簡易檢索 / 詳目顯示

研究生: 林宗翰
Lin, Tzong-Han
論文名稱: 異域種化與過去種間基因交流形塑臺灣攀蜥的演化歷史
Allopatric speciation and ancient gene flow shape the evolutionary history of dragon lizards (Genus: Diploderma) in Taiwan
指導教授: 林思民
Lin, Si-Min
口試委員: 廖培鈞
Liao, Pei-Chun
黃仁磐
Huang, Jen-Pan
林思民
Lin, Si-Min
口試日期: 2024/01/09
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: 2024
畢業學年度: 112
語文別: 英文
論文頁數: 111
中文關鍵詞: 雙重酶切DNA定序龍蜥基因流種化物種界定
英文關鍵詞: ddRAD-seq, Diploderma, gene flow, speciation, species delimitation
研究方法: 調查研究主題分析
DOI URL: http://doi.org/10.6345/NTNU202400254
論文種類: 學術論文
相關次數: 點閱:80下載:0
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
  • 自達爾文時期以來,物種形成一直是生態演化學者熱衷探索的議題。地理阻隔造成的異域種化是早期被用來解釋分化機制的假說之一,而有限的播遷能力亦被認為會限制物種的活動距離,並強化遺傳上的分化。然而,最近的研究結果表明這僅涉及種化過程的一部分,而雜交物種起源或二次接觸的基因滲入也同樣影響物種分化的過程。在本研究中,我的目標是檢測臺灣產龍蜥屬(Diploderma)的種化過程中是否受到地理阻隔與基因交流事件的影響。這個類群包括五個播遷能力不佳且具有高度形態多樣性的物種,其中多個物種被視為具有潛在的雜交事件或隱蔽種。我們首先透過親緣分析顯示了種內與種間的高度分化,並發現分化情形和族群分布有關,顯示地理距離和地形的潛在影響。使用粒線體和核基因序列進行的物種界定分析則顯示了不一致的結果。為了更進一步了解龍蜥的遺傳結構,我們使用雙重酶切DNA 定序技術(ddRAD)進行了多個族群結構分析,一致地得到了七個分群。我們發現在部份共域物種存在過去的遺傳滲入事件,包括短肢龍蜥(D. brevipes)的北部族群和多稜龍蜥(D. polygonatum)的西部族群,以及短肢龍蜥的中部到南部族群和牧氏龍蜥(D. makii)。我們也檢測了雜交地區族群的形態和生態棲位,發現共有的形態特徵和介於之間的生態棲位。藉由多物種溯祖與遺傳滲入模型(MSCi)估算了這些遺傳滲入事件的時間和方向,發現同時具有分化前和分化後基因流事件的模型具有最高的機率。總結來說,我們發現這些高度分化的物種有三次主要的古老基因流事件。這些事件發生在物種分化的初期,並造成形態和氣候棲位上的混雜,而直到生殖隔離的強化,才中斷了種間雜交事件。這項研究的發現提供了散佈能力有限的物種仍具有種化期間基因交流的例子,也有助於我們了解這些特有物種的種化歷史,並提供未來研究的方向和保育相關的資訊。

    Allopatric speciation is one of the earliest proposed hypotheses to interpret the underlying mechanism of differentiation. Concordantly, limited dispersal and niche conservatism constrain distribution ranges and thus facilitate genetic differentiation. However, recent findings have challenged this aspect, emphasizing that the detection of gene flow events during species divergence could provide more detailed information. In this study, we aimed to infer the presence of gene flow in dragon lizards (Agamidae: Diploderma) from Taiwan. This group of lizards comprises five species with limited migration ability and high ornamentation polymorphism, that are suspected with potential hybridization events or cryptic diversity. Our phylogenetic analysis showed deep divergence within and among species that was consistent with geographic distribution, indicating the potential effect of distance and topography. Results from species delimitation using mitochondrial and nuclear sequences were inclusive, masked by the effect of population structure. Seven clusters were identified using ddRAD-seq data in population structure analysis, where gene flow existed within two pairs of clusters that exhibit narrowly distributional overlapping. There were three major ancient gene flow events demonstrated by comparing the multispecies coalescent model with introgression (MSCi). These admixture events occurred during the initial stages of speciation and left traces in morphology, while the enforcement of the reproductive barrier later developed with the effect of genetic drift and niche evolution. Our findings provide an example of speciation with gene flow, and further highlight the potential impacts of niche conservatism and divergence on the completion of allopatric speciation.

