DNA BARCODING OF GECKOS (SQUAMATA: GEKKONIDAE: GEKKO) IN SOUTHERN VIETNAM
Main Article Content
Abstract
DNA barcoding is a quick tool for species identification using a fragment of DNA sequence which is short, genetically informative, and easy to amplify. In the southern Vietnam, there are eight species of geckos genus Gekko (Squamata: Gekkonidae). Most of them are morphologically similar and used for food, medicine, and pet trade. Based on thesamples of all theeight species collected from the area, this study seeks to build the standard DNA barcodes of these species which will be then used for species identification and searching the origin of traded geckos. The first set of DNA barcodes (681 bp, COI gene, 11 sequences) of all the eight geckos livingin thesouthern Vietnam with GenBank accession numbers MN062174-MN062184 was found. Six of the eight species collected from their type localities can be considered for standard DNA barcodes for these geckos. Mean genetic distance between species is 20.3%, ranging from 17.6% to 25.3%. The phylogenetic trees strongly support all species but do not clearly resolve their interspecific relationships.
Keywords
DNA barcoding, Gekkos, southern Vietnam
Article Details
References
Bain, R. H. (2010). Gekko grossmanni. The IUCN Red List of Threatened Species. e.T178613A7581244.
Che, J., Chen, H., Yang, J., Jin, J., Jiang, K., Yuan, Z., Murphy, R. W., & Zhang, Y. (2012). Universal COI primers for DNA barcoding amphibians. Molecular Ecology Resources, 12, 247-258. https://doi.org/10.1111/j.1755099-8.2011.03090.x
Felsenstein, J. (2004). Inferring phylogenies. Sinauer Associates.
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. Molecular Marine Biology and Biotechnology, 3, 294-299.
Fritz, U. (2002). Herpetology and herpetological type specimens at the Museum für Tierkunde Dresden with the bibliography of herpetological contributions by Fritz Jürgen Obst (Amphibian, Reptilia). Faunistische Abhandlungen, 23, 3-34.
Günther, R. (1994). A new species of the genus Gekko (Reptilia, Squamata, Gekkonidae) from southern Vietnam. Zoologischer Anzeiger, 233, 57-67.
Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., & Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, 103, 968-971. http://doi.org/10.1073/pnas.0510466103
Hillis, D. M., & Bull, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systems Biology, 42, 182-192.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003a). Biological identifications through DNA barcodes. Proceedings Biological Sciences, 270, 313-321. http://doi.org/10.1098/rspb.2002.2218
Hebert, P. D. N., deWaard, J. R., & Landry, J. F. (2009). DNA barcodes for 1/1000 of the animal kingdom. Biology Letters, 6, 359-362. https://doi.org/10.10-98/rsbl.2009.0848
Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society London B, Supplement 1, 270, S96-S99. https://doi.org/10.10-98/rsbl.2003.0025
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through DNA barcodes. PLoSBiology, 2(10), e312. https://doi.org/-10.1371/journal.pbio.0020312
Ivanova, N. V., Zemlak, T. S., Hanner, R. H., & Hebert, P. D. N. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7, 544-548. http://doi.org/10.1111/j.1471-8286.2007.01748.x
Kress, W. J., & Erickson, D. L. (2012). DNA Barcodes: Methods and Protocols. in W. J. Kress & D. L. Erickson (Eds.). DNA Barcodes-Methods and Protocols (pp. 3-8). Human Press.
Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., & Janzen, D. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, 102, 8369-8374. http://doi.org/10.1073pnas.0503-123102
Kumar, S., Stecher, G., Christina, K., & Kamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35,1547-1549. https://doi.org/0.1093/molbev/msy096
Luu, V. Q., Calame, T., Nguyen, T. Q., Le, M. D., & Ziegler, T. (2015). Morphological and molecular review of the Gekko diversity of Laos with descriptions of three new species. Zootaxa, 3986, 279-306. http://dx.doi.org/10.11646/zootaxa.3986.3.2
Marshall, E. (2005). Will DNA bar codes breathe life into classification?. Science, 307, 1037. http://doi.org/10.1126/science.307.5712.1037
Nagy, Z. T., Sonet, G., Glaw, F., & Vences, M. (2012). First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoSONE, 7(3), e34506. https://doi.org/10.1371/journal.pone.0034506
Ngo, T. V., Bauer, A. M., Wood, P. L. J., & Grismer, J. L. (2009). A new species of Gekko Laurenti, 1768 (Squamata: Gekkonidae) from Dong Nai Province, Southeastern Vietnam. Zootaxa, 2238, 33-42.
