Footprints of speciation and hybridization in the genomes of Galápagos iguanas

火山岛可以被视为进化的“天然实验室”，因为与大陆环境相比，许多重要的进化过程可以在更简单的条件下观察和重建。在这些岛屿上发生的主要进化过程之一是物种在岛屿上的到来和随后的进化，通常由有限数量的创始人代表。在到达后，物种必须适应新的环境条件，这往往会导致新物种的进化，有时还会导致整个物种的适应性辐射。加拉帕戈斯群岛可能是最著名的纯海洋火山岛，有特有的物种，其中一些成为进化生物学的教科书例子。南美蜥蜴在1000多万年前到达这个群岛，在加拉帕戈斯群岛上的物种多样化，分为陆地蜥蜴属(Conolophus属)和海生鬣蜥属(Amblyrigenchus属)。与世界上任何其他蜥蜴不同，海洋鬣蜥已经完全适应了海洋环境。此外，海洋鬣蜥的不同岛屿种群提供了一个独特的系统来研究两种主要进化力量--局部适应/物种形成与杂交的影响。通过对南美大陆的加拉帕戈斯鬣蜥及其姊妹类群(Cachryx属和Ctenosaura属的物种)的基因组测序，我们将分别揭示加拉帕戈斯鬣蜥的分化以及随后陆地鬣蜥和海洋鬣蜥的分化的基因组特征。这将使我们能够确定当物种在岛屿上面临新的环境条件时，通常处于选择之下的基因组区域(基因)，更具体地说，是构成蜥蜴物种对海洋环境独特适应的基因。基于海洋鬣蜥和陆地鬣蜥的完整参考基因组，我们将进一步检验我们的假设，即局部适应和杂交导致局部适应的基因组等价物通过反复杂交事件整合到海洋鬣蜥的共同物种基因库中。这样的过程将增强一个物种的进化潜力。根据我们的假设，我们将首先进行一项当地的实地研究，提供对圣克里斯托巴尔岛上当地适应和杂交过程的最新见解。其次，通过将这一快照的见解整合到一个更广泛的进化框架中，我们将分析这两种影响对种群基因组学以及转录/蛋白质组水平的影响。为此，我们将包括以低覆盖率基因组和转录图谱为代表的海洋鬣蜥岛屿种群。观察到的基因组模式将与加拉帕戈斯陆地鬣蜥系统中发现的模式进行比较，在进化时间尺度上，没有杂交的系统发育差异(物种形成)是明显的。

Volcanic islands can be seen as “natural laboratories” of evolution as many important evolutionary processes can be observed and reconstructed under simpler conditions compared to mainland settings. One of the major evolutionary processes that take place on such islands, is the arrival and subsequent evolution of species on islands usually represented by a limited number of founder individuals. Following arrival, species have to adapt to new environmental conditions often resulting into the evolution of new species and sometimes entire adaptive radiations of species. The Galápagos archipelago is probably the most famous setting of purely oceanic volcanic islands with endemic species, some of which became textbook examples of evolutionary biology. Having arrived more than 10 million years ago on the archipelago, a lineage of South-American lizards diversified on the Galápagos archipelago into land (genus Conolophus) and marine iguanas (genus Amblyrhynchus). Like no other lizard worldwide, marine iguanas have fully adapted to the marine environment. Moreover, the various island populations of marine iguanas provide a unique system to study the effects of two major evolutionary forces – local adaptation/speciation versus hybridization. By sequencing the genomes of Galápagos iguanas and their sister taxa from the South-American mainland (species of the genera Cachryx and Ctenosaura), we will unravel genomic signatures of the divergence of Galápagos iguanas and the subsequent differentiation of land and marine iguanas, respectively. This will allow us to identify genomic regions (genes) that are in general under selection when species face new environmental conditions on islands and more specific, genes that underlie the unique adaptation of a lizard species to the marine environment. Based on the full reference genomes of marine and land iguanas, we will further test our hypothesis that local adaptation and hybridization result into the integration of the genomic equivalents of adaptations on a local level into a common species gene pool of the marine iguana by recurrent hybridization events. Such a process would enhance the evolutionary potential of a species. We will follow up our hypothesis by first conducting a local field study, which provides a current insight on the processes of local adaptation and hybridization on the island of San Cristóbal. Second, by integrating the insights from this snapshot into a broader evolutionary framework, we will analyse the consequences of both effects on a population genomics as well as transcriptomic/proteomic level. To do so, we will include island populations of the marine iguana represented by low coverage genomes and transcriptomic profiles. Observed genomic patterns will be compared with patterns found for the system of the Galápagos land iguanas, in which phylogenetic divergence (speciation) without hybridization is evident on an evolutionary time scale.