    摘要 I Abstract II Content III Introduction 1 Material and methods 4 Study species and region 4 Sample collection and Molecular data preparation 5 ddRADseq data preparation 6 SNP data assembly 6 Phylogenetic analysis 7 Species delimitation by sequence data 9 Divergence time estimation 11 Population structure analysis 12 Morphological and ornamentation measurement analysis 14 Niche comparative analysis 16 Isolation mechanism analysis 17 Gene flow detection 18 Divergence with gene flow and species delimitation by BPP analysis 20 Demographic history reconstruction 22 Paleo-distribution modeling 23 Results 24 Sequence and ddRAD-seq data compilation 24 Geographic effect and intraspecific mitonuclear discordances in phylogenetic trees 25 Incongruent species delimitation from mitochondrial and nuclear genes 27 Deep divergence time uncovered by fossil-calibrated tree 28 Distinct population structure and shared co-ancestry between D. polygonatum and D. brevipes in contact zone 28 IBD and IBRclim as underlying mechanism for within island differentiation for D. p. xanthostomum, but not in D. brevipes 30 Pholidosis and morphometric traits in identified clusters 31 Diverse ornamentation among identified clusters with traces of potential hybrid 32 Niche analysis provided opposite pattern in divergent clusters 32 Interspecific gene flow between sympatric populations for sister taxa 33 Speciation with pre- and post- divergence gene flow favored by BPP 35 Evidence of demographic contraction after interspecific divergence 36 Overlapped paleo-distribution in pairs of clusters with gene flow 37 Discussion 37 Mito-nuclear discordance 38 Obscure results of species delimitation 39 Taxonomic revisions and recommendation 40 Ancient gene flow as potential source of ornamentation polymorphism in D. brevipes 41 Niches, demography, and dispersal ability 43 Conclusion 44 Reference 46 Tables 69

    Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J., Bierne, N., ... & Zinner, D. (2013). Hybridization and speciation. Journal of evolutionary biology, 26(2), 229-246.
    Ahmadi, M., Hemami, M. R., Kaboli, M., & Shabani, F. (2023). MaxEnt brings comparable results when the input data are being completed; Model parameterization of four species distribution models. Ecology and Evolution, 13(2), e9827.
    Aiello‐Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B., & Anderson, R. P. (2015). spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography, 38(5), 541-545.
    Anderson, R. P., & Gonzalez Jr, I. (2011). Species-specific tuning increases robustness to sampling bias in models of species distributions: an implementation with Maxent. Ecological Modelling, 222(15), 2796-2811.
    Anderson, S. A., & Weir, J. T. (2022). The role of divergent ecological adaptation during allopatric speciation in vertebrates. Science, 378(6625), 1214-1218.
    Andersen, M. J., McCullough, J. M., Gyllenhaal, E. F., Mapel, X. M., Haryoko, T., Jønsson, K. A., & Joseph, L. (2021). Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds. Molecular Ecology, 30(9), 2087-2103.
    Andrade, P., Pinho, C., Pérez i de Lanuza, G., Afonso, S., Brejcha, J., Rubin, C. J., ... & Carneiro, M. (2019). Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proceedings of the National Academy of Sciences, 116(12), 5633-5642.
    Barley, A. J., Nieto-Montes de Oca, A., Manríquez-Morán, N. L., & Thomson, R. C. (2022). The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization. Science, 377(6607), 773-777.
    Barrera-Guzmán, A. O., Aleixo, A., Shawkey, M. D., & Weir, J. T. (2018). Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proceedings of the National Academy of Sciences, 115(2), E218-E225.
    Benkovský, N., Moravec, J., Javůrková, V. G., Šifrová, H., Gvoždík, V., & Jandzik, D. (2021). Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe. PeerJ, 9, e12482.
    Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., ... & Drummond, A. J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650.
    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. The American Journal of Human Genetics, 81(5), 1084-1097.
    Browning, B. L., Zhou, Y., & Browning, S. R. (2018). A one-penny imputed genome from next-generation reference panels. The American Journal of Human Genetics, 103(3), 338-348.
    Burridge, C. P., & Waters, J. M. (2020). Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes. Evolution, 74(9), 1954-1965.
    Burriel-Carranza, B., Estarellas, M., Riaño, G., Talavera, A., Tejero-Cicuéndez, H., Els, J., & Carranza, S. (2023). Species boundaries to the limit: integrating species delimitation methods is critical to avoid taxonomic inflation in the case of the Hajar Banded Ground Gecko (Trachydactylus hajarensis). Molecular Phylogenetics and Evolution, 107834.
    Cai, B., Zhang, M., Li, J., Du, S., Xie, F., Hou, M., ... & Jiang, J. (2022). Three New Species of Diploderma Hallowell, 1861 (Reptilia: Squamata: Agamidae) from the Shaluli Mountains in Western Sichuan, China. Asian Herpetological Research, 13(4), 205-223A.
    Camargo, A., Morando, M., Avila, L. J., & Sites Jr, J. W. (2012). Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution, 66(9), 2834-2849.
    Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013). How to fail at species delimitation. Molecular ecology, 22(17), 4369-4383.
    Cerca, J., Maurstad, M. F., Rochette, N. C., Rivera‐Colón, A. G., Rayamajhi, N., Catchen, J. M., & Struck, T. H. (2021). Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms. Methods in Ecology and Evolution, 12(5), 805-817.
    Chambers, E. A., & Hillis, D. M. (2020). The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology, 69(1), 184-193.
    Chan, K. O., & Grismer, L. L. (2022). GroupStruct: An R package for allometric size correction. Zootaxa, 5124(4), 471-482.
    Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015.