Ngo, T. V., & Gamble, T. (2010). A new species of Gekko (Squamata: Gekkonidae) from Ta Kou Nature Reserve, Binh Thuan Province, southern Vietnam. Zootaxa, 2346, 17-28.
Ngo, T. V., & Gamble, T. (2011). Gekko canaensis sp. nov. (Squamata: Gekkonidae), a new gecko from southern Vietnam. Zootaxa, 2890, 53-64.
Nguyen, N. S. (2010). A new poreless species of Gekko Laurenti, 1768 (Gekkonidae: Squamata) from An Giang Province, southern Vietnam. Zootaxa, 2501, 54-60.
Nguyen, S. N., Golynsky, E., Milto, K., & Nguyen, T. Q. (2018b). Gekko badenii. The IUCN Red List of Threatened Species 2018, e.T178554A112309489. http://dx.doi.org/10.2305/IUCN.UK.20182.RLTS.T178554A112309489.en
Nguyen, S. N., & Hoang, D. D. (2005). Dan lieu sinh hoc tac ke hoa can Gekko ulikovskii tai nui Ba Den, Tay Ninh [Biological data of Golden Gecko Gekko ulikovskii at mount Ba Den, Tay Ninh Province]. The basic research problems in life science, 718-721.
Nguyen, S. N., Jin, J., Vo, B. D., Nguyen, L. T., Zhou, W., Che, J., Murphy, R. W., & Zhang, Y. (2019). A new species of Acanthosaura Gray 1831 (Reptilia: Agamidae) from central Vietnam. Zootaxa, 4612, 555-565. https://doi.o-rg/10.11646/zootaxa.4612.4.7
Nguyen, S. N., Milto, K., & Golynsky, E. (2018c). Gekko grossmanni. The IUCN Red List of Threatened Species 2018, e.T178613A112331071. http://dx.doi.org/10.2305/IU-CN.UK.20182.RLTS.T178613A112331071.en
Nguyen, S. N., Nguyen, T. L., Nguyen, V. D. H., Orlov, N. L., & Murphy, R. W. (2018a). A new skink of the genus Sphenomorphus Fitzinger, 1843 (Squamata: Scincidae) from Hon Ba Nature Reserve, southern Vietnam. Zootaxa, 4438, 313-326. https://doi.org/10.11646/zootaxa.4438.2.6
Nguyen, S. V., Ho, C. T., & Nguyen, T. Q. (2009). Herpetofauna of Vietnam. Andreas S. Brahm.
Nguyen, T. Q., Schmitz, A., & Böhme, W. (2010). Gekko ulikovskii Darevsky and Orlov, 1994: a junior synonym of Gekko badenii Szczerbak and Nekrasova, 1994. Bonn Zoological Bulletin, 57, 15-17.
Nylander, J. A. A. (2004). MrModeltest v2. Program distributed by the author. Uppsala University, Evolutionary Biology Centre.
Phung, T. M., & Ziegler, T. (2011). Another new Gekko species (Squamata: Gekkonidae) from Southern Vietnam. Zootaxa, 3129, 51-61.
Ronquist, R. R., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. https://doi.org/10.1093/bioinformatics/btg180
Rosler, H., Bauer, A. M., Heinicke, M. P., Greenbaum, E., Jackman, T., Nguyen, T. Q., & Ziegler, T. (2011). Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae). Zootaxa, 2989, 1-50. http://dx.doi.org/10.11646/zootaxa.2989.1.1
Stamatakis, A. S., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systems Biology, 57, 758-771. https://doi.org/10.1080/10635150802429642
Thompson, J. D., Higgins, D., & Gibson, T. J (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, 4670-4680.
Trinh, T. M. D., Hoang, M. D, Luu, H. T., & Vu, N. L. (2013). Dong vat thuong bi khai thac tai Khu Bao ton Thien nhien Takou [Animals commonly exploited by local communities in Takou Nature Reserve]. The 4thScientific report on ecology and biological resource, 508-514.
