title: Resources for phylogenomic analyses of Australian terrestrial vertebrates.
abstract: High-throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci, and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for four species of birds, four frogs, seven lizards and seven mammals. We also use exon data from the marsupial transcriptomes we generated to examine an approach for choosing a moderate number (dozens or hundreds) of phylogenetically informative exons based on a single transcriptome sequence, and a relatively distant reference genome.
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT, 0200, Australia.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Bragg
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT, 0200, Australia.
authors.forename: Sally
authors.initials: S
authors.lastname: Potter
authors.affiliation: Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
authors.forename: Ke
authors.initials: K
authors.lastname: Bi
authors.affiliation: Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
authors.forename: Renee
authors.initials: R
authors.lastname: Catullo
authors.affiliation: South Australian Museum, North Terrace, Adelaide, SA, 500, Australia.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Donnellan
authors.affiliation: Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW, 2010, Australia.
authors.forename: Mark D B
authors.initials: MDB
authors.lastname: Eldridge
authors.affiliation: The Commonwealth Scientific and Industrial Research Organization, National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia.
authors.forename: Leo
authors.initials: L
authors.lastname: Joseph
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT, 0200, Australia.
authors.forename: J Scott
authors.initials: JS
authors.lastname: Keogh
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT, 0200, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Oliver
authors.affiliation: Museum Victoria, Melbourne, Vic, 3001, Australia.
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Rowe
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT, 0200, Australia.
authors.forename: Craig
authors.initials: C
authors.lastname: Moritz
mesh_terms: D000818:Animals; D001315:Australia; D020869:Gene Expression Profiling / Q000379:methods*; D010802:Phylogeny; D014714:Vertebrates / Q000145:classification* / Q000235:genetics*
keywords: amphibians; birds; mammals; phylogenomics; reptiles; transcriptomics