    Chang, J. T., Chao, C. T., Nakamura, K., Liu, H. L., Luo, M. X., & Liao, P. C. (2022). Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. Frontiers in Plant Science, 13, 957.
    Chen, I. P., Stuart-Fox, D., Hugall, A. F., & Symonds, M. R. (2012). Sexual selection and the evolution of complex color patterns in dragon lizards. Evolution, 66(11), 3605-3614.
    Chhatre, V. E., & Emerson, K. J. (2017). StrAuto: automation and parallelization of STRUCTURE analysis. BMC bioinformatics, 18(1), 1-5.
    Chifman, J., & Kubatko, L. (2014). Quartet inference from SNP data under the coalescent model. Bioinformatics, 30(23), 3317-3324.
    Chifman, J., & Kubatko, L. (2015). Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of theoretical biology, 374, 35-47.
    Chou, C. A. (2007). Phylogeography of the Endemic Species Japalura brevipes of Taiwan Based on cytochrome b Sequences and Morphology. Master thesis of National Sun Yat-sen University. National Digital Library of Theses and Dissertations in Taiwan. https://hdl.handle.net/11296/7h72g5
    Chou, M. H., Tseng, W. Z., Sang, Y. D., Morgan, B., De Vivo, M., Kuan, Y. H., ... & Huang, J. P. (2021). Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus). Biological Journal of the Linnean Society, 134(3), 745-759.
    Clement, M., Snell, Q., Walker, P., Posada, D., & Crandall, K. (2002, April). TCS: estimating gene genealogies. In Parallel and Distributed Processing Symposium, International (Vol. 3, pp. 0184-0184). IEEE Computer Society.
    Corl, A., & Ellegren, H. (2013). Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Molecular Phylogenetics and Evolution, 67(2), 358-366.
    Crossman, C. A., Taylor, E. B., & Barrett‐Lennard, L. G. (2016). Hybridization in the Cetacea: widespread occurrence and associated morphological, behavioral, and ecological factors. Ecology and evolution, 6(5), 1293-1303.
    Crottini, A., Dordel, J., Köhler, J., Glaw, F., Schmitz, A., & Vences, M. (2009). A multilocus phylogeny of Malagasy scincid lizards elucidates the relationships of the fossorial genera Androngo and Cryptoscincus. Molecular Phylogenetics and Evolution, 53(1), 345-350.
    Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., ... & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158.
    Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature methods, 9(8), 772-772.
    Denburgh, V. (1912). Concerning certain species of reptiles and amphibians from China, Japan, the Loo Choo Islands, and Formosa. Proc California Acad Sci, 3, 187-258.
    Degnan, J. H., & Rosenberg, N. A. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in ecology & evolution, 24(6), 332-340.
    Degnan, J. H. (2018). Modeling hybridization under the network multispecies coalescent. Systematic biology, 67(5), 786-799.
    De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., ... & Fraïsse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications, 16(2), 542-559.
    Dellicour, S., & Flot, J. F. (2018). The hitchhiker's guide to single‐locus species delimitation. Molecular Ecology Resources, 18(6), 1234-1246.
    De Queiroz, K. (2007). Species concepts and species delimitation. Systematic biology, 56(6), 879-886.
    DeRaad, Devon A. 2021. Permanent DOI for RADStackshelpR to come.
    Di Cola, V., Broennimann, O., Petitpierre, B., Breiner, F. T., d'Amen, M., Randin, C., ... & Guisan, A. (2017). ecospat: an R package to support spatial analyses and modeling of species niches and distributions. Ecography, 40(6), 774-787.
    Dietz, L., Eberle, J., Mayer, C., Kukowka, S., Bohacz, C., Baur, H., ... & Ahrens, D. (2023). Standardized nuclear markers improve and homogenize species delimitation in Metazoa. Methods in Ecology and Evolution, 14(2), 543-555.
    Dixon, P. (2003). VEGAN, a package of R functions for community ecology. Journal of vegetation science, 14(6), 927-930.
    Dolinay, M., Nečas, T., Zimkus, B. M., Schmitz, A., Fokam, E. B., Lemmon, E. M., ... & Gvoždík, V. (2021). Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Molecular Phylogenetics and Evolution, 163, 107258.
    Dong, F., Li, S. H., Chiu, C. C., Dong, L., Yao, C. T., & Yang, X. J. (2020). Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Molecular phylogenetics and evolution, 153, 106941.
    Dool, S. E., Picker, M. D., & Eberhard, M. J. (2022). Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot. Molecular Ecology, 31(1), 279-295.
    Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS biology, 4(5), e88.
    Dufresnes, C., Poyarkov, N., & Jablonski, D. (2023). Acknowledging more biodiversity without more species. Proceedings of the National Academy of Sciences, 120(40), e2302424120.
    Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011). Testing for ancient admixture between closely related populations. Molecular biology and evolution, 28(8), 2239-2252.
    Earl, D. A., & VonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation genetics resources, 4, 359-361.
    Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797.
    Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology, 14(8), 2611-2620.
    Ezard, T., Fujisawa, T., & Barraclough, T. G. (2009). splits: Species’ LImits by Threshold Statistics. R package version 1.0-14/r31.
