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A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA.
Mol Phylogenet Evol. 2015 Jun; 87:14-27.MP

Abstract

To investigate phylogenetic relationships within the grass subfamily Pooideae we studied about 50 taxa covering all recognized tribes, using one plastid DNA (cpDNA) marker (matK gene-3'trnK exon) and for the first time four nuclear single copy gene loci. DNA sequence information from two parts of the nuclear genes topoisomerase 6 (Topo6) spanning the exons 8-13 and 17-19, the exons 9-13 encoding plastid acetyl-CoA-carboxylase (Acc1) and the partial exon 1 of phytochrome B (PhyB) were generated. Individual and nuclear combined data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All of the phylogenetic results show Brachyelytrum and the tribe Nardeae as earliest diverging lineages within the subfamily. The 'core' Pooideae (Hordeeae and the Aveneae/Poeae tribe complex) are also strongly supported, as well as the monophyly of the tribes Brachypodieae, Meliceae and Stipeae (except PhyB). The beak grass tribe Diarrheneae and the tribe Duthieeae are not monophyletic in some of the analyses. However, the combined nuclear DNA (nDNA) tree yields the highest resolution and the best delimitation of the tribes, and provides the following evolutionary hypothesis for the tribes: Brachyelytrum, Nardeae, Duthieeae, Meliceae, Stipeae, Diarrheneae, Brachypodieae and the 'core' Pooideae. Within the individual datasets, the phylogenetic trees obtained from Topo6 exon 8-13 shows the most interesting results. The divergent positions of some clone sequences of Ampelodesmos mauritanicus and Trikeraia pappiformis, for instance, may indicate a hybrid origin of these stipoid taxa.

Authors+Show Affiliations

Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Neuwerk 21, 06108 Halle (Saale), Germany. Electronic address: anne.hochbach@botanik.uni-halle.de.Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Neuwerk 21, 06108 Halle (Saale), Germany. Electronic address: julia.schneider@botanik.uni-halle.de.Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Neuwerk 21, 06108 Halle (Saale), Germany. Electronic address: martin.roeser@botanik.uni-halle.de.

Pub Type(s)

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

Language

eng

PubMed ID

25804934

Citation

Hochbach, Anne, et al. "A Multi-locus Analysis of Phylogenetic Relationships Within Grass Subfamily Pooideae (Poaceae) Inferred From Sequences of Nuclear Single Copy Gene Regions Compared With Plastid DNA." Molecular Phylogenetics and Evolution, vol. 87, 2015, pp. 14-27.
Hochbach A, Schneider J, Röser M. A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. Mol Phylogenet Evol. 2015;87:14-27.
Hochbach, A., Schneider, J., & Röser, M. (2015). A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. Molecular Phylogenetics and Evolution, 87, 14-27. https://doi.org/10.1016/j.ympev.2015.03.010
Hochbach A, Schneider J, Röser M. A Multi-locus Analysis of Phylogenetic Relationships Within Grass Subfamily Pooideae (Poaceae) Inferred From Sequences of Nuclear Single Copy Gene Regions Compared With Plastid DNA. Mol Phylogenet Evol. 2015;87:14-27. PubMed PMID: 25804934.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. AU - Hochbach,Anne, AU - Schneider,Julia, AU - Röser,Martin, Y1 - 2015/03/21/ PY - 2014/09/24/received PY - 2015/03/06/revised PY - 2015/03/12/accepted PY - 2015/3/26/entrez PY - 2015/3/26/pubmed PY - 2015/9/15/medline KW - Nuclear single copy KW - Phylogeny KW - Poaceae KW - Pooideae KW - Topo6 KW - matK SP - 14 EP - 27 JF - Molecular phylogenetics and evolution JO - Mol Phylogenet Evol VL - 87 N2 - To investigate phylogenetic relationships within the grass subfamily Pooideae we studied about 50 taxa covering all recognized tribes, using one plastid DNA (cpDNA) marker (matK gene-3'trnK exon) and for the first time four nuclear single copy gene loci. DNA sequence information from two parts of the nuclear genes topoisomerase 6 (Topo6) spanning the exons 8-13 and 17-19, the exons 9-13 encoding plastid acetyl-CoA-carboxylase (Acc1) and the partial exon 1 of phytochrome B (PhyB) were generated. Individual and nuclear combined data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All of the phylogenetic results show Brachyelytrum and the tribe Nardeae as earliest diverging lineages within the subfamily. The 'core' Pooideae (Hordeeae and the Aveneae/Poeae tribe complex) are also strongly supported, as well as the monophyly of the tribes Brachypodieae, Meliceae and Stipeae (except PhyB). The beak grass tribe Diarrheneae and the tribe Duthieeae are not monophyletic in some of the analyses. However, the combined nuclear DNA (nDNA) tree yields the highest resolution and the best delimitation of the tribes, and provides the following evolutionary hypothesis for the tribes: Brachyelytrum, Nardeae, Duthieeae, Meliceae, Stipeae, Diarrheneae, Brachypodieae and the 'core' Pooideae. Within the individual datasets, the phylogenetic trees obtained from Topo6 exon 8-13 shows the most interesting results. The divergent positions of some clone sequences of Ampelodesmos mauritanicus and Trikeraia pappiformis, for instance, may indicate a hybrid origin of these stipoid taxa. SN - 1095-9513 UR - https://www.unboundmedicine.com/medline/citation/25804934/A_multi_locus_analysis_of_phylogenetic_relationships_within_grass_subfamily_Pooideae__Poaceae__inferred_from_sequences_of_nuclear_single_copy_gene_regions_compared_with_plastid_DNA_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1055-7903(15)00067-6 DB - PRIME DP - Unbound Medicine ER -