Low genetic diversity and no genetic differentiation between maleo hatched at coastal and inland nesting grounds in North Sulawesi, Indonesia
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Abstract. Saputra AW, Yuda P. 2020. Low genetic diversity and no genetic differentiation between maleo hatched at coastal and inland nesting grounds in North Sulawesi, Indonesia. Biodiversitas 21: 4772-4777. Maleo Senkawor (Macrocephalon maleo), an endemic and endangered bird of Sulawesi (Indonesia), is burrow-nesting megapodes that incubate its eggs in communal nesting sites in soils heated by sun on beaches and by volcanic activity in inland. The aims of this study were to assess genetic diversity of the Maleo and examine whether those which have different nesting sites have become genetically differentiated. In total, 24 eggshell membranes of Maleo were collected from Tanjung Binerean (coastal nesting ground) and Tambun (inland nesting ground), and the DNA was extracted using silica spin-column kit. PCR was applied to amplify the hypervariable region 1 (HV1) and partial mtDNA control region of HV2 using a specific primer set designed for Maleo. The PCR products were sequenced, resulted in 612 bp, and showed 9 polymorphic sites and 9 haplotypes (H). Further sequences analysis suggested that there was no genetic differentiation between coastal nesting population and inland nesting population (Fst = 0.0009; P = 0.431). As expected, the genetic diversity of Maleo was relatively low (coastal nesting population, Hd: 0.727270, ?: 0.002377 and inland nesting population Hd: 0.848480, ?: 0.002203).
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References
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Baker, G., & Dekker, R. (2000). Lunar synchrony in the reproduction of the Moluccan Megapode. Ibis, 142, 382–388.
Bandelt, H.-J., Forster, P., & Rohl, A. (1999). Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Biology and Evolution, 16(1), 37–48.
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Davey, J. L., & Blaxter, M. W. (2010). RADseq: Next-generation population genetics. Briefings in Functional Genomics, 9(5–6), 416–423. https://doi.org/10.1093/bfgp/elq031
Dekker, R. (1990). The distribution and status of nesting grounds of the Maleo Macrocephalon maleo in Sulawesi, Indonesia. Biological Conservation, 51(2), 139–150. https://doi.org/10.1016/0006-3207(90)90108-2
Dekker, R., & Brom, T. (1992). Megapode phylogeny and the interpretation of incubation strategies. Zoologische Verhandelingen, 278, 19–31.
Dong, L., Zhang, J., Sun, Y., Liu, Y., Zhang, Y., & Zheng, G. (2010). Phylogeographic Patterns and Conservation Units of a Vulnerable Species, Cabot’s Tragopan (Tragopan caboti), Endemic to Southeast China. Conservation Genetics, 11, 2231–2242. https://doi.org/10.1007/s10592-010-0108-6
Excoffier, L., & Lischer, H. E. L. (2010). Arlequin Suite Ver 3.5?: a New Series of Programs to Perform Population Genetics Analyses Under Linux and Windows. Molecular Ecology Resources, 10, 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data. Genetics, 131(2), 479–491. https://doi.org/10.1007/s00424-009-0730-7
Frankham, R. (2003). Genetics and Conservation Biology. Comptes Rendus Biologies, 326, 22–29. https://doi.org/10.1016/S1631-0691(03)00023-4
Gorog, A. J., Pamungkas, B., & Lee, R. J. (2005). Nesting Ground Abandonment by The Maleo (Macrocephalon maleo) in North Sulawesi: Identifying Conservation Priorities for Indonesia’s Endemic Megapode. Biological Conservation, 126(4), 548–555. https://doi.org/10.1016/j.biocon.2005.07.006
Göth, A., & Vogel, U. (2004). Is Monogamy in the Polynesian Megapode (Megapodius Pritchardii) Related To Its High Relative Egg-Weight? The Auk, 121(2), 308. https://doi.org/10.1642/0004-8038(2004)121[0308:imitpm]2.0.co;2
Hall, T. A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. In Nucleic Acids Symposium Series (Vol. 41, pp. 95–98). https://doi.org/citeulike-article-id:691774
Harris, R. B., Birks, S. M., & Leaché, A. D. (2014). Incubator Birds: Biogeographical Origins and Evolution of Underground Nesting in Megapodes (Galliformes: Megapodiidae). Journal of Biogeography, 41(11), 2045–2056. https://doi.org/10.1111/jbi.12357
Huang, Z., & Ke, D. (2017). Organization and variation of the tetraonidae (Aves: Galliformes) mitochondrial dna control region. Mitochondrial DNA Part B: Resources, 2(2), 568–570. https://doi.org/10.1080/23802359.2017.1361345
Huang, Z., Liu, N., Liang, W., Zhang, Y., Liao, X., Ruan, L., & Yang, Z. (2010). Phylogeography of Chinese Bamboo Partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in South China: Inference from Mitochondrial DNA Control-Region Sequences. Molecular Phylogenetics and Evolution, 56(1), 273–280. https://doi.org/10.1016/j.ympev.2010.01.028
Hunowu, I., & Patandung, A. (2015). Laporan Program Konservasi Maleo dan Sumber Daya Pesisir di Tanjung Binerean.
