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研究生: 黃郁芯
Huang, Yu-Hsin
論文名稱: 白花蝴蝶蘭複合群之親緣地理與物種界定
Phylogeography and Species Delimitation of Phalaenopsis amabilis Complex
指導教授: 廖培鈞
Liao, Pei-Chun
李勇毅
Lee, Yung-I
口試委員: 廖培鈞
Liao, Pei-Chun
李勇毅
Lee, Yung-I
黃仁磐
Huang, Jen-Pan
口試日期: 2024/07/24
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: 中文
論文頁數: 96
中文關鍵詞: ddRADseq親緣地理蝴蝶蘭屬複合群物種界定
英文關鍵詞: ddRADseq, Phalaenopsis, phylogeography, species complex, species delimitation
DOI URL: http://doi.org/10.6345/NTNU202401747
論文種類: 學術論文
相關次數: 點閱:62下載:0
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  • 白花蝴蝶蘭複合群 (Phalaenopsis amabilis complex) 包含白花蝴蝶蘭 (P. aphrodite)、南洋白花蝴蝶蘭 (P. amabilis)、桑德蝴蝶蘭 (P. sanderiana) 及數個亞種。目前此複合群的分類觀點僅基於有限的形態特徵、地理分布及少量的分子標記,可能導致其物種界定和演化推論疑義。本研究在其分布範圍內採樣171個樣本,透過雙限制酶切位點標定法 (ddRADseq) 並結合形態學數據重建該複合群的親緣關係。本研究旨在闡明其物種界定並釐清演化歷史。綜合基因組資料和形態分析結果,P. amabilis中包含三個遺傳分群,分化過程中伴隨有限的基因交流,但形態上無法區分,顯示此類群尚處於分化早期。P. aphrodite中沒有明顯的遺傳分群,且P. aphrodite和P. sanderiana在遺傳和形態上皆無法區分別,分化過程中保持持續的基因交流。白花蝴蝶蘭複合群的演化歷史受到多次的播遷和隔離事件影響,其中,過去的氣候震盪導致的植被變化可能為P. amabilis遺傳分化的原因。基於綜合分類學,本研究結果不支持目前對於白花蝴蝶蘭複合群的分類觀點,建議將P. aphrodite和 P. sanderiana視為同一物種,且不再針對P. amabilis和P. aphrodite做進一步的種下位階劃分。

    The Phalaenopsis amabilis complex comprises P. aphrodite, P. amabilis, P. sanderiana, and several subspecies. The taxonomy of this complex was based on limited morphological traits, geographical distribution, and few genetic markers, which may have led to misconceptions in species delineation and evolutionary inference. This study sampled 171 individuals across their distribution range, employing ddRADseq to reconstruct their phylogenetic relationships. The aim was to elucidate species delimitation further and clarify the evolutionary history by combining molecular data and morphological analysis. Based on genomic data and morphological analysis, P. amabilis group consists of three distinct genetic groups, with limited gene flow during the speciation process. However, they are morphologically indistinguishable, suggesting that P. amabilis group is in the early stages of speciation. In contrast, the P. aphrodite group does not show any distinct genetic group. P. aphrodite and P. sanderiana are genetically and morphologically indistinguishable, with continous gene flow during the speciation process. The evolutionary history of the complex has been shaped by dispersal and vicariance events. The genetic differentiation within P. amabilis group appears to be influenced by vegetation changes stemming from climatic oscillations.
    Based on the integrative taxonomy, the current taxonomy of the Phalaenopsis amabilis complex is not corroborated. The results of this study do not support the current classification views regarding the Phalaenopsis aphrodite complex, suggesting that P. aphrodite and P. sanderiana should be considered the same species. Further infraspecific categorization between P. amabilis and P. aphrodite should no longer be pursued.

    前言 1 物種形成連續體 (speciation continuum) 1 白花蝴蝶蘭複合群概述 2 白花蝴蝶蘭複合群之分類沿革 4 白花蝴蝶蘭複合群之形態、地理分布與分子研究 6 東南亞島嶼之生物地理研究 8 綜合分類學與次世代定序於分類研究之應用 10 研究目的與問題 12 材料與方法 14 樣本採集 14 ddRADseq定序和取得遺傳變異資訊 14 遺傳結構檢測與遺傳多樣性指數 16 親緣關係樹重建 17 物種界定分析 17 形態分析 18 種內基因交流檢測 20 生物地理重建與分化時間分析 22 族群動態歷史模擬 24 結果 25 族群遺傳結構與遺傳多樣性指數 25 親緣關係樹重建 27 物種界定 28 形態分析 28 種內基因交流檢測 32 生物地理重建與分化時間 33 族群動態歷史模擬 36 討論 37 白花蝴蝶蘭複合群的族群結構與親緣關係 37 P. amabilis之族群結構與物種界定 38 P. aphrodite之族群結構與物種界定 42 P. amabilis類群之生物地理重建 45 P. aphrodite類群之生物地理重建 47 結論 50 參考文獻 52

    Ackerman, J. D., Sabat, A., & Zimmerman, J. (1996). Seedling establishment in an epiphytic orchid: an experimental study of seed limitation. Oecologia, 106, 192-198.
    Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655-1664.
    Alexandersson, R., & Ågren, J. (2000). Genetic structure in the nonrewarding, bumblebee-pollinated orchid Calypso bulbosa. Heredity, 85(4), 401-409.
    Anderson, B. M., Binks, R. M., Byrne, M., Crawford, A. D., & Shepherd, K. A. (2023). Using RADseq to resolve species boundaries in a morphologically complex group of yellow-flowered shrubs (Geleznowia, Rutaceae). Australian Systematic Botany, 36(4), 277-311.
    Arditti, J. (1992). Fundamentals of orchid biology. New York: John Wiley & Sons.
    Asa, M., & Kaviani, B. (2020). In vitro propagation of orchid Phalaenopsis amabilis (L.) Blume var. Jawa. Iranian Journal of Plant Physiology, 10(2), 3113-3123.
    Atkins, H. J., Bramley, G. L., Johnson, M. A., Kartonegoro, A., Nishii, K., Kokubugata, G., Moeller, M., & Hughes, M. (2020). A molecular phylogeny of Southeast Asian Cyrtandra (Gesneriaceae) supports an emerging paradigm for Malesian plant biogeography. Frontiers of Biogeography, 12(1), e44814.
    Avise, J. C. (2000). Phylogeography: the history and formation of species. Harvard university press.
    Beheregaray, L. B., Cooke, G. M., Chao, N. L., & Landguth, E. L. (2015). Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia. Frontiers in Genetics, 5, 477.
    Binks, R. M., & Byrne, M. (2022). Species delimitation, hybridization and possible apomixis in a rapid radiation of Western Australian Leptospermum (Myrtaceae). Botanical Journal of the Linnean Society, 200(3), 378-394.
    Blume, C. L. (1825). Bijdragen tot de flora van Nederlandsch Indië (Vol. 1). ter Lands Drukkerij.
    Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.
    Brown, R., & Diesmos, A. (2002). Application of lineage-based species concepts to oceanic island frog populations: the effects of differing taxonomic philosophies on the estimation of Philippine biodiversity. Silliman Journal, 42(1), 133-162.
    Brown, R. M., Siler, C. D., Oliveros, C. H., Esselstyn, J. A., Diesmos, A. C., Hosner, P. A., Linkem, C. W., Barley, A. J., Oaks, J. R., & Sanguila, M. B. (2013). Evolutionary processes of diversification in a model island archipelago. Annual Review of Ecology, Evolution, and Systematics, 44, 411-435.
    Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29(8), 1917-1932.
    Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., He, Y., Xu, Q., & Bian, C. (2015). The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics, 47(1), 65-72.
    Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22(11), 3124-3140.
    Chalker-Scott, L. K. (2018). How are Hydrangea Flower Colors Determined? Washington State University Extension.
    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), s13742-13015-10047-13748.
    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.
    Chang, S.-B., Chen, W.-H., Chen, H.-H., Fu, Y.-M., & Lin, Y.-S. (2000). RFLP and inheritance patterns of chloroplast DNA in intergeneric hybrids of Phalaenopsis and Doritis. Botanical Bulletin of Academia Sinica, 41.
    Chao, Y. T., Chen, W. C., Chen, C. Y., Ho, H. Y., Yeh, C. H., Kuo, Y. T., Su, C. L., Yen, S. H., Hsueh, H. Y., & Yeh, J. H. (2018). Chromosome‐level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. Plant Biotechnology Journal, 16(12), 2027-2041.
    Chen, J.-h., Huang, Y., Brachi, B., Yun, Q.-z., Zhang, W., Lu, W., Li, H.-n., Li, W.-q., Sun, X.-d., & Wang, G.-y. (2019). Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot. Nature Communications, 10(1), 5230.
    Christenson, E. A. (2001). Phalaenopsis. Timber Press.
    Chugh, S., Guha, S., & Rao, I. U. (2009). Micropropagation of orchids: a review on the potential of different explants. Scientia Horticulturae, 122(4), 507-520.
