The comparative genomic landscape of adaptive radiation in Crater Lake cichlid fishes

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 the factors promoting increased species numbers and phenotypic divergence in two closely related lineages is notably different. We investigated one such natural experiment using two de novo assembled and 40 re-sequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; non-radiating), 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 only 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.

Methods
The method for the genomes and transcriptomes assemblies was described in the paper "The Comparative Genomic Landscape of Adaptive Radiation in Crater Lake Cichlid Fishes".

从生态机遇到基因组构成的各类因素，或可解释为何仅有部分演化支系能够发生适应性辐射（adaptive radiation）。尽管这类天然实验较为罕见，但特定的研究系统可在相同的生态背景下提供天然实验场景——在此场景中，驱动两个近缘演化支系的物种数量增长与表型分化的核心因素存在显著差异。本研究利用两个从头组装（de novo assembly）基因组与40个重测序基因组，针对上述一类天然实验展开探究，旨在揭示为何两个近缘新热带区慈鲷鱼类演化支系会产生截然不同的演化结果：其一为橘色双冠丽鱼物种复合体（*Amphilophus citrinellus*，即迈达斯慈鲷，发生适应性辐射），其二为棘鳍慈鲷（*Archocentrus centrarchus*，即飞鱼慈鲷，未发生适应性辐射）。尽管两个支系均栖息于尼加拉瓜的诸多湖泊生境中，但基于全基因组推断的种群动态分析显示，优先效应（priority effect）并非导致二者演化差异的唯一原因。此外，两个支系在全基因组选择强度、转座因子（transposable element）动态、基因家族扩张、大型染色体重排以及受正选择作用的基因数量等方面均无显著差异。为更细致地探究迈达斯慈鲷中发生适应性分化的特定基因组区域，本研究还通过对反复分化的适应性性状进行QTL定位（quantitative trait locus mapping），以检验是否存在分子预适应（molecular pre-adaptation）相关的证据。尽管多数分析未能明确指向显著的基因组差异，但本研究确实鉴定出了一批受正选择作用的基因所在的功能类别，这些类别可作为未来探究迈达斯慈鲷适应性辐射倾向的候选研究靶点。本研究结果表明，相较于全基因组层面的因素，局部基因组因素在这类慈鲷的适应性辐射倾向中发挥了更为关键的作用。

方法
基因组与转录组的组装方法已在论文《火山口湖慈鲷适应性辐射的比较基因组图谱》（"The Comparative Genomic Landscape of Adaptive Radiation in Crater Lake Cichlid Fishes"）中予以详述。