Refugia and Speciation in North American Scarlet Snakes (Cemophora)
Scarlet Snakes (Cemophora coccinea) are monotypic, poorly studied, semifossorial habitat specialists from southeastern United States that traditionally include three subspecies based on color pattern and morphology. We sequenced two mitochondrial and two nuclear loci for 62 individuals from across the species range, and analyzed data with the use of parsimony and Bayesian phylogenetic methods to test a previously proposed phylogenetic hypothesis for C. coccinea. Our results suggest two Pliocene or Pleistocene refugia for Cemophora, one in southern Texas, and the other in the region extending from southeastern Louisiana through Florida. In light of our results we elevate Cemophora coccinea lineri to a full species, C. lineri, that differs from C. coccinea sensu stricto genetically and phenotypically.Abstract
Distribution, sampling and haplotype networks for Cemophora coccinea. Colors indicate C. c. coccinea (blue), Cemophora c. copei (red), Cemophora c. lineri (yellow), and the intergrade zone of C. c. coccinea and C. c. copei (purple). (A) Geographic ranges and sampling localities for C. c. coccinea (triangles), C. c. copei (squares), C. c. lineri (diamonds), and the intergrade zone of C. c. coccinea and C. c. copei (circles). Haplotype networks: (B) COI codon 1, (C) ND4 codon 1, (D) GAD2 intron 15 + SPTBN1 intron 1 (concatenated), (E) COI codon 3 + ND4 codon 3 (concatenated), (F) tRNA-Histidine, (G) COI, (H) ND4, (I) GAD2 intron 15 (phased), and (J) SPTBN1 intron 1 (phased); numbers are the individual ID numbers (Appendix 1); letters “a” and “b”, when following individual ID numbers, indicate the two alleles carried by individuals heterozygous at GAD2 intron 15 or SPTBN1 intron 1. The range map is adapted from Conant and Collins (1998) and the photograph of C. coccinea is used with permission from Paul Marcellini.
BEAST phylogenetic trees for COI and ND4 loci. BEAST trees for (A) COI and (B) ND4 loci; numbers at internal nodes indicate posterior probabilities. Colored shapes at tips indicate subspecies: Cemophora c. coccinea (blue triangles), Cemophora c. copei (red squares), Cemophora c. lineri (yellow triangles), or C. c. coccinea and C. c. copei intergrade zone (purple circles). Individual ID numbers (Appendix 1) and locality information are also indicated at tree tips. Clades collapsed as triangles indicate a set of individuals that share the same haplotype; phylogenies are represented as simple cladograms (branch lengths are not proportional to divergence) so that posterior probabilities could be displayed.
BEAST phylogenetic trees for phased nuclear loci. BEAST trees for (A) SPTBN1 intron 1 (phased) and (B) GAD2 intron 15 (phased); numbers at internal nodes indicate posterior probabilities. Colored shapes at tips indicate subspecies: Cemophora c. coccinea (blue triangles), Cemophora c. copei (red squares), Cemophora c. lineri (yellow triangles), or C. c. coccinea and C. c. copei intergrade zone (purple circles). Individual ID numbers (Appendix 1) and locality information are also indicated at tree tips. Clades collapsed as triangles indicate a set of individuals that share the same haplotype. For individuals heterozygous at GAD2 intron 15 or SPTBN1 intron 1, the letters “a” and “b” are added to the end of the individual's ID number to indicate the two alleles carried by that individual; phylogenies are represented as simple cladograms (branch lengths are not proportional to divergence) so that posterior probabilities could be displayed.
(A) Cephalic scalation of Cemophora lineri (formerly C. c. lineri), specimen AMNHR 108916, Jim Hogg County, Texas; (B) time-calibrated mitochondrial (ND4 + COI) phylogeny of Cemophora; asterisks indicate clades with posterior probability >0.95; horizontal gray bars at internal nodes indicate clade age (95% HPD). Individual ID numbers (Appendix 1) and locality information are indicated at tree tips.
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