長久以來，鳥類的種化被認為是由族群在空間上的隔離所啟動，空間隔離所導致的族群間基因交流中斷及族群量的縮減，會進一步促使各分隔族群內的遺傳漂變，而造成族群分化，最終以致種化。然而，對於陸生脊椎動物中運動能力最強的鳥類而言，地理屏障對其族群間基因交流所形成的障礙，是不近情理的假設，卻少被質疑。在我論文的第二章，我以核基因片段為材料，說明分布於澳洲的皇家琵鷺（Platalea regia)之物種形成，無法由前提是起始於少數奠基者及物種形成過程中完全缺乏與其姊妹種黑面琵鷺（P. minor)間進行“分化後基因交流“（post-divergence gene flow）的奠基者種化（founder speciation）模式加以解釋；相對的，我的遺傳證據較支持包含“分化後基因交流“的種化模式； 我的結果也顯示 ，奠基者種化所需的瓶頸事件(bottleneck)即便存在，所歷時間應極為短暫，或者所謂奠基者的數目會遠大於一般所設想。我同時也發現皇家琵鷺與黑面琵鷺的祖先在兩者開始分化之後，彼此間仍有相當程度的基因交流，而這樣交流所歷時間，更佔兩者分化至今一半以上的時間。在第三章中，以核基因序列所推估的遺傳有效族群量（effective population size）及普查族群量（census population size）之比例，作為評估物種內族群結構化（population structuring）的指標，我的結果顯示了部份琵鷺的祖先物種可能是由數量大且不具明顯結構的族群所構成。我也發現所有琵鷺的共祖及琵鷺與紅鹮（Eudocimus ruber）的共祖之有效族群量都出奇的大，這現象可能是由於這兩者的族群結構是更近似於Wright所提出的島嶼模式，也就是物種由幾個分化但彼此間持續進行基因交流的族群所構成。這些結果都指出選汰壓力在物種的分化上，較阻斷基因交流（地理隔離）扮演更重要的角色。最後在第四章中，我應用近似貝氏計算（approximate Bayesian calculation)分析黑面琵鷺的微衛星多態性數據，發現這個瀕危物種的有效族群量縮減，受到最近一次冰期啟動之影響，遠勝於近期人為干擾的效應；而根據核基因座及微衛星多態性所估出的現時黑面琵鷺有效族群量並不大，因此持續以人為努力減少環境波動對其族群數量的影響，應為維持黑面琵鷺長期存續之必要措施。在最末章中，我針對以上的結果作出綜合討論，並提出未來研究的展望。

Avian speciation has long been attributed to spatial isolation that prohibits gene flow and that is accompanied by population size reduction, which enhances genetic drift. However, given that birds are the most mobile of terrestrial vertebrates, that geographic barrier should pose such impediment to gene flow is rather counterintuitive and yet seldom questioned. In Chapter 2 of my dissertation, I show that founder effect model, which assumes a small founder population size and the absence of post-divergence gene flow, failed to apply to the speciation of the royal spoonbill (Platalea regia) from the black-faced spoonbill (P. minor); rather, models that considered post-divergence gene flow was much more probable for these species, and speciational bottleneck, if any, would have been very brief or the founder size would have needed to be much larger. Furthermore, post-divergence gene flow was estimated to be quite substantial and span well over half of the divergence history. In Chapter 3, using the ratio of effective to census population size as a proxy for the level of population structuring, I showed that ancestral populations of the most recent common ancestors of some spoonbill species (Platalea spp.) may be large and panmictic. Furthermore, I found that population size of the common ancestor of all spoonbills and the common ancestor of the spoonbills and the scarlet ibis (Eudocimus ruber) was surprisingly large, and reasoned that this may be due to population structuring which can be depicted by a Wrightian island model- that is, one in which populations exchange migrants persistently but remain genetically differentiated. Taken together, these results suggest a more important role for selection in promoting divergence despite gene flow. Finally, applying the ABC method to mirosatellite genotype data of the endangered black-faced spoonbill, I found that rather than anthropogenic disturbances, climatic changes at the onset of the last glacial period have had the greatest impact in reducing the species' effective population size. Moreover, current effective population size of black-faced spoonbill was estimated to be small, and calls for continuous human efforts to reduce environmental stochasticity in the hope of bettering the species' chances of persisting in the long run.

