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      Next-Generation Sequencing of an 88-Year-Old Specimen of the Poorly Known Species Liagora japonica (Nemaliales, Rhodophyta) Supports the Recognition of Otohimella gen. nov.

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          Abstract

          Liagora japonica is a red algal species distributed in temperate regions of Japan. This species has not been collected from its type locality on the Pacific coast of Japan since 1927 and seems to have become extinct in this area. For molecular characterization of L. japonica, we extracted DNA from the topotype material of L. japonica collected in 1927, analyzed seven genes using Illumina next-generation sequencing, and compared these data with sequences from modern samples of similar red algae collected from the Japan Sea coast of Japan. Both morphological and molecular data from modern samples and historical specimens (including the lectotype and topotype) suggest that the specimens from the Pacific and Japan Sea coasts of Japan should be treated as a single species, and that L. japonica is phylogenetically separated from the genus Liagora. Based on the phylogenetic results and examination of reproductive structures, we propose Otohimella japonica gen. et comb. nov., characterized morphologically by diffuse carposporophytes, undivided carposporangia, and involucral filaments initiated only from the cortical cell on the supporting cell.

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          Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs.

          The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to >30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the New World, along with a comprehensive panel of modern dogs and wolves. The mitochondrial genomes of all modern dogs are phylogenetically most closely related to either ancient or modern canids of Europe. Molecular dating suggests an onset of domestication there 18,800 to 32,100 years ago. These findings imply that domestic dogs are the culmination of a process that initiated with European hunter-gatherers and the canids with whom they interacted.
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            Ancient DNA damage.

            Under favorable conditions DNA can survive for thousands of years in the remains of dead organisms. The DNA extracted from such remains is invariably degraded to a small average size by processes that at least partly involve depurination. It also contains large amounts of deaminated cytosine residues that are accumulated toward the ends of the molecules, as well as several other lesions that are less well characterized.
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              The European database on small subunit ribosomal RNA.

              J Wuyts (2002)
              The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 July 2016
                2016
                : 11
                : 7
                : e0158944
                Affiliations
                [1 ]Kobe University Research Center for Inland Sea, Awaji, Hyogo, Japan
                [2 ]Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
                [3 ]National Institute of Polar Research, Midori-cho, Tachikawa-shi, Tokyo, Japan
                [4 ]Transdisciplinary Research Integration Center, Toranomon, Minato-ku, Tokyo, Japan
                [5 ]Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
                [6 ]Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, Setagaya-ku, Tokyo, Japan
                [7 ]Faculty of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
                [8 ]Bioresource Sciences, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
                [9 ]Department of Biology, Graduate School of Science, Kobe University, Rokkodai, Nada-ku, Kobe, Japan
                [10 ]Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
                [11 ]The Hokkaido University Museum, Hokkaido University, Sapporo, Hokkaido, Japan
                [12 ]Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
                [13 ]Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
                Tel-Aviv University, ISRAEL
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: MS TS HN. Performed the experiments: MS TS AA. Analyzed the data: HM TS RO MS. Contributed reagents/materials/analysis tools: MS TS HM AA AK HS TK TA KK HK HN. Wrote the paper: MS TS HM HN.

                Article
                PONE-D-15-48206
                10.1371/journal.pone.0158944
                4936710
                27388436
                f232a25a-c2d8-4cc2-9173-686803cfd5d2
                © 2016 Suzuki et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 November 2015
                : 24 June 2016
                Page count
                Figures: 4, Tables: 2, Pages: 17
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 26840125
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 24247042
                Award Recipient :
                MS and HN were supported by Grants-in-Aid for Scientific Research (grant numbers 26840125 and 24247042) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI ( https://www.jsps.go.jp/english/e-grants/).
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