    Coyne, J. A. (1992). Genetics and speciation. Nature, 355(6360), 511-515.
    Crayn, D. M., Costion, C., & Harrington, M. G. (2015). The Sahul–Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. Journal of Biogeography, 42(1), 11-24.
    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. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158.
    Dayrat, B. (2005). Towards integrative taxonomy. Biological Journal of the Linnean Society, 85(3), 407-417.
    De Bruyn, M., Stelbrink, B., Morley, R. J., Hall, R., Carvalho, G. R., Cannon, C. H., van den Bergh, G., Meijaard, E., Metcalfe, I., & Boitani, L. (2014). Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity. Systematic Biology, 63(6), 879-901.
    de Queiroz, K. (2005). A unified concept of species and its consequences for the future of taxonomy. Proceedings of the California Academy of Sciences.
    De Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56(6), 879-886.
    DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., Del Angel, G., Rivas, M. A., & Hanna, M. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5), 491-498.
    DeRaad, D. A., McCormack, J. E., Chen, N., Peterson, A. T., & Moyle, R. G. (2022). Combining species delimitation, species trees, and tests for gene flow clarifies complex speciation in scrub-jays. Systematic Biology, 71(6), 1453-1470.
    Dickerson, R. E., Merrill, E. D., McGregor, R. C., Schultze, W., Taylor, E. H., & Herre, A. W. (1928). Distribution of Life in the Philippines. Bureau of printing.
    Dong, W., Li, E., Liu, Y., Xu, C., Wang, Y., Liu, K., Cui, X., Sun, J., Suo, Z., & Zhang, Z. (2022). Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family. BMC Biology, 20(1), 1-25.
    Dong, X., Yi, W., Zheng, C., Zhu, X., Wang, S., Xue, H., Ye, Z., & Bu, W. (2022). Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. Zoologica Scripta, 51(2), 185-198.
    Doyle, J. J. (1990). Isolation of plant DNA from faesh tissue. Focus, 12, 13-15.
    Díaz, B. G., Zucchi, M. I., Alves‐Pereira, A., de Almeida, C. P., Moraes, A. C. L., Vianna, S. A., Azevedo-Filho, J., & Colombo, C. A. (2021). Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species. PLoS One, 16(7), e0241025.
    Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One, 6(5), e19379.
    Endler, J. A. (1977). Geographic variation, speciation, and clines. Princeton University Press.
    Esposito, S., Cardi, T., Campanelli, G., Sestili, S., Díez, M. J., Soler, S., Prohens, J., & Tripodi, P. (2020). ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean ‘da serbo’type long shelf-life germplasm. Horticulture Research, 7.
    Esselstyn, J. A., Timm, R. M., & Brown, R. M. (2009). Do geological or climatic processes drive speciation in dynamic archipelagos? The tempo and mode of diversification in Southeast Asian shrews. Evolution, 63(10), 2595-2610.
    Evans, B. J., Brown, R. M., McGuire, J. A., Supriatna, J., Andayani, N., Diesmos, A., Iskandar, D., Melnick, D. J., & Cannatella, D. C. (2003). Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Systematic Biology, 52(6), 794-819.
    Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C., & Foll, M. (2013). Robust demographic inference from genomic and SNP data. PLoS Genetics, 9(10), e1003905.
    Ezard, T., Fujisawa, T., & Barraclough, T. (2017). SPecies’ LImits by Threshold Statistics. R package version [Online]. Available online at: https://R-Forge.Rproject.org/projects/splits/ (accessed May 20, 2021).
    Feder, J. L., Egan, S. P., & Nosil, P. (2012). The genomics of speciation-with-gene-flow. Trends in Genetics, 28(7), 342-350.
    Fowlie, J. A., & Miller, J. (1975). Notes on the distribution of Phalaenopsis in the Philippines, with a useful climate summary Part III. Orchid Digest, 38, 219-221.
    Freeman, H. (1974). Computer processing of line-drawing images. ACM Computing Surveys (CSUR), 6(1), 57-97.
    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.
    Gante, H. F., Matschiner, M., Malmstrøm, M., Jakobsen, K. S., Jentoft, S., & Salzburger, W. (2016). Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Molecular Ecology, 25(24), 6143-6161.
    Ghaedi, Z., Badri, S., Saberi-Pirooz, R., Vaissi, S., Javidkar, M., & Ahmadzadeh, F. (2021). The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara). Zoological Journal of the Linnean Society, 192(4), 1123-1136.
