研究生: |
林俊佑 Lin, Chun-Yu |
---|---|
論文名稱: |
多次跨島播遷與基因交流驅動菲律賓特有雙葉塔冠角蟬種群的多樣化 Overseas Dispersal with Gene Flow Drives Diversification of Endemic Treehoppers, Pyrgonota bifoliata Species Complex, in the Philippines |
指導教授: |
林仲平
Lin, Chung-Ping |
口試委員: |
曾惠芸
Tseng, Hui-Yun 廖培鈞 Liao, Pei-Chun 林仲平 Lin, Chung-Ping |
口試日期: | 2023/06/21 |
學位類別: |
碩士 Master |
系所名稱: |
生命科學系 Department of Life Science |
論文出版年: | 2023 |
畢業學年度: | 111 |
語文別: | 英文 |
論文頁數: | 57 |
中文關鍵詞: | 露盾角蟬亞科 、隱蔽種 、島嶼生物地理學 、長距離播遷 、次世代定序 |
英文關鍵詞: | Centrotinae, Cryptic species, Island biogeography, Long-distance dispersal, Membracidae, Next generation sequencing |
研究方法: | 實驗設計法 |
DOI URL: | http://doi.org/10.6345/NTNU202300651 |
論文種類: | 學術論文 |
相關次數: | 點閱:89 下載:0 |
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海洋島嶼因其獨特的獨立性、特有性和相對年輕等特徵被廣泛認為是研究演化的天然實驗室。擁有豐富的動物相和超過7,000個島嶼的菲律賓群島,為研究島嶼生物多樣性提供了寶貴的機會。本研究調查了菲律賓特有東亞塔冠角蟬種群Pyrgonota bifoliata的多樣化,推測它們的多樣化主要是受到更新世冰期循環的影響,抑或是早期板塊活動或現有的島嶼界線所造成。藉由簡化基因組定序(RADseq)資料,我訂出12個P. bifoliata物種群的分類操作單元。這些分類操作單元的分化事件發生在更新世冰期循環期間,顯示更新世複合島群(PAIC)可能影響了它們的多樣化。然而祖先分布重建結果顯示了數個PAIC之間的播遷事件,暗示著海洋島嶼和PAIC之間的海洋隔離並未強烈地阻礙P. bifoliata角蟬的播遷。此外,我們使用近似貝葉斯計算與隨機森林(ABC-RF)方法推測了島嶼內、島嶼間、以及PAIC間的譜系分化情境。結果顯示,不論島嶼內或島嶼間分化分化的族群,在末次冰盛期後至今仍持續地有基因交流。在PAIC之間的物種分化的初期也偵測到遺傳交流。因此這篇研究結果顯示,跨海播遷與持續的基因流推動了P. bifoliata物種群的多樣化。此外,長距離跨海播遷可能比以前想像的更頻繁。
Oceanic islands have been widely recognized as valuable natural laboratories for studying evolution due to their unique characteristics of isolation, endemism, and relative youth. The Philippines archipelagos, with their diverse fauna and over 7,000 islands, offer a valuable opportunity to investigate island biodiversity. This study investigates the diversification of the Pyrgonota bifoliata species complex, which consists of endemic treehoppers in the Philippines. The objective is to assess whether their diversification was predominantly shaped by Pleistocene glaciation cycles, which cyclically connected and fragmented the Pleistocene Aggregate Island Complex (PAIC) through fluctuating sea levels, or if other factors like ancient tectonic activities and current island boundaries played significant roles. Using restriction site-associated DNA sequencing (RADseq) data, we identified 12 operational taxonomic units within the P. bifoliata species complex, with divergence occurring during the Pleistocene glaciation cycle. This suggests that PAICs may have influenced their diversification. However, our ancestral range reconstruction results also unveiled several instances of dispersal between PAICs, implying that the oceanic barriers between islands and PAICs may not have strongly impeded dispersal. Furthermore, we inferred the demographic history of within and between islands population divergence, as well as between PAIC speciation, using the approximated Bayesian computation random forest (ABC-RF) framework. The outcomes of the ABC-RF analysis reveal the presence of continuous gene flow, even after the last glacial maximum when the PAIC broke up into separate islands, in both within island and between islands population divergence scenarios. Additionally, gene flow was also detected at the initial stages of speciation between PAICs. Overall, our findings suggest that overseas dispersal with continuous gene flow drove the diversification of the P. bifoliata species complex. Moreover, our results suggest that long-distance dispersal, possibly through rafting on vegetation, may occur more frequently than previously thought.
