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Sequence Data from New Plastid and Nuclear COSII Regions Resolves Early Diverging Lineages in Coffea (Rubiaceae)

Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) pro... Full description

Journal Title: Systematic botany 2012-10, Vol.37 (4), p.995-1005
Main Author: Nowak, Michael D
Other Authors: Davis, Aaron P , Yoder, Anne D
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: American Society of Plant Toxonomists
ID: ISSN: 0363-6445
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recordid: cdi_gale_infotracacademiconefile_A315809358
title: Sequence Data from New Plastid and Nuclear COSII Regions Resolves Early Diverging Lineages in Coffea (Rubiaceae)
format: Article
creator:
  • Nowak, Michael D
  • Davis, Aaron P
  • Yoder, Anne D
subjects:
  • Alliances
  • Biological taxonomies
  • Coffea
  • Coffea, COSII
  • Cosii
  • Datasets
  • Evolution
  • Genomes
  • Incongruence
  • Nucleotide sequence
  • Oceans
  • Parsimony
  • Phylogenetics
  • Phylogeny
  • Plant genetics
  • Plants
  • Plastid
  • Plastids
  • Rubiaceae
ispartof: Systematic botany, 2012-10, Vol.37 (4), p.995-1005
description: Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the rest of the genus, and that the dry adapted baracoffea alliance from western Madagascar falls outside of previously defined East Africa/Indian Ocean and Indian Ocean clades. Well-supported patterns of phylogenetic incongruence are observed between plastid and nuclear data in several species, suggesting a potential role for hybridization in their evolutionary history. The results also provide further evidence for the paraphyly of African Coffea and support the supposition that the evolutionary history of the genus is more complicated than previously proposed.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 0363-6445
fulltext: fulltext
issn:
  • 0363-6445
  • 1548-2324
url: Link


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titleSequence Data from New Plastid and Nuclear COSII Regions Resolves Early Diverging Lineages in Coffea (Rubiaceae)
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creatorNowak, Michael D ; Davis, Aaron P ; Yoder, Anne D
creatorcontribNowak, Michael D ; Davis, Aaron P ; Yoder, Anne D
descriptionResolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the rest of the genus, and that the dry adapted baracoffea alliance from western Madagascar falls outside of previously defined East Africa/Indian Ocean and Indian Ocean clades. Well-supported patterns of phylogenetic incongruence are observed between plastid and nuclear data in several species, suggesting a potential role for hybridization in their evolutionary history. The results also provide further evidence for the paraphyly of African Coffea and support the supposition that the evolutionary history of the genus is more complicated than previously proposed.
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subjectAlliances ; Biological taxonomies ; Coffea ; Coffea, COSII ; Cosii ; Datasets ; Evolution ; Genomes ; Incongruence ; Nucleotide sequence ; Oceans ; Parsimony ; Phylogenetics ; Phylogeny ; Plant genetics ; Plants ; Plastid ; Plastids ; Rubiaceae
ispartofSystematic botany, 2012-10, Vol.37 (4), p.995-1005
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abstractResolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the rest of the genus, and that the dry adapted baracoffea alliance from western Madagascar falls outside of previously defined East Africa/Indian Ocean and Indian Ocean clades. Well-supported patterns of phylogenetic incongruence are observed between plastid and nuclear data in several species, suggesting a potential role for hybridization in their evolutionary history. The results also provide further evidence for the paraphyly of African Coffea and support the supposition that the evolutionary history of the genus is more complicated than previously proposed.
pubAmerican Society of Plant Toxonomists
doi10.1600/036364412X656482
tpages11