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Discordance Between ITS and Chloroplast Topologies in the Boykinia Group (Saxifragaceae)

To assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual... Full description

Journal Title: Systematic botany 1996-04-01, Vol.21 (2), p.169-185
Main Author: Soltis, Douglas E.
Other Authors: Johnson, Leigh A. , Looney, Christopher
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: American Society of Plant Taxonomists
ID: ISSN: 0363-6445
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recordid: cdi_crossref_primary_10_2307_2419746
title: Discordance Between ITS and Chloroplast Topologies in the Boykinia Group (Saxifragaceae)
format: Article
creator:
  • Soltis, Douglas E.
  • Johnson, Leigh A.
  • Looney, Christopher
subjects:
  • Biological taxonomies
  • Chloroplasts
  • Datasets
  • Genera
  • Internal transcribed spacers
  • Parsimony
  • Phylogenetics
  • Sequencing
  • Taxa
  • Topology
ispartof: Systematic botany, 1996-04-01, Vol.21 (2), p.169-185
description: To assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual alignment of sequences in the Boykinia group to be extremely difficult; we therefore explored different alignment strategies using CLUSTAL W and assessed the impact of different gap-open and gap-extension weights. To accomodate the multiple alignments possible with our ITS data set, we also employed the "elision" approach. Both cpDNA and matK sequences provide essentially identical topologies for the Boykinia group and differ from the ITS trees only in the placement of Suksdorfia ranunculifolia. The chloroplast trees place S. ranunculifolia as sister to Boykinia; in the ITS trees, S. ranunculifolia appears in a clade with S. violacea and Bolandra, a placement in agreement with morphology. The chloroplast-based and nuclear-based positions for S. ranunculifolia are each strongly supported, having high bootstrap values. This discordance could be the result of ancient hybridization and chloroplast capture between S. ranunculifolia and a species of Boykinia, resulting in chloroplast-based topologies that do not accurately reflect organismal relationships.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 0363-6445
fulltext: fulltext
issn:
  • 0363-6445
  • 1548-2324
url: Link


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titleDiscordance Between ITS and Chloroplast Topologies in the Boykinia Group (Saxifragaceae)
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descriptionTo assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual alignment of sequences in the Boykinia group to be extremely difficult; we therefore explored different alignment strategies using CLUSTAL W and assessed the impact of different gap-open and gap-extension weights. To accomodate the multiple alignments possible with our ITS data set, we also employed the "elision" approach. Both cpDNA and matK sequences provide essentially identical topologies for the Boykinia group and differ from the ITS trees only in the placement of Suksdorfia ranunculifolia. The chloroplast trees place S. ranunculifolia as sister to Boykinia; in the ITS trees, S. ranunculifolia appears in a clade with S. violacea and Bolandra, a placement in agreement with morphology. The chloroplast-based and nuclear-based positions for S. ranunculifolia are each strongly supported, having high bootstrap values. This discordance could be the result of ancient hybridization and chloroplast capture between S. ranunculifolia and a species of Boykinia, resulting in chloroplast-based topologies that do not accurately reflect organismal relationships.
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subjectBiological taxonomies ; Chloroplasts ; Datasets ; Genera ; Internal transcribed spacers ; Parsimony ; Phylogenetics ; Sequencing ; Taxa ; Topology
ispartofSystematic botany, 1996-04-01, Vol.21 (2), p.169-185
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descriptionTo assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual alignment of sequences in the Boykinia group to be extremely difficult; we therefore explored different alignment strategies using CLUSTAL W and assessed the impact of different gap-open and gap-extension weights. To accomodate the multiple alignments possible with our ITS data set, we also employed the "elision" approach. Both cpDNA and matK sequences provide essentially identical topologies for the Boykinia group and differ from the ITS trees only in the placement of Suksdorfia ranunculifolia. The chloroplast trees place S. ranunculifolia as sister to Boykinia; in the ITS trees, S. ranunculifolia appears in a clade with S. violacea and Bolandra, a placement in agreement with morphology. The chloroplast-based and nuclear-based positions for S. ranunculifolia are each strongly supported, having high bootstrap values. This discordance could be the result of ancient hybridization and chloroplast capture between S. ranunculifolia and a species of Boykinia, resulting in chloroplast-based topologies that do not accurately reflect organismal relationships.
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abstractTo assess whether discord exists between nuclear- and chloroplast-based phylogenetic trees within the Boykinia group (Saxifragaceae), we compared topologies obtained from analyses of ITS sequences with those acquired earlier via analyses of cpDNA restriction sites and matK sequences. We found manual alignment of sequences in the Boykinia group to be extremely difficult; we therefore explored different alignment strategies using CLUSTAL W and assessed the impact of different gap-open and gap-extension weights. To accomodate the multiple alignments possible with our ITS data set, we also employed the "elision" approach. Both cpDNA and matK sequences provide essentially identical topologies for the Boykinia group and differ from the ITS trees only in the placement of Suksdorfia ranunculifolia. The chloroplast trees place S. ranunculifolia as sister to Boykinia; in the ITS trees, S. ranunculifolia appears in a clade with S. violacea and Bolandra, a placement in agreement with morphology. The chloroplast-based and nuclear-based positions for S. ranunculifolia are each strongly supported, having high bootstrap values. This discordance could be the result of ancient hybridization and chloroplast capture between S. ranunculifolia and a species of Boykinia, resulting in chloroplast-based topologies that do not accurately reflect organismal relationships.
pubAmerican Society of Plant Taxonomists
doi10.2307/2419746