Chapter 1
Bateson W (1909). Heredity and variation in modern lights. In Darwin and Modern Science (ed. Seward AC). Cambridge University Press, Cambridge.
Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian Computation in Population Genetics. Genetics, 162,: 2025-2035.
Crow JF (1990) R. A. Fisher, a centennial view. Genetics, 124, 207-211.
Crow JF (1992) Centennial: J. B. S. Haldane, 1892-1964. Genetics, 130, 1-6.
Darwin C (1859). The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London.
Dobzhansky T (1937). Genetic and the Origin of Species. Columbia University Press, New York.
Grant PR, Grant BR (1997) Genetics and the origin of bird species. PNAS, 94, 7768-7775.
Grant BR, Grant PR (2008) Fission and fusion of Darwin's finches populations. Philosophical Transactions of the Royal Society of London B, 363, 2821-2829.
Hey J (1994). Bridging phylogenetics and population genetics with gene tree models. In Molecular Ecology and Evolution: Approaches and Applications (eds. Schierwater B, Wagner GP, DeSalle R) Birkhâuser, Basel, Verlag, Switzerland.
Hey J (2005) On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology, 3(6): e193.
Huxley J (1942) Evolution, the Modern Synthesis. Allen & Unwin, London.
Kingman JFC (1982) The coalescent. Stochastic Process and their Applications, 13, 235-248.
Kliman RM, Andolfatto P, Coyne JA et al. (2000). The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics, 156, 1913-1931.
Kuhner, M. K. (2008). "Coalescent genealogy samplers: windows into population history." Trends in Ecology & Evolution, 24: 86-93.
Lynch M (1991) Methods for the analysis of comparative data in evolutionary biology. Evolution, 45, 1065-1080.
Losos JB, Glor RE (2003) Phylogenetic comparative methods and the geography of speciation. Trends in Ecology and Evolution, 18, 220-227.
Lovette IJ (2005) Glacial cycles and the tempo of avian speciation. Trends in Ecology and Evolution, 20, 57-59.
Machado CA, Kliman RM, Markert J et al. (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution, 19, 472-488.
Mayr E (1942) Systematics and the Origin of Species. Columbia University Press, New York.
Mayr E (1954) Changes in genetic environment and evolution. In Evolution as a process (eds. Huxley JS, Hardy AC, Ford EB) Allen & Unwin, London.
Mayr E (1963) Animal species and evolution. Harvard University Press, Cambridge.
Moya A, Galiana A, Ayala FJ (1995) Founder-effect speciation theory: failure of experimental corroboration. PNAS, 92: 3983-3986.
Muller HJ (1942) Isolating mechanisms, evolution, and temperature. Biology Symposium, 6, 71-125.
Orr HA (1996) Dobzhansky, Bateson, and the genetics of speciation. Genetics, 144, 1331-1335.
Powell JR (1987) “In the Air"- Theodosius Dobzhansky's Genetics and the Origin of Species. Genetics, 117, 363-366.
Price T (2008) Speciation in Birds. Roberts & Company, Greenwood Village, CO.
Takahata N (1993) Mechanisms of molecular evolution: introduction to molecular paleopopulation biology. Sinauer Associates, Sunderland, MA.
Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics, 145, 847-855.
Weir J, Schluter D (2004) Ice sheets promote speciation in boreal birds. Proceedings of Biological Sciences, 22, 1881-1887.