    Feder, J. L., Egan, S. P., & Nosil, P. (2012). The genomics of speciation-with-gene-flow. Trends in genetics, 28(7), 342-350.
    Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
    Firneno Jr, T. J., O’Neill, J. R., Itgen, M. W., Kihneman, T. A., Townsend, J. H., & Fujita, M. K. (2021). Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance. Ecology and Evolution, 11(18), 12739-12753.
    Fitak, R. R. (2021). OptM: estimating the optimal number of migration edges on population trees using Treemix. Biology Methods and Protocols, 6(1), bpab017.
    Fitch, W. M. (1970). Distinguishing homologous from analogous proteins. Systematic zoology, 19(2), 99-113.
    Fitzpatrick, B. M., Fordyce, J. A., & Gavrilets, S. (2009). Pattern, process and geographic modes of speciation. Journal of evolutionary biology, 22(11), 2342-2347.
    Fitzpatrick, S. W., & Reid, B. N. (2019). Does gene flow aggravate or alleviate maladaptation to environmental stress in small populations?. Evolutionary Applications, 12(7), 1402-1416.
    Flouri, T., Jiao, X., Rannala, B., & Yang, Z. (2020). A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Molecular biology and evolution, 37(4), 1211-1223.
    Flury, J. M., Meusemann, K., Martin, S., Hilgers, L., Spanke, T., Böhne, A., ... & Schwarzer, J. (2023). Potential contribution of ancient introgression to the evolution of a derived reproductive strategy in ricefishes. Genome Biology and Evolution, 15(8), evad138.
    Fontaneto, D., Herniou, E. A., Boschetti, C., Caprioli, M., Melone, G., Ricci, C., & Barraclough, T. G. (2007). Independently evolving species in asexual bdelloid rotifers. PLoS biology, 5(4), e87.
    Fonseca, E. M., Duckett, D. J., & Carstens, B. C. (2021). P2C2M. GMYC: An R package for assessing the utility of the Generalized Mixed Yule Coalescent model. Methods in Ecology and Evolution, 12(3), 487-493.
    Forsdick, N. J., Martini, D., Brown, L., Cross, H. B., Maloney, R. F., Steeves, T. E., & Knapp, M. (2021). Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Global Ecology and Conservation, 28, e01681.
    Frugone, M. J., Cole, T. L., López, M. E., Clucas, G., Matos‐Maraví, P., Lois, N. A., ... & Vianna, J. A. (2021). Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation. Diversity and Distributions, 27(11), 2277-2296.
    Fujisawa, T., & Barraclough, T. G. (2013). Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic biology, 62(5), 707-724.
    Galante, P. J., Alade, B., Muscarella, R., Jansa, S. A., Goodman, S. M., & Anderson, R. P. (2018). The challenge of modeling niches and distributions for data‐poor species: a comprehensive approach to model complexity. Ecography, 41(5), 726-736.
    Galtier, N., & Daubin, V. (2008). Dealing with incongruence in phylogenomic analyses. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1512), 4023-4029.
    Ge, D., Wen, Z., Feijó, A., Lissovsky, A., Zhang, W., Cheng, J., ... & Yang, Q. (2023). Genomic consequences of and demographic response to pervasive hybridization over time in climate-sensitive Pikas. Molecular Biology and Evolution, 40(1), msac274.
    Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology, 59(3), 307-321.
    Hallowell, E. (1861). [1860] Report upon the Reptilia of the North Pacific exploring expedition, under command of Capt. John Roger. In Proc Acad Nat Sci Phil (Vol. 1860, pp. 480-510).
    Harrisson, K. A., Magrath, M. J., Yen, J. D., Pavlova, A., Murray, N., Quin, B., ... & Sunnucks, P. (2019). Lifetime fitness costs of inbreeding and being inbred in a critically endangered bird. Current Biology, 29(16), 2711-2717.
    Havird, J. C., & Miyamoto, M. M. (2010). The importance of taxon sampling in genomic studies: an example from the cyclooxygenases of teleost fishes. Molecular Phylogenetics and Evolution, 56(1), 451-455.
    He, Z., Li, X., Yang, M., Wang, X., Zhong, C., Duke, N. C., ... & Shi, S. (2019). Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. National Science Review, 6(2), 275-288.
    Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014). The fossilized birth–death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences, 111(29), E2957-E2966.
    Heathcote, R. J., While, G. M., MacGregor, H. E., Sciberras, J., Leroy, C., D'Ettorre, P., & Uller, T. (2016). Male behaviour drives assortative reproduction during the initial stage of secondary contact. Journal of evolutionary biology, 29(5), 1003-1015.
    Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: improving the ultrafast bootstrap approximation. Molecular biology and evolution, 35(2), 518-522.
    Hoelzel, A. R. (2023). Where to now with the evolutionarily significant unit?. Trends in Ecology & Evolution.
    Holt, R. D. (1987). On the relation between niche overlap and competition: the effect of incommensurable niche dimensions. Oikos, 110-114.
    Huang, W. S. (2007). Ecology and reproductive patterns of the agamid lizard Japalura swinhonis on an east Asian island, with comments on the small clutch sizes of island lizards. Zoological Science, 24(2), 181-188.
