Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus)

Author:

Myers Edward A12,Rautsaw Rhett M1,Borja Miguel3,Jones Jason4,Grünwald Christoph I45,Holding Matthew L16ORCID,Grazziotin Felipe G7,Parkinson Christopher L1ORCID

Affiliation:

1. Clemson University Department of Biological Sciences, , Clemson, SC 29634, USA

2. California Academy of Sciences Department of Herpetology, , San Francisco, CA 94118, USA

3. Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia Facultad de Ciencias Biológicas, , Gómez Palacio, Durango 35010, Mexico

4. Herp.mx A.C. C.P. 28989 , Villa de Álvarez, Colima, Mexico

5. Avenida de la Ribera #203 Biodiversa A.C., , C.P. 45900, Chapala, Jalisco, Mexico

6. Life Sciences Institute, University of Michigan , Ann Arbor, MI 48109 , USA

7. Laboratório de Coleções Zoológicas, Instituto Butantan , Avenida Vital Brasil, São Paulo, 05503-900 , Brazil

Abstract

Abstract Abstract.—Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.

Funder

National Science Foundation

Fundação de Amparo à Pesquisa do Estado de São Paulo

CNPq

National Institute of General Medical Sciences of the National Institutes of Health

Publisher

Oxford University Press (OUP)

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