Uetz, P., Freed, P., & Jirí, H. (2019). The Reptile Database. Retrieved May 13, 2019 from http://www.reptile-database.org
Wood, P. L., Guo, X., Travers, S. L., Su, Y., Olson, K. V., Bauer, A. M., Grismer, L. L., Siler, C. D., Moyle, R. G., Andersen, M. J., & Brown, R. M. (2020). Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements. Molecular Phylogenetics and Evolution, 146, 106731. https://doi.org/10.1016/j.ympev.2020.106731
Ziegler, T., Rauhaus, A., Nguyen, T. Q., & Nguyen, K. V. (2015). Südlichster Nachweis von Gekko badenii Szczerbak & Nekrasova, 1994, mit Bemerkungen zur Herpetofauna der Hon-Me-Auffangstation in der Provinz Kien Giang, Südvietnam [Southernmost record of Gekko badenii Szczerbak & Nekrasova, 1994, with remarks on the herpetofauna of the Hon Me Rescue Station in Kien Giang Province, Southern Vietnam]. Sauria, 37, 3-14.
Che, J., Chen, H., Yang, J., Jin, J., Jiang, K., Yuan, Z., Murphy, R. W., & Zhang, Y. (2012). Universal COI primers for DNA barcoding amphibians. Molecular Ecology Resources, 12, 247-258. https://doi.org/10.1111/j.1755099-8.2011.03090.x
Felsenstein, J. (2004). Inferring phylogenies. Sinauer Associates.
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. Molecular Marine Biology and Biotechnology, 3, 294-299.
Fritz, U. (2002). Herpetology and herpetological type specimens at the Museum für Tierkunde Dresden with the bibliography of herpetological contributions by Fritz Jürgen Obst (Amphibian, Reptilia). Faunistische Abhandlungen, 23, 3-34.
Günther, R. (1994). A new species of the genus Gekko (Reptilia, Squamata, Gekkonidae) from southern Vietnam. Zoologischer Anzeiger, 233, 57-67.
Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., & Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, 103, 968-971. http://doi.org/10.1073/pnas.0510466103
Hillis, D. M., & Bull, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systems Biology, 42, 182-192.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003a). Biological identifications through DNA barcodes. Proceedings Biological Sciences, 270, 313-321. http://doi.org/10.1098/rspb.2002.2218
Hebert, P. D. N., deWaard, J. R., & Landry, J. F. (2009). DNA barcodes for 1/1000 of the animal kingdom. Biology Letters, 6, 359-362. https://doi.org/10.10-98/rsbl.2009.0848
Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society London B, Supplement 1, 270, S96-S99. https://doi.org/10.10-98/rsbl.2003.0025
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through DNA barcodes. PLoSBiology, 2(10), e312. https://doi.org/-10.1371/journal.pbio.0020312
Ivanova, N. V., Zemlak, T. S., Hanner, R. H., & Hebert, P. D. N. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7, 544-548. http://doi.org/10.1111/j.1471-8286.2007.01748.x
Kress, W. J., & Erickson, D. L. (2012). DNA Barcodes: Methods and Protocols. in W. J. Kress & D. L. Erickson (Eds.). DNA Barcodes-Methods and Protocols (pp. 3-8). Human Press.
Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., & Janzen, D. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, 102, 8369-8374. http://doi.org/10.1073pnas.0503-123102
Kumar, S., Stecher, G., Christina, K., & Kamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35,1547-1549. https://doi.org/0.1093/molbev/msy096
Luu, V. Q., Calame, T., Nguyen, T. Q., Le, M. D., & Ziegler, T. (2015). Morphological and molecular review of the Gekko diversity of Laos with descriptions of three new species. Zootaxa, 3986, 279-306. http://dx.doi.org/10.11646/zootaxa.3986.3.2
Marshall, E. (2005). Will DNA bar codes breathe life into classification?. Science, 307, 1037. http://doi.org/10.1126/science.307.5712.1037
Nagy, Z. T., Sonet, G., Glaw, F., & Vences, M. (2012). First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoSONE, 7(3), e34506. https://doi.org/10.1371/journal.pone.0034506
Ngo, T. V., Bauer, A. M., Wood, P. L. J., & Grismer, J. L. (2009). A new species of Gekko Laurenti, 1768 (Squamata: Gekkonidae) from Dong Nai Province, Southeastern Vietnam. Zootaxa, 2238, 33-42.
Ngo, T. V., & Gamble, T. (2010). A new species of Gekko (Squamata: Gekkonidae) from Ta Kou Nature Reserve, Binh Thuan Province, southern Vietnam. Zootaxa, 2346, 17-28.
Ngo, T. V., & Gamble, T. (2011). Gekko canaensis sp. nov. (Squamata: Gekkonidae), a new gecko from southern Vietnam. Zootaxa, 2890, 53-64.
Nguyen, N. S. (2010). A new poreless species of Gekko Laurenti, 1768 (Gekkonidae: Squamata) from An Giang Province, southern Vietnam. Zootaxa, 2501, 54-60.