    Ghimire, B., Son, S., Kim, J. H., & Jeong, M. J. (2020). Gametophyte and embryonic ontogeny: understanding the reproductive calendar of Cypripedium japonicum Thunb.(Cypripedoideae, Orchidaceae), a lady’s slipper orchid endemic to East Asia. BMC Plant Biology, 20, 1-14.
    Greenleaf, S. S., Williams, N. M., Winfree, R., & Kremen, C. (2007). Bee foraging ranges and their relationship to body size. Oecologia, 153, 589-596.
    Grismer, L. L., Wood Jr, P. L., Anuar, S., Muin, M. A., Quah, E. S., McGuire, J. A., Brown, R. M., Van Tri, N., & Hong Thai, P. (2013). Integrative taxonomy uncovers high levels of cryptic species diversity in Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia. Zoological Journal of the Linnean Society, 169(4), 849-880.
    Grohar, M. C., Medic, A., Ivancic, T., Veberic, R., & Jogan, J. (2022). Color variation and secondary metabolites’ footprint in a taxonomic complex of Phyteuma sp.(Campanulaceae). Plants, 11(21), 2894.
    Haelewaters, D., De Kesel, A., & Pfister, D. H. (2018). Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds. Scientific Reports, 8(1), 15966.
    Hall, R. (1998). The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. Biogeography and Geological Evolution of SE Asia, 99-131.
    Hall, R. (2009). Southeast Asia's changing palaeogeography. Blumea-Biodiversity, Evolution and Biogeography of Plants, 54(1-2), 148-161.
    Hamilton, R., Amano, N., Bradshaw, C. J., Saltré, F., Patalano, R., Penny, D., Stevenson, J., Wolfhagen, J., & Roberts, P. (2024). Forest mosaics, not savanna corridors, dominated in Southeast Asia during the Last Glacial Maximum. Proceedings of the National Academy of Sciences, 121(1), e2311280120.
    Hamrick, J. L., & Trapnell, D. W. (2011). Using population genetic analyses to understand seed dispersal patterns. Acta Oecologica, 37(6), 641-649.
    Hanebuth, T. J., Voris, H. K., Yokoyama, Y., Saito, Y., & Okuno, J. i. (2011). Formation and fate of sedimentary depocentres on Southeast Asia's Sunda Shelf over the past sea-level cycle and biogeographic implications. Earth-Science Reviews, 104(1-3), 92-110.
    Harrison, R. G., & Larson, E. L. (2014). Hybridization, introgression, and the nature of species boundaries. Journal of Heredity, 105(S1), 795-809.
    Haug, J. T., Haug, G. T., Zippel, A., van der Wal, S., Müller, P., Gröhn, C., Wunderlich, J., Hoffeins, C., Hoffeins, H.-W., & Haug, C. (2021). Changes in the morphological diversity of larvae of lance lacewings, mantis lacewings and their closer relatives over 100 million years. Insects, 12(10), 860.
    Haywood, A. M., Dowsett, H. J., Valdes, P. J., Lunt, D. J., Francis, J. E., & Sellwood, B. W. (2009). Introduction. Pliocene climate, processes and problems. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367(1886), 3-17.
    Heaney, L. R. (1985). Zoogeographic evidence for middle and upper Pleistocene land bridges to the Philippine islands. Modern Quaternary Research in Southeast Asia, 9, 127-143.
    Holloway, J. D., & Hall, R. (1998). SE Asian geology and biogeography: an introduction. Biogeography and geological evolution of SE Asia, 1-23.
    Honnay, O., & Jacquemyn, H. (2007). Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conservation Biology, 21(3), 823-831.
    Hou, Y., Nowak, M. D., Mirre, V., Bjorå, C. S., Brochmann, C., & Popp, M. (2015). Thousands of RAD-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus Diapensia (Diapensiaceae). PLoS One, 10(10), e0140175.
    Huang, J. P. (2020). Is population subdivision different from speciation? From phylogeography to species delimitation. Ecology and Evolution, 10(14), 6890-6896.
    Husson, L., Boucher, F. C., Sarr, A. C., Sepulchre, P., & Cahyarini, S. Y. (2020). Evidence of Sundaland’s subsidence requires revisiting its biogeography. Journal of Biogeography, 47(4), 843-853.
    Iwata, H., Niikura, S., Matsuura, S., Takano, Y., & Ukai, Y. (2000). Diallel analysis of root shape of Japanese radish (Raphanus sativus L.) based on elliptic Fourier descriptors. Breeding Science, 50(2), 73-80.