    Huang, J. P. (2020). Is population subdivision different from speciation? From phylogeography to species delimitation. Ecology and Evolution, 10(14), 6890-6896.
    Huson, D. H. (1998). SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics (Oxford, England), 14(1), 68-73.
    Ivanov, V., Lee, K. M., & Mutanen, M. (2018). Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression. Molecular Ecology, 27(7), 1681-1695.
    Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801-1806.
    Johnson, J. B., Macedo, D. C., Passow, C. N., & Rosenthal, G. G. (2014). Sexual ornaments, body morphology, and swimming performance in naturally hybridizing swordtails (Teleostei: Xiphophorus). PLoS One, 9(10), e109025.
    Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405.
    Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC genetics, 11(1), 1-15.
    Jones, G. (2014). STACEY package documentation: species delimitation and species tree estimation with BEAST2.
    Jones, G. (2017). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of mathematical biology, 74, 447-467.
    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.
    Kapli, P., Lutteropp, S., Zhang, J., Kobert, K., Pavlidis, P., Stamatakis, A., & Flouri, T. (2017). Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics, 33(11), 1630-1638.
    Karger, D. N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R. W., ... & Kessler, M. (2017). Climatologies at high resolution for the earth’s land surface areas. Scientific data, 4(1), 1-20.
    Karger D.N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R.W., Zimmermann, N.E,, Linder, H.P., Kessler, M.. Data from: Climatologies at high resolution for the earth’s land surface areas. Dryad Digital Repository.http://dx.doi.org/doi:10.5061/dryad.kd1d4
    Karney, C. F. (2013). Algorithms for geodesics. Journal of Geodesy, 87, 43-55.
    Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C. L., Pinilla‐Buitrago, G. E., Boria, R. A., ... & Anderson, R. P. (2021). ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution, 12(9), 1602-1608.
    Knaus, B. J., & Grünwald, N. J. (2017). vcfr: a package to manipulate and visualize variant call format data in R. Molecular ecology resources, 17(1), 44-53.
    Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A., & Mayrose, I. (2015). Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular ecology resources, 15(5), 1179-1191.
    Kozak, K. H., & Wiens, J. (2006). Does niche conservatism promote speciation? A case study in North American salamanders. Evolution, 60(12), 2604-2621.
    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.
    Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012). Inference of population structure using dense haplotype data. PLoS genetics, 8(1), e1002453.
    Leigh, J. W., & Bryant, D. (2015). POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6(9), 1110-1116.
    Lin, Jun-yi., & Lu, Kau-hung. (1982). Population ecology of the lizard Japalura swinhonis formosensis (Sauria: Agamidae) in Taiwan. Copeia, 425-434.
    Liu, X., & Fu, Y. X. (2020). Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome biology, 21(1), 1-9.
    Liu, S., Hou, M., Ananjeva, N. B., & Rao, D. (2023). Four new species of the genus Diploderma Hallowell, 1861 (Squamata, Agamidae) from China. ZooKeys, 1148, 167.
    Lopes, F., Oliveira, L. R., Beux, Y., Kessler, A., Cárdenas-Alayza, S., Majluf, P., ... & Bonatto, S. L. (2023). Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator. Science Advances, 9(18), eadf6601.
    Luu, K., Bazin, E., & Blum, M. G. (2017). pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular ecology resources, 17(1), 67-77.
    Ma, Y., Wang, J. I., Hu, Q., Li, J., Sun, Y., Zhang, L., ... & Mao, K. (2019). Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex. Communications Biology, 2(1), 213.
    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.
    Malinsky, M., Svardal, H., Tyers, A. M., Miska, E. A., Genner, M. J., Turner, G. F., & Durbin, R. (2018). Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature ecology & evolution, 2(12), 1940-1955.
    Malinsky, M., Matschiner, M., & Svardal, H. (2021). Dsuite‐Fast D‐statistics and related admixture evidence from VCF files. Molecular ecology resources, 21(2), 584-595.
    Mario dos Reis (2023). bppr: An R package for BPP. R package version 0.6.3.
    Mao, Yu Han. (2023). phyformat: Format Bioinformatics Data. R package version 0.0.0.9000.
    McLean, C. A., Bartle, R. A., Dong, C. M., Rankin, K. J., & Stuart-Fox, D. (2020). Divergent male and female mate preferences do not explain incipient speciation between lizard lineages. Current Zoology, 66(5), 485-492.
    McQuillan, M. A., Roth, T. C., Huynh, A. V., & Rice, A. M. (2018). Hybrid chickadees are deficient in learning and memory. Evolution, 72(5), 1155-1164.
    Medina, I., Wang, I. J., Salazar, C., & Amézquita, A. (2013). Hybridization promotes color polymorphism in the aposematic harlequin poison frog, O ophaga histrionica. Ecology and evolution, 3(13), 4388-4400.
    Meirmans, P. G. (2014). Nonconvergence in B ayesian estimation of migration rates. Molecular ecology resources, 14(4), 726-733.