IUCN. (2020). The IUCN Red List of Threatened Species. Version 2019-3.
Lee, Y. J., Bhuiyan, M. S. A., Chung, H. J., Jung, W. Y., Choi, K. D., Jang, B. G., Paek, W. K., Jeon, J. T., Park, C. S. &, & Lee, J. H. 2007. (2007). Mitochondrial DNA Diversity of Korean Ogol Chicken. Asian-Australasian Journal of Animal Sciences, 20(4), 477–481.
Leigh, J. W., & Bryant, D. (2015). POPART?: Full-Feature Software for Haplotype Network Construction. Methods in Ecology AndEvolution, 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410
Lucchini, V., & Randi, E. (1999). Molecular evolution of the mtDNA control-region in galliform birds. Proceedings 22 International Ornithological Congress.
MacKinnon, J. (1981). Methods For The Conservation of Maleo Birds, Macrocephalon maleo on the Island of Sulawesi, Indonesia. Biological Conservation, 20(3), 183–193. https://doi.org/10.1016/0006-3207(81)90028-8
Martins, F. M. S., Dawson, D. A., Goth, A., Wells, D. A., Eiby, Y. A., Wilmer, J. W., Horsburgh, G. H., Booth, D. T., Jones, D. N., & Burke, T. (2014). Phylogeographical Population Structure in A Mound-Building Megapode, the Australian Brush-Turkey (Alectura lathami lathami). Molecular Ecology Laboratory, Dept of Animal and Plant Sciences, NERC-BAF.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7(5). https://doi.org/10.1371/journal.pone.0037135
Ravindran, P. N., Bentzen, P., Bradbury, I. R., & Beiko, R. G. (2019). RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Molecular Ecology Resources, 19(1), 272–282. https://doi.org/10.1111/1755-0998.12954
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Bology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248
Ruokonen, M., & Kvist, L. (2002). Structure and Evolution of The Avian Mitochondrial Control Region. Molecular Phylogenetics and Evolution, 23(3), 422–432. https://doi.org/10.1016/S1055-7903(02)00021-0
Slack, K. E., Delsuc, F., Mclenachan, P. A., Arnason, U., & Penny, D. (2007). Resolving The Root of The Avian Mitogenomic Tree by Breaking Up Long Branches. Molecular Phylogenetics and Evolution, 42(1), 1–13. https://doi.org/10.1016/j.ympev.2006.06.002
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3-New Capabilities and Interfaces. Nucleic Acids Research, 40(15), 1–12. https://doi.org/10.1093/nar/gks596
Yuda, P. (2008). Conservation Genetics of the Java sparrow (Padda oryzivora) and an analysis of its viability. James Cook University.
Yuda, P., & Saputra, A. W. (2020). Eggshell membrane for DNA sexing of the endangered Maleo (Macrocephalon maleo). F1000Research.
Zein, M., & Sulandari, S. (2008). Keragaman Genetik Ayam Lombok Berdasarkan Sekuen D-LOOP DNA Mitokondria. Jurnal Ilmu Ternak Dan Veteriner, 13(4), 308–314.
Zein, M., & Sulandari, S. (2012). Keragaman Genetik dan Distribusi Haplogrup Ayam Kampung dengan Menggunakan Hipervariabel-I Daerah Kontrol DNA Mitokondria. Jurnal Ilmu Ternak Dan Veteriner, 17(2), 120–131.
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000). A Greedy Algorithm for Aligning DNA Sequences. Journal Of Computational Biology, 7(1/2), 203–214.
Aquadro, C. F., & Greenberg, B. D. (1983). Human Mitochondrial DNA Variation and Evolution?: Analysis of Nucleotide Sequences from Seven Individuals. Genetics, 103, 287–312.
