title: Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?
abstract: Obtaining accurate phylogenies and effective species discrimination using a small standardized set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 of 13 New Caledonian Araucaria species, an evolutionarily young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
authors.forename: Markus
authors.initials: M
authors.lastname: Ruhsam
authors.affiliation: Department of Wildland Resources, Utah State University, 5230 Old Main Hill, Logan, UT, 84322, USA.
authors.forename: Hardeep S
authors.initials: HS
authors.lastname: Rai
authors.affiliation: The Arnold Arboretum of Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mathews
authors.affiliation: Department of Botany, University of British Columbia, 3529-6270 University Blvd., Vancouver, BC, Canada, V6T 1Z4.
authors.forename: T Gregory
authors.initials: TG
authors.lastname: Ross
authors.affiliation: Department of Botany, University of British Columbia, 3529-6270 University Blvd., Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Central Washington University, University Way, Ellensburg, WA, 98926-7537, USA.
authors.forename: Linda A
authors.initials: LA
authors.lastname: Raubeson
authors.affiliation: Central Washington University, University Way, Ellensburg, WA, 98926-7537, USA.|Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Mei
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
authors.forename: Philip I
authors.initials: PI
authors.lastname: Thomas
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
authors.forename: Martin F
authors.initials: MF
authors.lastname: Gardner
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, West Main Rd, Edinburgh, EH3 9JT, UK.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Ennos
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Hollingsworth
mesh_terms: D058893:DNA Barcoding, Taxonomic; D054627:Genome, Plastid; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010139:Pacific Islands; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D017422:Sequence Analysis, DNA; D064028:Tracheophyta / Q000145:classification* / Q000235:genetics*
keywords: Araucaria; DNA barcoding; next generation sequencing; phylogeny; plastid genome