Study on Phylogenetic Status of Javan Plover Bird (Charadrius, Charadriidae, Charadriiformes) through DNA Barcoding Analysis

Hidayat Ashari, Dwi Astuti


Javan Plover named Charadrius javanicus is taxonomically under controversy and phylogenetically unresolved yet. Through an analysis of DNA barcode, this study aims (1) to confirm whether Javan Plover is separated species named Charadrius javanicus or a subspecies of C. alexandrinus which named C. a. javanicus and (2) to determine a relationship within this genus. Totally 666 bp DNA sequences of COI barcode gene were analyzed.  The results showed that a sequence divergence between Javan Plover and C. alexandrinus alexandrinus was only 1.2%, while sequence divergences between C.a.alexandrinus and others species, or between Javan Plover and others species were ranged from 9-12%.  Neighbour-joining (NJ) and maximum-parsimony (MP) analyses showed that all individuals of both Javan Plover and Kenith Plover were clustered together, and supported by 99 % and 100 % of bootstrap value in NJ and MP, respectively. This study tends to support the previous findings that Javan Plover was not a separated species named C. javanicus, but it was as a subspecies of C. alexandrinus; named C. a. javanicus. There were two groups of Plover in this study; (C. leschenaultii and C. javanicus + C.a.alexandrinus), and (C.dubius and C. melodus + C. semipalmatus). DNA barcoding analysis can give certainty taxonomic status of the bird. Then, this study has implication as a basic data that can be used to provide and support the planning of Javan plover conservation programs. 


Phylogenetic status; Javan plover; Charadrius; COI gene; DNA barcoding

Full Text:



Astuti, D., Sulandari, S. (2010). The DNA sequnce performance of COI gene in white cockcatoos (Cacatua, Psittaciformes). Treubia, 37, 1-14.

Astuti, D. (2011). Variasi gen mitokondria cytochrome b pada dua jenis burung kakatua putih (Cacatua alba dan C. moluccensis). Jurnal Biologi Indonesia, 7(2), 263-276.

Astuti, D., & Prijono, S. N. (2015). Nucleotide variation in the NADH Subunit-2 gene sequences of lorikeet (genus: Trichoglossua) birds from Sulawesi isaland. Proceeding of the 4th International Conference on Biological Science. Yogyakarta 18-19 September 2015. AIP Conference Proceeding 1744 (020014), 1-5

Avise, J. C. (1994). Molecular Marker, Natural History and Evolution. New York: Chapman & Hall.

Ball Jr, R. M., & Avise, J. C. (1992). Mitochondrial phylogrographic differentiation among avian populations and the evolutionary significance of subspecies. The Auk, 109, 626-636.

Bamford, M., Watkins, D., Bancroft, W., Tischler, G., & Wahl, J. (2008). Migratory shorebirds of the East Asian–Australasian Flyway; population estimates and Internationally Important Sites. Australia: Wetlands International-Oceania, Canberra.

Barth, J. M., Matschiner, M., & Robertson, B. C. (2013). Phylogenetic position and subspecies divergence of endangered New Zealand Dotterel (Charadrius obscurus). PloSONE, 8(10), e78068.

Chasen, F. N. (1938). Vier neue Vogelrassen aus Malaysia. Ornith. Monatsber, 46(1), 5-8.

Cracraft, J. (1983). Species concepts and speciation analysis. Pp. 425 in R. F. Johnston, ed. Current ornithology. London: Plenum Press.

del Hoyo J., Elliot, A., & Sargatal, J. (1996). Handbook of the birds of the world. Vol. 3. Houstin to Auks. Barcelona: Lynnx Editions.

del Hoyo J., Elliot, A., Sargatal, J., & Christie, D. A. (2004). Handbook of the birds of the world. Vol. 3. Houstin to Auks. Barcelona: Lynnx Editions.

Dickinson, E. C., Howard & Moore. (2003). Complet Checklist of the birds of the birds of world. 3rd ed. London: Christopher Helm.

Dos Remedios, N., Lee, P. L., Burke, T., Székely, T., & Küpper, C. (2015). North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade. Molecular phylogenetics and evolution, 89, 151-159.

