The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes.
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes.
复制标题
火山口丽鱼科学鱼类自适应辐射的比较基因组景观。
DOI：
10.1111/mec.15774
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发表时间：
2021-03
影响因子：
4.9
通讯作者：
Franchini P
中科院分区：
文献类型：
--
作者：
Xiong P;Hulsey CD;Fruciano C;Wong WY;Nater A;Kautt AF;Simakov O;Pippel M;Kuraku S;Meyer A;Franchini P
从生态机会到基因组组成的各种因素可能解释了为什么只有一些谱系形成适应性辐射。虽然罕见，但某些系统可以在相同的生态环境中提供自然实验，其中两个密切相关的谱系的物种数量和表型差异明显不同。我们研究了一个这样的自然实验，使用了两个重新组装的基因组和40个重新测序的基因组，并询问为什么两个密切相关的新热带慈鲷鱼系，Amphilophus citrinellus物种复合体（Midas慈鲷；辐射）和Archocentrus centrarchus（飞慈鲷；非辐射）会导致如此不同的进化结果。尽管这两个血统都居住在尼加拉瓜的许多相同的湖泊中，但全基因组推断的人口统计学表明，优先效应不太可能是造成差异的原因。此外，全基因组范围内的选择水平、转座因子动力学、基因家族扩展、主要染色体重排和正选择下的基因数量在两个谱系之间没有显著差异。为了更细致地研究Midas慈鲷中经历了适应性分化的特定基因组亚群，我们还研究了在重复分化适应性状的QTL定位中确定的区域是否存在“分子预适应”的证据。虽然我们的大多数分析都未能确定基因组的实质性差异，但我们确实确定了包含许多正选择基因的功能类别，为未来研究迈达斯鲷的辐射倾向提供了候选基因。我们的研究结果指出，这些慈鲷鱼适应辐射的倾向背后，是局部因素而不是全基因组因素的不成比例的作用。
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole‐genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome‐wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for ‘molecular pre‐adaptation’ in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome‐wide factors underlying the propensity for these cichlid fishes to adaptively radiate.
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影响因子：
3.3
作者：
Elmer, Kathryn R.;Lehtonen, Topi K.;Meyer, Axel
通讯作者：
Meyer, Axel
影响因子：
12.3
作者：
Dalgleish, Raymond;Flicek, Paul;Maglott, Donna R.
通讯作者：
Maglott, Donna R.
影响因子：
10.7
作者：
Baalsrud HT;Tørresen OK;Solbakken MH;Salzburger W;Hanel R;Jakobsen KS;Jentoft S
通讯作者：
Jentoft S
影响因子：
10.7
作者：
Franchini, Paolo;Xiong, Peiwen;Meyer, Axel
通讯作者：
Meyer, Axel
影响因子：
64.8
作者：
Barluenga, M;Stölting, KN;Meyer, A
通讯作者：
Meyer, A