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研究生: 曾書萍
Shu-Ping Tseng
論文名稱: 利用多基因座遺傳資訊與溯祖理論推論種化模式:以草蜥屬為例
Inferring the speciation model with coalescent-based multi-locus approach: A case of Takydromus spp.
指導教授: 林思民
Lin, Si-Min
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: 2012
畢業學年度: 100
語文別: 英文
論文頁數: 60
中文關鍵詞: 454定序技術草蜥基因交流種化
英文關鍵詞: 454 sequencing, Takydromus species, gene flow, speciation
論文種類: 學術論文
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  • 異域種化描述兩族群在受到地理阻隔之後,由於基因交流中斷,變異在兩族群內逐漸累積,因而導致種化的發生。過去認為基因交流的存在會弭平兩個族群的差異,因此異域種化一直被視為物種形成的典型模式。然而近年來的證據顯示種化的過程在有少量基因交流的情況下仍然可能發生,這一類非典型的種化模式(如鄰域種化及同域種化)也因此逐漸受到演化學家的重視。本研究旨在檢測翠斑草蜥(Takydromus viridipunctatus)、鹿野草蜥(T. luyeanus)、雪山草蜥(T. hsuehshanensis)三種草蜥分化期間的基因交流量,以推論此三種草蜥的種化模式。我們利用454高通量定序技術取得翠班及鹿野草蜥的cDNA序列,篩選出20組核基因的分子標記,並利用Isolation with migration analysis(IMA2)程式與approximate Bayesian computation(ABC)方法進行分析,以推估三種草蜥種化過程中的基因交流量,並釐清基因交流發生的時間點。結果發現三種草蜥在分化過程中的基因交流值顯著偏離零,顯示種化過程中保有一定程度的基因交流,典型的異域種化模型被拒絕。而ABC的分析結果則顯示翠斑草蜥及鹿野草蜥基因交流的時間發生在分化之後,並持續了一段時間,之後基因交流停止至現今。這個結果顯示IMA2所偵測的基因交流來自早期基因交流的模式,而非因為二次接觸造成的近期交流。總結來說,鄰域種化模式比異域種化模式更適合描述這三個物種的種化模式。

    Allopatric speciation is the dominant view of speciation among evolutionists. It is the process, where an ancestral population splits into two populations because of a geographic barrier. Genetic divergence gradually accumulates between the two descendant populations and ultimately results in two reproductively isolated entities. Under this scenario, speciation seems unlikely to proceed with the existence of gene flow. However, alternative geographic speciation modes allowing certain amount of gene flow (i.e. parapatic and sympatric modes) during speciation have gained more attention and related studies been published in recent years.
    In this study, we aim to test the existence of historical gene flow to evaluate the predominance of allopatric isolation during the speciation process across three reciprocally monophyletic species: Takydromus viridipunctatus, T. luyeanus and T. hsuehshanensis. The EST database of Takydromus spp. was constructed by using 454 sequencing, and 20 nuclear loci were successfully identified and amplified from the lizards for genetic investigations. IMA2 analyses revealed significant gene flows among the three species disfavouring a strictly allopatric speciation model. An approximate Bayesian computation (ABC) model choice procedure further indicated that an “early gene flow model” but not an “secondary contact model” fits better with the empirical data (T. viridipunctatus and T. luyeanus). Hence, historical but contemporary gene flow has occurred between T. viridipunctatus and T. luyeanus. We concluded that “parapatric” rather than “allopatric” is the predominant mode of speciation across Takydromus species.

    Introduction……………………………………………………………………1 Materials and methods…………………………………………………6 Results……………………………………………………………………………16 Discussion………………………………………………………………………20 Conclusion………………………………………………………………………25 References………………………………………………………………………26 Table 1……………………………………………………………………………35 Table 2……………………………………………………………………………37 Table 3……………………………………………………………………………38 Table 4……………………………………………………………………………39 Table 5……………………………………………………………………………40 Table 6……………………………………………………………………………41 Table 7……………………………………………………………………………42 Table 8……………………………………………………………………………43 Table 9……………………………………………………………………………44 Figure 1…………………………………………………………………………45 Figure 2…………………………………………………………………………46 Figure 3…………………………………………………………………………47 Figure 4…………………………………………………………………………48 Figure 5…………………………………………………………………………50 Figure 6…………………………………………………………………………51 Figure 7…………………………………………………………………………52 Figure 8…………………………………………………………………………53 Figure 9…………………………………………………………………………54 Appendix I………………………………………………………………………55 Appendix II……………………………………………………………………56 Appendix III …………………………………………………………………57 Appendix IV……………………………………………………………………59 Appendix V………………………………………………………………………60

    Anderson RA, Vitt LJ (1990) Sexual selection versus alternative causes of sexual dimorphism in teiid lizards. Oecologia 84, 145-157.
    Arnold EN (1997) Interrelationships and evolution of the East Asian grass lizards,Takydromus(Squamata: Lacertidae). Zool J Linn Soc 119, 267-296.
