簡易檢索 / 詳目顯示

研究生: 傅雨辰
Fu, Yuchen
論文名稱: 探討台灣特有種台灣鉤嘴鹛近期適應的遺傳基礎
Genetic bases of recent adaptation in an island endemic babbler Taiwan Scimitar Babbler, Pomatorhinus musicus
指導教授: 李壽先
Li, Shou-Hsien
口試委員: 洪志銘
Hung, Chih-Ming
廖本揚
Liao, Ben-Yang
可文亞
Ko, Wen-Ya
李壽先
Li, Shou-Hsien
口試日期: 2022/05/04
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: 2022
畢業學年度: 110
語文別: 英文
論文頁數: 65
中文關鍵詞: 適應性基因漸滲既有變異新突變正向選擇台灣鉤嘴鹛
英文關鍵詞: adaptive introgression, standing variation, novel mutation, positive selection, Taiwan Scimitar Babbler
研究方法: 實驗設計法
DOI URL: http://doi.org/10.6345/NTNU202200445
論文種類: 學術論文
相關次數: 點閱:102下載:2
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 適應是指族群中的變異性狀受到選擇,因而提升生物生存概率和繁殖能力的過程。表型性狀變異的遺傳來源包括三種不同類型:新突變、既有變異、與漸滲。然而,它們在基因組中組成佔比如何,及對物種適應產生的相對貢獻仍然不為人知。本研究中,我以廣泛分佈于中國大陸南部、東南部、東部和海南島的棕頸鉤嘴鹛(Pomatorhinus ruficollis, Timaliidae, Aves)和它在台灣島的姐妹種,特有種台灣鉤嘴鹛(Pomatorhinus musicus)作為評估不同遺傳變異對近期適應相對貢獻的生物系統。為了評估台灣鉤嘴鹛的適應性遺傳變異的組成和來源,首先組裝了棕頸鉤嘴鹛高質量的染色體水平參考基因組。接著,我將台灣鉤嘴鹛基因組內遺傳變異分為三類:兩種鉤嘴鹛分化以來出現的新突變(5,431,390个SNPs,占總基因组SNPs的8. 87%),保持在台灣鉤嘴鹛內的既有變異(55,769,269个SNPs,占總基因组SNPs的91.04%),以及從棕頸鉤嘴鹛漸滲引入的變異(59,126个ABBA-BABA计数的SNPs,占總基因组SNPs的0.096%)。然後,我使用nSL test檢測台灣鉤嘴鹛支系中受到近期正向選擇的基因組區域。在受到正向選擇的基因組區域內,既有變異是台灣鉤嘴鹛近期適應的主要遺傳來源(642,823个SNPs,占既有變異總數的1.15%)。從棕頸鉤嘴鹛而來的漸滲基因占全部基因組的0.096%,漸滲基因中沒有顯著受到高比例的正向選擇(79個基因中有2個受到正向選擇)。儘管漸滲基因對台灣鉤嘴鹛基因組貢獻不大,但這些與生物基礎功能相關的基因可能仍對物種適應有重要作用。

    Adaptation is the process that trait variations of a population was selected to enhance its survival and reproduction probabilities. Three types of genetic sources underpin the phenotypic variations of a population, namely novel mutation, standing variation, and introgression. However, their relative contributions to genomic variation and adaptation are still poorly understood. In this thesis, I used the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis, Timaliidae, Aves) that is widely resides in south, southeast, and eastern China mainland and Hainan Island, and its sister species Taiwan Scimitar Babbler (Pomatorhinus musicus), an endemic to Taiwan Island, as a system to evaluate how different sources of genetic variants contributed to recent adaptation. To evaluate sources of adaptive genetic variants in the Taiwan Scimitar Babbler lineage, high quality chromosome-level reference genomes for the Streak-breasted Simitar Babbler was assembled at the first. Then, I categorized the genetic variants in the Taiwan Scimitar Babbler to three classes: the novel mutations arose since the split of the two scimitar babbler species (5,431,390 SNPs, 8.87% of total genomic SNPs), the standing genetic variation maintained in the Taiwan Scimitar Babbler and outgroup species (55,769,269 SNPs, 91.04% of total genomic SNPs), and the genetic variants introgressed from the Steak-breasted Scimitar Babbler (59,126 ABBA-BABA counts SNPs, accounting for 0.096% of total genome SNPs). Then I used the nSL test to detect signatures of genomic region under recent positively selection in the Taiwan Scimitar Babbler lineage. Among these SNPs, the standing genetic variant is the dominant sources for recent adaptation in the Taiwan Scimitar Babbler genomes (642,823 SNPs, 1.15% of total standing variation SNPs). Although the introgressed variation only contribute 0.096% to genomic variations of the Taiwan Scimitar Babbler, I detected the signature of recent positive selection for two of 79 introgressed genes. My results suggest that different genetic sources contribute differently to genomic configuration. Although introgressed variants only have minor contributions to the extant Taiwan Scimitar Babbler genome, it could play a role to introduce beneficial genetic variants into a lineage.