Baker, A. J., & Marshal, H. D. (1997). Mitochondrial Control Region Sequences as Tools for Understanding Evolution. In D. P. Mindell (Ed.), Avian Molecular Evolution and Systematics. Academic Press.
Baker, G., & Dekker, R. (2000). Lunar synchrony in the reproduction of the Moluccan Megapode. Ibis, 142, 382–388.
Bandelt, H.-J., Forster, P., & Rohl, A. (1999). Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Biology and Evolution, 16(1), 37–48.
BirdLife International. (2001). Threatened Birds of Asia: the BirdLife International Red Data Book. BirdLife International.
Budiarsa, I. M., Artama, I. W. T., Sembiring, L., & Situmorang, J. (2009a). Diversitas genetik burung Maleo (Macrocephalon maleo) berdasarkan sekuen gen dehydrogenase sub-Unit 2 (ND2) mitokondria. Berkala Penelitian Hayati Edisi Khusus, 3B(June), 11–15.
Budiarsa, I. M., Artama, I. W. T., Sembiring, L., & Situmorang, J. (2009b). Diversitas Genetik Burung Maleo (Macrocephalon maleo) Berdasarkan Intron Satu Gen Rhodopsin Nukleus (RDP1). Seminar Nasional Penelitian, Pendidikan Dan Penerapan MIPA, 81–85.
Crowe, T. M., Bowie, R. C. K., Bloomer, P., Mandiwana, T. G., Hedderson, T. a J., Randi, E., Pereira, S. L., & Wakeling, J. (2006). Phylogenetics, Biogeography and Classification of, and Character Evolution in, Gamebirds (Aves: Galliformes): Effects of Character Exclusion, Data Partitioning and Missing Data. Cladistics, 22, 495–532. https://doi.org/10.1111/j.1096-0031.2006.00120.x
Davey, J. L., & Blaxter, M. W. (2010). RADseq: Next-generation population genetics. Briefings in Functional Genomics, 9(5–6), 416–423. https://doi.org/10.1093/bfgp/elq031
Dekker, R. (1990). The distribution and status of nesting grounds of the Maleo Macrocephalon maleo in Sulawesi, Indonesia. Biological Conservation, 51(2), 139–150. https://doi.org/10.1016/0006-3207(90)90108-2
Dekker, R., & Brom, T. (1992). Megapode phylogeny and the interpretation of incubation strategies. Zoologische Verhandelingen, 278, 19–31.
Dong, L., Zhang, J., Sun, Y., Liu, Y., Zhang, Y., & Zheng, G. (2010). Phylogeographic Patterns and Conservation Units of a Vulnerable Species, Cabot’s Tragopan (Tragopan caboti), Endemic to Southeast China. Conservation Genetics, 11, 2231–2242. https://doi.org/10.1007/s10592-010-0108-6
Excoffier, L., & Lischer, H. E. L. (2010). Arlequin Suite Ver 3.5?: a New Series of Programs to Perform Population Genetics Analyses Under Linux and Windows. Molecular Ecology Resources, 10, 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data. Genetics, 131(2), 479–491. https://doi.org/10.1007/s00424-009-0730-7
Frankham, R. (2003). Genetics and Conservation Biology. Comptes Rendus Biologies, 326, 22–29. https://doi.org/10.1016/S1631-0691(03)00023-4
Gorog, A. J., Pamungkas, B., & Lee, R. J. (2005). Nesting Ground Abandonment by The Maleo (Macrocephalon maleo) in North Sulawesi: Identifying Conservation Priorities for Indonesia’s Endemic Megapode. Biological Conservation, 126(4), 548–555. https://doi.org/10.1016/j.biocon.2005.07.006
Göth, A., & Vogel, U. (2004). Is Monogamy in the Polynesian Megapode (Megapodius Pritchardii) Related To Its High Relative Egg-Weight? The Auk, 121(2), 308. https://doi.org/10.1642/0004-8038(2004)121[0308:imitpm]2.0.co;2
Hall, T. A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. In Nucleic Acids Symposium Series (Vol. 41, pp. 95–98). https://doi.org/citeulike-article-id:691774
Harris, R. B., Birks, S. M., & Leaché, A. D. (2014). Incubator Birds: Biogeographical Origins and Evolution of Underground Nesting in Megapodes (Galliformes: Megapodiidae). Journal of Biogeography, 41(11), 2045–2056. https://doi.org/10.1111/jbi.12357
Huang, Z., & Ke, D. (2017). Organization and variation of the tetraonidae (Aves: Galliformes) mitochondrial dna control region. Mitochondrial DNA Part B: Resources, 2(2), 568–570. https://doi.org/10.1080/23802359.2017.1361345
Huang, Z., Liu, N., Liang, W., Zhang, Y., Liao, X., Ruan, L., & Yang, Z. (2010). Phylogeography of Chinese Bamboo Partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in South China: Inference from Mitochondrial DNA Control-Region Sequences. Molecular Phylogenetics and Evolution, 56(1), 273–280. https://doi.org/10.1016/j.ympev.2010.01.028
Hunowu, I., & Patandung, A. (2015). Laporan Program Konservasi Maleo dan Sumber Daya Pesisir di Tanjung Binerean.
