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Published October 26, 2012 | Version v1
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Barcoding, molecular taxonomy, and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

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Jacquet, François, Nicolas, Violaine, Bonillo, Celine, Cruaud, Corinne, Denys, Christiane (2012): Barcoding, molecular taxonomy, and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea). Zoological Journal of the Linnean Society 166 (3): 672-687, DOI: 10.1111/j.1096-3642.2012.00856.x, URL: http://dx.doi.org/10.1111/j.1096-3642.2012.00856.x

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urn:lsid:plazi.org:pub:FFF1FFD2FFECFF939F75FFDF4759FF85

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References

  • Abdo Z, Golding GB. 2007. A step toward barcoding life: a modelbased, decision theoretic method to assign genes to pre-existing species groups. Systematic Biology 56: 44-56.
  • Akaike H. 1973. Information theory as an extension of the maximum likelihood principle. In: Petrov BN, Csaki F, eds. Proceedings of the 2nd international symposium on information theory. Budapest, Hungary: Akademiai Kiado, 267- 281.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
  • Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C. 2009. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics 10: S10.
  • Bannikova AA, Abramov AV, Borisenko AV, Lebedev VS, Rozhnov VV. 2011. Mitochondrial diversity of the whitetoothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam. Zootaxa 2812: 1-20.
  • Bannikova AA, Dokuchaev NE, Yudina EV, Bobretzov AV, Sheftel BI, Lebedev VS. 2010. Holarctic phylogeography of the tundra shrew (Sorex tundrensis) based on mitochondrial genes. Biological Journal of the Linnean Society 101: 721-746.
  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2011. GenBank. Nucleic Acids Research 39: D32-D37.
  • Borisenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PDN. 2008. DNA barcoding in surveys of small mammal communities: a field study in Suriname. Molecular Ecology Resources 8: 471-479.
  • Churchfield S, Barriere P, Hutterer R, Colyn M. 2004. First results on the feeding ecology of sympatric shrews (Insectivora: Soricidae) in the Tai National Park, Ivory Coast. Acta Theriologica 49: 1-15.
  • Coe M. 1975. Mammalian ecological studies on Mount Nimba, Liberia. Mammalia 39: 523-588.
  • Dayrat B. 2005. Towards integrative taxonomy. Biological Journal of the Linnean Society 85: 407-415.
  • Denys C, Lecompte E, Granjon L, Baylac M, Cordeiro P, Cornette R, Dobigny G, Fichet-Calvet E, Hugot JP, Meslage C, Millien-Parra V, Petrillo P, Volobouev V, Weltz M. 2003. Integrative systematics: the importance of combining techniques, for increasing knowledge in African Murinae. In: Singleton GR, Hinds LA, Krebs CJ, Spratt DM, eds. Rats, mice and people: rodent biology and management. Canberra: Australian Centre for International Agricultural Research, 499-506.
  • DeSalle R. 2006. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conservation Biology 20: 1545-1547.
  • DeSalle R, Egan MG, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 360: 1905-1916.
  • Dubey S, Salamin N, Ruedi M, Barriere P, Colyn M, Vogel P. 2008. Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 48: 953-963.
  • Dubey S, Zaitsev M, Cosson JF, Abdukadier A, Vogel P. 2006. Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group). Molecular Phylogenetics and Evolution 38: 635-647.
  • Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AVZ, Mallet J, Jiggins CD. 2007. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal Society B 274: 2881-2889.
  • Ferguson JWH. 2002. On the use of genetic divergence for identifying species. Biological Journal of the Linnean Society 75: 509-516.
  • Fumagalli L, Taberlet P, Stewart DT, Gielli L, Hausser J, Vogel P. 1999. Molecular phylogeny and evolution of Sorex shrews (Soricidae: Insectivora) inferred from mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution 11: 222-235.
  • Goldman N, Anderson JP, Rodrigo AG. 2000. Likelihoodbased tests of topologies in phylogenetics. Systematic Biology 49: 652-670.
  • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
  • Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, USA 103: 968-971.
  • Hajibabaei M, Singer GA, Clare EL, Hebert PD. 2007a. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology 5: 24.
  • Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. 2007b. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 23: 167-172.
  • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symposium Series 41: 95-98.
