臺灣博碩士論文加值系統

近期人類活動正快速地改變全球地貌及氣候型態，促使生物面臨新的選汰壓力。因此，瞭解生物如何因應快速的環境改變，不但是演化生物學的基本問題，也成為生物多樣性保育的重要議題。本研究以海拔適應做為檢測局域適應遺傳基礎的研究系統，並以近期與亞洲大陸族群分化（約四萬年前）且廣泛分布於台灣不同海拔的粉紅鸚嘴（Sinosuthora webbianus bulomachus）作為實驗物種。我先建立一隻雄性粉紅鸚嘴的基因組草圖，再自東西部高（> 2000公尺）與低（< 100公尺）海拔族群中，選取四十隻個體進行基因組重定序（平均定序深度約六倍），利用基因組掃描的方式找尋高低海拔族群局域適應的證據。我們發現107個可能與海拔適應相關的候選區域（candidate regions），且有79個基因落於這些候選區域中或附近，其中有九個基因與供氧階梯（oxygen cascade）、溫度調控（thermoregulation）及防止UV侵害（UV protection）相關。我們在這107個候選區域中，分別於台灣東西邊找到了199個及187個與海拔適應相關的SNP位點，且這些位點大部分與亞洲大陸族群共有（約91%）；此外，這些位點皆落於非編碼區。這些結果顯示，相對於編碼區改變而導致功能上的變化，調控區的改變對於局域適應可能佔有更重要的地位；而既有變異可能是海拔適應的過程中，供應有利遺傳變異的主要來源。本研究除了提供局域適應背後可能的遺傳機制外，也提供我們推測物種能否克服環境變遷的依據。

Anthropogenic activities are reconfiguring the global landscape and altering climate in an unprecedented rate. Whether organisms could cope with such rapid environmental changes is largely dependent on the nature of genetic basis of local adaptation. Here, I used altitudinal adaptation of vinous-throated parrotbills (Sinosuthora webbianus bulomachus) in Taiwan to investigate the relative role of novel and standing genetic variation in local adaptation. I firstly sequenced a male parrotbill genome (1.06GB) as the reference and re-sequenced other 40 individuals from two pairs of high- (over than 2000 m)/low-altitude (lower than 100 m) populations from both sides of Taiwan (~6X mean coverage), and 40 individuals from Asian mainland (~12X mean coverage). After calling SNP, I found that 60% of SNPs in Taiwan population are shared with the mainland conspecific population. Results of whole genome scan revealed that 107 10 kb genomic regions spanning entire genome that could be responsible to altitudinal adaptation. I found 79 candidate genes were harbored within these or nearby regions. Among these 79 candidate genes, nine were presumably related to oxygen cascade (N = 6), thermoregulation (N = 1), and UV protection (N = 2). In addition, I identified 199 and 187 causal SNPs, which might be corresponding to altitudinal adaption, in the east and west Taiwan population pairs separately. I found that 91% of the causal SNPs for altitudinal adaptation were shared with the mainland population. It implies that standing genetic variation should be the major source to supply advantage alleles in altitudinal adaptation. In addition, I surprisingly found that none of these causal SNPs located within coding regions of the candidate genes. It suggests that modifications of gene regulation, instead of functional changes, are critical to altitudinal adaptation. My results not only illuminate the genetic mechanism of altitudinal adaptation, but also provide a new insight into how organisms could respond to a changing environment.