    Miñano, M. R., While, G. M., Yang, W., Burridge, C. P., Sacchi, R., Zuffi, M., ... & Uller, T. (2021). Climate shapes the geographic distribution and introgressive spread of color ornamentation in common wall lizards. The American Naturalist, 198(3), 379-393.
    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.
    Morales, N. S., Fernández, I. C., & Baca-González, V. (2017). MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review. PeerJ, 5, e3093.
    Mussmann, S. M., Douglas, M. R., Chafin, T. K., & Douglas, M. E. (2019). BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data. Methods in Ecology and Evolution, 10(10), 1808-1813.
    Nabhan, A. R., & Sarkar, I. N. (2012). The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Briefings in bioinformatics, 13(1), 122-134.
    Naciri, Y., & Linder, H. P. (2015). Species delimitation and relationships: the dance of the seven veils. Taxon, 64(1), 3-16.
    Niemiller, M. L., Fitzpatrick, B. M., & Miller, B. T. (2008). Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Molecular ecology, 17(9), 2258-2275.
    Noguerales, V., & Ortego, J. (2022). Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution, 76(11), 2618-2633.
    Nosil, Patrik. "Speciation with gene flow could be common." (2008): 2103-2106.
    Ord, T. J., & Stuart‐Fox, D. (2006). Ornament evolution in dragon lizards: multiple gains and widespread losses reveal a complex history of evolutionary change. Journal of Evolutionary Biology, 19(3), 797-808.
    Ortego, J., Gutiérrez-Rodríguez, J., & Noguerales, V. (2021). Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers. Evolution, 75(8), 1998-2013.
    Ortiz, E.M. 2019. vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis. DOI:10.5281/zenodo.2540861
    Ota, H. (1989). Japalura brevipes Gressitt (Agamidae: Reptilia), a valid species from a high altitude area of Taiwan. Herpetologica, 55-60.
    Ota, H. (1991). Taxonomic redefinition of Japalura swinhonis Günther (Agamidae: Squamata), with a description of a new subspecies of J. polygonata from Taiwan. Herpetologica, 280-294.
    Ota, H. (2003). A new subspecies of the agamid lizard, Japalura polygonata (Hallowell, 1861)(Reptilia: Squamata), from Yonagunijima Island of the Yaeyama Group, Ryukyu Archipelago. Current Herpetology, 22(2), 61-71.
    Pamilo, P., & Nei, M. (1988). Relationships between gene trees and species trees. Molecular biology and evolution, 5(5), 568-583.
    Paradis, E., & Schliep, K. (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526-528.
    Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in parameter space: a road map for stacks. Methods in Ecology and Evolution, 8(10), 1360-1373.
    Pembleton, L. W., Cogan, N. O., & Forster, J. W. (2013). St AMPP: An R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations. Molecular ecology resources, 13(5), 946-952.
    Perry, B. W., Card, D. C., McGlothlin, J. W., Pasquesi, G. I., Adams, R. H., Schield, D. R., ... & Castoe, T. A. (2018). Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution, 10(8), 2110-2129.
    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.
    Peterson, A. T., & Nyari, A. S. (2008). Ecological niche conservatism and Pleistocene refugia in the thrush-like mourner, Schiffornis sp., in the Neotropics. Evolution, 62(1), 173-183.
    Petkova, D., Novembre, J., & Stephens, M. (2016). Visualizing spatial population structure with estimated effective migration surfaces. Nature genetics, 48(1), 94-100.
    Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximum entropy modeling of species geographic distributions. Ecological modelling, 190(3-4), 231-259.
    Pickrell, J., & Pritchard, J. (2012). Inference of population splits and mixtures from genome-wide allele frequency data. Nature Precedings, 1-1.
    Pinho, C., & Hey, J. (2010). Divergence with gene flow: models and data. Annual review of ecology, evolution, and systematics, 41, 215-230.
    Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., ... & Vogler, A. P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic biology, 55(4), 595-609.
    Popescu, A. A., Harper, A. L., Trick, M., Bancroft, I., & Huber, K. T. (2014). A novel and fast approach for population structure inference using kernel-PCA and optimization. Genetics, 198(4), 1421-1431.
    Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
    Puillandre, N., Lambert, A., Brouillet, S., & Achaz, G. J. M. E. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular ecology, 21(8), 1864-1877.
    Radosavljevic, A., & Anderson, R. P. (2014). Making better Maxent models of species distributions: complexity, overfitting and evaluation. Journal of biogeography, 41(4), 629-643.
    Rahbek, C., Borregaard, M. K., Antonelli, A., Colwell, R. K., Holt, B. G., Nogues-Bravo, D., ... & Fjeldså, J. (2019). Building mountain biodiversity: Geological and evolutionary processes. Science, 365(6458), 1114-1119.
    Rambaut, A. 2018. FigTree v.1.4.4. http://tree.bio.ed.ac.uk/software/figtree/ [accessed 23 January 2023].
    Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic biology, 67(5), 901-904.
    Rannala, B., & Yang, Z. (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164(4), 1645-1656.
    Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, https://imagej.nih.gov/ij/, 1997-2018.
