title: Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.
abstract: Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia kieren.mitchell@adelaide.edu.au alan.cooper@adelaide.edu.au.
authors.forename: Kieren J
authors.initials: KJ
authors.lastname: Mitchell
authors.affiliation: Department of Evolution, Ecology and Genetics, The Australian National University, Canberra, ACT, Australia.
authors.forename: Renae C
authors.initials: RC
authors.lastname: Pratt
authors.affiliation: Department of Obstetrics and Gynaecology, Research Centre for Reproductive Health, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Laura N
authors.initials: LN
authors.lastname: Watson
authors.affiliation: Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
authors.forename: Gillian C
authors.initials: GC
authors.lastname: Gibb
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Bastien
authors.initials: B
authors.lastname: Llamas
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Marta
authors.initials: M
authors.lastname: Kasper
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Janette
authors.initials: J
authors.lastname: Edson
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Blair
authors.initials: B
authors.lastname: Hopwood
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Dean
authors.initials: D
authors.lastname: Male
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Kyle N
authors.initials: KN
authors.lastname: Armstrong
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
authors.affiliation: Department of Biology, University of York, York, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Austin
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, AustraliaSouth Australian Museum, Adelaide, SA, Australia.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Donnellan
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, AustraliaSouth Australian Museum, Adelaide, SA, Australia.
authors.forename: Michael S Y
authors.initials: MS
authors.lastname: Lee
authors.affiliation: School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Phillips
authors.affiliation: Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, Australia kieren.mitchell@adelaide.edu.au alan.cooper@adelaide.edu.au.
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D004272:DNA, Mitochondrial / Q000032:analysis; D017753:Ecosystem; D019143:Evolution, Molecular; D008394:Marsupialia / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: ancestral state reconstruction; mammal; mitochondrion; supermatrix