Abstract i
摘要 iii
Introduction 1
Methods and materials 5
Reference genome 5
Sampling and DNA extraction 5
Genomic library preparation and sequencing 5
Reference de novo assembly 5
Contamination removal 6
Constructing putative chromosome base on the shared synteny 6
Genome annotation 7
Gene structure annotation 7
Gene functional annotation 7
Population re-sequencing 7
Population sampling 7
Whole genome re-sequencing 8
Re-sequencing mapping 8
Variants calling 9
Divergence demography of the vinous-throated parrotbill 9
Genome scan 10
Calculating summary statistics of genetic variations 10
Finding outlier regions and genes 11
Defining causal SNPs within the candidate region 13
Definition of the state of selective sweep in altitudinal adaptation 13
Inferring standing genetic variation and new mutation 14
Genes related to high altitude adaptation 14
Results 17
Reference genome assemble 17
Genome sequencing and assembling 17
Repeat content 17
Contamination removal 18
Putative chromosome base on the shared synteny 18
Genome annotation 18
Genome structure annotation 18
Genome functional annotation 19
Variants calling 19
Divergence demography 20
Genome scan 20
Genomic regions related to altitudinal adaptation 20
Genes related to altitudinal adaptation 21
Higher proportion of candidate regions complete selective sweep in the low altitude populations 23
Most of causal SNPs are standing genetic variation 24
Discussion 25
Evidences of altitudinal adaptation 25
Role of standing genetic variation in altitudinal adaptation 26
Role of regulatory regions in altitudinal adaptation 27
Purifying selection could cause noise signal in high FST regions 29
Literature cited 32
Figures 44
Tables 53
Supplementary figures 59
Supplementary tables 97

Armstrong, B. K., & Kricker, A. (2001). The epidemiology of UV induced skin cancer. Journal of Photochemistry and Photobiology B: Biology, 63(1), 8-18.
Barrett, R.D.H., & Schluter, D. (2008). Adaptation from standing genetic variation. Trends in Ecology & Evolution, 23, 38-44.
Barrier, M., Robichaux, R. H., & Purugganan, M. D. (2001). Accelerated regulatory gene evolution in an adaptive radiation. Proceedings of the National Academy of Sciences, 98(18), 10208-10213.
Barton, N. (1998). Evolutionary biology: The geometry of adaptation. Nature, 395(6704), 751-752.
Bell, M. A. & Foster, S. A. The Evolutionary Biology of the Threespine Stickleback (Oxford Science, New York, 1994).
Blunier, T., Schwander, J., Stauffer, B., Stocker, T., Dällenbach, A., Indermühle, A., ... & Barnola, J. M. (1997). Timing of the Antarctic Cold Reversal and the atmospheric CO2 increase with respect to the Younger Dryas event. Geophysical Research Letters, 24(21), 2683-2686.
Bradshaw, W. E., & Holzapfel, C. M. (2006). Evolutionary response to rapid climate change. Science(Washington), 312(5779), 1477-1478.
Burri, R., Nater, A., Kawakami, T., Mugal, C. F., Olason, P. I., Smeds, L., ... & Hogner, S. (2015). Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome research, 25(11), 1656-1665.
Carroll, S. B. (2008). Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell, 134(1), 25-36.
Ceballos, G., Ehrlich, P. R., Barnosky, A. D., García, A., Pringle, R. M., & Palmer, T. M. (2015). Accelerated modern human–induced species losses: Entering the sixth mass extinction. Science Advances, 1(5), e1400253.
Cheung, E. C., Ludwig, R. L., & Vousden, K. H. (2012). Mitochondrial localization of TIGAR under hypoxia stimulates HK2 and lowers ROS and cell death. Proceedings of the National Academy of Sciences, 109(50), 20491-20496.
Collier, R. J., Hernandez, L. L., & Horseman, N. D. (2012). Serotonin as a homeostatic regulator of lactation. Domestic animal endocrinology, 43(2), 161-170.
Cutter, A. D., & Payseur, B. A. (2013). Genomic signatures of selection at linked sites: unifying the disparity among species. Nature Reviews Genetics, 14(4), 262-274.
Chang, K. C. (1989). The Neolithic Taiwan Strait. Kaogu, (6), 541569.
Charlesworth, B. (2009). Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10(3), 195-205.
Chu, J. H., Lin, R. C., Yeh, C. F., Hsu, Y. C., & Li, S. H. (2012). Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves). BMC genomics, 13 (1), 149.
Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21 (18), 3674-3676.
Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow.Molecular Ecology, 23(13), 3133-3157.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., ... & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27 (15), 2156-2158.
De Robertis, E. M. (2008). Evo-devo: variations on ancestral themes. Cell, 132(2), 185-195.
Diepgen, T. L., & Mahler, V. (2002). The epidemiology of skin cancer. British Journal of Dermatology, 146(s61), 1-6.
Dirzo, R., Young, H. S., Galetti, M., Ceballos, G., Isaac, N. J., & Collen, B. (2014). Defaunation in the Anthropocene. Science, 345(6195), 401-406.
Dutta, B., Yan, R., Lim, S. K., Tam, J. P., & Sze, S. K. (2014). Quantitative profiling of chromatome dynamics reveals a novel role for HP1BP3 in hypoxia-induced oncogenesis. Molecular & Cellular Proteomics, 13(12), 3236-3249.
Ellegren, H. (2010). Evolutionary stasis: the stable chromosomes of birds. Trends in ecology & evolution, 25 (5), 283-291.
Ellegren, H. (2011). Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nature reviews genetics, 12(3), 157-166.
Ellegren, H., Smeds, L., Burri, R., Olason, P. I., Backström, N., Kawakami, T., ... & Wolf, J. B. (2012). The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491(7426), 756-760.
Endler, J. A. (1986). Natural selection in the wild (No. 21). Princeton University Press.
Falasca, M., & Maffucci, T. (2007). Role of class II phosphoinositide 3-kinase in cell signalling. Biochemical Society Transactions, 35(2), 211-214.
Fayngerts, S. A., Wu, J., Oxley, C. L., Liu, X., Vourekas, A., Cathopoulis, T., ... & Lemmon, M. A. (2014). TIPE3 is the transfer protein of lipid second messengers that promote cancer. Cancer cell, 26(4), 465-478.
Flamant, F., Gauthier, K., & Samarut, J. (2007). Thyroid hormones signaling is getting more complex: STORMs are coming. Molecular Endocrinology, 21(2), 321-333.
Fraser, H. B. (2013). Gene expression drives local adaptation in humans. Genome research, 23(7), 1089-1096.
Frisancho, A. R. (2013). Developmental functional adaptation to high altitude: review. American Journal of Human Biology, 25(2), 151-168.
Ganesan, A. K., Ho, H., Bodemann, B., Petersen, S., Aruri, J., Koshy, S., ... & Farmer, P. (2008). Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. PLoS Genet, 4(12).
Gemmell, N. J. & Akiyama, S. (1996). An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics, 12, 338–339.
Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., ... & Jaffe, D. B. (2011). High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences, 108 (4), 1513-1518.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., ... & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology, 29 (7), 644-652.
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26 (9), 1145-1151.
Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., & Siepel, A. (2011). Bayesian inference of ancient human demography from individual genome sequences. Nature genetics, 43(10), 1031-1034.
Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith Jr, R. K., Hannick, L. I., ... & White, O. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic acids research, 31 (19), 5654-5666.
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., ... & Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature protocols, 8 (8), 1494-1512.
Hachisuka M, Udagawa T: Contributions to the ornithology of Formosa part II. Quarterly J Taiwan Museum 1951, 4:1-180.
Hampe, A., & Petit, R. J. (2005). Conserving biodiversity under climate change: the rear edge matters. Ecology letters, 8(5), 461-467.
Hansen, J., Ruedy, R., Sato, M., & Lo, K. (2010). Global surface temperature change. Reviews of Geophysics, 48(4).
Hedrick, P. W. (2001). Conservation genetics: where are we now? Trends in Ecology & Evolution, 16(11), 629-636.
Hedrick, P. W., Ginevan, M. E., & Ewing, E. P. (1976). Genetic polymorphism in heterogeneous environments. Annual Review of Ecology and Systematics, 1-32.
Hermisson, J., Pennings, P.S. (2005). Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169, 2335-2352.
Hewitt, G. M. (2004). Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 359(1442), 183-195.
Hoekstra, H. E., & Coyne, J. A. (2007). The locus of evolution: evo devo and the genetics of adaptation. Evolution, 61(5), 995-1016.
Hoffmann, A. A., & Sgrò, C. M. (2011). Climate change and evolutionary adaptation. Nature, 470(7335), 479-485.
Hsu, Y. C., Shaner, P. J., Chang, C. I., Ke, L., & Kao, S. J. (2014). Trophic niche width increases with bill‐size variation in a generalist passerine: a test of niche variation hypothesis. Journal of animal ecology, 83(2), 450-459.
Hudson, R. R., Slatkin, M., & Maddison, W. P. (1992). Estimation of levels of gene flow from DNA sequence data. Genetics, 132 (2), 583-589.
Innan, H., & Kim, Y. (2004). Pattern of polymorphism after strong artificial selection in a domestication event. Proceedings of the National Academy of Sciences of the United States of America, 101(29), 10667-10672.
Kaplan, N. L., Hudson, R. R., & Langley, C. H. (1989). The" hitchhiking effect" revisited. Genetics, 123(4), 887-899.
Kim, Y., & Stephan, W. (2002). Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics, 160(2), 765-777.
Körner, C. (2007). The use of ‘altitude’in ecological research. Trends in ecology & evolution, 22, 569-574.
Lambeck, K., & Chappell, J. (2001). Sea level change through the last glacial cycle. Science, 292(5517), 679-686.
Lee, J. W., Lee, Y. K., & Hatchwell, B. J. (2010a). Natal dispersal and philopatry in a group-living but noncooperative passerine bird, the vinous-throated parrotbill. Animal Behaviour, 79, 1017-1023.
Lester, S. E., Ruttenberg, B. I., Gaines, S. D., & Kinlan, B. P. (2007). The relationship between dispersal ability and geographic range size. Ecology Letters, 10(8), 745-758.
Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27(21), 2987-2993.
Li, Y., Reynolds, A., Boyko, A. R., Wayne, R. K., Wu, D. D., & Zhang, Y. P. (2013). Artificial selection on brain-expressed genes during the domestication of dog. Molecular biology and evolution, 30(8), 1867-1876.
Lu, W. C., Liew, P. M., & Li, H. C. (2009). Paleoenvironmental study of the Yueh Tan core II in Sun Moon Lake, central Taiwan. West. Pac. Earth Sci., 9, 119-136.
McCracken, K. G., Bulgarella, M., Johnson, K. P., Kuhner, M. K., Trucco, J., Valqui, T. H., ... & Peters, J. L. (2009). Gene flow in the face of countervailing selection: adaptation to high-altitude hypoxia in the βA hemoglobin subunit of yellow-billed pintails in the Andes. Molecular Biology and Evolution, 26, 815-827.
McDonald, J. F., & Ayala, F. J. (1974). Genetic response to environmental heterogeneity. Nature, 250, 572-574.
McDonald, J. F., Chambers, G. K., David, J., & Ayala, F. J. (1977). Adaptive response due to changes in gene regulation: a study with Drosophila. Proceedings of the National Academy of Sciences, 74(10), 4562-4566.
Meisel, R. P., & Connallon, T. (2013). The faster-X effect: integrating theory and data. Trends in Genetics, 29(9), 537-544.
Moritz, C., & Agudo, R. (2013). The future of species under climate change: resilience or decline?. Science, 341(6145), 504-508.
Nillni, E. A., Xie, W., Mulcahy, L., Sanchez, V. C., & Wetsel, W. C. (2002). Deficiencies in pro-thyrotropin-releasing hormone processing and abnormalities in thermoregulation in Cpefat/fat mice. Journal of Biological Chemistry, 277(50), 48587-48595.
Nosil, P. (2012) Ecological Speciation. Oxford University Press, Oxford, UK.
Nosil, P., Crespi, B. J., & Sandoval, C. P. (2002). Host-plant adaptation drives the parallel evolution of reproductive isolation. Nature, 417(6887), 440-443.