Won YJ, Hey J (2005) Divergence population genetics of chimpanzees. Molecular Biology and Evolution, 22, 297-307.
Won YJ, Sivasundar A, Wong Y et al. (2005) On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence. Proceedings of the National Acadmy of Sciences, 102(suppl. 1), 6581-6586.
Wright S (1968) Evoution and the Genetics of Populations, Vol. 1: Genetics and Biometric Foundations. University of Chicago Press, Chicago.
Wright S (1969) Evolution and the Genetis of Populations, Vol. 2: The Theory of Gene Frequencies. University of Chicago Press, Chicago.
Wright S (1977) Evolution and the Genetics of Populations, Vol. 3: Experimental Results and Evolutionary Deductions. University of Chicago Press, Chicago.
Wright S (1978) Evolution and the Genetics of Populations, Vol. 4: Variability Within and Among Populations. University of Chicago Press, Chicago.

Chapter 2
Allen RP (1942) The Roseate Spoonbill. Research Report No. 2. National Audubon Society, New York.
Anisimova M, Gascuel O (2006) Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Systematic Biology, 55, 539-552.
Backström N, Brandström M, Gustafsson L, et al. (2006) Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics, 174, 337-386.
Barr KR, Lindsay DL, Athrey G, et al. (2008) Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery. Molecular Ecology, 17, 3628-3639.
Barraclough TG, Vogler AP (2000) Detecting the geographical pattern of speciation from species-level phylogenies. The American Naturalist, 155, 419-434.
Barton NH (1996) Natual selection and random genetic drift as causes of evolution on islands. Philosophical Transactions of the Royal Society of London B, 351, 785-795.
Barton NH, Charlesworth B (1984) Genetic revolutions, founder effects, and speciation. Annual Reviews of Ecology and Systematics, 15, 133-164.
Bearhop S, Fiedler W, Furness RW, et al. (2005) Assortative mating as a mechanism for rapid evolution of a migratory divide. Science, 310, 502-504.
Beaumont MA (2007) Simulations, genetics and Human Prehistory- A focus on Islands University of Cambridge, Cambridge, UK.
Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 2025-2035.
Burg T (2007) Phylogeography of chestnut-backed chickadees in western North America. In Ecology and Behavior of Chickadees and Titmice: An Integrated Approach (ed. Otter KA). Oxford University Press, Oxford.
Carson HL (1968) The population flush and its genetic consequences. In Population Biology and Evolution (ed. Lewinton RC). Syracuse University Press, Syracuse, NY.
Carson HL, Templeton A (1984) Genetic revolutions in relation to speciation phenomena: The founding of new populations. Annual Reviews of Ecology and Systematics, 15, 97-131.
Charlesworth B, Rouhani S (1988) The probability of peak shifts in a founder population. II. An additive polygenic trait. Evolution, 42, 1129-1145.
Charlesworth B, Smith DB (1982) A computer model of founder effect speciation. Genetics Research Cambridge, 39, 227-236.
Chen F-C, Li W-H (2001) Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics, 68, 444-456.
Chesser RT, Zink RM (1994) Modes of speciation in birds: a test of Lynch's method. Evolution, 48, 490-497.
Clegg SM, Degnan SM, Kikkawa J, et al. (2002) Genetic consequences of sequential founder events by an island-colonizing bird. Proceedings of the National Acadmy of Sciences, 99, 8127-8132.
Coyne JA, Orr HA (2004) Speciation Sinauer Associates, Sunderland.
Endler JA (1977) Geographic Variation, Speciation, and Clines Princeton University Press, Princeton.
Felsenstein J (2004) Inferring Phylogenies Sinauer Associates, Sunderland, MA.
Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genetics Research (Cambridge), 66, 95-107.
Friesen VL, Anderson DJ (1997) Phylogeny and evolution of the Sulidae (Aves: Pelecaniformes): a test of alternative modes of speciation. Molecular Phylogenetics and Evolution, 7, 252-260.