    摘要 ii Abstract iii Introduction 1 Materials and Methods 5 1. Reference genome 5 2. Chromosome-level assembly with Hi-C technology 5 3. Synteny analysis 6 4. Genome annotation 6 5. Genome resequencing 7 6. Reads mapping and variants calling 7 7. Phylogenetic relationship and population structuring analyses 8 a) Principal component analysis and population structuring analysis 8 b) Phylogenetic trees of populations 8 8. Geographic historical demography 9 9. Categorizing genetic variants in the Taiwan Scimitar Babbler 9 a) Introgressed SNPs detection 9 b) Standing variation and novel mutation detection 10 10. Adaptive gene detection 11 11. Candidate adaptive introgressed genes 11 Results 11 1. Genome sequencing, assembly, and synteny mapping 11 2. Genome annotation and gene content 12 3. Variants calling 12 4. Higher genomic diversity of the Steak-breasted Scimitar Babbler 13 5. Population structure and phylogenetic analysis 13 6. Phylogenetic relationship 14 7. Demographic history 14 8. Characterization of SNPs in the Taiwan Scimitar Babbler 14 a) Detection of genetic introgression 14 b) Characterizations of standing variation and novel mutation 15 9. Signatures of recent positive selection 15 Discussion 16 Further study 20 Conclusion 21 Reference 22

    Alaei Kakhki, N., Aliabadian, M., & Schweizer, M. (2016). Out of Africa: Biogeographic history of the open-habitat chats (Aves, Muscicapidae: Saxicolinae) across arid areas of the old world. Zoologica Scripta, 45(3), 237–251. https://doi.org/10.1111/zsc.12151
    Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655–1664. https://doi.org/10.1101/gr.094052.109
    Allen, C. E., Beldade, P., Zwaan, B. J., & Brakefield, P. M. (2008). Differences in the selection response of serially repeated color pattern characters: Standing variation, development, and evolution. BMC Evolutionary Biology, 8(1), 94. https://doi.org/10.1186/1471-2148-8-94
    Anderson, E., & Hubricht, L. (1938). Hybridization in Tradescantia. Iii. The Evidence for Introgressive Hybridization. American Journal of Botany, 25(6), 396–402. https://doi.org/10.1002/j.1537-2197.1938.tb09237.x
    Anderson, E., & Stebbins, G. L. (1954). Hybridization as an Evolutionary Stimulus. Evolution, 8(4), 378–388. https://doi.org/10.2307/2405784
    Arnold, M. L., & Hodges, S. A. (1995). Are natural hybrids fit or unfit relative to their parents? Trends in Ecology & Evolution, 10(2), 67–71. https://doi.org/10.1016/S0169-5347(00)88979-X
    Arnold, M. L., & Martin, N. H. (2010). Hybrid fitness across time and habitats. Trends in Ecology & Evolution, 25(9), 530–536. https://doi.org/10.1016/j.tree.2010.06.005
    Barrett, R. D. H., & Schluter, D. (2008). Adaptation from standing genetic variation. Trends in Ecology & Evolution, 23(1), 38–44. https://doi.org/10.1016/j.tree.2007.09.008
    Barry, C. P., Xie, J., Lemmon, V., & Young, A. P. (1993). Molecular characterization of a multi-promoter gene encoding a chicken filamin protein. Journal of Biological Chemistry, 268(34), 25577–25586. https://doi.org/10.1016/S0021-9258(19)74430-5
    Barton, N. H. (2000). Genetic hitchhiking. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 355(1403), 1553–1562.