    Iwata, H., & Ukai, Y. (2002). SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity, 93(5), 384-385.
    Jang, S., Choi, S.-C., Li, H.-Y., An, G., & Schmelzer, E. (2015). Functional characterization of Phalaenopsis aphrodite flowering genes PaFT1 and PaFD. PLoS One, 10(8), e0134987.
    Joyce, E. M., Pannell, C. M., Rossetto, M., Yap, J. Y. S., Thiele, K. R., Wilson, P. D., & Crayn, D. M. (2021). Molecular phylogeography reveals two geographically and temporally separated floristic exchange tracks between Southeast Asia and northern Australia. Journal of Biogeography, 48(5), 1213-1227.
    Kartonegoro, A., Mota de Oliveira, S., & van Welzen, P. C. (2022). Historical biogeography of the Southeast Asian and Malesian tribe Dissochaeteae (Melastomataceae). Journal of Systematics and Evolution, 60(2), 237-252.
    Kartzinel, T. R., Trapnell, D. W., & Shefferson, R. P. (2013). Critical importance of large native trees for conservation of a rare Neotropical epiphyte. Journal of Ecology, 101(6), 1429-1438.
    Kashiwaya, K., Ochiai, S., Sakai, H., & Kawai, T. (2001). Orbit-related long-term climate cycles revealed in a 12-Myr continental record from Lake Baikal. Nature, 410(6824), 71-74.
    Kim, D., Bauer, B. H., & Near, T. J. (2022). Introgression and species delimitation in the longear sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae). Systematic Biology, 71(2), 273-285.
    Kuhl, F. P., & Giardina, C. R. (1982). Elliptic Fourier features of a closed contour. Computer Graphics and Image Processing, 18(3), 236-258.
    Kyriazis, C. C., Alam, B., Wjodyla, M., Hackett, S., Hosner, P., Mays Jr, H. L., Heaney, L. R., & Reddy, S. (2018). Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines. Molecular Phylogenetics and Evolution, 121, 121-131.
    Lee, Y.-I., Chung, M.-C., Kuo, H.-C., Wang, C.-N., Lee, Y.-C., Lin, C.-Y., Jiang, H., & Yeh, C.-H. (2017). The evolution of genome size and distinct distribution patterns of rDNA in Phalaenopsis (Orchidaceae). Botanical Journal of the Linnean Society, 185(1), 65-80.
    Lee, Y.-I., Tseng, Y. F., Lee, Y.-C., & Chung, M.-C. (2020). Chromosome constitution and nuclear DNA content of Phalaenopsis hybrids. Scientia Horticulturae, 262, 109089.
    Leroy, T., Roux, C., Villate, L., Bodénès, C., Romiguier, J., Paiva, J. A., Dossat, C., Aury, J. M., Plomion, C., & Kremer, A. (2017). Extensive recent secondary contacts between four European white oak species. New Phytologist, 214(2), 865-878.
    Lexer, C., & Widmer, A. (2008). The genic view of plant speciation: recent progress and emerging questions. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1506), 3023-3036.
    Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
    Li, M.-R., Wang, H.-Y., Ding, N., Lu, T., Huang, Y.-C., Xiao, H.-X., Liu, B., & Li, L.-F. (2019). Rapid divergence followed by adaptation to contrasting ecological niches of two closely related columbine species Aquilegia japonica and A. oxysepala. Genome Biology and Evolution, 11(3), 919-930.
    Lohman, D. J., de Bruyn, M., Page, T., von Rintelen, K., Hall, R., Ng, P. K., Shih, H.-T., Carvalho, G. R., & von Rintelen, T. (2011). Biogeography of the Indo-Australian archipelago. Annual Review of Ecology, Evolution, and Systematics, 42, 205-226.
    Lundberg, J. G., Marshall, L. G., Guerrero, J., Horton, B., Malabarba, M., & Wesselingh, F. (1998). The stage for Neotropical fish diversification: a history of tropical South American rivers. Phylogeny and Classification of Neotropical Fishes, 27, 13-48.
    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.
    Maeda, H., Akagi, T., & Tao, R. (2018). Quantitative characterization of fruit shape and its differentiation pattern in diverse persimmon (Diospyros kaki) cultivars. Scientia Horticulturae, 228, 41-48.
    Mallet, B., Martos, F., Blambert, L., Pailler, T., & Humeau, L. (2014). Evidence for isolation-by-habitat among populations of an epiphytic orchid species on a small oceanic island. PLoS One, 9(2), e87469.
    Mallet, J. (2008). Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1506), 2971-2986.