  • Happold DCD. 1996. Mammals of the Guinea-Congo rain forest. Proceedings of the Royal Society of Edinburgh 104B: 243-284.
  • He K, Li YJ, Brandley MC, Lin LK, Wanga YX, Zhang YP, Jiang XL. 2010. A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Molecular Phylogenetics and Evolution 56: 734- 746.
  • Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, Biological Sciences 270: 313-321.
  • Hebert PDN, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852-859.
  • Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004a. Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, USA 101: 14812-14817.
  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004b. Identification of birds through DNA barcodes. PLoS Biology 2: 1657-1663.
  • Heim de Balsac H. 1958. La reserve naturelle integrale du mont Nimba. XIV. Mammiferes insectivores. Memoires de l'Institut fondamental d'Afrique noire 53: 339-357.
  • Heim de Balsac H. 1968. Recherches sur la faune des Soricidae de l'ouest africain (du Ghana au Senegal). Mammalia 32: 379-418.
  • Heim de Balsac H. 1974. Les insectivores de Lamto (Cote d'Ivoire). Mammalia 38: 637-646.
  • Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
  • Hurst GDD, Jiggins FM. 2005. Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings of the Royal Society, Series B, Biological Sciences 272: 1525-1534.
  • Hutterer R. 2003. Two replacement names and a note on the author of the shrew family Soricidae (Mammalia). Bonner Zoologische Beitrage 50: 369-370.
  • Hutterer R. 2005. Order Soricomorpha. In: Wilson DE, Reeder DM, eds. Mammal species of the world: a taxonomic and geographic reference, 3rd edn. Baltimore: Johns Hopkins University Press, 220-310.
  • Hutterer R, Happold DCD. 1983. The shrews of Nigeria (Mammalia: Soricidae). Bonner Zoologische Monographien 18: 1-79.
  • Hutterer R, Montermann C. 2009. A large new species of Sylvisorex (Mammalia: Soricidae) from Nigeria and the first record of Sylvisorex ollula from the country. Bonner Zoologische Beitrage 56: 201-208.
  • Hutterer R, Riegert J, Sedlacek O. 2009. A tiny new species of Sylvisorex (Mammalia: Soricidae) from the Bamenda Highlands, Cameroon. Bonner Zoologische Beitrage 56: 151-157.
  • Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution 32: 128-144.
  • Jacquet F. 2009. Taxonomie des musaraignes (Mammalia, Soricidae) du Mont Nimba (Guinee, Afrique occidentale): approche moleculaire, morphologique et morphometrique. Master Systematique, Evolution et Paleontologie, Museum National d'Histoire Naturelle.
  • Kang HJ, Kadjo B, Dubey S, Jacquet F, Yanagihara R. 2011. Molecular evolution of Azagny virus, a newfound hantavirus harbored by the West African pygmy shrew (Crocidura obscurior) in Cote d'Ivoire. Virology Journal 8: 373.
  • Kerbis Peterhans J, Stanley WT, Hutterer R, Demos TC, Agwanda B. 2009. A new species of Surdisorex Thomas, 1906 (Mammalia, Soricidae) from western Kenya. Bonner Zoologishe Beitrage 56: 175-183.
  • Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequences data, and the branching order in Hominoidea. Journal of Molecular Evolution 29: 170-179.
  • Klempa B, Fichet-Calvet E, Lecompte E, Auste B, Aniskin V, Meisel H, Barriere P, Koivogui L, ter Meulen J, Kruger DH. 2007. Novel hantavirus sequences in shrew, Guinea. Emerging Infectious Diseases 13: 520- 522.
  • Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in mammals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences, USA 86: 6196-6200.
  • Lamotte M, Roy R. 2003. Le peuplement animal du Mont Nimba (Guinee, Cote d'ivoire, Liberia). Paris: Museum National d'Histoire Naturelle, CD-ROM.
  • Lorenz JG, Jackson WE, Beck JC, Hanner R. 2005. The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philosophical Transactions of the Royal Society, Series B, Biological Sciences 360: 1869-1877.
  • Maddison WP, Maddison DR. 2000. Macclade: analysis of phylogeny and character evolution. Version 4.0. Sunderland, MA: Sinauer Associates.
