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，在全球变化面前更是至关重要。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。另一些人则在许多平行进化的例子中看到了自然选择的决定性特征。在适应度景观中存在类似的自适应峰值是并行性的潜在原因，但不一定是唯一的解释。密切相关的物种之间的共同基因组背景和发育限制也可能影响生物学变化的方向，在这种情况下，遗传平行性预计是平行表型进化的基础。在这里，我的目标是确定密切相关的物种的平行表型进化的基础上，起源于共同的发展途径的共同选择的遗传平行。本研究拟对四川米达斯丽鱼视觉敏感性的适应性进化进行研究。这个物种群提供了一个自然的实验，以解决这个问题，因为多个清晰的火山口湖泊具有相似的光照条件独立殖民从混浊的五大湖，他们的辐射发生最近导致小基因组的分歧，和他们的系统发育关系是很好的理解。迈达斯慈鲷的视觉灵敏度已经迅速发展，并在殖民化后的火山口湖从五大湖平行。此外，衍生的火山口湖物种的视觉敏感性类似于在青少年从祖先五大湖。因此，我假设：1）在适应性进化过程中，发育途径被选择为适应新的条件，因此，2）在火山口湖谱系中，潜在的分子机制具有高度的平行性。正向和反向遗传学相结合的方法将被用来实证检验这些假设。首先，我将测试视网膜转录组中差异表达基因之间的正相关性，这些基因是进化分歧的基础（即，火山口与五大湖）和祖先群体中那些潜在的个体发生变化（即，五大湖）如第一种假设所预测的那样。第二个假设预测这些基因在不同火山口湖泊的物种中是相同的。然后，我将在两个独立的祖先衍生的杂交组合中通过eQTL分析研究视觉敏感性的遗传结构。共同的基因组区域，预计在两个十字架影响视觉灵敏度的基因表达的平行变化的基础。最后，我将使用基因组编辑来功能性地挑战所识别的基因座。该项目增加了关于进化可预测性的长期争论，并将进一步加深我们对视觉敏感性发展和适应性差异机制的理解。