Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 30, 2019 - Issue 4
250
Views
1
CrossRef citations to date
0
Altmetric
Research Article

DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province

, , , , ORCID Icon, & show all
Pages 592-601 | Received 19 Nov 2018, Accepted 03 Feb 2019, Published online: 05 Apr 2019

References

  • Aguilera P, Frenich A, Torres J, Castro H, Vidal JM, Canton M. 2001. Appliction of the Kohonen neural network in coastal water management: methodological development for the assessment and prediction of water quality. Water Res. 35:4053–4062.
  • April J, Mayden RL, Hanner RH, Bernatchez L. 2011. Genetic calibration of species diversity among North Americas' freshwater fishes. Proc Natl Acad Sci USA. 26:10606–10607.
  • Berbuto M, Galimberti A, Ferri E, Labra M, Malandra R, Galli P, Casiraghi M. 2010. DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Res Int. 43:376–381.
  • Chon TS, Park YS, Moon KH, Cha EY. 1996. Patternizing communities by using an artificial neural network. Ecol Model. 90:69–78.
  • Dimmick WW, Edds DR. 2002. Evolution genetics of the endemic schizorathicine (Cypriniformes: Cprinidae) fishes of Lake Rara, Nepal. Biochem Syst Ecol. 30:919–929.
  • Foody GM. 1999. Applications of the self-organising feature map neural network in community data analysis. Ecoll Model. 120:97–107.
  • Frezal L, Leblois R. 2008. Four years of DNA barcoding: current advances and prospects. Infect Genet Evol. 8:727–736.
  • Gibbs J. 2009. Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae). Zootaxa. 2032:1–38.
  • Giraudel JL, Lek S. 2001. A comparison of self-organizing map algorithm and some conventional statistical methods for ecological community ordination. Ecol Model. 146:329–339.
  • He D, Chen Y. 2006. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequecnes. J Biogeography. 33:1448–1460.
  • He D, Chen Y. 2007. Biogeography and molecular phylogeny of the highly specialized schizothoracine fishes. Chin Sci Bull. 52:303–312.
  • He D, Chen Y, Chen Y, Chen Z. 2003. Molecular phylogeny of the specialized Schizothoricine fishes and the uplift of Qinghai-Tibetan Plateau. Chin Sci Bull. 48:2354–2362.
  • Hebert PDN, Ratnasingham S, R.deWaard J. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Royal Soc B. 270:S96–S99.
  • Hebert PDN, Cywinska A, Bal SL, R.deWaard J. 2003. Biological identifications through DNA barcodes. Proc Royal Soc B. 270:313–321.
  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. Plos Biol. 2:e312.
  • Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PloS One 3:e2490.
  • Jabiol J, Corbara B, Dejean A, Cereghino R. 2009. Structure of aquatic insect communities in tank-bromeliads in a East-Amazonian rainforest in French Guiana. Forest Ecol Manage. 257:351–360.
  • Janzen DH. 2004. Now is the time. Philos Trans Royal Soc B. 359:731–732.
  • Kangur K, Park Y-S, Kangur A, Kangur P, Lek S. 2007. Patterning long-term changes of fish community in large shallow Lake Peisi. Ecol Model. 203:34–44.
  • Kelley RP, Sarkar IN, Eernisse DJ, Desalle R. 2007. DNA barcoding using chitons (genus Mopalia). Mol Ecol Notes. 7:177–183.
  • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111–120.
  • Kohonen T, Makisara K, Saramaki T. 1984. Phonotopic maps – insightful representation of phonological features for speech recognition. In: Proceedings of 71COR, International Conference on Pattern Recognition. Los Alamitos, CA: IEEE Computer Society Press. p. 182–185.
  • Kundu S, Das KC, Ghosh SK. 2013. Taxonomic rank of Indian tortoise: revisit with DNA barcoding perspective. DNA Barcodes. 1:39–45.
  • Laskar BA, Bhattacharjee MJ, Dhar B, Mahadani P, Kundu S, Ghosh SK. 2013. The species dilemma of Northeast Indian Mahseer (Actinopterygii: Cyprinidae): DNA barcoding in clarifying the riddle. PloS One 8:e53704.
  • Lasne E, Lek S, Laffaille P. 2007. Patterns in fish assemblags in the Loire floodplain: the role of hydrological connectivity and implications for conserve- ation. Biol Conserv. 139:258–268.
  • Le P, Chen Y. 1998. China Endangered Animals Red Book: fishes. Beijing: Science Publishing House.
  • Li G, Peng Z, Zhang R, Tang Y, Tong C, Feng C, Zhang C, Zhao K. 2016. Mito-nuclear phylogeography of the cyprinid fish Gymnodiptychus dybowskii in the arid Tien Shan region of central Asia. Biol J Linnean Soc. 118:304–314.
  • Liang Y, He D, Jia Y, Sun H, Chen Y. 2017. Phylogeographic studies of schizothoracine fishes on the central Qinghai-Tibetan Plateau reveal the highest known glacial microrefugia. Sci Rep. 7:10983.
  • Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Lim BK. 2012. Preliminary assessment of neotropical mammal DNA barcodes: an underestimation of biodiversity. Open Zool J. 5:10–17.
  • Lowenstein JH, Burger J, Jeitner CW, Amato G, Kolokotronis S-O, Gochfeld M. 2010. DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biol Lett. 6:692–695.
  • Meyer CP, Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. Plos Biol. 3:e422.
  • Nei M. 1987. Molecular evolution genetics. Columbia: Columbia University Press.