Hebert, P. D., Cywinska, A., & Ball, S. L. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270(1512), 313-321.

Hebert, P. D., Ratnasingham, S., & de Waard, J. R. (2003a). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences, 270(Suppl 1), S96-S99.

Hebert, P. D., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through DNA barcodes. Plos biol, 2(10), 1657-1662.

Hebert, P. D., Penton, E. H., Burns, J. M., Janzen, D. H., & 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 of the United States of America, 101(41), 14812-14817.

Hajibabaei, M., Smith, M., Janzen, D. H., Rodriguez, J. J., Whitfield, J. B., & Hebert, P. D. (2006). A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6(4), 959-964.

Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., & Hebert, P. D. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America, 103(4), 968-971.

Iqbal, M., Taufiqurrahman, I., Yordan, K., & van Balen, B. (2013). The distribution, abundance and conservation status of the Javan Plover Charadrius javanicus. Wader Study Group Bulletin, 120(1), 75-79.

Johns, G. C., & Avise, J. C. (1998). A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution, 15(11), 1481-1490.

Kaur, S. (2015). DNA Barcoding and Its Applications. International Journal of Engineering Research and General Science, 3(2), 602-604

Kerr, K. C., Stoeckle, M. Y., Dove, C. J., Weigt, L. A., Francis, C. M., & Hebert, P. D. (2007). Comprehensive DNA barcode coverage of North American birds. Molecular ecology notes, 7(4), 535-543.

Klicka, J., & Zink, R. M. (1997). The importance of recent ice ages in speciation: a failed paradigm. Science, 277(5332), 1666-1669.

Luo, A., Zhang, A., Ho, S. Y., Xu, W., Zhang, Y., Shi, W., ... & Zhu, C. (2011). Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. Bmc genomics, 12(1), 84.

MacKinnon. (1998). Field Guide Birds of Java and Bali. Yogyakarta: Gadjah Mada University Press.

Monroe, B. L. Jr, & Sibley, C. G. (1993). A world checklist of Birds. New Haven: Yale University Press.

Mutanen, M., Hausmann, A., Hebert, P. D., Landry, J. F., de Waard, J. R., & Huemer, P. (2012). Allopatry as a Gordian knot for taxonomists: Patterns of DNA barcode divergence in arctic-alpine Lepidoptera. PLoS One, 7(10), e47214.

Nagy, Z. T., Backeljau, T., De Meyer, M., & Jordaens, K. (Eds.). (2013). DNA barcoding: a practical tool for fundamental and applied biodiversity research (Vol. 365). PenSoft Publishers LTD.

Purty, R. S., & Chatterjee, S. (2016). DNA Barcoding: An Effective Technique in Molecular Taxonomy. Austin J Biotechnol Bioeng, 3(1), 1059.

Rach, J., DeSalle, R., Sarkar, I. N., Schierwater, B., & Hadrys, H. (2008). Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society of London B: Biological Sciences, 275(1632), 237-247.

Rheindt, F. E., Székely, T., Edwards, S. V., Lee, P. L., Burke, T., Kennerley, P. R., ... & Liu, W. T. (2011). Conflict between genetic and phenotypic differentiation: the evolutionary history of a ‘lost and rediscovered’shorebird. PLoS One, 6(11), e26995.

Shaffer, H. B., Fellers, G. M., Magee, A., & Voss, S. R. (2000). The genetics of amphibian declines: population substructure and molecular differentiation in the Yosemite Toad, Bufo canorus (Anura, Bufonidae) based on single‐strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data. Molecular Ecology, 9(3), 245-257.

Starkey, D. E., Shaffer, H. B., Burke, R. L., Forstner, M. R., Iverson, J. B., Janzen, F. J., ... & Ultsch, G. R. (2003). Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complex. Evolution, 57(1), 119-128.

Weibel, A. C., & Moore, W. S. (2002). Molecular phylogeny of a cosmopolitan group of woodpeckers (genus Picoides) based on COI and cyt b mitochondrial gene sequences. Molecular phylogenetics and evolution, 22(1), 65-75.



  • There are currently no refbacks.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.