Andolfatto, P., D. Davison, D. Erezyilmaz, T. T. Hu, J. Mast, T. Sunayama-Morita, and D. L. Stern. 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21: 610-617.
Andrews, K. R., J. M. Good, M. R. Miller, G. Luikart, and P. A. Hohenlohe. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17: 81-92.
Baird, N. A., P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver, Z. A. Lewis, E. U. Selker, W. A. Cresko, and E. A. Johnson. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
Borowiec, M. L. 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4: e1660.
Bouckaert, R., T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. De Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C.-H. Wu, D. Xie, C. Zhang, T. Stadler, and A. J. Drummond. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comp Biol 15: e1006650.
Brown, R. M., and A. C. Diesmos. 2001. Application of lineage-based species concepts to oceanic island frog populations: the effects of differing taxonomic philosophies on the estimation of philippine biodiversity. Silliman J 42.
Brown, R. M., and A. C. Diesmos. 2009. Philippines, biology, pp. 723-732. In R. G. Gillespie and D. A. Clague (eds.), Encyclopedia of Islands, 1 ed. University of California Press.
Brown, R. M., C. D. Siler, C. H. Oliveros, J. A. Esselstyn, A. C. Diesmos, P. A. Hosner, C. W. Linkem, A. J. Barley, J. R. Oaks, M. B. Sanguila, L. J. Welton, D. C. Blackburn, R. G. Moyle, A. T. Peterson, and A. C. Alcala. 2013. Evolutionary processes of diversification in a model island archipelago. Annu Rev Ecol Evol Syst 44: 411-435.
Catchen, J., P. A. Hohenlohe, S. Bassham, A. Amores, and W. A. Cresko. 2013. Stacks: an analysis tool set for population genomics. Mol Ecol 22: 3124-3140.
Chen, S., Y. Zhou, Y. Chen, and J. Gu. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34: i884-i890.
da Fonseca, R. R., A. Albrechtsen, G. E. Themudo, J. Ramos-Madrigal, J. A. Sibbesen, L. Maretty, M. L. Zepeda-Mendoza, P. F. Campos, R. Heller, and R. J. Pereira. 2016. Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Mar Genomics 30: 3-13.
Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, M. A. DePristo, R. E. Handsaker, G. Lunter, G. T. Marth, S. T. Sherry, G. McVean, R. Durbin, and G. P. A. Group. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156-2158.
Esselstyn, J. A., and R. M. Brown. 2009. The role of repeated sea-level fluctuations in the generation of shrew (Soricidae: Crocidura) diversity in the Philippine Archipelago. Mol Phylogen Evol 53: 171-181.
Ewels, P., M. Magnusson, S. Lundin, and M. Käller. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32: 3047-3048.
Excoffier, L., and H. E. L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
Excoffier, L., I. Dupanloup, E. Huerta-Sánchez, V. C. Sousa, and M. Foll. 2013. Robust demographic inference from genomic and SNP data. PLoS Genet 9: e1003905.
Ezard, T., Fujisawa, T., and Barraclough, T. 2017. SPecies’ LImits by Threshold Statistics. R package version [Online]. Available from: https://R-Forge.R-project.org/projects/splits/ (accessed September 4, 2022).
Frichot, E., and O. François. 2015. LEA: An R package for landscape and ecological association studies. Methods Ecol Evol 6: 925-929.
Frichot, E., F. Mathieu, T. Trouillon, G. Bouchard, and O. François. 2014. Fast and efficient estimation of individual ancestry coefficients. Genetics 196: 973-983.
Fujisawa, T., and T. G. Barraclough. 2013. Delimiting species using single-locus data and the generalized mixed yule coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol 62: 707-724.
Green, M. R., and J. Sambrook. 2017. Precipitation of DNA with isopropanol. Cold Spring Harb Protoc 2017: pdb.prot093385.
Guindon, S., J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
Heads, M. 2014. Biogeography of the Philippines, pp. 356-401, Biogeography of Australasia: a molecular analysis. Cambridge University Press, Cambridge.
