，在适应性多样化过程中驱动生态相关的基因表达分歧。
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.7
作者：
Karvonen A;Lucek K;Marques DA;Seehausen O
通讯作者：
Seehausen O
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
DOI：
10.1073/pnas.1719798115
发表时间：
2018-07-03
影响因子：
11.1
作者：
Conith, Moira R.;Hu, Yinan;Albertson, R. Craig
通讯作者：
Albertson, R. Craig
影响因子：
9.2
作者：
Conte, Matthew A.;Joshi, Rajesh;Kocher, Thomas D.
通讯作者：
Kocher, Thomas D.