Mitochondrial Dna Phylogeography of the Polytypic North American Rat Snake (Elaphe Obsoleta): A Critique of the Subspecies Concept

Abstract

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.

A new species of the genus Rhabdophis Fitzinger, 1843 (Squamata: Colubridae) from Guangdong Province, southern China

“…The polymerase chain reaction (PCR) was used for amplification of both the cyt b and c-mos genes. For amplification of the cyt b gene, the forward primer was L14910 (5′-GAC CTG TGA TMT GAA AAA CCA YCG TTG T-3′) according to de Queiroz et al (2002), and the reverse primer was H16064 (5′-CTT TGG TTT ACA AGA ACA ATG CTT TA-3′) according to Burbrink et al (2000). For amplification of the c-mos gene segment, the primers S77 (5′-CAT GGA CTG GGA TCAGTT ATG-3′) and S78 (5′-CCT TGGGTG TGA TTT TCT CAC CT-3′) (Slowinski & Lawson 2002) were used.…”

Surviving the ice: Northern refugia and postglacial colonization

“…In North America, some studies have uncovered reduced levels of genetic variation in northern populations supporting expansions from southern refugia (7)(8)(9). However, phylogeographic surveys of the central U.S. are incomplete, and recolonization scenarios have not been adequately tested (10,11).…”

Northward dispersal of sea kraits (Laticauda semifasciata) beyond their typical range

“…For this study, we targeted Cytb because there are comparable data in GenBank. We amplified partial sequences of the Cytb gene using the primers L14910 and H16064 [25]. DNA was amplified using a SimpliAmp Thermal Cycler (Life Technologies, Carlsbad, CA, USA) in 25 μl reaction volumes, consisting of 10 ng of template DNA, 1.25 U of ELPIS rTaq DNA polymerase (ELPIS, Daejeon, South Korea), 2.5 μl of 10x PCR buffer, 2 μl of 10 mM dNTP mix (2.5 mM each) and 0.5 μl of each primer (10 pmol).…”

“…DNA was amplified using a SimpliAmp Thermal Cycler (Life Technologies, Carlsbad, CA, USA) in 25 μl reaction volumes, consisting of 10 ng of template DNA, 1.25 U of ELPIS rTaq DNA polymerase (ELPIS, Daejeon, South Korea), 2.5 μl of 10x PCR buffer, 2 μl of 10 mM dNTP mix (2.5 mM each) and 0.5 μl of each primer (10 pmol). The cycling conditions for PCR were as follows: 94°C for 4 min, followed by 35 cycles at 94°C for 30 s, 57°C for 30 s and 72°C for 1 min with a final extension step of 72°C for 7 min [25]. We verified PCR products by electrophoresis on 1.5% agarose gels, and purified products using an AccuPrep ® PCR Purification Kit (Bioneer, Daejeon, South Korea).…”