Nguyen, S. N., Golynsky, E., Milto, K., & Nguyen, T. Q. (2018b). Gekko badenii. The IUCN Red List of Threatened Species 2018, e.T178554A112309489. http://dx.doi.org/10.2305/IUCN.UK.20182.RLTS.T178554A112309489.en
Nguyen, S. N., & Hoang, D. D. (2005). Dan lieu sinh hoc tac ke hoa can Gekko ulikovskii tai nui Ba Den, Tay Ninh [Biological data of Golden Gecko Gekko ulikovskii at mount Ba Den, Tay Ninh Province]. The basic research problems in life science, 718-721.
Nguyen, S. N., Jin, J., Vo, B. D., Nguyen, L. T., Zhou, W., Che, J., Murphy, R. W., & Zhang, Y. (2019). A new species of Acanthosaura Gray 1831 (Reptilia: Agamidae) from central Vietnam. Zootaxa, 4612, 555-565. https://doi.o-rg/10.11646/zootaxa.4612.4.7
Nguyen, S. N., Milto, K., & Golynsky, E. (2018c). Gekko grossmanni. The IUCN Red List of Threatened Species 2018, e.T178613A112331071. http://dx.doi.org/10.2305/IU-CN.UK.20182.RLTS.T178613A112331071.en
Nguyen, S. N., Nguyen, T. L., Nguyen, V. D. H., Orlov, N. L., & Murphy, R. W. (2018a). A new skink of the genus Sphenomorphus Fitzinger, 1843 (Squamata: Scincidae) from Hon Ba Nature Reserve, southern Vietnam. Zootaxa, 4438, 313-326. https://doi.org/10.11646/zootaxa.4438.2.6
Nguyen, S. V., Ho, C. T., & Nguyen, T. Q. (2009). Herpetofauna of Vietnam. Andreas S. Brahm.
Nguyen, T. Q., Schmitz, A., & Böhme, W. (2010). Gekko ulikovskii Darevsky and Orlov, 1994: a junior synonym of Gekko badenii Szczerbak and Nekrasova, 1994. Bonn Zoological Bulletin, 57, 15-17.
Nylander, J. A. A. (2004). MrModeltest v2. Program distributed by the author. Uppsala University, Evolutionary Biology Centre.
Phung, T. M., & Ziegler, T. (2011). Another new Gekko species (Squamata: Gekkonidae) from Southern Vietnam. Zootaxa, 3129, 51-61.
Ronquist, R. R., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. https://doi.org/10.1093/bioinformatics/btg180
Rosler, H., Bauer, A. M., Heinicke, M. P., Greenbaum, E., Jackman, T., Nguyen, T. Q., & Ziegler, T. (2011). Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae). Zootaxa, 2989, 1-50. http://dx.doi.org/10.11646/zootaxa.2989.1.1
Stamatakis, A. S., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systems Biology, 57, 758-771. https://doi.org/10.1080/10635150802429642
Thompson, J. D., Higgins, D., & Gibson, T. J (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, 4670-4680.
Trinh, T. M. D., Hoang, M. D, Luu, H. T., & Vu, N. L. (2013). Dong vat thuong bi khai thac tai Khu Bao ton Thien nhien Takou [Animals commonly exploited by local communities in Takou Nature Reserve]. The 4thScientific report on ecology and biological resource, 508-514.
Uetz, P., Freed, P., & Jirí, H. (2019). The Reptile Database. Retrieved May 13, 2019 from http://www.reptile-database.org
Wood, P. L., Guo, X., Travers, S. L., Su, Y., Olson, K. V., Bauer, A. M., Grismer, L. L., Siler, C. D., Moyle, R. G., Andersen, M. J., & Brown, R. M. (2020). Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements. Molecular Phylogenetics and Evolution, 146, 106731. https://doi.org/10.1016/j.ympev.2020.106731
Ziegler, T., Rauhaus, A., Nguyen, T. Q., & Nguyen, K. V. (2015). Südlichster Nachweis von Gekko badenii Szczerbak & Nekrasova, 1994, mit Bemerkungen zur Herpetofauna der Hon-Me-Auffangstation in der Provinz Kien Giang, Südvietnam [Southernmost record of Gekko badenii Szczerbak & Nekrasova, 1994, with remarks on the herpetofauna of the Hon Me Rescue Station in Kien Giang Province, Southern Vietnam]. Sauria, 37, 3-14.