Heaney, L. 1985. Zoogeographic evidence for Middle and Late Pleistocene landbridges to the Philippine islands. Modern Quaternary research in Southeast Asia. Vol. 9 9: 127-143.
Heaney, L. R. 1986. Biogeography of mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biol J Linn Soc 28: 127-165.
Hoang, D. T., O. Chernomor, A. von Haeseler, B. Q. Minh, and L. S. Vinh. 2017. UFBoot2: Improving the ultrafast bootstrap approximation. Mol Biol Evol 35: 518-522.
Hosner, P. A., N. C. Boggess, P. Alviola, L. A. Sánchez-gonzález, C. H. Oliveros, R. Urriza, and R. G. Moyle. 2013. Phylogeography of the Robsonius ground-warblers (Passeriformes: Locustellidae) reveals an undescribed species from northeastern Luzon, Philippines. The Condor 115: 630-639.
Huang, J.-P. 2020. Is population subdivision different from speciation? From phylogeography to species delimitation. Ecol Evol 10: 6890-6896.
Jombart, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405.
Jombart, T., and I. Ahmed. 2011. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27: 3070-3071.
Jombart, T., S. Devillard, and F. Balloux. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11: 94.
Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler, and L. S. Jermiin. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14: 587-589.
Kapli, P., S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, and T. Flouri. 2017. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33: 1630-1638.
Keightley, P. D., R. W. Ness, D. L. Halligan, and P. R. Haddrill. 2014. Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics 196: 313-320.
Keightley, P. D., A. Pinharanda, R. W. Ness, F. Simpson, K. K. Dasmahapatra, J. Mallet, J. W. Davey, and C. D. Jiggins. 2015. Estimation of the spontaneous mutation rate in Heliconius melpomene. Mol Biol Evol 32: 239-243.
Kier, G., H. Kreft, T. M. Lee, W. Jetz, P. L. Ibisch, C. Nowicki, J. Mutke, and W. Barthlott. 2009. A global assessment of endemism and species richness across island and mainland regions. Proc Natl Acad Sci U.S.A. 106: 9322-9327.
Knaus, B. J., and N. J. Grünwald. 2017. VCFR: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour 17: 44-53.
Kyriazis, C. C., B. Alam, M. Wjodyla, S. Hackett, P. Hosner, H. L. Mays, L. R. Heaney, and S. Reddy. 2018. Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines. Mol Phylogen Evol 121: 121-131.
Leaché, A. D., B. L. Banbury, J. Felsenstein, A. n.-M. de Oca, and A. Stamatakis. 2015. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for Inferring SNP phylogenies. Syst Biol 64: 1032-1047.
Lemmon, E. M., and A. R. Lemmon. 2013. High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst 44: 99-121.
Linkem, C. W., R. M. Brown, C. D. Siler, B. J. Evans, C. C. Austin, D. T. Iskandar, A. C. Diesmos, J. Supriatna, N. Andayani, and J. A. McGuire. 2013. Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina). J Biogeogr 40: 507-520.
Losos, J. B., and R. E. Ricklefs. 2009. Adaptation and diversification on islands. Nature 457: 830-836.
Matzke, N. J. 2013. Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Front Biogeogr 5: 242-248.
Matzke, N. J. 2014. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Syst Biol 63: 951-970.
Matzke, N. J. 2022. Statistical comparison of DEC and DEC+J is identical to comparison of two ClaSSE submodels, and is therefore valid. J Biogeogr 49: 1805-1824.
McCormack, J. E., S. M. Hird, A. J. Zellmer, B. C. Carstens, and R. T. Brumfield. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66: 526-538.
Metcalf, Z. P., and V. Wade. 1965. General catalogue of the Homoptera. A supplement to fascicle I – Membracidae of the general catalogue of Hemiptera. Membracoidea, North Carolina State University, Raleigh.
Minh, B. Q., H. A. Schmidt, O. Chernomor, D. Schrempf, M. D. Woodhams, A. von Haeseler, and R. Lanfear. 2020. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37: 1530-1534.
Myers, N., R. A. Mittermeier, C. G. Mittermeier, G. A. B. da Fonseca, and J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
NAMRIA. 2017. Administrator Tiangco welcomes 2017. Accessed 5 March, 2023. (https://www.namria.gov.ph/list.php?id=1032&alias=administrator-tiangco-welcomes-2017&Archive=1).
