title: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes.
abstract: Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents. We estimate species trees inferred from phylogenomic scale data (304 loci) while exploring several strategies that consider topological error from each individual gene tree. With a dated species tree, we examine taxonomy and test previous hypotheses that suggest the ratsnakes originated in the Old World (OW) and dispersed to New World (NW). Furthermore, we determine if dispersal to the NW represented a source of ecological opportunity, which should show elevated rates of species diversification. We show that ratsnakes originated in the OW during the mid-Oligocene and subsequently dispersed to the NW by the mid-Miocene; diversification was also elevated in a subclade of NW taxa. Finally, the optimal biogeographic region-dependent speciation model shows that the uptick in ratsnake diversification was associated with colonization of the NW. We consider several alternative explanations that account for regionally distinct diversification rates.
authors.affiliation: Dept. of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, United States; Dept. of Biology, The Graduate School and University Center, The City University of New York, 365 Fifth Ave., New York, NY 10016, United States; Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, United States. Electronic address: chenx1122@gmail.com.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, United States.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, United States.
authors.forename: R Alexander
authors.initials: RA
authors.lastname: Pyron
authors.affiliation: Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, United States.
authors.forename: Frank T
authors.initials: FT
authors.lastname: Burbrink
mesh_terms: D000818:Animals; D044822:Biodiversity; D002138:Calibration; D017812:Colubridae / Q000235:genetics*; D056426:Genetic Loci; D049810:Genetic Speciation; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D058974:Phylogeography; D011336:Probability; D013045:Species Specificity; D013997:Time Factors
keywords: Biogeography; Diversification; GeoSSE; Phylogenomics; Ratsnakes