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Phylogeny and Polyploidy: Resolving the Classification of Cyprinine Fishes (Teleostei: Cypriniformes)

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Accepted Manuscript Phylogeny and Polyploidy: Resolving the Classification of Cyprinine Fishes (Teleostei: Cypriniformes) Lei Yang, Tetsuya Sado, M. Vincent Hirt, Emmanuel Pasco-Viel, M. Arunachalam, Junbing Li, Xuzhen Wang, Jörg Freyhof, Kenji Saitoh, Andrew M. Simons, Masaki Miya, Shunping He, Richard L. Mayden PII: S1055-7903(15)00028-7 DOI: http://dx.doi.org/10.1016/j.ympev.2015.01.014 Reference: YMPEV 5112 To appear in: Molecular Phylogenetics and Evolution Received Date: 12 April 2014 Revised Date: 29 January 2015 Accepted Date: 30 January 2015 Please cite this article as: Yang, L., Sado, T., Vincent Hirt, M., Pasco-Viel, E., Arunachalam, M., Li, J., Wang, X., Freyhof, J., Saitoh, K., Simons, A.M., Miya, M., He, S., Mayden, R.L., Phylogeny and Polyploidy: Resolving the Classification of Cyprinine Fishes (Teleostei: Cypriniformes), Molecular Phylogenetics and Evolution (2015), doi: http://dx.doi.org/10.1016/j.ympev.2015.01.014 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 2 Phylogeny and Polyploidy: Resolving the Classification of Cyprinine Fishes 3 (Teleostei: Cypriniformes) 4 5 Lei Yang 1,†,*, Tetsuya Sado2, M. Vincent Hirt3, Emmanuel Pasco-Viel4, 6 M. Arunachalam5, Junbing Li6, Xuzhen Wang6, Jörg Freyhof7, Kenji Saitoh8, 7 Andrew M. Simons9, Masaki Miya2, Shunping He6, Richard L. Mayden 1,* 8 9 1Department of Biology, Saint Louis University, St. Louis, MO 63103, USA 10 11 2Department of Zoology, Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, 12 Chuo-ku, Chiba 260-8682, Japan 13 14 3Graduate Program in Ecology, Evolution, and Behavior, University of Minnesota, St. 15 Paul, MN 55108, USA 16 17 4 - 18 19 , Lyon, 69007, France 20 21 5Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar 22 University, Alwarkurichi - 627 412, Tamil Nadu, India 23 24 6Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese 25 Academy of Sciences, Wuhan 430072, China 26 27 7German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 28 Deutscher Platz 5e, 04103 Leipzig, Germany 29 30 8National Research Institute of Fisheries Science, Aquatic Genomics Research Center, 31 Fukuura, Kanazawa, Yokohama 236-8648, Japan 32 33 9Department of Fisheries, Wildlife, and Conservation Biology and Bell Museum of 34 Natural History, University of Minnesota, St. Paul, MN 55108, USA 35 36 †Present address: Hollings Marine Laboratory, College of Charleston, Charleston, SC 37 29401, USA 38 39 40 41 42 1 43 *To whom correspondence should be addressed: 44 45 Lei Yang & Richard L. Mayden 46 Department of Biology, 47 3507 Laclede Ave, 48 Saint Louis University, 49 St. Louis, MO 63103, USA. 50 Phone: +001-314-977-3910 51 Fax: +001-314-977-3658 52 Emails: [email protected] (LY); [email protected] (RLM) 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 2 74 Abstract: 75 Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and 76 contains more polyploid species (~400) than any other group of fishes. We examined the 77 phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and 78 genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the 79 phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: 80 two mitochondrial gene datasets (465 and 791 taxa, 5604bp), a mitogenome dataset (85 81 taxa, 14,771bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497 bp). Based on 82 resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; 83 Probarbus + Catlocarpio), Labeonini Bleeker, 1859 (Labeo & allies), Torini Karaman, 84 1971 (Tor, Labeobarbus & allies), Smiliogastrini Bleeker, 1863 (Puntius, Enteromius & 85 allies), Poropuntiini (Poropuntius & allies), Cyprinini Rafinesque, 1815 (Cyprinus & 86 allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus), 87 Schizothoracini McClelland, 1842 (Schizothorax & allies), Schizopygopsini Mirza, 1991 88 (Schizopygopsis & allies), and Barbini Bleeker, 1859 (Barbus & allies). Phylogenetic 89 relationships within each tribe were discussed. Two or three distinct RAG1 lineages were 90 identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, 91 indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western 92 Asian Capoeta are likely derived from two independent hybridization events between 93 their respective maternal tetraploid ancestors and Cyprinion. 94 95 Keywords: Biogeography; Cyprinidae; Evolution; Hexaploids; Taxonomy; Tetraploids 96 97 98 99 100 101 102 103 104 3 105 1. Introduction 106 Within vertebrates, phylogenetic resolution of the largest group, Actinopterygii or 107 ray-finned fishes, lags behind other taxa, due to the large number of species and the 108 difficulties obtaining and identifying specimens. Another challenge in actinopterygian 109 phylogeny is the evolution of genome duplications producing polyploids. Genome 110 duplications have occurred multiple times in actinopterygian evolution but are 111 particularly prevalent in Cypriniformes, the largest clade of freshwater fishes (Amores, et 112 al. 1998; Leggatt & Iwama, 2003; Taylor et al. 2003). Within Cypriniformes, the 113 Cyprininae contains more than 1300 freshwater species in over 120 genera, accounting 114 for nearly 4% of bony fish diversity (Eschmeyer, 2015). Most species of this subfamily 115 inhabit waters of southern Eurasia and Africa. Some are well known, such as the common 116 carp (Cyprinus carpio) and Goldfish (Carassius auratus). The Cyprininae contains 117 around 400 closely related polyploid species (Arai, 2011; Froese & Pauly, 2015), more 118 than other polyploid fish lineages, such as Acipenseriformes, Salmoniformes, and 119 Catostomidae (all <250 species; Eschmeyer, 2015). Over 30 genera in this subfamily 120 consist only of polyploid species (Leggatt & Iwama, 2003; Arai, 2011). Most polyploids 121 in this subfamily are either tetraploids (2n = ca.100) or hexaploids (2n = ca.150). The 122 species Ptychobarbus dipogon has an amazingly large number of chromosomes (2n = 123 446, Cui et al. 1991; 2n= 424-432, Wu et al. 1999). 124 The classification of the subfamily Cyprininae is still under discussion as various 125 numbers of formal or informal groups have been recognized within it (Tables 1&S1). 126 Many molecular studies have been conducted on the phylogenetic relationships of the 127 Cyprininae; however, most were limited by restricted taxon or character sampling or 128 limited geographical sampling. Most importantly, these studies either did not use nuclear 129 genes or used, but ignored the issue of paralogy associated with polyploid taxa. If a 130 nuclear gene has only one copy in diploids, it is expected to have two copies in 131 tetraploids, three copies in hexaploids, and four copies in octoploids. In polyploids, 132 especially allopolyploids, the different nuclear gene copies could be quite divergent and 133 belong to distinct clades in a gene tree (e.g. Evans et al. 2005; Saitoh et al. 2010). Direct 134 amplification of these nuclear genes with PCR (polymerase chain reaction) without using 135 specially designed paralog-specific primers will likely result in a mixture of gene copies. 4 136 If nuclear copies are not sorted appropriately, homology cannot be confidently 137 established, potentially misleading phylogenetic studies. In the present study, extensive 138 DNA cloning was performed and multiple alleles were used in phylogeny reconstruction 139 of all major diploid and polyploid lineages of the subfamily Cyprininae. These data and 140 molecular phylogenies inferred from mitochondrial genes made it possible for us to 141 explore the phylogenetic relationships and subdivisions of this subfamily as well as the 142 evolution of polyploidy. 143 The major objectives of this study are: 1) to investigate the phylogenetic 144 relationships and subdivisions of the subfamily Cyprininae based on the largest taxon, 145 geographical, and genomic sampling to date; and 2) to propose a classification for this 146 group. The evolution of polyploid lineages; the distribution of some morphological 147 characters important in classification; and biogeography of some taxa will be discussed. 148 149 2. Materials and Methods 150 2.1 Taxon sampling and datasets 151 Four datasets were analyzed in this study: 1) a mitochondrial gene dataset with 465 152 taxa (465-taxon mt dataset); 2) an expanded mitochondrial gene dataset with 791 taxa 153 (791-taxon mt dataset); 3) a mitochondrial genome dataset with 85 taxa (mitogenome 154 dataset); and 4) a cloned RAG1 dataset with 97 taxa (RAG1 dataset). 155 In the 465-taxon mt dataset, most taxa (97.4%) were represented by sequences from 156 five mitochondrial genes: cytochrome oxidase subunit I (COI), Cytochrome b (Cyt b), 157 16S ribosomal RNA (16S rRNA), NADH dehydrogenase subunit 4 (ND4), and NADH 158 dehydrogenase subunit 5 (ND5); remaining taxa (2.6%) were represented by sequences 159 from at least three genes. This dataset has good representation for major lineages
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  • A Synopsis of the Scientific Information and Utilization Potential of the Assamese Kingfish

