Sains Malaysiana 45(7)(2016): 1089–1095

 

Phylogenetic Relationships of Waders (Charadriiformes: Scolopacidae) in Sarawak Inferred from Cytochrome Oxidase I and Recombinant Activating Gene 1

(Hubungan Filogenetik Burung Laut (Charadriiformers: Scolopacidae) di Sarawak yang Tersimpul daripada Sitokrom Oksidase I dan Rekombinan Gen Pengaktif 1)

 

NURUL ASHIKEEN AB RAZAK1*, MUSTAFA ABDUL RAHMAN2 & ANDREW ALEK TUEN1

 

1Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak

94300Kota Samarahan, Sarawak, Malaysia

 

2University College Sabah Foundation, Jalan Sanzac, 88100 Sembulan, Kota Kinabalu, Sabah Negeri di Bawah Bayu, Malaysia

 

Diserahkan: 25 November 2014/Diterima: 30 Januari 2016

 

ABSTRACT

Family Scolopacidae includes the sandpipers, shanks, snipes, godwits and curlews. Systematic classifications of shorebirds at the higher level have been successfully resolved. Nevertheless, the phylogeny of shorebirds in the familial level is still poorly understood. Thus, this phylogenetic study on Scolopacidae was conducted upon the framework provided by the first sequence-based species-level phylogeny within the shorebirds to determine the phylogenetic relationships among family members of Scolopacidae in West Borneo, Sarawak using combined gene markers, mtDNA Cytochrome Oxidise I (COI) and nucDNA Recombinant Activating Gene 1 (RAG1). A total of 1,342 base pair (bp) were inferred from both COI and RAG1 gene from 45 sequences constituted of 15 species Scolopacidae sampled from Sarawak namely Xenus cinereus, Actitis hypoleucos, Tringa totanus, Tringa glareola, Tringa stagnatilis, Heteroscelus brevipes, Calidris alba, Calidris ruficollis, Calidris ferruginea, Calidris tenuirostris, Calidris alpina, Gallinago stenura, Gallinago megala, Numenius arquata, and Numenius phaeopus. The phylogenetic tree was constructed with Charadrius mongulus derived as an outgroup. The Bayesian Inference (BI) tree constructed supported grouping of species into several lineages of Numeniinae, Calidrinae, Scolopacinae and Tringinae. The groupings of species into several lineages correlate with morphological features that contribute to their adaptation and ability of the species to fit to their ecosystems.

 

Keywords: Cytochrome Oxidase I; phylogenetic; Recombinant Activating Gene 1; waders

 

ABSTRAK

Famili Scolopacidae merangkumi burung kedidi biasa, burung kedidi kaki merah, burung berkek dan burung kedidi kendi. Pengelasan sistematik burung laut pada peringkat lebih tinggi telah berjaya diselesaikan. Namun, filogeni burung laut pada peringkat famili masih belum difahami. Sehubungan itu, kajian filogenetik ke atas Scolopacidae telah dijalankan mengikut rangka kerja yang diberikan oleh filogeni berasaskan-urutan-pertama aras-spesies dalam kalangan burung laut untuk mengenal pasti hubungan filogenetik dalam kalangan family Scolopacidae di barat Borneo, Sarawak, menggunakan penanda molekul berbeza; mtDNA Siktokrom Oksidase I (COI) dan nucDNA Recombinan Gen Pengaktif 1 (RAG1). Sejumlah 1,342 pasangan asas (bp) diperoleh daripada kedua-dua jenis gen COI dan RAG1 daripada 45 jujukan merangkumi 15 spesies Scolopacidae yang disampel dari Sarawak iaitu Xenus cinereus, Actitis hypoleucos, Tringa totanus, Tringa glareola, Tringa stagnatilis, Heteroscelus brevipes, Calidris alba, Calidris ruficollis, Calidris ferruginea, Calidris tenuirostris, Calidris alpina, Gallinago stenura, Gallinago megala, Numenius arquata dan Numenius phaeopus. Pokok filogenetik telah dibina menggunakan Charadrius mongulus sebagai kumpulan luar. Pokok Bayesian Inference (BI) yang dibina menyokong perkumpulan spesies mengikut keturunan masing-masing iaitu Numeniinae, Calidrinae, Scolopacinae dan Tringinae. Perkumpulan spesies kepada beberapa keturunan berkait rapat dengan ciri morfologi yang telah menyumbang kepada adaptasi dan kebolehan spesies ini menyesuaikan diri dalam ekosistem mereka.

Kata kunci: Burung laut; filogenetik; Rekombinan Gen Pengaktif 1; Sitokrom Oksidase 1

 

 

RUJUKAN

 

Avise, J.C. 2004. Molecular Markers, Natural History, and Evolution. 2nd ed. Sunderland, Massachusetts: Sinauer.

Baker, A.J., Pereira, S.L. & Paton, T.A. 2007. Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biology Letters 3: 205-209.

Banks, J., van Buren, A., Cherel, Y. & Whitfield, J.B. 2006. Genetic evidence for three species of Rockhopper Penguins Eudyptes chrysocome. Polar Biol. DOI 10.1007/s00300- 006-0160-3.