    Massatti, R., Reznicek, A. A., & Knowles, L. L. (2016). Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae. American Journal of Botany, 103(2), 337-347.
    Matzke, N. J. (2014). Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Systematic Biology, 63(6), 951-970.
    Mayr, E. (1963). Animal species and evolution. Harvard University Press.
    Mayr, E. (1999). Systematics and the origin of species, from the viewpoint of a zoologist. Harvard University Press.
    McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., & Daly, M. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303.
    Mitra, G. (1971). Studies on seeds, shoot-tips and stem-discs of an orchid grown in aseptic culture.
    Mohtadi, M., Prange, M., & Steinke, S. (2016). Palaeoclimatic insights into forcing and response of monsoon rainfall. Nature, 533(7602), 191-199.
    Morley, R. J. (2003). Interplate dispersal paths for megathermal angiosperms. Perspectives in Plant Ecology, Evolution and Systematics, 6(1-2), 5-20.
    Morley, R. J. (2012). A review of the Cenozoic palaeoclimate history of Southeast Asia. Biotic Evolution and Environmental Change in Southeast Asia, 79-114.
    Muellner, A. N., Pannell, C. M., Coleman, A., & Chase, M. W. (2008). The origin and evolution of Indomalesian, Australasian and Pacific island biotas: insights from Aglaieae (Meliaceae, Sapindales). Journal of Biogeography, 35(10), 1769-1789.
    Naish, T. R., & Wilson, G. S. (2009). Constraints on the amplitude of Mid-Pliocene (3.6–2.4 Ma) eustatic sea-level fluctuations from the New Zealand shallow-marine sediment record. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367(1886), 169-187.
    Nathan, R. (2006). Long-distance dispersal of plants. Science, 313(5788), 786-788.
    Nathan, R., Katul, G. G., Horn, H. S., Thomas, S. M., Oren, R., Avissar, R., Pacala, S. W., & Levin, S. A. (2002). Mechanisms of long-distance dispersal of seeds by wind. Nature, 418(6896), 409-413.
    Nauheimer, L., Boyce, P. C., & Renner, S. S. (2012). Giant taro and its relatives: a phylogeny of the large genus Alocasia (Araceae) sheds light on Miocene floristic exchange in the Malesian region. Molecular Phylogenetics and Evolution, 63(1), 43-51.
    Nichols, R. (2001). Gene trees and species trees are not the same. Trends in Ecology & Evolution, 16(7), 358-364.
    Okuyama, Y., Goto, N., Nagano, A. J., Yasugi, M., Kokubugata, G., Kudoh, H., Qi, Z., Ito, T., Kakishima, S., & Sugawara, T. (2020). Radiation history of Asian Asarum (sect. Heterotropa, Aristolochiaceae) resolved using a phylogenomic approach based on double-digested RAD-seq data. Annals of Botany, 126(2), 245-260.
    Padial, J. M., Miralles, A., De la Riva, I., & Vences, M. (2010). The integrative future of taxonomy. Frontiers in Zoology, 7(1), 1-14.
    Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290.
    Paran, F. J., Ikeo, K., Asakura, A., & Nakano, T. (2023). Species divergence despite minimal morphological differentiation and habitat overlap in the Patelloida saccharina (Patellogastropoda: Lottiidae) species complex. Biological Journal of the Linnean Society, 139(2), 173-191.
    Patton, A. H., Margres, M. J., Stahlke, A. R., Hendricks, S., Lewallen, K., Hamede, R. K., Ruiz-Aravena, M., Ryder, O., McCallum, H. I., & Jones, M. E. (2019). Contemporary demographic reconstruction methods are robust to genome assembly quality: a case study in Tasmanian devils. Molecular Biology and Evolution, 36(12), 2906-2921.
    Pedersen, M. P., Irestedt, M., Joseph, L., Rahbek, C., & Jønsson, K. A. (2018). Phylogeography of a ‘great speciator’(Aves: Edolisoma tenuirostre) reveals complex dispersal and diversification dynamics across the Indo‐Pacific. Journal of Biogeography, 45(4), 826-837.
    Pelser, P. B., Nickrent, D. L., van Ee, B. W., & Barcelona, J. F. (2019). A phylogenetic and biogeographic study of Rafflesia (Rafflesiaceae) in the Philippines: Limited dispersal and high island endemism. Molecular Phylogenetics and Evolution, 139, 106555.
    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.
    Petit, R. J., & Excoffier, L. (2009). Gene flow and species delimitation. Trends in Ecology & Evolution, 24(7), 386-393.
