The Rattlesnake Tree of Life: A Genome-Wide Perspective

Parkinson, Christopher                                                                                                                                                                             Department of Biological Sciences         

Department of Forestry and Environmental Conservation

Clemson University

Clemson, South Carolina, USA 


Holding, Matthew L.*                             

Department of Biological Sciences                                                                                                                           

Clemson University

Clemson, South Carolina, USA 


Strickland, Jason L.                                                                                                                                            Rautsaw, Rhett M.

Mason, Andrew J.

Hofmann, Erich P.                                                                                                                                      Department of Biological Science*    

Florida State University                                                                                                                             

Tallahassee, Florida, USA


Borja, Miguel

Facultad de Ciencias Biológicas                                  

Universidad Juárez del Estado de Durango

Av. Universidad s/n. Fracc. Filadelfia, C.P. 35070                                                                                           Gómez Palacio, Durango, Mexico


Grünwald, Christoph I.

Jones, Jason M. A.C.

Villa del Álvarez, Colima, Mexico


de la Torre-Loranca, Miguel Angel

Instituto Lorancai

Km 32 Carretera Federal Orizaba-Zongolica Ocotepec

Los Reyes, Veracruz, México


Castañeda, Gamaliel   Facultad de Ciencias Biológicas

Universidad Juárez del Estado de Durango

Av. Universidad s/n. Fracc

Filadelfia, C.P. 35070

Gómez Palacio, Durango, Mexico


Grazziotin, Felipe

Laboratório de Coleções Zoológicas

Instituto Butantan

São Paulo, Brazil


Junqueira-de-Azevedo, Inacio

Laboratório Especial de Toxinologia Aplicada                                                                                        


Instituto Butantan

São Paulo, Brazil


Gibbs, H. Lisle                                                                                                   

Department of Evolution, Ecology and Organismal Biology

Ohio State University                                        

Columbus, Ohio, USA


Rokyta, Darin                                                                                                                      

Department of Biological Science                                                                                                                    Florida State University                                                            

Tallahassee, Florida, USA


The rattlesnakes (Crotalus and Sistrurus) are the most speciose group of vipers, consisting of ~50 currently described species. Rattlesnakes contribute the majority of snakebites in North America and are flagships for curiosity, culture, and conservation of snakes. As such, they have been extensively studied through time from an ecological and evolutionary perspective. Despite being the focus of countless phylogenetic studies, the evolutionary history of rattlesnakes remains clouded and the phylogenetic placement of many species is uncertain. Here, we use the largest dataset assembled and the most complete sampling of putative lineages to infer the phylogeny of rattlesnakes. We used > 1400 coding gene sequences recovered from venom gland transcriptomes of 147 individual snakes, representing 55 putative rattlesnake lineages. We provide strong evidence for 3 major clades within Crotalus, the dusky rattlesnakes and rock rattlesnakes, the montane rattlesnakes including C. willardi, and the large-bodied rattlesnakes such as C. durissus and C. scutulatus. We clearly support a monophyletic C. viridis complex, a montane radiation that includes C. pricei, C. transversus, C. intermedius, and C. willardi, and a monophyletic C. durissus complex. Interestingly, we support C. horridus as sister to the rest of the clade of large-bodied Crotalus species, which differs considerably from its place in previous phylogenies. The recovery of novel relationships, and apparent paraphyly of certain taxa suggest that several groups may be in need of taxonomic revision. Despite the unprecedented size of our dataset, the persistence of a few recalcitrant nodes suggests that the early diversification of rattlesnakes may include hard polytomies, or require targeted whole genome comparisons to resolve. Overall, we provide new, high resolution insight into the evolutionary history of this complex and iconic group to date. We expect that the phylogeny generated here will provide a stalwart backbone for testing a variety of ecological and evolutionary hypotheses in the future.

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