    Bitter, M. C., Kapsenberg, L., Gattuso, J.-P., & Pfister, C. A. (2019). Standing genetic variation fuels rapid adaptation to ocean acidification. Nature Communications, 10(1), 5821. https://doi.org/10.1038/s41467-019-13767-1
    Browning, B. L., Zhou, Y., & Browning, S. R. (2018). A One-Penny Imputed Genome from Next-Generation Reference Panels. American Journal of Human Genetics, 103(3), 338–348. https://doi.org/10.1016/j.ajhg.2018.07.015
    Browning, S. R., & Browning, B. L. (2007). Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering. American Journal of Human Genetics, 81(5), 1084–1097.
    Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013). Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology, 31(12), 1119–1125. https://doi.org/10.1038/nbt.2727
    Casacuberta, E., & González, J. (2013). The impact of transposable elements in environmental adaptation. Molecular Ecology, 22(6), 1503–1517. https://doi.org/10.1111/mec.12170
    Chen, S., Krinsky, B. H., & Long, M. (2013). New genes as drivers of phenotypic evolution. Nature Reviews Genetics, 14(9), 645–660. https://doi.org/10.1038/nrg3521
    Chen, S., Zhang, Y. E., & Long, M. (2010). New genes in Drosophila quickly become essential. Science (New York, N.Y.), 330(6011), 1682–1685. https://doi.org/10.1126/science.1196380
    Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England), 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560
    Chénais, B., Caruso, A., Hiard, S., & Casse, N. (2012). The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments. Gene, 509(1), 7–15. https://doi.org/10.1016/j.gene.2012.07.042
    Chernomor, O., von Haeseler, A., & Minh, B. Q. (2016). Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Systematic Biology, 65(6), 997–1008. https://doi.org/10.1093/sysbio/syw037
    Clements, J. F. (2007). The Clements checklist of birds of the world (6th ed). Comstock Pub. Associates/Cornell University Press.
    Collar, N. J. (2006). A partial revision of the Asian babblers (Timaliidae). Forktail, 22, 85.
    Collar, N. J., & Robson, C. (2007). Handbook of the Birds of the World. Volume 12: Family Timaliidae (babblers). Ostrich: Journal of African Ornithology, 12, 165–171. https://doi.org/10.2989/OSTRICH.2008.79.2.20.594
    Darwin, C., Wallace, A. R., Lyell, S. C., & Hooker, J. D. (1858). On the tendency of species to form varieties: And on the perpetuation of varieties and species by natural means of selection.
    Dasmahapatra, K. K., Walters, J. R., Briscoe, A. D., Davey, J. W., Whibley, A., Nadeau, N. J., Zimin, A. V., Hughes, D. S., Ferguson, L. C., & Martin, S. H. (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487(7405), 94.
    DeWoody, J. A., Harder, A. M., Mathur, S., & Willoughby, J. R. (2021). The long-standing significance of genetic diversity in conservation. Molecular Ecology, 30(17), 4147–4154. https://doi.org/10.1111/mec.16051
    Dickinson, E. C., & Howard, R. (2003). The Howard and Moore complete checklist of the birds of the world. Christopher Helm.
    Dong, F., Li, S.-H., Zou, F.-S., Lei, F.-M., Liang, W., Yang, J.-X., & Yang, X.-J. (2014). Molecular systematics and plumage coloration evolution of an enigmatic babbler (Pomatorhinus ruficollis) in East Asia. Molecular Phylogenetics and Evolution, 70, 76–83. https://doi.org/10.1016/j.ympev.2013.09.008
    Dong, F., Zou, F.-S., Lei, F.-M., Liang, W., Li, S.-H., & Yang, X.-J. (2014). Testing hypotheses of mitochondrial gene-tree paraphyly: Unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Molecular Ecology, 23(23), 5855–5867. https://doi.org/10.1111/mec.12981
    Ferrer-Admetlla, A., Liang, M., Korneliussen, T., & Nielsen, R. (2014). On detecting incomplete soft or hard selective sweeps using haplotype structure. Molecular Biology and Evolution, 31(5), 1275–1291. https://doi.org/10.1093/molbev/msu077
    Feuk, L., Carson, A. R., & Scherer, S. W. (2006). Structural variation in the human genome. Nature Reviews Genetics, 7(2), 85–97. https://doi.org/10.1038/nrg1767
    Freeman, J. L., Perry, G. H., Feuk, L., Redon, R., McCarroll, S. A., Altshuler, D. M., Aburatani, H., Jones, K. W., Tyler-Smith, C., Hurles, M. E., Carter, N. P., Scherer, S. W., & Lee, C. (2006). Copy number variation: New insights in genome diversity. Genome Research, 16(8), 949–961. https://doi.org/10.1101/gr.3677206
    Gemmell, N. J., & Akiyama, S. (1996). An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics, 12(9), 338–339.
    Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., … Regev, A. (2011). Trinity: Reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology, 29(7), 644–652. https://doi.org/10.1038/nbt.1883
    Graham, A. M., Peters, J. L., Wilson, R. E., Muñoz-Fuentes, V., Green, A. J., Dorfsman, D. A., Valqui, T. H., Winker, K., & McCracken, K. G. (2021). Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity, 127(1), 107–123. https://doi.org/10.1038/s41437-021-00437-6
    Haenel, Q., Roesti, M., Moser, D., MacColl, A. D. C., & Berner, D. (2019). Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish. Evolution Letters, 3(1), 28–42. https://doi.org/10.1002/evl3.99
    Harris, K., & Nielsen, R. (2016). The Genetic Cost of Neanderthal Introgression. Genetics, 203(2), 881–891. https://doi.org/10.1534/genetics.116.186890
    Hedrick, P. W. (2013). Adaptive introgression in animals: Examples and comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology, 22(18), 4606–4618.
    Hermisson, J., & Pennings, P. S. (2005). Soft Sweeps. Genetics, 169(4), 2335–2352. https://doi.org/10.1534/genetics.104.036947
    Hoekstra, H. E., & Coyne, J. A. (2007). The Locus of Evolution: Evo Devo and the Genetics of Adaptation. Evolution, 61(5), 995–1016. https://doi.org/10.1111/j.1558-5646.2007.00105.x
    Hof, A. E. van’t, Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., Hall, N., Darby, A. C., & Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. Nature, 534(7605), 102–105. https://doi.org/10.1038/nature17951
    Jenkins, B. R., Vitousek, M. N., Hubbard, J. K., & Safran, R. J. (2014). An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population. Proceedings of the Royal Society B: Biological Sciences, 281(1790), 20141302. https://doi.org/10.1098/rspb.2014.1302
    Jones, M. R., Mills, L. S., Alves, P. C., Callahan, C. M., Alves, J. M., Lafferty, D. J., Jiggins, F. M., Jensen, J. D., Melo-Ferreira, J., & Good, J. M. (2018). Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science, 360(6395), 1355–1358.
    Lai, Y.-T., Yeung, C. K., Omland, K. E., Pang, E.-L., Hao, Y., Liao, B.-Y., Cao, H.-F., Zhang, B.-W., Yeh, C.-F., & Hung, C.-M. (2019). Standing genetic variation as the predominant source for adaptation of a songbird. Proceedings of the National Academy of Sciences, 116(6), 2152–2157.
    Lamichhaney, S., Berglund, J., Almén, M. S., Maqbool, K., Grabherr, M., Martinez-Barrio, A., Promerová, M., Rubin, C.-J., Wang, C., Zamani, N., Grant, B. R., Grant, P. R., Webster, M. T., & Andersson, L. (2015). Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature, 518(7539), 371–375. https://doi.org/10.1038/nature14181
    Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R., & Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s finches. Science (New York, N.Y.), 359(6372), 224–228. https://doi.org/10.1126/science.aao4593
    Lande, R. (1975). The maintenance of genetic variability by mutation in a polygenic character with linked loci. Genetics Research, 26(3), 221–235. https://doi.org/10.1017/S0016672300016037
    Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–359. https://doi.org/10.1038/nmeth.1923
    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.
    Linnen, C. R., Kingsley, E. P., Jensen, J. D., & Hoekstra, H. E. (2009). On the origin and spread of an adaptive allele in deer mice. Science (New York, N.Y.), 325(5944), 1095–1098. https://doi.org/10.1126/science.1175826
    Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. PLoS Computational Biology, 14(1), e1005944.
