title: Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.
abstract: Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences.
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia; Kings Park and Botanic Garden, Fraser Ave, Kings Park, WA 6005, Australia; School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia. Electronic address: anna.williams@graduate.uwa.edu.au.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Williams
authors.affiliation: National Research Collections Australia, CSIRO National Facilities and Collections, GPO Box 1600, Canberra, ACT 2601, Australia; Division of Environmental Biology, National Science Foundation, 4201 Wilson Blvd, Arlington, VA 22230, USA.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Miller
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Small
authors.affiliation: Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia; Kings Park and Botanic Garden, Fraser Ave, Kings Park, WA 6005, Australia; School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Nevill
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Boykin
mesh_terms: D000045:Acacia / Q000235:genetics*; D001499:Bayes Theorem; D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D066264:Datasets as Topic; D014644:Genetic Variation / Q000235:genetics; D054628:Genome, Chloroplast / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny
chemical_list: D018742:DNA, Chloroplast
keywords: Acacia; ExaBayes; Integrative systematics; RAxML; Whole chloroplast genome