    Prata, E. M., Sass, C., Rodrigues, D. P., Domingos, F. M., Specht, C. D., Damasco, G., Ribas, C. C., Fine, P. V., & Vicentini, A. (2018). Towards integrative taxonomy in Neotropical botany: disentangling the Pagamea guianensis species complex (Rubiaceae). Botanical Journal of the Linnean Society, 188(2), 213-231.
    Qin, X., Liu, Y., Mao, S., Li, T., Wu, H., Chu, C., & Wang, Y. (2011). Genetic transformation of lipid transfer protein encoding gene in Phalaenopsis amabilis to enhance cold resistance. Euphytica, 177, 33-43.
    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.
    Rancilhac, L., Goudarzi, F., Gehara, M., Hemami, M.-R., Elmer, K. R., Vences, M., & Steinfarz, S. (2019). Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Molecular Phylogenetics and Evolution, 133, 189-197.
    Rasmussen, H. N. (2002). Recent developments in the study of orchid mycorrhiza. Plant and Soil, 244, 149-163.
    Rice, W. R., & Hostert, E. E. (1993). Laboratory experiments on speciation: what have we learned in 40 years? Evolution, 47(6), 1637-1653.
    Rittmeyer, E. N., & Austin, C. C. (2012). The effects of sampling on delimiting species from multi-locus sequence data. Molecular Phylogenetics and Evolution, 65(2), 451-463.
    Rohlf, F. J., & Archie, J. W. (1984). A comparison of Fourier methods for the description of wing shape in mosquitoes (Diptera: Culicidae). Systematic Zoology, 33(3), 302-317.
    Schemske, D. W., & Bierzychudek, P. (2001). Perspective: evolution of flower color in the desert annual Linanthus parryae: Wright revisited. Evolution, 55(7), 1269-1282.
    Schiestl, F. P., & Schlüter, P. M. (2009). Floral isolation, specialized pollination, and pollinator behavior in orchids. Annual Review of Entomology, 54(1), 425-446.
    Scopece, G., Musacchio, A., Widmer, A., & Cozzolino, S. (2007). Patterns of reproductive isolation in Mediterranean deceptive orchids. Evolution, 61(11), 2623-2642.
    Sheldon, F. H., Lim, H. C., & Moyle, R. G. (2015). Return to the Malay Archipelago: the biogeography of Sundaic rainforest birds. Journal of Ornithology, 156, 91-113.
    Sholihah, A., Delrieu-Trottin, E., Condamine, F. L., Wowor, D., Rüber, L., Pouyaud, L., Agnèse, J.-F., & Hubert, N. (2021). Impact of Pleistocene eustatic fluctuations on evolutionary dynamics in Southeast Asian biodiversity hotspots. Systematic Biology, 70(5), 940-960.
    Shrestha, M., Tai, K.-C., Dyer, A. G., Garcia, J. E., Yang, E.-C., Jentsch, A., & Wang, C.-N. (2024). Flower colour and size-signals vary with altitude and resulting climate on the tropical-subtropical islands of Taiwan. Frontiers in Plant Science, 15, 1304849.
    Siler, C. D., Oaks, J. R., Welton, L. J., Linkem, C. W., Swab, J. C., Diesmos, A. C., & Brown, R. M. (2012). Did geckos ride the Palawan raft to the Philippines? Journal of Biogeography, 39(7), 1217-1234.
    Skeels, A., Boschman, L., McFadden, I. R., Joyce, E. M., Hagen, O., Jiménez Robles, O., Bach, W., Boussange, V., Keggin, T., & Jetz, W. (2023). Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace’s Line. Science, 381(6653), 86-92.
    Skeels, A., Dinnage, R., Medina, I., & Cardillo, M. (2021). Ecological interactions shape the evolution of flower color in communities across a temperate biodiversity hotspot. Evolution Letters, 5(3), 277-289.
    Slatkin, M. (1987). Gene flow and the geographic structure of natural populations. Science, 236(4803), 787-792.
    Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution, 75(6), 1256-1273.
    Stanton, D. W., Frandsen, P., Waples, R. K., Heller, R., Russo, I.-R. M., Orozco-terWengel, P. A., Pedersen, C.-E. T., Siegismund, H. R., & Bruford, M. W. (2019). More grist for the mill? Species delimitation in the genomic era and its implications for conservation. Conservation Genetics, 20, 101-113.
    Su, Y. C., & Saunders, R. M. (2009). Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea. BMC Evolutionary Biology, 9, 1-19.