    Martin, S. H., Dasmahapatra, K. K., Nadeau, N. J., Salazar, C., Walters, J. R., Simpson, F., Blaxter, M., Manica, A., Mallet, J., & Jiggins, C. D. (2013). Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research, 23(11), 1817–1828. https://doi.org/10.1101/gr.159426.113
    Martin, S. H., Davey, J. W., & Jiggins, C. D. (2015). Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci. Molecular Biology and Evolution, 32(1), 244–257. https://doi.org/10.1093/molbev/msu269
    Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press. https://doi.org/10.7312/nei-92038
    Nei, M. (2007). The new mutation theory of phenotypic evolution. Proceedings of the National Academy of Sciences, 104(30), 12235–12242. https://doi.org/10.1073/pnas.0703349104
    Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32(1), 268–274. https://doi.org/10.1093/molbev/msu300
    O’Donnell, D. R., Parigi, A., Fish, J. A., Dworkin, I., & Wagner, A. P. (2014). The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies. PLoS ONE, 9(6), e100163. https://doi.org/10.1371/journal.pone.0100163
    Ottenburghs, J. (2019). Multispecies hybridization in birds. Avian Research, 10(1), 20. https://doi.org/10.1186/s40657-019-0159-4
    Ottenburghs, J., Megens, H.-J., Kraus, R. H. S., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M., & Prins, H. H. T. (2017). A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evolutionary Biology, 17(1), 201. https://doi.org/10.1186/s12862-017-1048-2
    Pickrell, J. K., & Pritchard, J. K. (2012). Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. PLOS Genetics, 8(11), e1002967. https://doi.org/10.1371/journal.pgen.1002967
    Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559–575. https://doi.org/10.1086/519795
    Räsänen, K., & Hendry, A. P. (2008). Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification. Ecology Letters, 11(6), 624–636. https://doi.org/10.1111/j.1461-0248.2008.01176.x
    Runemark, A., Trier, C. N., Eroukhmanoff, F., Hermansen, J. S., Matschiner, M., Ravinet, M., Elgvin, T. O., & Sætre, G.-P. (2018). Variation and constraints in hybrid genome formation. Nature Ecology & Evolution, 2(3), 549–556. https://doi.org/10.1038/s41559-017-0437-7
    Rutherford, S., van der Merwe, M., Wilson, P. G., Kooyman, R. M., & Rossetto, M. (2019). Managing the risk of genetic swamping of a rare and restricted tree. Conservation Genetics, 20(5), 1113–1131. https://doi.org/10.1007/s10592-019-01201-4
    Samaniego Castruita, J. A., Westbury, M. V., & Lorenzen, E. D. (2020). Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role. BMC Genomics, 21(1), 543. https://doi.org/10.1186/s12864-020-06940-0
    Sankararaman, S., Mallick, S., Patterson, N., & Reich, D. (2016). The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans. Current Biology, 26(9), 1241–1247. https://doi.org/10.1016/j.cub.2016.03.037
    Schumer, M., Cui, R., Powell, D. L., Rosenthal, G. G., & Andolfatto, P. (2016). Ancient hybridization and genomic stabilization in a swordtail fish. Molecular Ecology, 25(11), 2661–2679. https://doi.org/10.1111/mec.13602
    Schweizer, M., Warmuth, V., Alaei Kakhki, N., Aliabadian, M., Förschler, M., Shirihai, H., Suh, A., & Burri, R. (2019). Parallel plumage colour evolution and introgressive hybridization in wheatears. Journal of Evolutionary Biology, 32(1), 100–110. https://doi.org/10.1111/jeb.13401
    Sibley, C. G., & Ahlquist, J. E. (1991). Phylogeny and Classification of the Birds: A Study in Molecular Evolution. Yale University Press. https://doi.org/10.2307/j.ctt1xp3v3r
    Sibley, C. G., & Monroe, B. L. (1990). Distribution and taxonomy of birds of the world. Yale University Press. https://scholar.google.com/scholar_lookup?title=Distribution+and+taxonomy+of+birds+of+the+world&author=Sibley%2C+C.G.&publication_year=1990
    Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210–3212.
    Singhal, S., Derryberry, G. E., Bravo, G. A., Derryberry, E. P., Brumfield, R. T., & Harvey, M. G. (2021). The dynamics of introgression across an avian radiation. Evolution Letters, 5(6), 568–581. https://doi.org/10.1002/evl3.256
    Smeds, L., Qvarnström, A., & Ellegren, H. (2016). Direct estimate of the rate of germline mutation in a bird. Genome Research, 26(9), 1211–1218. https://doi.org/10.1101/gr.204669.116
    Smith, J. M., & Haigh, J. (1974). The hitch-hiking effect of a favourable gene. Genetics Research, 23(1), 23–35.
