Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish.
The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m(2) pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high-resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20-10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration.
Department of Animal Science, University of California, One Shields Avenue, Davis, CA, 95616, USA.|Ecological Sciences Research Laboratories, Department of Biology, Hacettepe University, Beytepe, 06800, Ankara, Turkey.
İsmaİl K
İK
Sağlam
Department of Animal Science, University of California, One Shields Avenue, Davis, CA, 95616, USA.|Center for Watershed Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
Jason
J
Baumsteiger
Abernathy Fish Technology Center, U.S. Fish and Wildlife Service, 1440 Abernathy Creek Road, Longview, WA, 98632, USA.
Matt J
MJ
Smith
Pacific Southwest Region, U.S. Fish and Wildlife Service, 2800 Cottage Way W-2606, Sacramento, CA, 95825, USA.
Javier
J
Linares-Casenave
Center for Watershed Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
Andrew L
AL
Nichols
Department of Animal Science, University of California, One Shields Avenue, Davis, CA, 95616, USA.
Sean M
SM
O'Rourke
Department of Animal Science, University of California, One Shields Avenue, Davis, CA, 95616, USA.|Center for Watershed Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
Michael R
MR
Miller
D000818:Animals; D005075:Biological Evolution; D003247:Conservation of Natural Resources; D003889:Desert Climate; D056727:Endangered Species; D051456:Gene Flow; D023281:Genomics; D007695:Killifishes / Q000235:genetics*; D008957:Models, Genetic; D059645:Mutation Rate; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014481:United States
ABBA-BABA; RAD sequencing; SNP assays; critically endangered; divergence estimates; multispecies coalescent