Gavrilets S, Hastings A (1996) Founder-effect speciation: A theoretical reassessment. American Naturalist, 147, 466-491.
Gemmell NJ, Akiyama S (1996) An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics, 12, 338-339.
Grant PR, Grant BR, Petren K (2001) A population founded by a single pair of individuals: establishment, expansion, and evolution. Genetica, 112-113, 359-382.
Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704.
Hamilton G, Stoneking M, Excoffier L (2005) Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proceedings of the National Acadmy of Sciences, 102, 7476-7480.
Hancock JA, Kushlan JA, Kahl MP (1992) Storks, ibises and spoonbills of the world Academic Press, London.
Hare MP, Cipriano F, Palumbi SR (2002) Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution, 56, 804-816.
Hendry AP, Nosil P, Rieseberg LH (2007) The speed of ecological speciation. Functional Ecology, 21, 455-464.
Hey J (2005) On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology, 3, e193.
Hornfeldt B, Hipkiss T, Fridolfsson A-K, Eklund U, Ellegren H (2000) Sex ratio and fledging success of supplementary-fed Tengmalm's owl broods. Molecular Ecology, 9, 187-192.
Hudson R (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337-338.
Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
Huelsenbeck JP, Rannala B (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology, 53, 904-913.
Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
Kaeuffer R, Coltman DW, Chapuis J-L, Pontier D, R(e)ale D (2007) Unexpected heterozygosity in an island mouflon population founded by a single pair of individuals. Proceedings of the Royal Society B: Biolgoical Sciences, 274, 527-533.
Kalinowski S, Taper M, Marshall T (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 1099-1100.
Kaneshiro KY (1980) Sexual isolation, speciation and the direction of evolution. Evolution, 34, 437-444.
Knowles LL, Futuyma DJ, Eanes WF, Rannala B (1999) Insight into speciation from historical demography in the phytophagous beetle genus Orphraella. Evolution, 53, 1846-1856.
Kondo B, Peters JL, Rosensteel BB, Omland KE (2008) Coalescent analyses of multiple loci support a new route to speciation in birds. Evolution, 62, 1182-1191.
Losos JB, Glor RE (2003) Phylogenetic comparative methods and the geography of speciation. Trends in Ecology and Evolution, 18, 220-227.
Machado CA, Kliman RM, Markert JA, Hey J (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution, 19, 472-488.
Madison DR, Madison PW (2000) MacClade 4: analysis of phylogeny and character evolution Sinauer Associates, Sunderland.
Mattern MY, McLennan DA (2000) Phylogeny and speciation of felids. Cladistics, 16, 232-253.
Mayr E (1942) Systematics and the Origin of Species Columbia University Press, New York.
Mayr E (1954) Changes in genetic environment and evolution. In: Evolution as a process (eds. Huxley JS, Hardy AC, Ford EB), pp. 156-180. Allen & Unwin, London.
McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics, 160, 1231-1241.
Moya A, Galiana A, Ayala FJ (1995) Founder-effect speciation theory: failure of experimental corroboration. PNAS, 92, 3983-3986.
Nicholls JA, Austin JJ, Moritz C, Goldizen AW (2007) Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus. Evolution, 60, 1279-1290.
Niemiller ML, Fitzpatrick BM, Miller BT (2008) Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Molecular Ecology, 17, 2258-2275.
Osada N, Wu C-I (2005) Inferring the mode of speciation from genomic data. Genetics, 169, 259-264.
Paulay G (2002) Diversification in the tropical Pacific: Comparisons between marine and terrestrial systems and the importance of founder speciation. Integrative and Comparative Biology, 42, 922-934.
Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Systematic Biology, 53, 793-808.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
Pulido F (2007) The genetics and evolution of avian migration. BioScience, 57, 165-174.
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
Ross-Ibarra J, Wright S, Foxe J, Kawabe A, DeRose-Wilson L (2008) Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE, 3, e2411-.
