第五章 結語
附表 3 作者於博士班期間協助實驗室進行的研究發表
2020
1. Yu, Tao, Jian Gao, Bing-Hong Huang, Buddhi Dayananda, Wen-Bao Ma, Yu-Yang Zhang, Pei-Chun Liao, Jun-Qing Li. 2020. Comparative plastome analyses and phylogenetic applications of Acer section Platanoidea. Forests 11(4): 462; doi: 10.3390/f11040462
2. Yang, Yong-Zhi, Run-Hong Gao, Min-Xin Luo, Bing-Hong Huang, Pei-Chun Liao. 2020.
Tissue-specific bioaccumulation of heavy metals in Ammopiptanthus mongolicus, the only evergreen shrub in the desert of Northwest China. Taiwania 65(2): 140-148; doi:
10.6165/tai.2020.65.140
3. Chao, Chien-Ti, Bing-Hong Huang, Jui-Tse Chang, Pei-Chun Liao. 2020. Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data. PhytoKeys 140:33-45; doi: 10.3897/phytokeys.140.48578
4. Jin, Wei-Yin, Hai-Wen Li, Ran Wei, Bing-Hong Huang, Bing Liu, Tian-Tian Sun, David J.
Mabberley, Pei-Chun Liao, Yong Yang. 2019. New insights into biogeographic disjunctions between Taiwan and the Eastern Himalayas: the case of Prinsepia (Rosaceae). Taxon (Accepted);
doi:10.1002/tax.12209
5. Yu, Tao, Bing-Hong Huang, Yuyang Zhang, Pei-Chun Liao*, Jun-Qing Li*. 2019. Chloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch.: gene organization, comparative and phylogenetic analysis. Physiology and Molecular Biology of Plants 26: 409-418.
DOI :10.1007/s12298-019-00736-7 2019
6. Bing-Hong Huang, Kanae Nishii, Chun-Neng Wang, Michael Moeller. 2019. Quantitative assessment of anisocotyly in Haberlea rhodopensis and Ramonda myconi. Edinburgh Journal of Botany 76: 377-391. DOI :10.1017/S0960428619000179
7. Tseng, Yi-Ting, Min-Xin Luo, Bing-Hong Huang, Pei-Chun Liao. 2019. Development of transferable expressed sequence tag-simple sequence repeat (EST-SSR) markers for delimitating two recently diverged gingers endemic to Taiwan. Taiwania 64(2): 209-216; doi:
10.6165/tai.2019.64.209
8. Luo, Min-Xin, Meng-Yuan Huang, Chih-Kai Yang, Yi-Zhou He, Bing-Hong Huang, Pei-Chun Liao 2019. Deviation from the Brownian motion expectation implies episodic adaptive divergences in traits of Lithocarpus species in Taiwan. Taiwania 64(2): 202-208; doi:
10.6165/tai.2019.64.202
9. Chang, Jui-Tse, Bing-Hong Huang, Pei-Chun Liao 2019. Genetic evidence of the southward founder speciation of Cycas taitungensis from ancestral C. revoluta along the Ryukyu Archipelagos. Conservation Genetics 20(5): 1045-1056; doi: 10.1007/s10592-019-01193-1 10. Wu, Shu-Hong, Bing-Hong Huang, Jian Gao, Siqi Wang, Pei-Chun Liao 2019. The effects of
afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties. PeerJ 7: e6147; doi: https://peerj.com/articles/6147/
80
2018
11. Yang, Chih-Kai, Yu-Chung Chiang, Bing-Hong Huang, Li-Ping Ju, Pei-Chun Liao 2018.
Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands. Botanical Studies 59:27; doi:
10.1186/s40529-018-0244-8
12. Huang, Bing-Hong, Yuan-Chien Lin, Chih-Wei Huang, Hsin-Pei Lu, Min-Xin Luo, Pei-Chun Liao 2018. Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species. BMC Genomics 19:692; doi:
10.1186/s12864-018-5081-3
13. Yang, Chih-Kai, Bing-Hong Huang, Shao-Wei Ho, Meng-Yuan Huang, Jenn-Che Wang, Jian Gao, Pei-Chun Liao 2018. Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae). BMC Plant Biology 18:196; doi: 10.1186/s12870-018-1420-4
14. Chiang, Yu-Chung, Bing-Hong Huang, Nan Li, Yi-Qing Gong, Hsien-Hui Shen, Shong Huang, Pei-Chun Liao 2018. Multilocus genome evidence for a paraphyletic relationship and past interspecific gene flow between species of Cycas Section Asiorientales. Memoirs of the New York Botanical Garden: 117: 230-249
15. Guo, Wuxia, Ying Liu, Wei Lun Ng, Pei-Chun Liao, Bing-Hong Huang, Weixi Li, Chunmei Li,Xianggang Shi, Yelin Huang 2018. Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion. BMC Genomics 19:392; doi: 10.1186/s12864-018-4784-9
16. Wu, Shu-Hong, Bing-Hong Huang, Chia-Lung Huang, Gang Li, Pei-Chun Liao 2018. The aboveground vegetation type and underground soil property mediate the divergence of soil microbiomes and the biological interactions. Microbial Ecology 75(2):434-446; doi:
10.1007/s00248-017-1050-7
17. Huang, Bing-Hong, Chun-Wen Chang, Chih Wei Huang, Jian Gao and Pei-Chun Liao 2018.
Composition and functional specialists of the gut microbiota of frogs reflect habitat differences and agricultural activity. Frontiers in Microbiology 8: 2670; doi: 10.3389/fmicb.2017.02670
2017
18. Gao, Jian, Bing-Hong Huang, Yu-Ting Wan, JenYu Chang, Jun-Qing Li, Pei-Chun Liao 2017.
Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes. Scientific Reports 7: 14830; doi:10.1038/s41598-017-13645-0 19. Huang, Bing-Hong, Chih-Wei Huang, Chia-Lung Huang, Pei-Chun Liao 2017. Continuation of
the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants. Scientific Reports 7: 5465; doi: 10.1038/s41598-017-05900-1
81
20. Hsiung, Huan-Yi, Bing-Hong Huang, Jui-Tse Chang, Yao-Moan Huang, Chih-Wei Huang, Pei-Chun Liao*. 2017. Local climate heterogeneity shapes population genetic structure of two undifferentiated insular Scutellaria species. Frontiers in Plant Science 8:159; doi:
10.3389/fpls.2017.00159 2016
21. Huang, Bing-Hong, Yi-Wen Chen, Chia-Lung Huang, Jian Gao, Pei-Chun Liao 2016.
Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes. Scientific Reports 6: 39031; doi:
10.1038/srep39031
22. Huang, Bing-Hong, Yi-Wen Chen, Chia-Lung Huang, Jian Gao, Pei-Chun Liao 2016.
Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species. BMC Evolutionary Biology 16:191; doi:
10.1186/s12862-016-0759-0
23. Chang, Chun-Wen, Bing-Hong Huang, Si-Min Lin, Chia-Lung Huang, Pei-Chun Liao*. 2016.
Changes of diet and dominant intestinal microbes in farmland frogs. BMC Microbiology 16: 33;
doi: 10.1186/s12866-016-0660-4
82
參考文獻
Ackerly, D.D. (2003) Community assembly, niche conservatism, and adaptive evolution in changing environments. International Journal of Plant Sciences, 164, S165-S184.
Albert B. Phillimore, C. David L. Orme, Gavin H. Thomas, Tim M. Blackburn, Peter M. