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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 王弘毅 | zh_TW |
| dc.contributor.advisor | Hurng-Yi Wang | en |
| dc.contributor.author | 彭翊倫 | zh_TW |
| dc.contributor.author | Yi-Lun Peng | en |
| dc.date.accessioned | 2025-02-13T16:11:48Z | - |
| dc.date.available | 2025-02-14 | - |
| dc.date.copyright | 2025-02-13 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-02-07 | - |
| dc.identifier.citation | 王玉婷 (2012)。島嶼中的島嶼: 從粒線體DNA 探討台灣不同高山地區台灣高山田鼠 (Microtus kikuchii) 的遺傳結構。﹝碩士論文。東海大學﹞台灣博碩士論文知識加值系統。 https://hdl.handle.net/11296/32mvww。
王敏男 (1989)。台灣山羌之生物學研究--分布現況及性別與年齡的辨別。﹝碩士論文。國立台灣師範大學﹞台灣博碩士論文知識加值系統。 https://hdl.handle.net/11296/5eg9ay。 王穎, 李壽先, 姚秋如, & 王佳琪。 (2004) 。台灣地區台灣山羌之保育遺傳分析研究（四）。台灣農業部林業及自然保育署，。 吳志仁 (1990)。動物園台灣山羌行為的研究。﹝碩士論文。國立台灣師範大學﹞台灣博碩士論文知識加值系統。 https://hdl.handle.net/11296/uqx8cd。 陳光祖。 (2000)。 試論台灣各時代的哺乳動物群及其相關問題——台灣地區動物考古學研究的基礎資料之一(下篇)。中央研究院歷史語言研究所集刊(71本2分), 367-457。 陳怡君 (2001)。瓦拉米地區台灣山羌之活動習性。﹝博士論文。國立台灣師範大學﹞台灣博碩士論文知識加值系統。 https://hdl.handle.net/11296/3h3aud。 黃紀瑜 (2018)。台灣山羌的分布及行為的海拔差異。﹝碩士論文。國立中山大學﹞台灣博碩士論文知識加值系統。 https://hdl.handle.net/11296/4pf2ub。 Aguirre, N. C., Filippi, C. V., Zaina, G., Rivas, J. G., Acuña, C. V., Villalba, P. V., García, M. N., González, S., Rivarola, M., & Martínez, M. C. (2019). Optimizing ddRADseq in non-model species: A case study in Eucalyptus dunnii Maiden. Agronomy, 9(9), 484. Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 19(9), 1655-1664. https://doi.org/10.1101/gr.094052.109 Avallone, A., Bartie, K. L., Selly, S. C., Taslima, K., Campos Mendoza, A., & Bekaert, M. (2020). Local ancestry inference provides insight into Tilapia breeding programmes. Sci Rep, 10(1), 18613. https://doi.org/10.1038/s41598-020-75744-9 Avise, J. C. (2012). Molecular markers, natural history and evolution. Springer Science & Business Media. Ayad, L. A., & Pissis, S. P. (2017). MARS: improving multiple circular sequence alignment using refined sequences. BMC Genomics, 18(1), 86. https://doi.org/10.1186/s12864-016-3477-5 Balmori-de la Puente, A., Ventura, J., Miñarro, M., Somoano, A., Hey, J., & Castresana, J. (2022). Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola. Scientific reports, 12(1), 4065. Broennimann O, D. C. V., Guisan A. (2023). ecospat: Spatial Ecology Miscellaneous Methods. In https://CRAN.R-project.org/package=ecospat Brown, J. L., Weber, J. J., Alvarado‐Serrano, D. F., Hickerson, M. J., Franks, S. J., & Carnaval, A. C. (2016). Predicting the genetic consequences of future climate change: The power of coupling spatial demography, the coalescent, and historical landscape changes. American Journal of Botany, 103(1), 153-163. Chapman, N. G. (2022). Reeves’ Muntjac Muntiacus reevesi (Ogilby, 1839). In Terrestrial Cetartiodactyla (pp. 29-50). Springer. Chen, C.-S., & Chen, Y.-L. (2003). The rainfall characteristics of Taiwan. Monthly Weather Review, 131(7), 1323-1341. Chen, G., Sun, Z., Shi, W., Wang, H., Shi, G., Hu, Y., Fan, H., Wu, Q., & Zhang, B. (2024). Climatic fluctuations, geographic features, and evolutionary forces: Shaping high genomic diversity and local adaptation in Muntiacus reevesi. Diversity and Distributions, 30(9), e13904. Chen, Y.-Y., Huang, W., Wang, W.-H., Juang, J.-Y., Hong, J.-S., Kato, T., & Luyssaert, S. (2019). Reconstructing Taiwan’s land cover changes between 1904 and 2015 from historical maps and satellite images. Scientific reports, 9(1), 3643. Combe, F. J., Jaster, L., Ricketts, A., Haukos, D., & Hope, A. G. (2022). Population genomics of free‐ranging Great Plains white‐tailed and mule deer reflects a long history of interspecific hybridization. Evolutionary Applications, 15(1), 111-131. Cortellari, M., Barbato, M., Talenti, A., Bionda, A., Carta, A., Ciampolini, R., Ciani, E., Crisà, A., Frattini, S., & Lasagna, E. (2021). The climatic and genetic heritage of Italian goat breeds with genomic SNP data. Scientific reports, 11(1), 10986. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. https://doi.org/10.1093/bioinformatics/btr330 Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. Gigascience, 10(2). https://doi.org/10.1093/gigascience/giab008 de Jong, M. J., Lovatt, F., & Hoelzel, A. R. (2021). Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events. Molecular Ecology, 30(7), 1642-1658. Dierckxsens, N., Mardulyn, P., & Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res, 45(4), e18. https://doi.org/10.1093/nar/gkw955 Dinnage, D. W. a. R. (2024). ENMTools: Analysis of Niche Evolution using Niche and Distribution Models. In https://CRAN.R-project.org/package=ENMTools Doublet, M., Degalez, F., Lagarrigue, S., Lagoutte, L., Gueret, E., Allais, S., & Lecerf, F. (2024). Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers. PloS one, 19(7), e0298565. Dray, S., & Dufour, A.-B. (2007). The ade4 package: implementing the duality diagram for ecologists. Journal of statistical software, 22, 1-20. Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC evolutionary biology, 7, 1-8. Dumont, B. L., & Payseur, B. A. (2008). Evolution of the genomic rate of recombination in mammals. Evolution, 62(2), 276-294. https://doi.org/10.1111/j.1558-5646.2007.00278.x Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797. Ehbrecht, M., Schall, P., Ammer, C., Fischer, M., & Seidel, D. (2019). Effects of structural heterogeneity on the diurnal temperature range in temperate forest ecosystems. Forest Ecology and Management, 432, 860-867. Ellegren, H., & Galtier, N. (2016). Determinants of genetic diversity. Nat Rev Genet, 17(7), 422-433. https://doi.org/10.1038/nrg.2016.58 Excoffier, L., Marchi, N., Marques, D. A., Matthey-Doret, R., Gouy, A., & Sousa, V. C. (2021). fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics, 37(24), 4882-4885. https://doi.org/10.1093/bioinformatics/btab468 Felton, A. M., Wam, H. K., Borowski, Z., Granhus, A., Juvany, L., Matala, J., Melin, M., Wallgren, M., & Mårell, A. (2024). Climate change and deer in boreal and temperate regions: From physiology to population dynamics and species distributions. Global Change Biology, 30(9), e17505. Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. International journal of climatology, 37(12), 4302-4315. Fitzpatrick, M. C., & Keller, S. R. (2015). Ecological genomics meets community‐level modelling of biodiversity: Mapping the genomic landscape of current and future environmental adaptation. Ecology letters, 18(1), 1-16. Flantua, S. G., Payne, D., Borregaard, M. K., Beierkuhnlein, C., Steinbauer, M. J., Dullinger, S., Essl, F., Irl, S. D., Kienle, D., & Kreft, H. (2020). Snapshot isolation and isolation history challenge the analogy between mountains and islands used to understand endemism. Global Ecology and Biogeography, 29(10), 1651-1673. GBIF Occurrence. (2024). https://doi.org/10.15468/dl.demzn82024-10-15 Goudarzi, F., Hemami, M.-R., Rancilhac, L., Malekian, M., Fakheran, S., Elmer, K. R., & Steinfartz, S. (2019). Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser’s spotted newt (Neurergus kaiseri). Scientific reports, 9(1), 6239. Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol Ecol Resour, 18(3), 691-699. https://doi.org/10.1111/1755-0998.12745 Hallmark, B., Karafet, T. M., Hsieh, P., Osipova, L. P., Watkins, J. C., & Hammer, M. F. (2019). Genomic evidence of local adaptation to climate and diet in indigenous Siberians. Molecular biology and evolution, 36(2), 315-327. Harrison, P. W., Amode, M. R., Austine-Orimoloye, O., Azov, A. G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., & Bhai, J. (2024). Ensembl 2024. Nucleic acids research, 52(D1), D891-D899. Hijmans, R. J. (2022). geosphere: Spherical Trigonometry. In https://CRAN.R-project.org/package=geosphere Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology: A Journal of the Royal Meteorological Society, 25(15), 1965-1978. Ho, C. (1986). A synthesis of the geologic evolution of Taiwan. Tectonophysics, 125(1-3), 1-16. Hsu, F.-H., Lin, F.-J., & Lin, Y.-S. (2001). Phylogeographic structure of the Formosan wood mouse, Apodemus semotus Thomas. Zoological Studies, 40(2), 91-102. Hsu, H.-H., & Chen, C.-T. (2002). Observed and projected climate change in Taiwan. Meteorology and Atmospheric Physics, 79, 87-104. Hu, P., Shao, Y., Xu, J., Wang, T., Li, Y., Liu, H., Rong, M., Su, W., Chen, B., & Cui, S. (2019). Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus. BMC Genomics, 20, 1-13. Jacques Dainat, D. H., Dr. K. D. Murray, Ed Davis, Ivan Ugrin, Kathryn Crouch, LucileSol, Nuno Agostinho, pascal-git, Zachary Zollman, tayyrov. (2024). AGAT: AGAT-v1.4.1 (v1.4.1). Jiao, X., Wu, L., Zhang, D., Wang, H., Dong, F., Yang, L., Wang, S., Amano, H. E., Zhang, W., & Jia, C. (2024). Landscape heterogeneity explains the genetic differentiation of a forest bird across the Sino-Himalayan Mountains. Molecular biology and evolution, 41(3), msae027. Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405. https://doi.org/10.1093/bioinformatics/btn129 Jouzel, J., Barkov, N., Barnola, J., Bender, M., Chappellaz, J., Genthon, C., Kotlyakov, V., Lipenkov, V., Lorius, C., & Petit, J. (1993). Extending the Vostok ice-core record of palaeoclimate to the penultimate glacial period. Nature, 364(6436), 407-412. Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., Von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature methods, 14(6), 587-589. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 16(2), 111-120. https://doi.org/10.1007/bf01731581 Knaus, B. J., & Grünwald, N. J. (2017). vcfr: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour, 17(1), 44-53. https://doi.org/10.1111/1755-0998.12549 Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution, 35(6), 1547-1549. Kuo, C.-C., Su, Y., Liu, H.-Y., & Lin, C.-T. (2021). Assessment of climate change effects on alpine summit vegetation in the transition of tropical to subtropical humid climate. Plant Ecology, 222(8), 933-951. Lavretsky, P., DaCosta, J. M., Sorenson, M. D., McCracken, K. G., & Peters, J. L. (2019). ddRAD-seq data reveal significant genome-wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America. Mol Ecol, 28(10), 2594-2609. https://doi.org/10.1111/mec.15091 Lepais, O., & Weir, J. T. (2014). SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches. Mol Ecol Resour, 14(6), 1314-1321. https://doi.org/10.1111/1755-0998.12273 Li, C. F., Chytrý, M., Zelený, D., Chen, M. Y., Chen, T. Y., Chiou, C. R., Hsia, Y. J., Liu, H. Y., Yang, S. Z., & Yeh, C. L. (2013). Classification of Taiwan forest vegetation. Applied Vegetation Science, 16(4), 698-719. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. https://doi.org/10.1093/bioinformatics/btp324 Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. https://doi.org/10.1093/bioinformatics/btp352 Li, K.-Y., Hsiao, C., Yen, S.-C., Hung, C.-Y., Lin, Y.-Z., Jheng, S.-W., Yu, P.-J., Hwang, M.-H., Weng, G.-J., & Chen, K.-L. (2023). Phylogenetic divergence associated with climate oscillations and topology illustrates the dispersal history of Formosan sambar deer (Rusa unicolor swinhoii) in Taiwan. Mammal Research, 68(3), 283-294. Lin, M.-F., Su, S.-H., Huang, L.-W., Chen, C.-W., Jeng, M.-R., & Wang, H.-H. (2017). Tree Leaf Choice by Formosan Reeve’s Muntjac in Relation to Nutrient Content. Taiwan J For Sci, 32(3), 237-249. Liu, X., & Fu, Y. X. (2020). Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol, 21(1), 280. https://doi.org/10.1186/s13059-020-02196-9 Lone, M. A., Yamoah, K. A., & Lin, T.-W. (2024). A brief review of climate in Taiwan. The Role of Tropics in Climate Change, 187-192. Malinsky, M., Trucchi, E., Lawson, D. J., & Falush, D. (2018). RADpainter and fineRADstructure: population inference from RADseq data. Molecular biology and evolution, 35(5), 1284-1290. MCBRIDE, J. L. (1995). Tropical cyclone formation. Global perspective on tropical cyclones, 63-105. McCullough, D. R., Pei, K. C., & Wang, Y. (2000). Home range, activity patterns, and habitat relations of Reeves' muntjacs in Taiwan. The Journal of wildlife management, 430-441. Merow, C., Smith, M. J., & Silander Jr, J. A. (2013). A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter. Ecography, 36(10), 1058-1069. Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., Von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular biology and evolution, 37(5), 1530-1534. Murakami, M., Nakatani, Y., Atsumi, G. I., Inoue, K., & Kudo, I. (2017). Regulatory Functions of Phospholipase A2. Crit Rev Immunol, 37(2-6), 127-195. https://doi.org/10.1615/CritRevImmunol.v37.i2-6.20 Nei, M., & Li, W.-H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 76(10), 5269-5273. NVIDIA. (2019). Clara Parabricks. In (Version 4.3.1) https://www.nvidia.com/en-us/clara/genomics/ Oksanen J, S. G., Blanchet F, Kindt R, Legendre P, MinchinP, O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M, Durand S, Evangelista H, FitzJohn R, Friendly M, Furneaux B, Hannigan G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T, Stier A, Ter Braak C, Weedon J. (2024). vegan: Community Ecology Package. In https://CRAN.R-project.org/package=vegan Oshida, T., Lin, L.-K., Chang, S.-W., Chen, Y.-J., & Lin, J.-K. (2011). Phylogeography of two sympatric giant flying squirrel subspecies, Petaurista alborufus lena and P. philippensis grandis (Rodentia: Sciuridae), in Taiwan. Biological Journal of the Linnean Society, 102(2), 404-419. Pacifici, M., Santini, L., Di Marco, M., Baisero, D., Francucci, L., Marasini, G. G., Visconti, P., & Rondinini, C. (2013). Generation length for mammals. Nature Conservation, 5, 89-94. Pagès, M. C. a. H. (2023). AnnotationForge: Tools for building SQLite-based annotation data packages. In https://bioconductor.org/packages/AnnotationForge Pearson, R. G., & Dawson, T. P. (2003). Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful? Global Ecology and Biogeography, 12(5), 361-371. Pei, C.-J. (1990). The reproductive biology of the Formosan Reeves' muntjac (Muntiacus reevesi micrurus) in Jiou-Jeng-Yang area, I-Lan, Taiwan, ROC. University of Montana. Pei, K., Taber, R., O’GARA, B., & Wang, Y. (1995). Breeding cycle of the Formosan Reeves muntjac (Muntiacus reevesi micrurus) in northern Taiwan, Republic of China. 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), e37135. Phillips, S. J., & Dudík, M. (2008). Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31(2), 161-175. Privé, F., Luu, K., Vilhjálmsson, B. J., & Blum, M. G. B. (2020). Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4. Mol Biol Evol, 37(7), 2153-2154. https://doi.org/10.1093/molbev/msaa053 Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, P. I., Daly, M. J., & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 81(3), 559-575. https://doi.org/10.1086/519795 Rochette, N. C., Rivera-Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol, 28(21), 4737-4754. https://doi.org/10.1111/mec.15253 Rosser, N., Seixas, F., Queste, L. M., Cama, B., Mori-Pezo, R., Kryvokhyzha, D., Nelson, M., Waite-Hudson, R., Goringe, M., & Costa, M. (2024). Hybrid speciation driven by multilocus introgression of ecological traits. Nature, 1-7. 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. Mol Biol Evol, 34(12), 3299-3302. https://doi.org/10.1093/molbev/msx248 Saitoh, T. (2021). High variation of mitochondrial DNA diversity as compared to nuclear microsatellites in mammalian populations. Ecological Research, 36(2), 206-220. Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4(4), 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454 Santiago, E., Novo, I., Pardiñas, A. F., Saura, M., Wang, J., & Caballero, A. (2020). Recent demographic history inferred by high-resolution analysis of linkage disequilibrium. Molecular biology and evolution, 37(12), 3642-3653. Savolainen, O., Lascoux, M., & Merilä, J. (2013). Ecological genomics of local adaptation. Nature Reviews Genetics, 14(11), 807-820. Sejian, V., Bhatta, R., Gaughan, J. B., Dunshea, F. R., & Lacetera, N. (2018). Review: Adaptation of animals to heat stress. Animal, 12(s2), s431-s444. https://doi.org/10.1017/s1751731118001945 Sibuet, J.-C., & Hsu, S.-K. (2004). How was Taiwan created? Tectonophysics, 379(1-4), 159-181. Singh, V. K., Joshi, B. D., Singh, A., Singh, S. K., Chandra, K., Sharma, L. K., & Thakur, M. (2022). Genetic diversity and population structure of the northern red muntjac (Muntiacus vaginalis) in Indian Himalayan region. Mammalian Biology, 102(2), 537-544. Stoltz, M., Baeumer, B., Bouckaert, R., Fox, C., Hiscott, G., & Bryant, D. (2021). Bayesian Inference of Species Trees using Diffusion Models. Syst Biol, 70(1), 145-161. https://doi.org/10.1093/sysbio/syaa051 Sun, Z., Wang, H., Zhou, W., Shi, W., Zhu, W., & Zhang, B. (2019). How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac (Muntiacus reevesi)? Diversity and Distributions, 25(1), 116-128. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3), 585-595. Tan, C.-j. (2017). Population structure of Formosan Reeves‘ muntjac (Muntiacus reevesi micrurus) and genetic diversity in isolated habitat, based on Mitochondrial DNA. National Sun Yat-sen University. QGIS Development Team. (2009). QGIS Geographic Information System. In http://qgis.org R Core Team. (2023). R: A Language and Environment for Statistical Computing. In https://www.R-project.org/ Terry, C. L. (2023). Phylogeography, demography, and environmental adaptation of Petaurista flying squirrels in Taiwan. National Taiwan University. Velo-Antón, G., Zamudio, K. R., & Cordero-Rivera, A. (2012). Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra). Heredity (Edinb), 108(4), 410-418. https://doi.org/10.1038/hdy.2011.91 Waelbroeck, C., Labeyrie, L., Michel, E., Duplessy, J.-C., Mcmanus, J. F., Lambeck, K., Balbon, E., & Labracherie, M. (2002). Sea-level and deep water temperature changes derived from benthic foraminifera isotopic records. Quaternary Science Reviews, 21(1-3), 295-305. Wang, B. (2002). Rainy season of the Asian–Pacific summer monsoon. Journal of Climate, 15(4), 386-398. Wang, S., Zhu, W., Gao, X., Li, X., Yan, S., Liu, X., Yang, J., Gao, Z., & Li, Y. (2014). Population size and time since island isolation determine genetic diversity loss in insular frog populations. Molecular Ecology, 23(3), 637-648. Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 1358-1370. Weng, M.-P., & Liao, B.-Y. (2017). modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets. Bioinformatics, 33(21), 3505-3507. White, T. A., & Searle, J. B. (2007). Genetic diversity and population size: island populations of the common shrew, Sorex araneus. Mol Ecol, 16(10), 2005-2016. https://doi.org/10.1111/j.1365-294X.2007.03296.x Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis. In Springer-Verlag New York. https://ggplot2.tidyverse.org Wu, T., Hu, E., Xu, S., Chen, M., Guo, P., Dai, Z., Feng, T., Zhou, L., Tang, W., Zhan, L., Fu, X., Liu, S., Bo, X., & Yu, G. (2021). clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb), 2(3), 100141. https://doi.org/10.1016/j.xinn.2021.100141 Yen, M. C., & Chen, T. C. (2000). Seasonal variation of the rainfall over Taiwan. International Journal of Climatology: A Journal of the Royal Meteorological Society, 20(7), 803-809. Yin, Y., Fan, H., Zhou, B., Hu, Y., Fan, G., Wang, J., Zhou, F., Nie, W., Zhang, C., & Liu, L. (2021). Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nature Communications, 12(1), 6858. Yuan, S. L., Lin, L. K., & Oshida, T. (2006). Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal. Mol Ecol, 15(8), 2119-2130. https://doi.org/10.1111/j.1365-294X.2006.02875.x Zhang, C., Yang, S., Huang, X., Dou, Y., Li, F., Xu, X., Hao, Q., & Gao, J. (2022). Sea level change and Kuroshio intrusion dominated Taiwan sediment source-to-sink processes in the northeastern South China Sea over the past 244 kyrs. Quaternary Science Reviews, 287, 107558. | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/96377 | - |
| dc.description.abstract | 台灣山羌Muntiacus reevesi micrurus (Sclater, 1875)是廣泛分布於台灣全島的小型鹿科動物。過去曾因過度獵捕被列為保育類，目前雖已脫離保育名錄，但其族群動態及遺傳多樣性仍需關注。以往研究多集中於粒線體DNA，缺乏基因體層級(genome-wide)的族群遺傳分析。本研究基於71個台灣各地山羌樣本，應用ddRADseq (Double Digest Restriction Associated DNA Sequencing)技術進行全基因組單核苷酸多態性(SNPs)分析，並結合資料庫中60隻中國山羌的全基因組資料，探討其族群結構、遺傳多樣性及歷史動態。台灣山羌在倒數第二次冰期(Penultimate glacial period)與中國山羌分化。台灣山羌族群結構可分為北部與南部兩大群，濁水溪與烏溪之間有混合群出現。台灣山羌南北族群基因交流仍存在，遺傳距離主要受到最小成本路徑影響。棲位分析顯示，南北族群棲息在不同環境中，進一步促成遺傳分化。環境變因分析指出，平均日溫差、年溫差和季節性降水是影響族群分布的可能因子。富集分析指出磷脂質酶A2活性(Phospholipase A2)受到選擇，影響毛披型態、神經發展、生殖系統以及離子穩態。近年來，人類活動導致族群數量下降，儘管遺傳多樣性在中性演化範疇內未見顯著變化，但台灣山羌的核苷酸多樣性相較於其他鹿科動物低。雖然台灣山羌已脫離保育名錄，但氣候變遷與人類活動仍可能威脅其族群穩定。族群動態與遺傳結構的研究有助於揭示其演化歷程與適應潛力。 | zh_TW |