    Beaumont MA (2010) Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41, 379-406.
    Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035.
    Becquet C, Przeworski M (2009) Learning about modes of speciation by computational approaches. Evolution 63, 2547-2562.
    Bertorelle G, Benazzo A, Mona S (2010) ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 19, 2609-2625.
    Carneiro M, Ferrand N, Nachman MW (2009) Recombination and speciation: loci near centromeres are more differentiated than loci near telomeres between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 181, 593-606.
    Creer S, Malhotra A, Thorpe RS, Chou WH (2001) Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan. Mol Ecol 10, 1967–1981.
    Chiang TY, Schaal BA (2006) Phylogeography of plants in Taiwan and the Ryukyu Archipelago.Taxon 55, 31-41
    Chou WH, Nguyen QT, Pauwels OSG (2001) A new species of Takydromus (Reptilia : Lacertidae) from Vietnam. Herpetologica 57, 497-508.
    Coyne J, Orr H (2004) Speciation. Sinauer Associatiates, Sunderland(MA).
    Csilléry K, Blum MG, Gaggiotti OE, François O (2010) Approximate Bayesian computation (ABC) in practice. Trends Ecol. Evol 25:410–18
    Darwin C (1859) On the Origin of Species. John Murray, London.
    Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24, 332-340.
    Doughty P, Sinervo B, Burghardt GM (1994) Sex-biased dispersal in a polygynous lizard, Uta stansburiana. Anim Behav 47, 227-229.
    Du WG, Yao ZJ (2007) Mating behavior of the northern grass lizard,Takydromus septentrionalis. Chinese J Zool 42, 392-394.
    Duvaux L, Belkhir K, Boulesteix M, Boursot P (2011) Isolation and gene flow: inferring the speciation history of European house mice. Mol Ecol 20, 5248-5264.
    Fay JC, Wu CI (2000) Hitchhiking under positive darwinian selection. Genetics 155, 1405-1413.
    Fijarczyk A, Nadachowska K, Hofman S, et al. (2011) Nuclear and mitochondrial phylogeography of the European fire-bellied toads Bombina bombina and Bombina variegata supports their independent histories. Mol Ecol 20, 3381-3398.
    Fitzpatrick BM, Fordyce JA, Gavrilets S (2009) Pattern, process and geographic modes of speciation. J Evol Biol 22, 2342-2347.
    Gavrilets S (2003) Perspective: models of speciation: what have we learned in 40 years? Evolution 57, 2197-2215.
    Gifford ME, Larson A (2008) In situ genetic differentiation in a Hispaniolan lizard (Ameiva chrysolaema): A multilocus perspective. Mol Phylogenet and Evol 49, 277-291.
    Guindon S, Dufayard JF, Lefort V, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59, 307-321.
    Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27, 570-580.
    Hey J (1991) A multi-dimensional coalescent process applied to multi-allelic selection models and migration models. Theor Popul Biol 39, 30-48.
    Hey J (2010a) The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol Biol Evol 27, 921-933.
    Hey J (2010b) Isolation with migration models for more than two populations. Mol Biol Evol 27, 905-920.
    Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747-760.
    Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci 104, 2785-2790.
    Hey J, Wakeley J (1997) A coalescent estimator of the population recombination rate. Genetics 145, 833-846.
    Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9, 1322-1332.
    Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
    Jeffreys H (1961) Theory of probability, 3rd ed. Oxford University Press, USA, London.
    Joyce P, Marjoram P (2008) Approximately sufficient statistics and Bayesian computation. Stat Appl Genet Mol Biol 7, Article26.
    Jukes TH, Cantor CR (1969) Evolution of protein molecule. In: Mammalian Protein Metabolism (ed. Munro HN), pp. 21-123. Academic Press, New York.
    Kelly JK (1997) A test of neutrality based on interlocus associations. Genetics 146, 1197-1206.
    Lawniczak MKN, Emrich SJ, Holloway AK, et al. (2010) Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 330, 512-514.
    Leaché AD (2009) Species tree discordance traces to phylogeographic clade boundaries in north american fence lizards (Sceloporus). Sys Biol 58, 547-559.
    Lin HD, Chen YR, Lin SM (2012) Strict consistency between genetic and topographic landscapes of the brown tree frog (Buergeria robusta) in Taiwan. Mol Phylogenet and Evol 62, 251-262.
    Li JW, Yeung CKL, Tsai PW et al. (2010) Rejecting strictly allopatric speciation on a continental island: prolonged postdivergence gene flow between Taiwan (Leucodioptron taewanus, Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis. Mol Ecol 19, 494-507.
    Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.
    Lin SM, Lue KY (2003) Phylogeny and phylogeographic studies of Takydromus in Taiwan and adjacent regions (Squamata: Lacertidae) PhD Dissertatio, National Taiwan Normal University.
    Lin SM, Lue KY (2008) Two new cryptic species of Takydromus (Squamata: Lacertidae) from Taiwan. Herpetologica 64, 379-395.
