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
Rosemary A. Barrett A , Michael J. Bayly A E , Marco F. Duretto B , Paul I. Forster C , Pauline Y. Ladiges A and David J. Cantrill D
+ Author Affiliations
- Author Affiliations
A School of BioSciences, The University of Melbourne, Vic. 3010, Australia.
B National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia.
C Queensland Herbarium, Department of Science, Information Technology & Innovation, Brisbane Botanic Gardens, Toowong, Qld 4066, Australia.
D Royal Botanic Gardens Victoria, Birdwood Avenue, South Yarra, Vic. 3141, Australia.
E Corresponding author. Email: mbayly@unimelb.edu.au
Australian Systematic Botany 31(1) 16-47 https://doi.org/10.1071/SB16034
Submitted: 23 August 2017 Accepted: 17 November 2017 Published: 28 February 2018
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.
Additional keywords: biogeography, chloroplast lineage sorting, hybrids, molecular phylogeny, nrDNA, taxonomy.
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