| dc.description.abstract | The Formosan Reeves’ muntjac (Muntiacus reevesi micrurus, Sclater, 1875) is a small cervid widely distributed across the entire Taiwan. Previously classified as a protected species due to overhunting, it has since been removed from the list of protected wildlife. However, its population dynamics and genetic diversity remain critical concerns. Previous studies have predominantly focused on mitochondrial DNA, lacking genome-wide population genetic analyses. In this study, we analyzed 71 Formosan muntjac samples using double digest restriction-site associated DNA sequencing (ddRADseq) to generate genome-wide single nucleotide polymorphism (SNP) data. We then combined these data with 60 whole genome sequences from Chinese muntjac to examined population structure, genetic diversity, and demographic history of this species. Our results indicate that Formosan muntjac diverged from Chinese muntjac during the Penultimate Glacial Period. Within Taiwan, the species exhibits a north-south population structure, with a contact zone identified between the Jhuoshuei River and Wu River. Despite this differentiation, gene flow persists between northern and southern populations, with genetic distance primarily shaped by least-cost path connectivity. Ecological niche analyses reveal that the northern and southern populations inhabit distinct environments, further promoting genetic differentiation. Environmental association analyses suggest that mean diurnal range, temperature annual range, and precipitation seasonality are key factors influencing population distribution. Functional enrichment analysis highlights Phospholipase A2 activity as a candidate under selection, potentially impacting coat morphology, neural development, reproductive physiology, and ion homeostasis. In recent years, human activities have contributed to population decline. While genetic diversity remains within the range expected under neutral evolution, nucleotide diversity in Formosan muntjac is relatively low compared to other cervids. While the Formosan muntjac is no longer listed as a protected species, ongoing climate change and anthropogenic disturbances may still impact its population stability. Research on population dynamics and genetic structure reveals its evolutionary history and adaptive potential. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-02-13T16:11:48Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-02-13T16:11:48Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
致謝 ii 摘要 iii Abstract iv 表次 viii 圖次 ix 前言 1 方法 5 樣本來源 5 DNA萃取與品質挑選 5 ddRADseq建庫及定序 5 ddRADseq 資料分析 6 連鎖不平衡(Linkage Disequilibrium，LD) 7 族群結構 7 族群遺傳 8 中國山羌(M. reevesi reevesi)樣本處理 8 粒線體基因(cytochrome b)定序與親緣關係樹 10 分化時間與有效族群量估算 11 氣候環境分析 12 潛在受到環境選擇點位 14 結果 17 定序以及資料集 17 族群結構與遺傳 17 分化時間與有效族群量估算 18 氣候環境分析 20 潛在受到環境選擇點位 23 討論 25 台灣山羌族群結構 25 分化時間與有效族群量變動 26 潛在受到選擇基因與環境適應 26 參考文獻 30 | - |
| dc.language.iso | zh_TW | - |
| dc.title | 利用基因組單核苷酸變異探討台灣山羌的族群結構與變動 | zh_TW |
| dc.title | Exploring Population Structure and Demography of the Taiwan Reeves's Muntjac (Muntiacus reevesi micrurus, Sclater, 1875) Using Genome-Wide Single Nucleotide Variations | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-1 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 張仕緯;陳宣汶;李承叡 | zh_TW |
| dc.contributor.oralexamcommittee | Shih-Wei Chang;Hsuan-Wen Chen;Cheng- Ruei Lee | en |
| dc.subject.keyword | 遺傳多樣性,族群結構,ddRADseq,保育遺傳, | zh_TW |
| dc.subject.keyword | genetic diversity,population structure,ddRADseq,conservation genetics, | en |
| dc.relation.page | 80 | - |
| dc.identifier.doi | 10.6342/NTU202500507 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2025-02-08 | - |
| dc.contributor.author-college | 生命科學院 | - |
| dc.contributor.author-dept | 生態學與演化生物學研究所 | - |
| dc.date.embargo-lift | 2026-02-28 | - |
| 顯示於系所單位： | 生態學與演化生物學研究所 | |
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