Rouhani S, Barton NH (1987) The probability of peak shifts in a founder population. Journal of Theoretical Biology, 126, 51-62.
Rozas J, Sánchez-DelBarrio JC, Messegyer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497.
Rundle HD, Nosil P (2005) Ecological speciation. Ecology Letters, 8, 336-352.
Slatkin M (1996) In defense of founder-flush theories of speciation. American Naturalist, 147, 493-505.
Stadler T, Arunyawat U, Stephan W (2008) Population genetics of speciation in two closely related wild tomatoes (Solanum Section Lycopersicon). Genetics, 178, 339-350.
Stemmer WPC (1994) DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proceedings of the National Acadmy of Sciences, 91, 10747-10751.
Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics, 76, 449-462.
Stephens M, Smith N, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526.
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetic Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
Templeton A (1980) The theory of speciation via the founder principle. Genetics, 94, 1011-1038.
Turner TL, Hahn MW, Nuzhdin SV (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3, e285.
Vestjens W (1975) Feeding behaviour of spoonbills at Lake Cowal, NSW. Emu, 75, 132-136.
Vincek V, O'Huigin C, Satta Y, et al. (1997) How large was the founding population of Darwin's finches? Proceedings of the Royal Society B: Biolgoical Sciences, 264, 111-118.
Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics, 145, 847-855.
Wakeley J (1999) Nonequilibrium migration in human history. Genetics, 153, 1863-1871.
Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evolution, 54, 1092-1101.
Walsh HE, Jones IL, Friesen VL (2005) A test of founder effect speciation using multiple loci in the auklets (Aethia spp.). Genetics, 171, 1885-1894.
Weir JW, Schluter D (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321-2328.
Won Y-J, Hey J (2005) Divergence population genetics of chimpanzees. Molecular Biology and Evolution, 22, 297-307.
Won Y-J, Sivasundar A, Wang Y, Hey J (2005) On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence. Proceedings of the National Acadmy of Sciences, 102, 6581-6586.
Wu C-I (2001) The genic view of the process of speciation. Journal of Evolutionary Biology, 14, 851-865.
Yeung CK-L, Yao C-T, Hsu Y-C, Wang J-P, Li S-H (2006) Assessment of the historical population size of an endangered bird, the black-faced spoonbill (Platalea minor) by analysis of mitochondrial DNA diversity. Animal Conservation, 9, 1-10.
Zhou R, Zeng K, Wu W, et al. (2007) Population genetics of speciation in nonmodel organisms: I. ancestral polymorphism in mangroves. Molecular Biology and Evolution, 24, 2746-2754.

Chapter 3
Axelsson E, Smith NGC, Sundström H, Berlin S, Ellegren H (2004) Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. Molecular Biology and Evolution, 21, 1538-1547.
Backström N, Karaiskou N, Leder EH, et al. (2008) A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene-order conservation during 100 million years of avian evolution. Genetics, 179, 1479-1495.
Berlin S, Tomaras D, Charlesworth B (2007) Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome. Heredity, 99, 389-396.
Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nature Reviews Genetics, 5, 618-625.
Chen F-C, Li W-H (2001) Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics, 68, 444-456.
Coyne JA, Orr HA (2004) Speciation Sinauer Associates, Sunderland.
Del Hoyo J, Elliot A, Sargatal J eds. (1992) Handbook of the Birds of the World. Vol. 1. Lynx Edicions, Barcelona
Endler JA (1977) Geographic Variation, Speciation, and Clines Princeton University Press, Princeton.
Ewens WJ (1989) The effective population size in the presence ofcatastrophes. In: Mathematical Evolutionary Theory (ed. Feldman MW). Princeton University Press, Princeton, New Jersey.
Fisher RA (1930) The Genetical Theory of Natural Selection Oxford University Press, Oxford, UK.
Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genetics Research (Cambridge), 66, 95-107.
