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Citation for Study 21451

Citation title: "Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA".

Study name: "Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA".

This study is part of submission 21451 (Status: Published).

Citation

Barrett R., Bayly M.J., Duretto M., Forster P.I., Ladiges P.Y., & Cantrill D.J. 2018. Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA. Australian Systematic Botany, 31: 16-47.

Authors

• Barrett R.
• Bayly M.J.
• Duretto M.
• Forster P.I.
• Ladiges P.Y.
• Cantrill D.J.

Abstract

This study presents a phylogeny of Zieria Sm. (Rutaceae) based on sequences of internal transcribed spacer and external transcribed spacer regions of nrDNA, and using Neobyrnesia suberosa J.A.Armstr. as the outgroup. The phylogeny includes 109 samples, representing 58 of the 60 currently recognised species of Zieria, with multiple accessions of most. Ten species were resolved as monophyletic on the basis of two, or in one case four, samples. Monophyly of four species was neither supported nor rejected, and all other species with more than one accession were resolved as polyphyletic or paraphyletic. Results showed that divergent paralogues of nrDNA are present in some individuals, although the underlying evolutionary process that gave rise to those paralogues is uncertain. Divergent paralogues within genomes could predate speciation and be variably retained or variably detected within the species sampled here; alternatively, they could represent novel nrDNA combinations formed through hybridisation after speciation. There was no strong evidence for recombination between paralogues or that paralogues represent pseudogenes. Variation of nrDNA sequences was clearly incongruent with previously published cpDNA variation, with the nrDNA potentially providing a better indication of species relationships in Zieria. Evidence for this comes from the greater level of congruence, in some species at least, between nrDNA and existing species-level taxonomy than between cpDNA and taxonomy. Incomplete lineage sorting is proposed as a plausible cause for much of the conflict between nrDNA and cpDNA in Zieria, although, in most cases, there was insufficient information to identify the underlying causes with confidence. Implications for species-level taxonomy are discussed.

External links

• DOI: 10.1071/SB16034
• Other URL: http://www.publish.csiro.au/SB/SB16034

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S21451
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref27545,
  	 author = {Rose  Barrett and Michael J. Bayly and Marco  Duretto and Paul I. Forster and Pauline Y Ladiges and David J. Cantrill},
  	 title = {Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA},
  	 year = {2018},
  	 keywords = {},
  	 doi = {10.1071/SB16034},
  	 url = {http://www.publish.csiro.au/SB/SB16034},
  	 pmid = {},
  	 journal = {Australian Systematic Botany},
  	 volume = {31},
  	 number = {},
  	 pages = {16--47},
  	 abstract = {This study presents a phylogeny of Zieria Sm. (Rutaceae) based on sequences of internal transcribed spacer and external transcribed spacer regions of nrDNA, and using Neobyrnesia suberosa J.A.Armstr. as the outgroup. The phylogeny includes 109 samples, representing 58 of the 60 currently recognised species of Zieria, with multiple accessions of most. Ten species were resolved as monophyletic on the basis of two, or in one case four, samples. Monophyly of four species was neither supported nor rejected, and all other species with more than one accession were resolved as polyphyletic or paraphyletic. Results showed that divergent paralogues of nrDNA are present in some individuals, although the underlying evolutionary process that gave rise to those paralogues is uncertain. Divergent paralogues within genomes could predate speciation and be variably retained or variably detected within the species sampled here; alternatively, they could represent novel nrDNA combinations formed through hybridisation after speciation. There was no strong evidence for recombination between paralogues or that paralogues represent pseudogenes. Variation of nrDNA sequences was clearly incongruent with previously published cpDNA variation, with the nrDNA potentially providing a better indication of species relationships in Zieria. Evidence for this comes from the greater level of congruence, in some species at least, between nrDNA and existing species-level taxonomy than between cpDNA and taxonomy. Incomplete lineage sorting is proposed as a plausible cause for much of the conflict between nrDNA and cpDNA in Zieria, although, in most cases, there was insufficient information to identify the underlying causes with confidence. Implications for species-level taxonomy are discussed. }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 27545
  AU  - Barrett,Rose 
  AU  - Bayly,Michael J.
  AU  - Duretto,Marco 
  AU  - Forster,Paul I.
  AU  - Ladiges,Pauline Y
  AU  - Cantrill,David J.
  T1  - Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA
  PY  - 2018
  KW  - 
  UR  - http://www.publish.csiro.au/SB/SB16034
  N2  - This study presents a phylogeny of Zieria Sm. (Rutaceae) based on sequences of internal transcribed spacer and external transcribed spacer regions of nrDNA, and using Neobyrnesia suberosa J.A.Armstr. as the outgroup. The phylogeny includes 109 samples, representing 58 of the 60 currently recognised species of Zieria, with multiple accessions of most. Ten species were resolved as monophyletic on the basis of two, or in one case four, samples. Monophyly of four species was neither supported nor rejected, and all other species with more than one accession were resolved as polyphyletic or paraphyletic. Results showed that divergent paralogues of nrDNA are present in some individuals, although the underlying evolutionary process that gave rise to those paralogues is uncertain. Divergent paralogues within genomes could predate speciation and be variably retained or variably detected within the species sampled here; alternatively, they could represent novel nrDNA combinations formed through hybridisation after speciation. There was no strong evidence for recombination between paralogues or that paralogues represent pseudogenes. Variation of nrDNA sequences was clearly incongruent with previously published cpDNA variation, with the nrDNA potentially providing a better indication of species relationships in Zieria. Evidence for this comes from the greater level of congruence, in some species at least, between nrDNA and existing species-level taxonomy than between cpDNA and taxonomy. Incomplete lineage sorting is proposed as a plausible cause for much of the conflict between nrDNA and cpDNA in Zieria, although, in most cases, there was insufficient information to identify the underlying causes with confidence. Implications for species-level taxonomy are discussed. 
  L3  - 10.1071/SB16034
  JF  - Australian Systematic Botany
  VL  - 31
  IS  - 
  SP  - 16
  EP  - 47
  ER  -