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Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough?
Mol Phylogenet Evol. 2002 Feb; 22(2):315-29.MP

Abstract

The clade of garter snakes (Thamnophis) includes some of the most abundant and well-studied snakes in North America. However, phylogenetic relationships within this group have been little studied. We used DNA sequences of four mitochondrial genes (cytochrome b and NADH dehydrogenase subunits 1, 2, and 4) to estimate relationships among 29 of the 31 recognized species of Thamnophis plus the related species Adelophis foxi. Both maximum parsimony (MP) and maximum-likelihood (ML) analyses of all these genes combined produced well-resolved trees with moderate (70-89%) to strong (90-100%) bootstrap support for most clades. MP and ML trees were very similar, with no strongly supported conflict between the two analyses. These analyses identify a clade of 12 species largely restricted to México (the "Mexican clade"), and a clade containing 15 species that collectively range from Central America to southern Canada (the "widespread clade"). These two groups are identified as sister taxa in both MP and ML analyses. A clade consisting of the ribbon snakes (T. sauritus and T. proximus) and the common garter snake (T. sirtalis) is placed as the sister group to all other Thamnophis (i.e., the Mexican + widespread clades) in our analyses. High bootstrap proportions at several levels in the tree support the inclusion of both Thamnophis validus, which has traditionally been placed in the genus Nerodia, and the poorly known species Adelophis foxi within Thamnophis. We used randomly sampled characters (i.e., standard bootstrapping) and randomly sampled contiguous blocks of characters to examine the effect of number of characters on resolution of and support for relationships within Thamnophis using MP. In general, these analyses indicate that we have reached a point of strongly diminishing returns with respect to the effect of adding mtDNA sequence characters for the current set of taxa; our sample of 3809 mtDNA characters is apparently "enough." The next steps to improve the phylogenetic estimate may be to add nuclear DNA sequences, morphology, or behavior, or to sequence additional mtDNA lineages within species.

Authors+Show Affiliations

Department of Environmental, Population and Organismic Biology and University Museum, University of Colorado, Boulder, Colorado 80309-0334, USA. dequeiro@stripe.colorado.eduNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

11820851

Citation

de Queiroz, Alan, et al. "Phylogenetic Relationships of North American Garter Snakes (Thamnophis) Based On Four Mitochondrial Genes: How Much DNA Sequence Is Enough?" Molecular Phylogenetics and Evolution, vol. 22, no. 2, 2002, pp. 315-29.
de Queiroz A, Lawson R, Lemos-Espinal JA. Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough? Mol Phylogenet Evol. 2002;22(2):315-29.
de Queiroz, A., Lawson, R., & Lemos-Espinal, J. A. (2002). Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough? Molecular Phylogenetics and Evolution, 22(2), 315-29.
de Queiroz A, Lawson R, Lemos-Espinal JA. Phylogenetic Relationships of North American Garter Snakes (Thamnophis) Based On Four Mitochondrial Genes: How Much DNA Sequence Is Enough. Mol Phylogenet Evol. 2002;22(2):315-29. PubMed PMID: 11820851.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough? AU - de Queiroz,Alan, AU - Lawson,Robin, AU - Lemos-Espinal,Julio A, PY - 2002/2/1/pubmed PY - 2002/4/4/medline PY - 2002/2/1/entrez SP - 315 EP - 29 JF - Molecular phylogenetics and evolution JO - Mol Phylogenet Evol VL - 22 IS - 2 N2 - The clade of garter snakes (Thamnophis) includes some of the most abundant and well-studied snakes in North America. However, phylogenetic relationships within this group have been little studied. We used DNA sequences of four mitochondrial genes (cytochrome b and NADH dehydrogenase subunits 1, 2, and 4) to estimate relationships among 29 of the 31 recognized species of Thamnophis plus the related species Adelophis foxi. Both maximum parsimony (MP) and maximum-likelihood (ML) analyses of all these genes combined produced well-resolved trees with moderate (70-89%) to strong (90-100%) bootstrap support for most clades. MP and ML trees were very similar, with no strongly supported conflict between the two analyses. These analyses identify a clade of 12 species largely restricted to México (the "Mexican clade"), and a clade containing 15 species that collectively range from Central America to southern Canada (the "widespread clade"). These two groups are identified as sister taxa in both MP and ML analyses. A clade consisting of the ribbon snakes (T. sauritus and T. proximus) and the common garter snake (T. sirtalis) is placed as the sister group to all other Thamnophis (i.e., the Mexican + widespread clades) in our analyses. High bootstrap proportions at several levels in the tree support the inclusion of both Thamnophis validus, which has traditionally been placed in the genus Nerodia, and the poorly known species Adelophis foxi within Thamnophis. We used randomly sampled characters (i.e., standard bootstrapping) and randomly sampled contiguous blocks of characters to examine the effect of number of characters on resolution of and support for relationships within Thamnophis using MP. In general, these analyses indicate that we have reached a point of strongly diminishing returns with respect to the effect of adding mtDNA sequence characters for the current set of taxa; our sample of 3809 mtDNA characters is apparently "enough." The next steps to improve the phylogenetic estimate may be to add nuclear DNA sequences, morphology, or behavior, or to sequence additional mtDNA lineages within species. SN - 1055-7903 UR - https://www.unboundmedicine.com/medline/citation/11820851/Phylogenetic_relationships_of_North_American_garter_snakes__Thamnophis__based_on_four_mitochondrial_genes:_how_much_DNA_sequence_is_enough L2 - https://linkinghub.elsevier.com/retrieve/pii/S1055790301910747 DB - PRIME DP - Unbound Medicine ER -