Frankham R, Ballou JD, Birscoe BA (2002). Introduction to Conservation Genetics. Cambridge University Press, Cambridge, UK.
Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693-709.
Gemmell NJ, Akiyama S (1996) An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics, 12, 338-339.
Gilpin M (1991) The genetic effective size of a metapopulation. Biological Journal of the Linnean Society, 42, 165-175.
Hancock JA, Kushlan JA, Kahl MP (1992) Storks, ibises and spoonbills of the world Academic Press, London.
Heath JA (2002) White Ibis (Eudocimus albus) reproductive physiology. PhD dissertation, University of Florida.
Hey J (2005) On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology, 3, e193.
Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Dorophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
Hornfeldt B, Hipkiss T, Fridolfsson A-K, Eklund U, Ellegren H (2000) Sex ratio and fledging success of supplementary-fed Tengmalm's owl broods. Molecular Ecology, 9, 187-192.
Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
Levins R (1970) Extinction. Lecture Notes in Mathematics, 2, 75-107.
Li J-W (2006) Geographic Model of Speciation in a Continental Island: Divergence Genetics of Hwameis (Garrulax canorus and G. taewanus) Master's thesis, National Taiwan Normal University.
Maruyama T, Kimura M (1980) Genetic variation and effective population size when local extinction and recolonization of subpopulations are frequent. Proceedings of the National Acadmy of Sciences, 77, 6710-6714.
Mayr E (1942) Systematics and the Origin of Species Columbia University Press, New York.
Nei M, Takahata N (1993) Effective population size, genetic diversity, and coalescence time in subdivided populations. Journal of Molecular Evolution, 37, 240-244.
Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics, 158, 885-896.
Osada N, Wu C-I (2005) Inferring the mode of speciation from genomic data. Genetics, 169, 259-264.
Pulido F (2007) The genetics and evolution of avian migration. BioScience, 57, 165-174.
Rannala B, Yang Z (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
Rozas J, Sánchez-DelBarrio JC, Messegyer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497.
Segrè D, DeLuna A, Church GM, Kishony R (2004) Modular epistasis in yeast metabolism. Nature Genetics, 37, 77-83.
Sibley CG, Ahlquist JE (1990) Phylogeny and classification of birds, a study in molecular evolution Yale University Press, New Haven (CT).
Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics, 76, 449-462.
Stephens M, Smith N, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
Studds CE, Marra PP (2005) Nonbreeding habitat occupancy and population processes: an upgrade experiment with a migratory bird. Ecology, 86, 2380-2385.
Takahata N, Satta Y (1997) Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences. PNAS, 94, 4811-4815.
Wade MJ, Goodnight CJ (1998) Perspective: The theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments. Evolution, 52, 1537-1553.
Weinreich DM, Chao L (2005) Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution, 59, 1175-1182.
Wetlands International (2002) Waterbird Population Estimates – Third Edition. Wetlands International Global Series No. 12. Wageningen, the Netherlands
Whitlock MC, Barton NH (1997) The effective size of a subdivided population. Genetics, 146, 427-441.
Won Y-J, Sivasundar A, Wang Y, Hey J (2005) On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence. Proceedings of the National Acadmy of Sciences, 102, 6581-6586.
Wright S (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.
Wright S (1943). Isolation by distance. Genetics, 28, 114-138.
Wright S (1978) Evolution and the Genetics of Populations. Vol. 4: Variability Within and Among Populations University of Chicago Press, Chicago.
Yeung CK-L, Yao C-T, Hsu Y-C, Wang J-P, Li S-H (2006) Assessment of the historical population size of an endangered bird, the black-faced spoonbill (Platalea minor) by analysis of mitochondrial DNA diversity. Animal Conservation, 9, 1-10.
Zeng K, Fu Y-X, Shi S, Wu C-I (2006) Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants. Genetics, 174, 1431-1439.