Parmesan, C. (2006). Ecological and evolutionary responses to recent climate change. Annual Review of Ecology, Evolution, and Systematics, 637-669.
Parsons, P. A. (1997). Extreme environmental change and evolution. Cambridge University Press.
Petit, R. J., Aguinagalde, I., de Beaulieu, J. L., Bittkau, C., Brewer, S., Cheddadi, R., ... & Mohanty, A. (2003). Glacial refugia: hotspots but not melting pots of genetic diversity. science, 300(5625), 1563-1565.
Pfeifer, B., Wittelsbürger, U., Ramos-Onsins, S. E., & Lercher, M. J. (2014). PopGenome: an efficient Swiss army knife for population genomic analyses in R. Molecular biology and evolution, msu136.
Pounds, J. A., Fogden, M. P., & Campbell, J. H. (1999). Biological response to climate change on a tropical mountain. Nature, 398(6728), 611-615.
Prud'homme, B., Gompel, N., & Carroll, S. B. (2007). Emerging principles of regulatory evolution. Proceedings of the National Academy of Sciences, 104(suppl 1), 8605-8612.
Radwan, J., & Babik, W. (2012). The genomics of adaptation. Proceedings of the Royal Society of London B: Biological Sciences, 279(1749), 5024-5028.
Robson C: Family Paradoxornithidae (Parrotbills). In Handbook of the birds of the world. Edited by Hoyo J, Elliott A, Christie DA. Barcelona: Lynx Edicions; 2007.
Roux-Buisson, N., Cacheux, M., Fourest-Lieuvin, A., Fauconnier, J., Brocard, J., Denjoy, I., ... & Le Marec, H. (2012). Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human. Human molecular genetics, 21(12), 2759-2767.
Rosenzweig, C., Karoly, D., Vicarelli, M., Neofotis, P., Wu, Q., Casassa, G., ... & Tryjanowski, P. (2008). Attributing physical and biological impacts to anthropogenic climate change. Nature, 453(7193), 353-357.
Rundle, H. D., Nagel, L., Boughman, J. W., & Schluter, D. (2000). Natural selection and parallel speciation in sympatric sticklebacks. Science, 287(5451), 306-308.
Scott, G. R., Schulte, P. M., Egginton, S., Scott, A. L., Richards, J. G., & Milsom, W. K. (2011). Molecular evolution of cytochrome c oxidase underlies high-altitude adaptation in the bar-headed goose. Molecular biology and evolution, 28, 351-363.
Severinghaus, L. L. (1992). Demographic Patterns of the Vinous-Throated Parrotbill. In Wildlife 2001: Populations (pp. 489-501). Springer Netherlands.
Sheridan, J. A., & Bickford, D. (2011). Shrinking body size as an ecological response to climate change. Nature climate change, 1(8), 401-406.
Smith, J. M., & Haigh, J. (1974). The hitch-hiking effect of a favourable gene. Genetical research, 23(01), 23-35.
Stanke, M., & Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19(suppl 2), ii215-ii225.
Storz, J. F., Runck, A. M., Moriyama, H., Weber, R. E., & Fago, A. (2010). Genetic differences in hemoglobin function between highland and lowland deer mice. The Journal of experimental biology, 213, 2565-2574.
Uchikawa, M., Takemoto, T., Kamachi, Y., & Kondoh, H. (2004). Efficient identification of regulatory sequences in the chicken genome by a powerful combination of embryo electroporation and genome comparison. Mechanisms of development, 121(9), 1145-1158.
Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27, 1153-1167.
Walther, G. R., Post, E., Convey, P., Menzel, A., Parmesan, C., Beebee, T. J., ... & Bairlein, F. (2002). Ecological responses to recent climate change. Nature, 416(6879), 389-395.
Woodward, F. I. (1987). Climate and plant distribution. Cambridge University Press.
Wray, G. A. (2007). The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics, 8(3), 206-216.
Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience,3(1), 26.