    Stanke, M., & Morgenstern, B. (2005). AUGUSTUS: A web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Research, 33(Web Server issue), W465–W467. https://doi.org/10.1093/nar/gki458
    Szpiech, Z. A., & Hernandez, R. D. (2014). selscan: An efficient multithreaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution, 31(10), 2824–2827. https://doi.org/10.1093/molbev/msu211
    Teixeira, J. C., & Huber, C. D. (2021). The inflated significance of neutral genetic diversity in conservation genetics. Proceedings of the National Academy of Sciences, 118(10), e2015096118. https://doi.org/10.1073/pnas.2015096118
    Terhorst, J., Kamm, J. A., & Song, Y. S. (2017). Robust and scalable inference of population history from hundreds of unphased whole-genomes. Nature Genetics, 49(2), 303–309. https://doi.org/10.1038/ng.3748
    Todesco, M., Pascual, M. A., Owens, G. L., Ostevik, K. L., Moyers, B. T., Hübner, S., Heredia, S. M., Hahn, M. A., Caseys, C., Bock, D. G., & Rieseberg, L. H. (2016). Hybridization and extinction. Evolutionary Applications, 9(7), 892–908. https://doi.org/10.1111/eva.12367
    Van der Auwera, G. A., & O’Connor, B. D. (2020). Genomics in the cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media.
    Van’t Hof, A. E., Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., Hall, N., Darby, A. C., & Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. Nature, 534(7605), 102–105. https://doi.org/10.1038/nature17951
    Veller, C., Edelman, N. B., Muralidhar, P., & Nowak, M. A. (2019). Recombination and selection against introgressed DNA [Preprint]. Evolutionary Biology. https://doi.org/10.1101/846147
    Vickrey, A. I., Bruders, R., Kronenberg, Z., Mackey, E., Bohlender, R. J., Maclary, E. T., Maynez, R., Osborne, E. J., Johnson, K. P., Huff, C. D., Yandell, M., & Shapiro, M. D. (2018). Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. ELife, 7, e34803. https://doi.org/10.7554/eLife.34803
    Wanker, E. E., Rovira, C., Scherzinger, E., Hasenbank, R., Wälter, S., Tait, D., Colicelli, J., & Lehrach, H. (1997). HIP-I: A huntingtin interacting protein isolated by the yeast two-hybrid system. Human Molecular Genetics, 6(3), 487–495. https://doi.org/10.1093/hmg/6.3.487
    Whitney, K. D., Randell, R. A., & Rieseberg, L. H. (2006). Adaptive Introgression of Herbivore Resistance Traits in the Weedy Sunflower Helianthus annuus. The American Naturalist, 167(6), 794–807. https://doi.org/10.1086/504606
    Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis (2nd ed. 2016). Springer International Publishing : Imprint: Springer. https://doi.org/10.1007/978-3-319-24277-4
    Wu, D.-D., Ding, X.-D., Wang, S., Wójcik, J. M., Zhang, Y. I., Tokarska, M., Li, Y., Wang, M.-S., Faruque, O., & Nielsen, R. (2018). Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nature Ecology & Evolution, 2(7), 1139–1145.
    Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A. R., Yu, Y., Hou, G., Zi, J., Zhou, R., Wen, B., Zhang, J., Chougule, K., Wang, M., Copetti, D., Peng, Z., Zhang, C., Zhang, Y., Ouyang, Y., … Long, M. (2019). Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution, 3(4), 679–690. https://doi.org/10.1038/s41559-019-0822-5
    Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science (New York, N.Y.), 343(6172), 769–772. https://doi.org/10.1126/science.1248286
    Zheng, G. X. Y., Lau, B. T., Schnall-Levin, M., Jarosz, M., Bell, J. M., Hindson, C. M., Kyriazopoulou-Panagiotopoulou, S., Masquelier, D. A., Merrill, L., Terry, J. M., Mudivarti, P. A., Wyatt, P. W., Bharadwaj, R., Makarewicz, A. J., Li, Y., Belgrader, P., Price, A. D., Lowe, A. J., Marks, P., … Ji, H. P. (2016). Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nature Biotechnology, 34(3), 303–311. https://doi.org/10.1038/nbt.3432

    下載圖示
    QR CODE