  • Obach M, Wagner R, Werner H, Schmidt H-H. 2001. Modelling population dynamics of aquatic insects with artificial neural networks. Ecol Model. 146:207–217.
  • Park Y-S, Kwak I-S, Chon T-S, Kim J-K, Jørgensen SE. 2001. Implementation of artificial nueral network in patterning and prediction of exergy in response to temporal dynamics of benthic macroinvertebrate communities in stream. Ecol Model. 146:143–157.
  • Penczak T, Kruk A, Park Y-S, Lek S. 2005. Patterning spatial variation in fish assemblage structures and diversity in the Pilica River system using a self- organizing map (SOM). In: Park YS, Lek S, editors. Modelling Community Structure in Freshwater Ecosystems. Berlin: Springer-Verlag; p. 100–113.
  • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol. 55:595–609.
  • Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol Notes. 21:1864–1887.
  • Qi D, Chao Y, Guo S, Zhao L, Li T, Wei F, Zhao X. 2012. Convergent, parallel and correlated evolution of trophic morphologies in the subfamily Schizothoracinae from the Qinghai-Tibetan Plateau. PloS One. 7:e34070.
  • Qi D, Guo S, Tang J, Zhao X, Liu J. 2007. Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei: Cyprinidae) in the Qinghai-Tibetan Plateau. J Fish Biol. 70:60–74.
  • Qi D, Guo S, Chao Y, Kong Q, Li C, Xia M, Xie B, Zhao K. 2015. The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai-Tibetan Plateau. Zoologica Scripta. 44:523–533.
  • Saccone C, Giorgi CD, Gissi C, Pesole G, Reyes A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene. 238:195–209.
  • Sambrook J, Fritsch E, Maniatis T. 1989. Molecular cloning: a laboratory manual. 2nd ed. New York: Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press.
  • Schindel DE, Stoeckle MY, Milensky C, Trizna M, Schmidt B, Gebhard C, Graves G. 2011. DNA barcodes of bird species in the National Museum of Natural History, Smithsonian Institution, USA. Zookeys. 152:87–91.
  • Shen Z. 2012. Illustrative plates of key aquatic organism of Qinghai Province. Xining, China: Qinghai Nationality Publishing House.
  • Shi J. 2008. Research on current situation and countermeasures of the resources protection of Gymnocypris przewalskii. Sci Technol, Qinghai. 6:13–16.
  • Song W, Yan X. 2004. China species red list. Red List. Vol. 1. Beijing: High Education Press.
  • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57:758–771.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30:2725–2729.
  • Tison J, Giraudel JL, Coste M, Park Y-S, Delmas F. 2004. Use of unsupervised neural networks for eco-regional zonation of hydrosystems through diatom communities: case study of Adour-Garonne watershed (France). Archiv Fur Hydrobiologie. 159:409–422.
  • Tong C, Lin Y, Zhang C, Shi J, Qi H, Zhao K. 2015. Transcriptome-wide identification, molecular evolution and expression analysis of Toll-like receptor family in a Tibet fish, Gymnocypris przewalskii. Fish Shellfish Immunol. 46:334–345.
  • Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. 2015. Molecular phylogeny of oysters belonging to the genus Crassoatrea through DNA barcoding. J Entomol Zool Stud. 3:21–26.
  • Trivedi S, Affan R, Alessa AHA, Ansari AA, Dhar B, Mahadani P, Ghosh SK. 2014. DNA barcoding of Red Sea fishes from Saudi Arabia – the first approach. DNA Barcodes. 2:17–20.
  • Vogler A. 2006. Will DNA barcoding advance efforts to conserve biodiversity more efficiently than traditional taxonomic methods? Front Ecol Environ. 4:268–273.
  • Wang T, Zhang Y, Guan L, Du Y, Lou Z, Jiao W. 2015. Current freshwater fish resources and the application of DNA barcoding in species identification in Gansu Province. Biol Divers. 23:306–313.
  • Wang Z, Guo Y, Liu X, Fan Y, Liu C. 2012. DNA barcoding South China Sea fishes. Mitochondrial DNA. 23:405–410.
  • Ward RD. 2009. DNA barcode divergence among species and genera of birds and fishes. Mol Ecol Resources. 9:1077–1085.
  • Ward RD, Hanner R, Hebert PDN. 2009. Review paper: the campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol. 74:329–356.
  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philos Trans Royal Soc Series B. 360:1847–1857.
  • Waugh J. 2007. DNA barcoding in animal species: progress, potential and pitfalls. Bioessays. 29:188–197.
  • Wong EH-K, Hanner RH. 2008. DNA barcoding detects market substitution in North American seafood. Food Res Int. 41:828–837.
  • Wu Y, Wu C. 1992. The fishes of the Qinghai-Xizang Plateau. Chendu, China: Sichuan Publishing House of Science & Technology.
  • Zhang D, Hewitt GM. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol Evol (Amst). 11:247–251.
  • Zhang R, Peng Z, Li G, Zhang C, Tang Y, Gan X, He S, Zhao K. 2013. Ongoing speciation in the Tibetan Plateau Gymnocypris species complex. PloS One. 8:e71331.
  • Zhang RL, Zhang B. 2014. Prospects of using DNA barcoding for species identification and evolution of the accuracy of sequence database for ticks (Acari: Ixodida). Ticks Tick-Borne Dis. 5:352–358.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.