Developmental Mechanisms of Scale Loss and Replacement in the Evolution of Catfishes

人们普遍认为，在进化过程中，一个结构的丢失伴随着产生该结构所需的遗传信息的丢失，从而阻止了该结构的再现。这种进化的不可逆性有一个明显的例外，那就是鲶鱼表皮的进化。这一群体的共同祖先失去了鳞片的外骨骼，导致大多数现存物种的“裸露”皮肤。然而，在几个“装甲”鲶鱼家族的皮肤中，一个外骨骼以被称为鳞片的骨板的形式重新出现。这个项目测试了一个假设，即制造鳞片的遗传程序在裸鲶鱼中以潜在的形式保留，并在铠甲鲶鱼鳞片的起源中被重新激活。确定生物体拥有过去适应的遗传“记忆”的程度，将有助于深入了解物种以进化而不是灭绝来应对环境变化的能力。该项目将为本科生、研究生和博士后学员提供研究机会，并为加强首席研究员在遗传学和鱼类生物学方面的本科课程提供材料。为这项工作而维持的鱼群将用于向中小学生介绍鲶鱼的各种不同寻常的繁殖行为。最后，将在科罗拉多大学自然历史博物馆准备一个关于鱼鳞结构和进化的展览（包括博物馆创始人一百多年前的相关工作）。本文将通过斑马鱼（代表祖先鳞片状态）、两种裸鲶和两种甲鱼的基因表达和调控的比较，研究鲶鱼躯干真皮骨架遗传程序保留和再激活的程度和性质。通过原位杂交分析，验证了裸鲶鳞片起始基因在甲鱼鳞片中丢失而在甲鱼鳞片中重新表达的假说。裸鲶鱼祖先鳞片中调节基因表达的顺式调控元件和/或反式作用因子被保留在裸鲶鱼中，并被用于鳞片的发育，这一假设将通过对多物种幼虫中斑马鱼和鲶鱼基因两侧的DNA进行报告基因转基因分析来验证。这些报告基因转基因实验，结合使用基于CRISPR/ cas9的基因组编辑删除斑马鱼顺式调控元件，也将提供对元件多向性功能的深入了解，这一功能可能在缺乏性状表达的情况下保留它们。使用保守的遗传程序的复杂结构的循环起源，作为对正在研究的系统的假设，已经被标记为“深度同源”，它的发现代表了进化发育生物学的胜利之一。所提出的研究将有助于理解深层同源性，不仅在基因表达的普遍研究水平，而且在潜在的基因组元件。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

It is generally thought that the loss of a structure in evolution is accompanied by the loss of the genetic information needed to produce it, thereby preventing its reappearance. An apparent exception to such irreversibility of evolution is provided by the evolution of the skin covering of catfishes. A common ancestor of this group lost its outer skeleton of scales, resulting in the "naked" skin characteristic of most living species. An outer skeleton has reappeared in the skin of several families of "armored" catfishes, however, in the form of bony plates known as scutes. This project tests the hypothesis that the genetic program for making scales is retained in a latent form in naked catfishes and was reactivated in the origin of armored catfish scutes. Determining the extent to which organisms possess a genetic "memory" of past adaptations will provide insight into the ability of species to respond to environmental change with evolution rather than extinction. The project will provide research opportunities for undergraduate, graduate, and post-doctoral trainees, as well as materials for enhancing the principal investigator's undergraduate courses in genetics and fish biology. Fish colonies maintained for the work will be used to introduce primary and secondary school students to a variety of unusual reproductive behaviors employed by catfishes. Finally, an exhibit will be prepared at the University of Colorado Natural History Museum on the structure and evolution of fish scales (including relevant work by the museum's founder conducted over a hundred years ago). The degree and nature of retention and reactivation of genetic programs for the trunk dermal skeleton in catfishes will be investigated by comparison of gene expression and regulation in the zebrafish (representing the ancestral scaled condition), two species of naked catfishes and two species of armored catfishes. The hypothesis that the expression of scale initiation genes was lost in naked catfishes and regained in the scutes of armored catfishes will be tested by in situ hybridization analysis. The hypothesis that cis-regulatory elements and/or trans-acting factors regulating gene expression in ancestral scales have been retained in naked catfishes and co-opted for the development of scutes will be tested by reporter transgenic analysis of DNA flanking zebrafish and catfish genes in larvae of multiple species. These reporter transgenic experiments, combined with deletion of zebrafish cis-regulatory elements using CRISPR/Cas9-based genome editing, will also provide insight into pleiotropic function of the elements, a feature likely to preserve them in the absence of trait expression. Recurrent origin of complex structures using conserved genetic programs, as hypothesized for the system under study, has been labeled "deep homology" and its discovery represents one of the triumphs of Evolutionary Developmental Biology. The proposed research will contribute to the understanding of deep homology not only at the commonly studied level of gene expression but at that of the underlying genomic elements as well.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.