Zhou R, Zeng K, Wu W, et al. (2007) Population genetics of speciation in nonmodel organisms: I. ancestral polymorphism in mangroves. Molecular Biology and Evolution, 24, 2746-2754.

Chapter 4
Anderson EC, Williamson EG, Thompson EA (2000) Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics, 156, 2109-2118.
Anselmetti FS, Ariztegui D, Hodell DA, et al. (2006) Late Quaternary climate-induced lake level variations in Lake Pete´n Itza´, Guatemala, inferred from seismic stratigraphic analysis. Palaeogeography, Palaeoclimatology, Palaeoecology, 230, 52-69.
Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
Beaumont MA (2007) Simulations, genetics and Human Prehistory- A focus on Islands University of Cambridge, Cambridge, UK.
Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian Computation in Population Genetics. Genetics, 162, 2025-2035.
Beck JW, Richards DA, Edwards RL, et al. (2001) Extremely large variations of atmospheric 14C concentration during the last glacial period. Science, 292, 2453-2458.
Berthier P, Beaumont MA, Cornuet J-M, et al. (2002) Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics, 160, 741-751.
Boakes EH, Wang J, Amos W (2006) An investigation of inbreeding depression and purging in captive pedigreed populations. Heredity, 98, 172-182.
Bos JAA, Sjoerd JPB, Janssen CR (2006) Lake-level fluctuations and small-scale vegetation patterns during the Late Glacial in the Netherlands Journal of Paleolimnology, 35, 211-238.
Busch JD, Waser PM, DeWoody A (2007) Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis). Molecular Ecology, 16, 2450-2462.
Cornuet J-M, Santos F, Beaumont MA, et al. (2008) Inferring population history with DIY ABC: a user-friendly approach to Approximate Bayesian Computation. Bioinformatics, 24, 2713-2719.
Del Hoyo J, Elliot A, Sargatal J eds. (1992) Handbook of the Birds of the World. Vol. 1. Lynx Edicions, Barcelona
England PR, Osler GHR, Woodworth LM, et al. (2003) Effects of intense versus diffuse population bottlenecks on microsatellite genetic diversity and evolutionary potential. Conservation Genetics, 4, 595-604.
Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genetics Research (Cambridge), 66, 95-107.
Frankham R, Ballou JD, Birscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press. Cambridge, UK.
Franklin IA (1980) Evolutionary changes in small populations. in Conservation biology: an evolutionary-ecological perspective. Soulé M, Wilcox BA (eds). Sinauer Associates. Sunderland, MA.
Gemmell NJ, Akiyama S (1996) An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics, 12, 338-339.
Goossens B, Chikhi L, Ancrenaz M, et al. (2006) Genetic Signature of Anthropogenic Population Collapse in Orang-utans. PLoS Biology, 4, e25.
Hailer F, Helander B, Folkestad AO, et al. (2006) Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline. Biology Letters, 2, 316-319.
Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genetical Research, 98, 625-640.
IUCN (2001) IUCN Red List Categories and Criteria – Version 3.1, IUCN-SSC. Available at :http://www.redlist.org/info/categories_criteria2001.html
Kalinowski T, Taper L, Marshall C (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 1099-1106.
Kennerley PR (1990) A review of the status and distribution of black-faced spoonbill. In The Hong Kong bird report 1989. Pickens V (ed) Hong Kong Bird Watching Society, Hong Kong.
Lande R (1995) Mutation and Conservation. Convservation Biology, 9, 782-791.
Lippe C, Dumont P, Bernatchez L (2006) High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time. Molecular Ecology, 15, 1769-1780.
Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. American Naturalist, 146, 489-518.
Marshal TC, Slate J, Kruuk LEB et al. (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7, 639-655.
Nei M, Tajima F (1981) Genetic drift and estimation of effective population size. Genetics, 98, 625-640.
