Research article summary (published 27 Feb 1999):

Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition.

Full Abstract

We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid-binding protein (IRBP), von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora, Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set, we recognized nine mitochondrial partitions (both stems and loops, for each of 12S rRNA, tRNA valine, and 16S rRNA; and first, second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony, minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99-100% bootstrap support for Afrotheria and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also high bootstrap support (89-100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic analyses. Mitochondrial-gene trees associate cow with horse, whereas nuclear-gene trees associate cow with hedgehog and these two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.

Author information

Author/s: Springer, M S (MS); Amrine, H M (HM); Burk, A (A); Stanhope, M J (MJ);

Affiliation: Department of Biology and Interdepartmental Graduate Program in Genetics, University of California, Riverside, California 92521, USA. mark.springer(-atsign-)ucr.edu

Journal and publication information

Publication Type: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal: Systematic biology (Syst Biol), published in England. (Language: eng)

Reference: 1999-Mar; vol 48 (issue 1) : pp 65-75

Dates: Created 2002/06/24; Completed 2002/07/25; Revised 2006/11/15;

PMID: 12078646, status: MEDLINE (last retrieval date: 2/18/2009, IMS Date: )

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Animals Base Composition Cell Nucleus - genetics Cytochrome b Group - genetics DNA, Mitochondrial - genetics Female Genes Mammals - classification; genetics

Mammals - classification; genetics Phylogeny Placenta Pregnancy RNA, Ribosomal - genetics RNA, Ribosomal, 16S - genetics RNA, Transfer, Val - genetics Rabbits - classification

Associated Chemicals: Cytochrome b Group (0) ; DNA, Mitochondrial (0) ; RNA, Ribosomal (0) ; RNA, Ribosomal, 16S (0) ; RNA, Transfer, Val (0) ; RNA, ribosomal, 12S (0)

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