Barrett, D. & Schluter, D. 2008. Adaptation from standing genetic variation. Trends in Ecology & Evolution 23(1): 38-44.

Braun, E.L. & Kimball, R.T. 2002. Examining basal avian divergences with mitochondrial sequences: model complexity, taxon sampling and sequence length. Syst. Biol. 51: 614-625.

Brown, W.M. 1983. Evolution of animal mitochondrial DNA. In Evolution of Genes and Proteins, edited by Nei, M. & Koehn, R.K. Sunderland, Massachussets: Sinauer Associates.

Clements, J.F., Schulenberg, T.S., Iliff, M.J., Sullivan, B.L. & Wood, C.L. 2010. The Clements Checklist of Birds of the World: Version 6.5. New York: Cornell University.

Cummings, M.P., Otto S.P. & Wakeley, J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12: 814-822.

Ericson, P.G.P., Envall, I., Irestedt, M. & Norman, J.A. 2003. Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data. BMC Evol. Biol. 3: 16.

Farris, J.S., KaČ llersjoČ, M., Kluge, A.G. & Bult, C. 1995. Constructing a significance test for incongruence. Syst. Biol. 44: 570-572.

Gibson, R. & Baker, A. 2012. Multiple gene sequences resolve phylogenetic relationships in shorebird suborder Scolopaci (Aves: Charadriiformes). Molecular Phylogenetics and Evolution 64: 66-72.

Gibson, R. 2010. Phylogenetic relationships among the Scolopaci (Aves: Charadriiformes): Implications for the study of behavioral evolution. M.Sc. Thesis. University of Toronto (Unpublished).

Grewe, P.M., Krueger, C.C., Aquadro, C.F., Bermingham, E., Kincaid, H.L. & May, B. 1993. Mitochondrial variation among lake trout (Salvenilus namaycush) strains stocked into Lake Ontario. Can. J. Fish. Aquat. Sci. 50: 2397-2403.

Groth, J.G. & Barrowclough, G.F. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12: 115-123.

Huelsenbeck, J.P. & Ronquist, F. 2001. Mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

Jehl Jr., J.R. 1968. Relationships in the Charadrii (shorebirds): a taxonomic study based on color patterns of the downy young. Mem. San Diego Soc. Nat. Hist. 3: 1-54.

Kimura, M. 1980. A simple method for estimating the evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.

Livezey, B.C. 2010. Progress and obstacles in the phylogenetics of modern birds. In Evolution of Modern Birds, edited by Dyke, G. & Chiappe, L. Berkeley: University of California Press. pp. 117-145.

Mayr, G. 2011. The phylogeny of Charadriii form birds (shorebirds and allies) - reassessing the conflict between morphology and molecules. Zool. J. Linn. Soc. 161: 916-934.

Myers, S. 2009. A Field Guide to the Birds of Borneo. UK: New Holland Publication.

Palumbi, S.A., Martin, S., Romano, W.O., McMillan, L., Stice, L. & Grabowski, G. 1991. The Simple Fool’s Guide to PCR. Honolulu, HI: Department of Zoology and Kewalo Marine Laboratory, Univ. of Hawaii.

Paton, T.A. & Baker, A.J. 2006. Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the charadriiform birds congruent with the nuclear RAG-1 tree. Molecular Phylogenetics and Evolution 39: 657-667.

Paton, T.A., Baker, A.J., Groth, J.G. & Barrowclough, G.F. 2003. RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet Evol. 29(2): 268-278.

Pereira, S.L. & Baker, A.J. 2005. Multiple gene evidence for parallel evolution and retention of ancestral morphological states in the shanks (Charadriiformes: Scolopacidae). Condor 107: 514-526.

Pereira, S.L., Baker, A.J. & Wajntal, A. 2002. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes Aves). Syst. Biol. 51: 946-958.

Rosenberg, N.A. & Feldman, M.W. 2001. The Relationship between Coalescence Times and Population Divergence Times. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press.

Saitou, N. & Nei, M. 1987. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.

Sibley, C. & Ahlquist, J. 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution. New Haven: Yale University Press.

Smythies, B. 1999. The Birds of Borneo. 4th ed. Kota Kinabalu: Natural History Publications Borneo.

Swofford, D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Massachusetts: Sinauer Associates.

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. 2011. MEGA 5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.

Thomas, G.H., Wills, M.A. & Székely, T. 2004. A super tree approach to shorebird phylogeny. BioMed Central Evolutionary Biology 4: 1-18.

Thompson, J.D., Gibson, T.J. & Plewniak, F. 1997. The clustal X windows interface: Flexible strategies for multiple sequence alignment aided by the quality analysis tools. Nucleic Acids Res. 24: 4876-4882.

Weibel, A.C. & Moore, W.S. 2002. Molecular phylogeny of a cosmopolitan group of woodpeckers (genus Picoides) gased on COI and cyt b mitochondrial gene sequences. Mol. Phylogenet. Evol. 22: 65-75.

 

 

*Pengarang untuk surat-menyurat; email: ekinrazak@gmail.com

 

 

 

 

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