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Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus, Trimeresurus: separate, simultaneous, and conditional data combination analyses.
Mol Biol Evol. 2003 Aug; 20(8):1240-51.MB

Abstract

A number of methods have been proposed for addressing how to optimize the analysis of multiple data sets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous, and conditional data combination methods to analyze 3,135 bp of data from four mitochondrial partitions and the seventh intron of the beta fibrinogen gene in the Asian pit viper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best-supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron resulted in much lower levels of homoplasy compared with the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels, respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa that were unresolved throughout all individual gene trees and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships than are the 12S and 16S ribosomal RNA partitions at the taxonomic levels under consideration.

Authors+Show Affiliations

School of Biological Sciences, University of Wales, Bangor, Gwynedd, United Kingdom. s.creer@bangor.ac.ukNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

12777535

Citation

Creer, Simon, et al. "Assessing the Phylogenetic Utility of Four Mitochondrial Genes and a Nuclear Intron in the Asian Pit Viper Genus, Trimeresurus: Separate, Simultaneous, and Conditional Data Combination Analyses." Molecular Biology and Evolution, vol. 20, no. 8, 2003, pp. 1240-51.
Creer S, Malhotra A, Thorpe RS. Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus, Trimeresurus: separate, simultaneous, and conditional data combination analyses. Mol Biol Evol. 2003;20(8):1240-51.
Creer, S., Malhotra, A., & Thorpe, R. S. (2003). Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus, Trimeresurus: separate, simultaneous, and conditional data combination analyses. Molecular Biology and Evolution, 20(8), 1240-51.
Creer S, Malhotra A, Thorpe RS. Assessing the Phylogenetic Utility of Four Mitochondrial Genes and a Nuclear Intron in the Asian Pit Viper Genus, Trimeresurus: Separate, Simultaneous, and Conditional Data Combination Analyses. Mol Biol Evol. 2003;20(8):1240-51. PubMed PMID: 12777535.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus, Trimeresurus: separate, simultaneous, and conditional data combination analyses. AU - Creer,Simon, AU - Malhotra,Anita, AU - Thorpe,Roger S, Y1 - 2003/05/30/ PY - 2003/6/5/pubmed PY - 2004/4/17/medline PY - 2003/6/5/entrez SP - 1240 EP - 51 JF - Molecular biology and evolution JO - Mol Biol Evol VL - 20 IS - 8 N2 - A number of methods have been proposed for addressing how to optimize the analysis of multiple data sets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous, and conditional data combination methods to analyze 3,135 bp of data from four mitochondrial partitions and the seventh intron of the beta fibrinogen gene in the Asian pit viper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best-supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron resulted in much lower levels of homoplasy compared with the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels, respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa that were unresolved throughout all individual gene trees and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships than are the 12S and 16S ribosomal RNA partitions at the taxonomic levels under consideration. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/12777535/Assessing_the_phylogenetic_utility_of_four_mitochondrial_genes_and_a_nuclear_intron_in_the_asian_pit_viper_genus_Trimeresurus:_separate_simultaneous_and_conditional_data_combination_analyses_ DB - PRIME DP - Unbound Medicine ER -