  • Meier R, Shiyang K, Vaidya G, Ng PK. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715-728.
  • Meyer CP, Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3: e422.
  • Mishler BD. 1985. The morphological, developmental, and phylogenetic basis of species concepts in bryophytes. The Bryologist 88: 207-214.
  • Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
  • Nicolas V, Barriere P, Tapiero A, Colyn M. 2009. Shrew species diversity and abundance in Ziama Biosphere Reserve (Guinea): comparison between primary forest, degraded forest and restoration plots. Biodiversity and Conservation 18: 2043-2061.
  • Nielsen R, Matz M. 2006. Statistical approaches for DNA barcoding. Systematic Biology 55: 162-169.
  • Palumbi SR, Martin AP, Romano SL, McMillan WO, Stice L, Grabowski G. 1991. The simple fool's guide to PCR. Honolulu, HI: Department of Zoology, University of Hawaii.
  • Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568- 583.
  • Pfunder M, Holzgang O, Frey JE. 2004. Developmentj of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers. Molecular Ecology 5: 1277-1286.
  • Posada D, Crandall K. 2001. A comparison of different strategies for selecting models of DNA substitution. Systematic Biology 50: 580-601.
  • Poulakakis N, Lymberakis P, Paragamian K, Mylonas M. 2005. Isolation and amplification of shrew DNA from barn owl pellets. Biological Journal of the Linnean Society 85: 331-340.
  • Querouil S, Barriere P, Colyn M, Hutterer R, Dudu A, Dillen M, Verheyen E. 2005. A molecular insight into the references of African Crocidura (Crocidurinae, Soricidae) using 16s rRNA sequences. In: Merritt JF, Churchfield S, Hutterer R, Sheftel BI, eds. Advances in the biology of shrews II. New York: International Society of Shrew Biologists, Special Publication No. 1, 99-113.
  • Querouil S, Hutterer R, Barriere P, Colyn M, Kerbis Peterhans JC, Verheyen E. 2001. Phylogeny and evolution of reference shrews (Mammalia: Soricidae) inferred from 16s rRNA sequences. Molecular Phylogenetics and Evolution 20: 185-195.
  • Ratnasingham S, Hebert PDN. 2007. BOLD: the barcode of life data system. Molecular Ecology Notes 7: 355-336. Available at: http://www.barcodinglife.org
  • Robins JH, Hingston M, Matisoo-Smith E, Ross HA. 2007. Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes 7: 717-729.
  • Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
  • Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. 2005. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society, Series B, Biological Sciences 360: 1805-1811.
  • Schilthuizen M. 2000. Ecotone: speciation-prone. Trends in Ecology and Evolution 15: 130-131.
  • Sikes RS, Gannon WL, the Animal Care and Use Committee of the American Society of Mammalogists. 2011. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. Journal of Mammalogy 92: 235-253.
  • Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
  • Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
  • Verschuren J, Meester J. 1977. Notes sur les Soricidae (Insectivora) du Nimba Liberien. Mammalia 41: 291- 299.
  • Vogel P, Cosson JF, Lopez Jurado LF. 2003. Taxonomic status and origin of the shrews (Soricidae) from the Canary Islands inferred from a mtDNA comparison with the European Crocidura species. Molecular Phylogenetics and Evolution 27: 271-282.
  • Vogler AP, Monaghan MT. 2007. Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research 45: 1-10.
  • Wada S, Oishi M, Yamada TK. 2003. A newly discovered species of living baleen whale. Nature 426: 278-281.
  • White F. 1981. The history of the Afromontane archipelago and the scientific need for its conservation. African Journal of Ecology 19: 33-54.
  • Winnepenninck B, Backeljau T, De Wachter R. 1993. Extraction of high molecular weight DNA from molluscs. Trends in Genetics 9: 407.
  • Yannic G, Basset P, Hausser J. 2008. A new perspective on the evolutionary history of western European Sorex araneus group revealed by paternal and maternal molecular markers. Molecular Phylogenetics and Evolution 47: 237- 250.
  • Yannic G, Dubey S, Hausser J, Basset P. 2010. Additional data for nuclear DNA give new insights into the phylogenetic position of Sorex granarius within the Sorex araneus group. Molecular Phylogenetics and Evolution 57: 1062- 1071.