Application of DNA Barcoding in Taxonomy and Phylogeny: An Individual Case of COI Partial Gene Sequencing from Seven Animal Species

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A part of the COI mitochondrial barcoding gene was sequenced from seven species of different taxonomical groups: Ambystoma mexicanum (Amphibia, Ambystomatidae), Darevskia lindholmi, Lacerta agilis exigua (Reptilia, Lacertidae), Erinaceus roumanicus (Mammalia, Erinaceidae), Macrobiotus sp. 1 and 2 (Eutardigrada, Macrobiotidae) and Cameraria ohridella (Insecta, Gracillariidae). The sequences were compared with available sequences from databases and positioned on phylogenetic trees when the taxa had not yet been sequenced. The presence of Mexican axolotls in herpetoculture in Ukraine was confirmed. The partial COI genes of the Crimean rock lizard and an eastern sub-species of the sand lizard were sequenced. We demonstrated the presence of two tardigrade mitochondrial lineages of the Macrobiotus hufelandi group in the same sample from the Zeya Natural Reserve in the Far East: one was nearly identical to the Italian M. macrocalix, and the other one is similar to M. persimilis and M. vladimiri. We also confirmed the presence of the invasive haplotype “A” of the horse chestnut leaf miner in Ukraine, in line with the hypothesized route of invasion from Central Europe.

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  • Aljanabi S. M. Martinez I. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25 4692–4693.

  • Andres C. Franke F Bleidorn C Bernhard D Schlegel M. 2014. Phylogenetic analysis of the Lacerta agilis subspecies complex. Syst Biodivers 12 43–54.

  • Bogdanov A. S. Bannikova A. A. Pirusskii Y. M. Formozov N. A. 2009. The First Genetic Evidence of Hybridization between West European and Northern White-breasted Hedgehogs (Erinaceus europaeus and E. roumanicus) in Moscow Region. Biol Bull Russ Acad Sci36 (6) 647–651.

  • Cesari M Guidetti R Rebecchi L Giovannini I Bertolani R. 2013. A DNA barcoding approach in the study of tardigrades. J Limnol72 23.

  • Ciobanu D. G. Grechko V. V. Kramerov D. A. Darevsky I. S. 2003. A New Subfamily of the Satellite DNA CLsatIV of the Lizard Darevskia lindholmi (Sauria Laceridae): Structure and Evolution. Dokl Biochem Biophys392 (1–6) 263–267.

  • De Carvalho M. R. Bockmann F. A. Amorim D. S. Brandao C. R. F. de Vivo M. de Figueiredo J. L. Britski H. A. de Pinna M. C. C. Menezes N. A. Marques F. P. L. Papavero N. Cancello E. M. Crisci J. V. McEachran J. D. Schelly R. C. Lundberg J. G. Gill A. C. Britz R. Wheeler Q. D. Stiassny M. L. J. Parenti L. R. Page L. M. Wheeler W. C. Faivovich J. Vari R. P. Grande L. Humphries C. J. DeSalle R. Ebach M. C. Nelson G. J. 2007. Taxonomic Impediment or Impediment to Taxonomy? A Commentary on Systematics and the Cybertaxonomic-Automation Paradigm. Evol Biol34 140–143.

  • Folmer O. Black M. Hoeh W. Lutz R. Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech3 (5) 294–299.

  • Grechko V. V. Ciobanu D. G. Darevsky I. S. Kosushkin S. A. Kramerov D. A. 2006. Molecular evolution of satellite DNA repeats and speciation of lizards of the genus Darevskia (Sauria: Lacertidae). Genome49 (10) 1297–1307.

  • Guil N. Sanchez-Moreno S. Machordom A. 2009. Local biodiversity patterns in micrometazoans: Are tardigrades everywhere? Syst Biodivers7 (3) 259–268.

  • Guglya Yu. Zinenko O. 2008. New Data on Expansion of the Leaf-Mining Moth Cameraria ochridella (Lepidoptera Gracillariidae) in Ukraine. Vestnik Zooogiil42 (3) 220.

  • Hall T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41 95–98.

  • He K. Chen J. H. Gould G. C. Yamaguchi N. Ai H-S. Wang Y-X. Zhang Y-P. Jiang X-L. 2012. An estimation of Erinaceidae phylogeny: a combined analysis approach. PLoS One 7: e39304.

  • Hebert P. D. N. Cywinska A. Ball S. L. de Waard J. R. 2003. Biological identifications through DNA barcodes. Proc Biol Sci270 (1512) 313–321.

  • Kaczmarek L. Gawlak M. Bartels P. J. Nelson D. R. Roszkowska M. 2017. Revision of the Genus Paramacrobiotus Guidetti et al. 2009 with the Description of a New Species Re-Descriptions and a Key. Ann Zool 67 627–656.

  • Kaczmarek L. Michalczyk L. 2017. The Macrobiotus hufelandi group (Tardigrada) revisited. Zootaxa4363 (1) 101–123.