    A Synopsis of the Scientific Information and Utilization Potential of the Assamese Kingfish

    Journal of Entomology and Zoology Studies 2019; 7(3): 1463-1469 E-ISSN: 2320-7078 P-ISSN: 2349-6800 A synopsis of the scientific information and JEZS 2019; 7(3): 1463-1469 © 2019 JEZS utilization potential of the Assamese Kingfish Received: 01-03-2019 Accepted: 05-04-2019 Aishwarya Sharma Aishwarya Sharma, Shahnawaz Ali, Prabhati Kumari Sahoo, Rupak Molecular Genetics Laboratory, Nath, Debajit Sarma and C Siva Directorate of Coldwater Fisheries Research, Bhimtal, Uttarakhand, India Abstract Assamese kingfish is one of the important cyprinids endemic to the Trans-Himalayan states of southern Shahnawaz Ali Asia, with considerable subsistence fishery value. As such it plays a crucial role in local livelihood, food Molecular Genetics Laboratory, security and occupies a prominent place in the diet of the hilly populace with traditionally identified Directorate of Coldwater pharmacological benefits in treating smallpox, stomachache, urinary and digestive problems. The Fisheries Research, Bhimtal, kingfish reportedly withstands a wide range of temperature and exhibits herbivores, but opportunistic Uttarakhand, India feeding behavior. In recent times, it has been identified as a potential species for diversification in hill aquaculture. On the other hand, C. Semiplotum population is declining in its natural habitat due to Prabhati Kumari Sahoo ICAR-Central Institute of overexploitation and related anthropogenic pressures. Presently, it has been classified as vulnerable in the Freshwater Aquaculture, IUCN red list of threatened species. In scientific terms, key questions regarding its breeding biology, Bhubaneswar, Odisha, India culture aspects, and conservation measures remain unanswered. Considering all the above, we have summarized the outcome of various studies carried on this vulnerable species regarding its taxonomic Rupak Nath ambiguity, ecology, behavior, growth, reproduction, nutrition, pharmacological benefit, fisheries, and St.