    Rieppel, O., Walker, A., & Odhiambo, I. (1992). A preliminary report on a fossil chamaeleonine (Reptilia: Chamaeleoninae) skull from the Miocene of Kenya. Journal of Herpetology, 26(1), 77-80.
    Rochette, N. C., Rivera‐Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Molecular ecology, 28(21), 4737-4754.
    Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., ... & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology, 61(3), 539-542.
    Rosenberg, M. S., & Kumar, S. (2001). Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences, 98(19), 10751-10756.
    Rossi, N., Benitez-Vieyra, S., Cocucci, A., Chiaraviglio, M., & Cardozo, G. (2019). Sexual dichromatism and color diversity in the spiny lava lizard Tropidurus spinulosus using lizard visual modelling. Scientific Reports, 9(1), 14270.
    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. Molecular biology and evolution, 34(12), 3299-3302.
    Safran, R. J., & Nosil, P. (2012). Speciation: the origin of new species. Nature Education Knowledge, 3(10), 17.
    Salces-Castellano, A., Andújar, C., López, H., Pérez-Delgado, A. J., Arribas, P., & Emerson, B. C. (2021). Flightlessness in insects enhances diversification and determines assemblage structure across whole communities. Proceedings of the Royal Society B, 288(1945), 20202646.
    Schield, D. R., Perry, B. W., Adams, R. H., Card, D. C., Jezkova, T., Pasquesi, G. I., ... & Castoe, T. A. (2019). Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation. Biological Journal of the Linnean Society, 128(1), 149-169.
    Schilthuizen, M. (2000). Dualism and conflicts in understanding speciation. BioEssays, 22(12), 1134-1141.
    Schmidt, E. M., & Pfennig, K. S. (2016). Hybrid female mate choice as a species isolating mechanism: environment matters. Journal of evolutionary biology, 29(4), 865-869.
    Schoener, T. W. (1968). The Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology, 49(4), 704-726.
    Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature methods, 9(7), 671-675.
    Shen, Y. Y., Chen, X., & Murphy, R. W. (2013). Assessing DNA barcoding as a tool for species identification and data quality control. PloS one, 8(2), e57125.
    Shang, G. S. (1997). Phylogenetic Relationships and Biogeography in the Genus Japalura of Taiwan Base on the Variation of mtDNA Sequences. Master thesis of National Taiwan Normal University. National Digital Library of Theses and Dissertations in Taiwan. https://hdl.handle.net/11296/82z8qu
    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.
    Singhal, S., Huang, H., Grundler, M. R., Marchán-Rivadeneira, M. R., Holmes, I., Title, P. O., ... & Rabosky, D. L. (2018). Does population structure predict the rate of speciation? A comparative test across Australia’s most diverse vertebrate radiation. The American Naturalist, 192(4), 432-447.
    Singhal, S., & Moritz, C. (2012). Testing hypotheses for genealogical discordance in a rainforest lizard. Molecular Ecology, 21(20), 5059-5072.
    Smith, K. T., & Gauthier, J. A. (2013). Early Eocene lizards of the Wasatch Formation near Bitter Creek, Wyoming: diversity and paleoenvironment during an interval of global warming. Bulletin of the Peabody Museum of Natural History, 54(2), 135-230.
    Stadler, T. (2010). Sampling-through-time in birth–death trees. Journal of theoretical biology, 267(3), 396-404.
    Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.
    Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution, 75(6), 1256-1273.
    Stuart–Fox, D. M., & Ord, T. J. (2004). Sexual selection, natural selection and the evolution of dimorphic coloration and ornamentation in agamid lizards. Proceedings of the Royal Society of London. Series B: Biological Sciences, 271(1554), 2249-2255.
    Stift, M., Kolář, F., & Meirmans, P. G. (2019). Structure is more robust than other clustering methods in simulated mixed-ploidy populations. Heredity, 123(4), 429-441.
    Suárez, D., Arribas, P., Jiménez-García, E., & Emerson, B. C. (2022). Dispersal ability and its consequences for population genetic differentiation and diversification. Proceedings of the Royal Society B, 289(1975), 20220489.
    Sukumaran, J., & Knowles, L. L. (2017). Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences, 114(7), 1607-1612.
    Talavera, G., Dincă, V., & Vila, R. (2013). Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods in Ecology and Evolution, 4(12), 1101-1110.
    Tallowin, O. J., Meiri, S., Donnellan, S. C., Richards, S. J., Austin, C. C., & Oliver, P. M. (2020). The other side of the Sahulian coin: biogeography and evolution of Melanesian forest dragons (Agamidae). Biological Journal of the Linnean Society, 129(1), 99-113.
    Thorpe, R. S. (1975). Quantitative handling of characters useful in snake systematics with particular reference to intraspecific variation in the ringed snake Natrix natrix (L.). Biological Journal of the Linnean society, 7(1), 27-43.
    Toews, D. P., & Brelsford, A. (2012). The biogeography of mitochondrial and nuclear discordance in animals. Molecular ecology, 21(16), 3907-3930.
    Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D., & Corander, J. (2019). Fast hierarchical Bayesian analysis of population structure. Nucleic acids research, 47(11), 5539-5549.