  • Kalyabina S. A. Milto K. D. Ananjeva N. B. Legal L. Joger U. Wink M. 2001. Phylogeography and systematics of Lacerta agilis based on mitochondrial cytochrome b gene sequences: first results. Russ J Herpetol 8 149–158.

  • Kalyabina-Hauf S. A. Ananjeva N. B. 2004. Phylogeography and intraspecies structure of wide distributed sand lizard Lacerta agilis L. 1758 (Lacertidae Sauria Reptilia). Trudy Zoologicheskogo Instituta 302 1–105.

  • Kapli P. Poulakakis N. Lymberakis P. Mylonas M. 2011. A re-analysis of the molecular phylogeny of Lacertidae with currently available data. Basic Appl Herpetol 25 97–104.

  • Kukushkin O. V. Doronin I. V. Tuniyev B. S. Ananjeva N. B. Doronina M. A. 2017. Introduction of Amphibians and Reptiles at the Caucasus and the Crimea: an Overview and Some Actual Data. Curr Stud Herpetol 17 157–197.

  • Kumar S. Stecher G. Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biol and Evol33 (7) 1870–1874.

  • Lee J. Rho H. S. Chang C. Y. 2017. Taxonomic Study of Marine Tardigrades from Korea III. A New Species of the Genus Orzeliscus (Heterotardigrada Halechiniscidae). Animal Syst Evol Divers 33 26–32.

  • Lees D. C. Lack H. W. Rougerie R. Hernandez-Lopez A. Raus T. Avtzis N. Augustin S. Lopez-Vaamonde C. 2011. Tracking origins of invasive herbivores through herbaria and archival DNA: the case of the horse-chestnut leaf miner. Front Ecol Environ 9 322–328.

  • MacCuloch R. D. Fu J. Darevsky I. S. Murphy R. W. 2000. Genetic evidence for species status of some Caucasian rock lizards in the Darevskia saxicola group. Amphibia–Reptilia 21 169–176.

  • Pérez-Pech W. A. Anguas-Escalante A. Cutz-Pool L. Q. Guidetti R. 2017. Doryphoribius chetumalensis sp. nov. (Eutardigrada: Isohypsibiidae) a new tardigrade species discovered in an unusual habitat of urban areas of Mexico. Zootaxa4344 (2) 345–356.

  • Pilato G. Binda M. G. 2001. Biogeography and limno-terrestrial tardigrades: are they truly incompatible binomials? Zool Anz 240 511–516.

  • Ratnasingham S. Hebert P. D. N. 2007. BOLD: The Barcode of Life Data System ( Mol Ecol Notes 7 355–364.

  • Ratnasingham S. Hebert P. D. N. 2013. A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. PLoS ONE 8 e66213

  • Tarkhnishvili D. Gabelaia M. Mumladze L. Murtskhvaladze M. 2016. Mitochondrial phylogeny of the Darevskia saxicola complex: two highly deviant evolutionary lineages from the easternmost part of the range. Herpetol J 26 175–182.

  • Valade R. Kenis M. Hernandez-Lopez A Augustin S. Mari Mena N. Magnoux E. Rougerie R. Lakatos F. Roques A. Lopez-Vaamonde C. 2009. Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera Gracillariidae). Mol Ecol 18 3458–3470.

  • Voss S. R. Woodcock M. R. Zambrano L. 2015. A tale of two axolotls. BioScience 65 1134–1140.

  • Zambrano L. Valiente E. Vander Zanden M. J. 2010. Food web overlap among native axolotl (Ambystoma mexicanum) and two exotic fishes: carp (Cyprinus carpio) and tilapia (Oreochromis niloticus) in Xochimilco Mexico City. Biol Invasions 12 3061–3069.

  • Zambrano L. Reidl P. M. McKay J. Griffiths R. Shaffer B. Flores-Villela O. ParraOlea G. Wake D. 2010. Ambystoma mexicanum. In: IUCN 2010. The IUCN Red List of Threatened Species. Version 2010. DOI: 10.2305/IUCN.UK.2010-2.RLTS.T1095A3229615.en.

  • Zerova M. D. Nikitenko G. N. Narolsky N. B. Gershenson Z. S. Sviridov S. V. Lukash O. V. Babidoritsh M. M. 2007. Horse-chestnut Leaf miner Cameraria ohridella in Ukraine. Kiev Ukraine Schmalhausen Institute of Zoology [In Russian].

  • Zinenko O. I. Drabkin P. L. Rudyk O. M. 2005. Contact zone between two subspecies of the Sand lizard: Lacerta agilis exigua Eichw. 1831 and Lacerta agilis chersonensis Andr. 1832 in three regions of the Left-bank Ukraine. In: Ananjeva N. Tsinenko O. eds. Herpetologica Petropolitana. Proceedings of the 12th Ordinary General Meeting Societas Europea HerpetologicaAugust 12–16 2003St. Petersburg Russian Federation: SEH 109–112.

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