DOI: 10.5061/dryad.393
title: Data from: Additional Support for Afrotheria and Paenungulata, the Performance of Mitochondrial versus Nuclear Genes, and the Impact of Data Partitions with Heterogeneous Base Composition

description: 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 (stems and loops, respectively, for 12S
 rRNA, tRNA valine, 16S rRNA; 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 and horse together, whereas nuclear-gene trees associate cow and
 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.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 (stems and loops,
 respectively, for 12S rRNA, tRNA valine, 16S rRNA; 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 and horse together, whereas
 nuclear-gene trees associate cow and 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.
description: Springer et al Data
 SetSpringer.htm