title: Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae).
abstract: With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.
authors.affiliation: Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Ave., Ann Arbor, Michigan 48109-1079, USA. knowlesl@umich.edu
authors.forename: Lacey L
authors.initials: LL
authors.lastname: Knowles
authors.forename: Pavel B
authors.initials: PB
authors.lastname: Klimov
mesh_terms: D000053:Acari / Q000145:classification* / Q000235:genetics*; D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D005796:Genes; D049810:Genetic Speciation; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D008925:Mites / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018840:HSP70 Heat-Shock Proteins; D020648:Peptide Elongation Factor 1; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S