IUCN. (2020). The IUCN Red List of Threatened Species. Version 2019-3.
Lee, Y. J., Bhuiyan, M. S. A., Chung, H. J., Jung, W. Y., Choi, K. D., Jang, B. G., Paek, W. K., Jeon, J. T., Park, C. S. &, & Lee, J. H. 2007. (2007). Mitochondrial DNA Diversity of Korean Ogol Chicken. Asian-Australasian Journal of Animal Sciences, 20(4), 477–481.
Leigh, J. W., & Bryant, D. (2015). POPART?: Full-Feature Software for Haplotype Network Construction. Methods in Ecology AndEvolution, 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410
Lucchini, V., & Randi, E. (1999). Molecular evolution of the mtDNA control-region in galliform birds. Proceedings 22 International Ornithological Congress.
MacKinnon, J. (1981). Methods For The Conservation of Maleo Birds, Macrocephalon maleo on the Island of Sulawesi, Indonesia. Biological Conservation, 20(3), 183–193. https://doi.org/10.1016/0006-3207(81)90028-8
Martins, F. M. S., Dawson, D. A., Goth, A., Wells, D. A., Eiby, Y. A., Wilmer, J. W., Horsburgh, G. H., Booth, D. T., Jones, D. N., & Burke, T. (2014). Phylogeographical Population Structure in A Mound-Building Megapode, the Australian Brush-Turkey (Alectura lathami lathami). Molecular Ecology Laboratory, Dept of Animal and Plant Sciences, NERC-BAF.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7(5). https://doi.org/10.1371/journal.pone.0037135
Ravindran, P. N., Bentzen, P., Bradbury, I. R., & Beiko, R. G. (2019). RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Molecular Ecology Resources, 19(1), 272–282. https://doi.org/10.1111/1755-0998.12954
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Bology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248
Ruokonen, M., & Kvist, L. (2002). Structure and Evolution of The Avian Mitochondrial Control Region. Molecular Phylogenetics and Evolution, 23(3), 422–432. https://doi.org/10.1016/S1055-7903(02)00021-0
Slack, K. E., Delsuc, F., Mclenachan, P. A., Arnason, U., & Penny, D. (2007). Resolving The Root of The Avian Mitogenomic Tree by Breaking Up Long Branches. Molecular Phylogenetics and Evolution, 42(1), 1–13. https://doi.org/10.1016/j.ympev.2006.06.002
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3-New Capabilities and Interfaces. Nucleic Acids Research, 40(15), 1–12. https://doi.org/10.1093/nar/gks596
Yuda, P. (2008). Conservation Genetics of the Java sparrow (Padda oryzivora) and an analysis of its viability. James Cook University.
Yuda, P., & Saputra, A. W. (2020). Eggshell membrane for DNA sexing of the endangered Maleo (Macrocephalon maleo). F1000Research.
Zein, M., & Sulandari, S. (2008). Keragaman Genetik Ayam Lombok Berdasarkan Sekuen D-LOOP DNA Mitokondria. Jurnal Ilmu Ternak Dan Veteriner, 13(4), 308–314.
Zein, M., & Sulandari, S. (2012). Keragaman Genetik dan Distribusi Haplogrup Ayam Kampung dengan Menggunakan Hipervariabel-I Daerah Kontrol DNA Mitokondria. Jurnal Ilmu Ternak Dan Veteriner, 17(2), 120–131.
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000). A Greedy Algorithm for Aligning DNA Sequences. Journal Of Computational Biology, 7(1/2), 203–214.
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