    Llopart A, Lachaise D, Coyne JA (2005) Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea. Genetics 171, 197-210.
    Lue KY, Tu MC, Hsian KS (1999) A field guide to amphibians and reptiles of Taiwan SWAN Press, Taipei, Taiwan.
    Massot M, Huey RB, Tsuji J, van Berkum FH (2003) Genetic, prenatal, and postnatal correlates of dispersal in hatchling fence lizards (Sceloporus occidentalis). Behav Ecol 14, 650-655.
    Mats O (1992) Contest success in relation to size and residency in male sand lizards, Lacerta agilis. Anim Behav 44, Part 2, 386-388.
    Mayr E (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia University Press, New York.
    Mayr E (1963) Animal Species and Evolution. Havard University Press, Cambridge, MA.
    Mayr E (1989) Toward a New Philosophy of Biology: Observations of an Evolutionist Harvard University Press.
    Mayr E (2001) What Evolution Is. Basic Books, New York.
    Nadachowska K, Babik W (2009) Divergence in the face of gene flow: the case of two newts (amphibia: salamandridae). Mol Biol Evol 26, 829-841.
    Nei M (1987) Molecular Evolutionary Genetics Columbia Univ, New York.
    Nei M, Takahata N (1993) Effective population size, genetic diversity, and coalescence time in subdivided populations. J Mol Evol 37, 240-244.
    Niemiller ML, Fitzpatrick BM, Miller BT (2008) Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Mol Ecol 17, 2258-2275.
    Nosil P (2008) Speciation with gene flow could be common. Mol Ecol 17, 2103-2106.
    Olsson M, Gullberg A, Tegelström H (1996) Malformed offspring, sibling matings, and selection against inbreeding in the sand lizard (Lacerta agilis). J Evol Biol 9, 229-242.
    Oshida T, Lee JK, Lin LK, Chen YJ (2006) Phylogeography of Pallas’s squirrel in Taiwan: geographical isolation in an arboreal small mammal. J Mammal 87, 247–254.
    Pavlidis P, Laurent S, Stephan W (2011) msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis. Mol Ecol Resour 10, 723-727.
    Pinho C, Hey J (2010) Divergence with gene flow: models and data. Annu Rev Ecol, Evol Syst 41, 215-230.
    Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25, 1253-1256.
    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multi-locus genotype data. Genetics 155, 945-959.
    Rocha S, Harris DJ, Posada D (2011) Cryptic diversity within the endemic prehensile-tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographical structure and isolation at the multi-locus level. Biol Linn Soc 104, 177-191.
    Runemark A, Hansson B, Pafilis P, Valakos E, Svensson E (2010) Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence? BMC Evol Biology 10, 269.
    Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264-279.
    Slotte T, Huang H, Lascoux M, Ceplitis A (2008) Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). Mol Biol Evol 25, 1472-1481.
    Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 76, 449-462.
    Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 68, 978-989.
    Strasburg JL, Rieseberg LH (2010) How robust are "isolation with migration" analyses to violations of the im model? A simulation study. Mol Biol Evol 27, 297-310.
    Strasburg JL, Rieseberg LH (2011) Interpreting the estimated timing of migration events between hybridizing species. Mol Ecol 20, 2353-2366.
    Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
    Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW (2008) Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles. Mol Phylogenet and Evol 47, 129-142.
    Turner TL, Hahn MW (2007) Locus- and population-specific selection and differentiation between incipient species of Anopheles gambiae. Mol Biol Evol 24, 2132-2138.
    Turner TL, Hahn MW, Nuzhdin SV (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biol 3, e285.
    Wang JP, Lin HD, Huang S, Pan CH, Chen XL, Chiang TY (2004) Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Mol Phylogenet Evol 31, 1143– 1156.
    Waples RS (2010) Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Mol Ecol Resour 10, 785-796.
    Waples RS, Yokota M (2007) Temporal estimates of effective population size in species with overlapping generations. Genetics 175, 219-233.
    Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7, 256-276.
    Wegmann D, Excoffier L (2010) Bayesian inference of the demographic history of chimpanzees. Mol Biol Evol 27, 1425-1435.
    Wegmann D, Leuenberger C, Excoffier L (2009) Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 182, 1207-1218.
    Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 11, 1-7.
    Woerner AE, Cox MP, Hammer MF (2007) Recombination-filtered genomic data sets by information maximization. Bioinformatics 23, 1851-1853.
    Won YJ, Hey J (2005) Divergence population genetics of chimpanzees. Mol Biol Evol 22, 297-307.
    Won YJ, Sivasundar A, Wang Y, Hey J (2005) On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence. Proc Natl Acad Sci 102, 6581-6586.
    Wright S (1943) Isolation by distance. Genetics 28, 114-138.
    Wu CI (2001) The genic view of the process of speciation. J Evo Biol 14, 851-865.
    Yang Z (2010) A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol Evol 2, 200-211.

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