title: Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.
abstract: The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.
authors.affiliation: School of Life Sciences, Fudan University, SongHu Road 2005, Shanghai 200438, China; The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan; School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama-cho, Kanagawa 240-0193, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Yonezawa
authors.affiliation: Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan; National Institute of Polar Research, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Segawa
authors.affiliation: Department of Biological Information, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mori
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289 Porto, 4050-123 Portugal.
authors.forename: Paula F
authors.initials: PF
authors.lastname: Campos
authors.affiliation: Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Hongoh
authors.affiliation: The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Endo
authors.affiliation: National Institute of Polar Research, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan.
authors.forename: Ayumi
authors.initials: A
authors.lastname: Akiyoshi
authors.affiliation: National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba City, Ibaraki 305-0005, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba City, Ibaraki, 305-8572, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Kohno
authors.affiliation: Biology, Science Education, Faculty of Education and Culture, University of Miyazaki, Gakuen-Kibanadai-Nishi 1-1, Miyazaki, Miyazaki 889-2192, Japan.
authors.forename: Shin
authors.initials: S
authors.lastname: Nishida
authors.affiliation: School of Life Sciences, Fudan University, SongHu Road 2005, Shanghai 200438, China; Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Jiaqi
authors.initials: J
authors.lastname: Wu
authors.affiliation: School of Life Sciences, Fudan University, SongHu Road 2005, Shanghai 200438, China.
authors.forename: Haofei
authors.initials: H
authors.lastname: Jin
authors.affiliation: The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan; School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama-cho, Kanagawa 240-0193, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Adachi
authors.affiliation: Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Hirohisa
authors.initials: H
authors.lastname: Kishino
authors.affiliation: Department of Biological Information, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.affiliation: National Institute of Polar Research, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan.
authors.forename: Yoshifumi
authors.initials: Y
authors.lastname: Nogi
authors.affiliation: School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama-cho, Kanagawa 240-0193, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Tanabe
authors.affiliation: Faculty of Vetrinary Medicine, Nippon Veterinary Science and Life Science University, Kyonancho 1-7-1, Musashino City, Tokyo 180-8602, Japan.
authors.forename: Harutaka
authors.initials: H
authors.lastname: Mukoyama
authors.affiliation: The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Kunio
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Department of Biological Anthropology and Paleontology, Faculty of Science, University of Antananarivo, BP 906, Antananarivo 101, Madagascar.
authors.forename: Armand
authors.initials: A
authors.lastname: Rasoamiaramanana
authors.affiliation: Yamashina Institute for Ornithology, Konoyama 115, Abiko City, Chiba 270-1145, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Yamagishi
authors.affiliation: National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba City, Ibaraki 305-0005, Japan; Yamashina Institute for Ornithology, Konoyama 115, Abiko City, Chiba 270-1145, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Hayashi
authors.affiliation: Tokyo University of Information Sciences, Onaridai 4-1, Wakaba-ku, Chiba City, Chiba, 265-8501, Japan; The Research Institute of Evolutionary Biology, Kamiyoga 2-4-28, Setagaya-ku, Tokyo, 158-0098, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Yoshida
authors.affiliation: The Kyushu University Museum, Hakozaki 6-10-1, Higashi-ku, Fukuoka City, Fukuoka 812-8581, Japan.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Koike
authors.affiliation: The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Yamashina Institute for Ornithology, Konoyama 115, Abiko City, Chiba 270-1145, Japan; Tokyo University of Agriculture, 1737 Funako, Atsugi-shi, Kanagawa 243-0034, Japan.
authors.forename: Fumihito
authors.initials: F
authors.lastname: Akishinonomiya
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. Electronic address: ewillerslev@snm.ku.dk.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: School of Life Sciences, Fudan University, SongHu Road 2005, Shanghai 200438, China; The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa City, Tokyo 190-8562, Japan; School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama-cho, Kanagawa 240-0193, Japan. Electronic address: masamihase@gmail.com.
authors.forename: Masami
authors.initials: M
authors.lastname: Hasegawa
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics; D019143:Evolution, Molecular; D053476:Extinction, Biological; D005580:Fossils; D016678:Genome; D023281:Genomics; D008957:Models, Genetic; D046108:Palaeognathae / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: Aepyornis; Lithornis; Mullerornis; Palaeognathae; ancient DNA