Ontogeny and evolution: parallel cooption of developmental pathways in the adaptive evolution of the visual system of Neotropical cichlid fish in recently colonized crater lakes

个体发育和进化：新热带火山口湖中慈鲷视觉系统适应性进化中发育途径的平行选择

• 批准号: 428846198
• 负责人: Professor Dr. Julián Torres-Dowdall, Ph.D.
• 金额: --
• 依托单位: Department of Biological Sciences
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/428846198?language=en
• 关键词: Ontogeny; evolution; parallel; cooption; developmental

Understanding the factors affecting biological change is an ultimate goal in evolutionary biology, even more crucial now in the face of global change. However, the predictability of evolution is a contested topic. Some authors argue that stochastic factors are predominant, and thus, biological change is inherently unpredictable. Others see in the many cases of parallel evolution the deterministic signature of natural selection. The presence of similar adaptive peaks in the fitness landscape is the potential cause of parallelisms, but not necessarily their only explanation. Common genomic backgrounds and developmental constraints among closely related species might also affect the direction of biological change, in which case, genetic parallelisms are expected to underlie parallel phenotypic evolution. Here, I aim to determine if parallel phenotypic evolution of closely related species is underpinned by genetic parallelisms originating from the cooption of common developmental pathways. I propose to study the adaptive evolution of visual sensitivity in Nicaraguan Midas cichlid fishes. This species flock offers a natural experiment to address this topic because multiple clear crater lakes with similar light conditions were independently colonized from turbid great lakes, their radiation occurred recently resulting in little genomic divergence, and their phylogenetic relationships are well understood. The visual sensitivity of Midas cichlids has evolved rapidly and in parallel after the colonization of the crater lakes from the great lakes. Also, the visual sensitivity of the derived crater lake species resembles that in juveniles from the ancestral great lakes. Thus, I hypothesize that 1) developmental pathways were coopted during adaptive evolution to the novel conditions and, hence, 2) a high degree of parallelism in the underlying molecular mechanisms is expected among crater lake lineages. An approach combining forward and reverse genetics will be used to empirically test these hypotheses. First, I will test retinal transcriptomes for a positive association between differentially expressed genes underlying evolutionary divergence (i.e., crater vs. great lakes) and those underlying ontogenetic changes in the ancestral population (i.e., great lakes) as predicted by the first hypothesis. The second hypothesis predicts those genes to be the same in the species from different crater lakes. Then, I will study the genetic architecture of visual sensitivity by eQTL analyses in two independent ancestral-derived hybrid crosses. Common genomic regions are expected to underlie parallel changes in expression of genes affecting visual sensitivity in both crosses. Finally, I will use genomic editing to functionally challenge the identified loci. This project adds to the longstanding debate about the predictability of evolution and will further our understanding of the mechanisms involved in development and adaptive divergence in visual sensitivity.

了解影响生物变化的因素是进化生物学的终极目标，在面对全球变化的今天，这一目标更加重要。然而，进化的可预测性是一个有争议的话题。一些作者认为，随机因素占主导地位，因此，生物变化本质上是不可预测的。其他人在许多平行进化的案例中看到了自然选择的确定性特征。在适应环境中出现类似的适应高峰是平行现象的潜在原因，但不一定是唯一的解释。密切相关物种之间的共同基因组背景和发育限制也可能影响生物变化的方向，在这种情况下，遗传平行有望成为平行表型进化的基础。在这里，我的目标是确定密切相关物种的平行表型进化是否由共同发育途径共同选择的遗传平行所支撑。我建议研究尼加拉瓜迈达鱼视觉敏感度的适应性进化。这一物种群体提供了一个解决这一问题的自然实验，因为多个具有相似光照条件的透明火山口湖泊是从浑浊的大湖中独立殖民的，它们的辐射最近发生，导致很小的基因组分歧，它们的系统发育关系被很好地理解。在五大湖中的火山口湖被殖民后，米达斯鱼的视觉敏感度迅速而平行地演变。此外，来自火山口湖物种的视觉敏感度与来自祖先五大湖的幼鱼相似。因此，我假设1)发育路径在适应新条件的进化过程中被增选，因此，2)潜在的分子机制在火山口湖谱系中预计具有高度的相似性。一种结合了正向遗传学和反向遗传学的方法将被用来对这些假说进行实证检验。首先，我将测试视网膜转录本，寻找导致进化分歧(即火山口和大湖)的差异表达基因与第一个假设预测的祖先种群(即大湖)潜在的个体发育变化之间的正相关性。第二种假设预测这些基因在来自不同火山口湖泊的物种中是相同的。然后，我将通过eQTL分析研究两个独立祖先衍生的杂交组合的视觉敏感性的遗传结构。在这两个杂交组合中，共同的基因组区域被认为是影响视觉敏感度的基因表达平行变化的基础。最后，我将使用基因组编辑来从功能上挑战已识别的基因座。这个项目增加了关于进化的可预测性的长期争论，并将进一步加深我们对视觉敏感度的发育和适应性差异所涉及的机制的理解。