    Wachter, G. A., Papadopoulou, A., Muster, C., Arthofer, W., Knowles, L. L., Steiner, F. M., & Schlick‐Steiner, B. C. (2016). Glacial refugia, recolonization patterns and diversification forces in Alpine‐endemic Megabunus harvestmen. Molecular Ecology, 25(12), 2904-2919.
    Wang, K., Che, J., Lin, S., Deepak, V., Aniruddha, D. R., Jiang, K., ... & Siler, C. D. (2019a). Multilocus phylogeny and revised classification for mountain dragons of the genus Japalura sl.(Reptilia: Agamidae: Draconinae) from Asia. Zoological Journal of the Linnean Society, 185(1), 246-267.
    Wang, K., Wu, J. W., Jiang, K., Chen, J. M., Miao, B. F., Siler, C. D., & Che, J. (2019b). A new species of Mountain Dragon (Reptilia: Agamidae: Diploderma) from the D. dymondi complex in southern Sichuan Province, China. Zoological Research, 40(5), 456.
    Wang, K., Ren, J., Wu, J., Jiang, K., Jin, J., Hou, S., ... & Che, J. (2021). Systematic revision of Mountain Dragons (Reptilia: Agamidae: Diploderma) in China, with descriptions of six new species and discussion on their conservation. Journal of Zoological Systematics and Evolutionary Research, 59(1), 222-263.
    Wang, K., Gao, W., Wu, J., Dong, W., Feng, X., Shen, W., ... & Che, J. (2021). Two New Species of Diploderma Hallowell, 1861 (Reptilia: Squamata: Agamidae) from the Hengduan Mountain Region in China and Rediscovery of D. brevicaudum (Manthey, Wolfgang, Hou, Wang, 2012). Zootaxa, 4941(1).
    Wang, K., Zhang, Y. P., & Li, X. Q. (2022). A New Species of Diploderma (Reptilia: Squamata: Agamidae) from the upper Salween River in Eastern Tibet, China. Zootaxa, 5099(2), 201-220.
    Waples, R. S., & Do, C. H. I. (2010). Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary applications, 3(3), 244-262.
    Warren, D. L., Glor, R. E., & Turelli, M. (2008). Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62(11), 2868-2883.
    Waters, J. M., Emerson, B. C., Arribas, P., & McCulloch, G. A. (2020). Dispersal reduction: causes, genomic mechanisms, and evolutionary consequences. Trends in Ecology & Evolution, 35(6), 512-522.
    While, G. M., Michaelides, S., Heathcote, R. J., MacGregor, H. E., Zajac, N., Beninde, J., ... & Uller, T. (2015). Sexual selection drives asymmetric introgression in wall lizards. Ecology Letters, 18(12), 1366-1375.
    Whiting, A. S., Bauer, A. M., & Sites Jr, J. W. (2003). Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae). Molecular phylogenetics and evolution, 29(3), 582-598.
    Wickham, H., & Wickham, H. (2016). Data analysis (pp. 189-201). Springer International Publishing.
    Wiens, J. J. (2003). Missing data, incomplete taxa, and phylogenetic accuracy. Systematic biology, 52(4), 528-538.
    Wilson, G. A., & Rannala, B. (2003). Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163(3), 1177-1191.
    Wisz, M. S., Hijmans, R. J., Li, J., Peterson, A. T., Graham, C. H., Guisan, A., & NCEAS Predicting Species Distributions Working Group. (2008). Effects of sample size on the performance of species distribution models. Diversity and distributions, 14(5), 763-773.
    Woodhead, J., Hand, S. J., Archer, M., Graham, I., Sniderman, K., Arena, D. A., ... & Price, E. (2016). Developing a radiometrically-dated chronologic sequence for Neogene biotic change in Australia, from the Riversleigh World Heritage Area of Queensland. Gondwana Research, 29(1), 153-167.
    Yang, Z. (2002). Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics, 162(4), 1811-1823.
    Yang, S. F., Komaki, S., Brown, R. M., & Lin, S. M. (2018). Riding the Kuroshio Current: stepping stone dispersal of the Okinawa tree lizard across the East Asian Island Arc. Journal of Biogeography, 45(1), 37-50.
    Yang, W., Feiner, N., Pinho, C., While, G. M., Kaliontzopoulou, A., Harris, D. J., ... & Uller, T. (2021). Extensive introgression and mosaic genomes of Mediterranean endemic lizards. Nature Communications, 12(1), 2762.
    Yang, Z., & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, 107(20), 9264-9269.
    Zerova, G. A., & Chkhikvadze, V. M. (1984). Review of Cenozoic lizards and snakes of the USSR. Izv. Akad. Nauk Gruz. SSR. Ser. Biol, 10, 319-126.
    Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869-2876.
    Zou, T., Kuang, W., Yin, T., Frantz, L., Zhang, C., Liu, J., ... & Yu, L. (2022). Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear. Proceedings of the National Academy of Sciences, 119(31), e2120307119.

    無法下載圖示 電子全文延後公開
    2029/02/01
    QR CODE