    Sumanon, P., Balslev, H., Utteridge, T. M., & Eiserhardt, W. L. (2023). A species‐level phylogenetic framework and infrageneric classification for the genus Maesa (Primulaceae). TAXON, 72(4), 791-810.
    Supple, M. A., Papa, R., Hines, H. M., McMillan, W. O., & Counterman, B. A. (2015). Divergence with gene flow across a speciation continuum of Heliconius butterflies. BMC Evolutionary Biology, 15(1), 1-12.
    Sweet, H. R. (1969). A revision of the genus Phalaenopis-VII. American Orchid Society Bulletin, 38, 681-694.
    Sweet, H. R. (1980). The genus Phalaenopsis. The Orchid Digest. Pomona, California.
    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.
    Thom, G., Amaral, F. R. D., Hickerson, M. J., Aleixo, A., Araujo-Silva, L. E., Ribas, C. C., Choueri, E., & Miyaki, C. Y. (2018). Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species. Systematic Biology, 67(4), 700-718.
    Thomas, D. C., Hughes, M., Phutthai, T., Ardi, W., Rajbhandary, S., Rubite, R., Twyford, A. D., & Richardson, J.-E. (2012). West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago. Journal of Biogeography, 39(1), 98-113.
    Toonen, R. J., Puritz, J. B., Forsman, Z. H., Whitney, J. L., Fernandez-Silva, I., Andrews, K. R., & Bird, C. E. (2013). ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ, 1, e203.
    Tsai, C.-C., Chou, C.-H., Wang, H.-V., Ko, Y.-Z., Chiang, T.-Y., & Chiang, Y.-C. (2015). Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs. BMC Plant Biology, 15(1), 1-16.
    Tsai, C., Chiang, Y., Huang, S., Chen, C., & Chou, C. (2010). Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA. Plant Systematics and Evolution, 288, 77-98.
    Van Dam, M. H., Anzano Cabras, A., & Lam, A. W. (2023). How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae). Systematic Biology, 72(3), 516-529.
    Van Welzen, P. C., Parnell, J. A., & Slik, J. F. (2011). Wallace's Line and plant distributions: two or three phytogeographical areas and where to group Java? Biological Journal of the Linnean society, 103(3), 531-545.
    Villalvazo-Hernández, A., Burgos-Hernández, M., & González, D. (2022). Phylogenetic analysis and flower color evolution of the Subfamily Linoideae (Linaceae). Plants, 11(12), 1579.
    Visher, S. S. (1925). Tropical cyclones and the dispersal of life from island to island in the Pacific. The American Naturalist, 59(660), 70-78.
    Viswanath, K. K., Huang, J.-Z., Chin, S.-W., & Chen, F.-C. (2021). Phalaenopsis Genome and Transcriptome Exploitation and Its Application for Breeding. The Orchid Genome, 49-65.
    Voris, H. K. (2000). Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27(5), 1153-1167.
    Wallbrunn, H. (1971). A second look at the" Revision of the genus Phalaenopsis".
    Wang, P., Clemens, S., Beaufort, L., Braconnot, P., Ganssen, G., Jian, Z., Kershaw, P., & Sarnthein, M. (2005). Evolution and variability of the Asian monsoon system: state of the art and outstanding issues. Quaternary Science Reviews, 24(5-6), 595-629.
    Werneck, F. P., Leite, R. N., Geurgas, S. R., & Rodrigues, M. T. (2015). Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga. BMC Evolutionary Biology, 15, 1-24.
    Wessinger, C. A., & Rausher, M. D. (2012). Lessons from flower colour evolution on targets of selection. Journal of Experimental Botany, 63(16), 5741-5749.
    Whitney, K. D., Ahern, J. R., Campbell, L. G., Albert, L. P., & King, M. S. (2010). Patterns of hybridization in plants. Perspectives in Plant Ecology, Evolution and Systematics, 12(3), 175-182.
    Woodruff, D. S., & Turner, L. M. (2009). The Indochinese–Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions. Journal of Biogeography, 36(5), 803-821.
    Yoshioka, Y., Iwata, H., Ohsawa, R., & Ninomiya, S. (2004). Analysis of petal shape variation of Primula sieboldii by elliptic Fourier descriptors and principal component analysis. Annals of Botany, 94(5), 657-664.
    Yu, Y., Harris, A. J., Blair, C., & He, X. (2015). RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Molecular Phylogenetics and Evolution, 87, 46-49.
    Zhang, Z., Gale, S. W., Li, J.-H., Fischer, G. A., Ren, M.-X., & Song, X.-Q. (2019). Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid. BMC Plant Biology, 19, 1-16.

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