title: Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography.
abstract: Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequencing alleviates this effect in phylogeography using a case study on the Sea of Japan lineage of the intertidal goby Chaenogobius annularis Eighty-three C. annularis individuals were collected and their mitogenomes were determined by high-throughput and low-cost parallel sequencing. Phylogenetic analysis of these mitogenome sequences was conducted to root the Sea of Japan lineage, which has a star-like phylogeny and had not been reliably rooted. The topologies of the bootstrap trees were investigated to determine whether the use of mitogenomes alleviated the random rooting effect. The mitogenome data successfully rooted the Sea of Japan lineage by alleviating the effect, which hindered phylogenetic analysis that used specific gene sequences. The reliable rooting of the lineage led to the discovery of a novel, northern lineage that expanded during an interglacial period with high bootstrap support. Furthermore, the finding of this lineage suggested the existence of additional glacial refugia and provided a new recent calibration point that revised the divergence time estimation between the Sea of Japan and Pacific Ocean lineages. This study illustrates the effectiveness of parallel mitogenome sequencing for solving the random rooting problem in phylogeographic studies.
authors.affiliation: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan ashirase@mail.ecc.u-tokyo.ac.jp iwasaki@bs.s.u-tokyo.ac.jp.
authors.forename: Shotaro
authors.initials: S
authors.lastname: Hirase
authors.affiliation: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Center for Research Promotion, Research Institute for Humanity and Nature, National Institutes for the Humanities, Kita-ku, Kyoto, Japan.
authors.forename: Hirohiko
authors.initials: H
authors.lastname: Takeshima
authors.affiliation: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan University of the Ryukyus, Nishihara, Okinawa, Japan.
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Nishida
authors.affiliation: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan ashirase@mail.ecc.u-tokyo.ac.jp iwasaki@bs.s.u-tokyo.ac.jp.
authors.forename: Wataru
authors.initials: W
authors.lastname: Iwasaki
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D050259:Genes, Mitochondrial; D005828:Genetics, Population; D054629:Genome, Mitochondrial; D007564:Japan; D010473:Perciformes / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Chaenogobius annularis; Sea of Japan; divergence time estimation; mitogenome; phylogeography; random rooting