Some of the most fundamental biological questions involve how, why, and how fast organisms can adapt to new environments and whether evolution would proceed down the same path if repeated in an independent event. Cases of repeated evolution offer a window into understanding whether certain types of genetic variants are more likely than others to consistently contribute to evolutionary change. For this work, we interrogate genomes for signatures left by local adaptation in cavefish. Cavefish in northern Mexico have lost their eyes and pigment and experience changes across their metabolism, sensory systems, and behavior.  Most notably, is the only known natural system to study fixed, derived sleep loss, and we are working to understand why cavefish can survive 1/4 of the sleep that surface fish need to function. This repeated evolution offers an opportunity to understand specific characteristics of targets of selection that are repeatedly responsible for phenotypic change.

Repeated evolution in cavefish —  

In order to identify the genetic bases of eye loss and and sleep loss,  our lab is leading the population genomic effort with support from other cavefish labs.  This community-wide effort has generated whole genome resequencing data from multiple independently evolved cave populations and multiple surface populations, and a closely related congener. 

By analyzing the most expansive sampling to date in this system, we've shown that 

1) at least two independent origins of cave phenotypes have evolved from two separate surface lineages

2) selection has played a central role in driving the evolution of both loss and gain of function traits, 

3) selection on standing genetic variation and de novo mutations has targeted the same genes repeatedly across cavefish lineages, and 

4) genes evolving repeatedly across cave lineages are longer and, thus, have a greater mutational opportunity compared to genes across the rest of the genome, a pattern that is primarily driven by genes with independent mutations across lineages. 

Our work presents strong evidence that repeated evolution of the canonical cavefish phenotypes was shaped by selection. More broadly, our work provides insight into the factors contributing to the repeatability of evolution and whether features such as coding sequence length may predictably bias evolution via novel mutations in certain genes. 

Pathway evolution in amniotes — 

Comparative analyses of central molecular networks uncover variation that can be targeted by biomedical research to develop insights and interventions into disease. The Insulin/Insulin-like Signaling and TOR (IIS/TOR) molecular network regulates metabolism, growth, and aging. With the development of new molecular resources for reptiles, we examined whether IIS/TOR is rapidly evolving within amniotes – mammals and reptiles (including birds). Additionally, we evaluated whether natural selection shaped the hormone-receptor binding relationships that initiate IIS/TOR signaling. Finally, we've used comparative molecular biology to identify repeated changes and losses across amniotes of key genes related to eye loss.