Pamilo P, Varvio-Aho S (1980) On the estimation of population size from allele frequency changes. Genetics, 95, 1055-1058.
Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity, 90, 502-503.
Pollak E (1983) A new method for estimating the effective population size from allele frequency changes. Genetics, 104, 531-548.
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
Soulé ME (1980) Thresholds for survival: maintaining fitness and evolutionary potential. in Conservation biology: an evolutionary-ecological perspective. Soulé M, Wilcox BA (eds). Sinauer Associates. Sunderland, MA.
Storz JF, Beaumont M, Alberts SC (2002) Genetic evidence for long-term population decline in a savannah-dwelling primate: Inferences from a hierarchical Bayesian model. Molecular Biology and Evolution, 19, 1981-1990.
Swindle WR, Bouzat JL (2006) Reduced inbreeding depression due to historical inbreeding in Drosophila melanogaster: evidence for purging. Journal of Evolutionary Biology, 19, 1257-1264.
Tajima F, Nei M (1984) Note on genetic drift and estimation of effective population size. Genetics, 106, 569-574.
Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research, 78, 243-257.
Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time Genetics, 163, 429-446.
Waples R (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, 121, 379-391.
Waples R, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753-756.
Wetlands International (2002) Waterbird Population Estimates – Third Edition. Wetlands International Global Series No. 12. Wageningen, the Netherlands
Willi Y, Bushkirk JV, Hoffmann AA (2006) Limits to the adaptive potential of small populations. Annual Review of Ecology and Evolution, 37, 433-458.
Williamson EG, Slatkin M (1999) Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics, 152, 755-761.
Woodworth LM, Montgomery ME, Briscoe DA, et al. (2002) Rapid genetic deterioration in captive populations: causes and conservation implications. Conservation Genetics, 3, 277-288.
Wright S (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.
Wright S (1943) Isolation by distance. Genetics, 28, 114-138.
Yeung CKL, Yao C-T, Hsu Y-C, et al. (2006) Assessment of the historical population size of an endangered bird, the black-faced spoonbill (Platalea minor) by analysis of mitochondrial DNA diversity. Animal Conservation, 9, 1-10.
Yeung CKL, Hsu Y-C, Yao C-T, et al. (2009) Isolation and characterization of 23 microsatellite loci in the black-faced spoonbill ( Platalea minor) and amplification in other Ciconiiformes waterbirds Conservation Genetics 10:1081-1084.

Chapter 5
Becquet C, Przeworski M (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Research, 17, 1505-1519.
Craddock EM (2000) Speciation processes in the adaptive radiation of
Hawaiian plants and animals. In Evolutionary Biology (eds. Hecht
MK, Maclntyre RJ, Clegg MT). Springer, New York.
Grant BR, Grant PR (2008) Fission and fusion of Darwin's finches
populations. Philosophical Transactions of the Royal Society of
London B, 363, 2821-2829.
Huber SK, León LFD, Hendry AP et al. (2007) Reproductive isolation of
sympatric morphs in a population of Darwin's finches. Proceedings
of Biological Sciences, 274, 1709-1714.
Hudson R (2002) Generating samples under a Wright-Fisher neutral
model of genetic variation. Bioinformatics, 18, 337-338.
Lovette IJ (2005) Glacial cycles and the tempo of avian speciation.
Trends in Ecology and Evolution, 20, 57-59.
Price T (2008) Speciation in Birds. Roberts & Company, Greenwood
Village, CO.
Ross-Ibarra JS, Wright SI, Foxe JP et al. (2008) Patterns of
polymorphism and demographic history in natural populations of
Arabidopsis lyrata. PLoS ONE 3(6): e2411.
Slatkin M, Pollack JL (2008) Subdivision i an ancestral species creates
asymmetry in gene trees. Molecular Biology and Evolution, 25, 2241-2246.
Wakeley J, Hey J (1997) Estimating ancestral population parameters.
Genetics, 145, 847-855.