Oaks, J. R., C. D. Siler, and R. M. Brown. 2019. The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago. Evolution 73: 1151-1167.
Oaks, J. R., P. L. Wood, C. D. Siler, and R. M. Brown. 2022. Generalizing Bayesian phylogenetics to infer shared evolutionary events. Proc Natl Acad Sci U.S.A. 119: e2121036119.
Paradis, E., and K. Schliep. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
Paris, J. R., J. R. Stevens, J. M. Catchen, and S. Johnston. 2017. Lost in parameter space: a road map for stacks. Methods Ecol Evol 8: 1360-1373.
Pudlo, P., J.-M. Marin, A. Estoup, J.-M. Cornuet, M. Gautier, and C. P. Robert. 2016. Reliable ABC model choice via random forests. Bioinformatics 32: 859-866.
R Core Team 2021. R: A language and environment for statistical computing computer program, version By R Core Team, Vienna, Austria.
Rambaut, A., A. J. Drummond, D. Xie, G. Baele, and M. A. Suchard. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67: 901-904.
Raynal, L., J.-M. Marin, P. Pudlo, M. Ribatet, C. P. Robert, and A. Estoup. 2019. ABC random forests for Bayesian parameter inference. Bioinformatics 35: 1720-1728.
Ree, R. H., and I. Sanmartín. 2018. Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection. J Biogeogr 45: 741-749.
Responte, M., Y.-F. Chiu, P. Peng, R. M. Brown, C.-Y. Dai, and Y.-C. Su. 2021. Northward geographic diversification of a kleptoparasitic spider Argyrodes lanyuensis (Araneae, Theridiidae) from the Philippine Archipelago to Orchid Island. Ecol Evol 11: 11241-11266.
Rochette, N. C., A. G. Rivera-Colón, and J. M. Catchen. 2019. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol 28: 4737-4754.
Siler, C. D., A. C. Diesmos, A. C. Alcala, and R. M. Brown. 2011. Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification. Mol Phylogenet Evol 59: 53-65.
Su, Y.-C., J.-F. Wang, R. J. T. Villanueva, O. M. Nuñeza, C.-P. Lin, and L. Heaney. 2014. Hopping out of Mindanao: Miocene-Pliocene geological processes and cross-island dispersal as major drivers of diversity for Philippine treehoppers. J Biogeogr 41: 1277-1290.
Veron, S., T. Haevermans, R. Govaerts, M. Mouchet, and R. Pellens. 2019. Distribution and relative age of endemism across islands worldwide. Sci Rep 9: 11693.
Wachi, N., K. W. Matsubayashi, and K. Maeto. 2018. Application of next-generation sequencing to the study of non-model insects. Entomol Sci 21: 3-11.
Wallace, M. S., and L. L. Deitz. 2004. Phylogeny and systematics of the treehopper subfamily Centrotinae (Hemiptera: Membracidae). Mem Entomol Int 19: i-iv:1–377.
Wallace, M. S., and L. L. Deitz. 2006. Australian treehoppers (Hemiptera: Membracidae: Centrotinae: Terentiini): phylogeny and biogeography. Invertebr Syst 20: 163-183.
Welton, L. J., C. D. Siler, D. Bennett, A. Diesmos, M. R. Duya, R. Dugay, E. L. B. Rico, M. Van Weerd, and R. M. Brown. 2010. A spectacular new Philippine monitor lizard reveals a hidden biogeographic boundary and a novel flagship species for conservation. Biol Lett 6: 654-658.
Wood, T. K. 1984. Life history patterns of tropical membracids (Homoptera: Membracidae). Sociobiology 8: 299–344.
Yeh, H.-Y., H.-Y. Tseng, C.-P. Lin, C.-P. Liao, J.-Y. Hsu, and W.-S. Huang. 2018. Rafting on floating fruit is effective for oceanic dispersal of flightless weevils. J Exp Biol 221.
Young, A. D., and J. P. Gillung. 2020. Phylogenomics — principles, opportunities and pitfalls of big-data phylogenetics. Syst Entomol 45: 225-247.
Yu, Y., C. Blair, and X. He. 2019. RASP 4: ancestral state reconstruction tool for multiple genes and characters. Mol Biol Evol 37: 604-606.
Zhang, J., P. Kapli, P. Pavlidis, and A. Stamatakis. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869-2876.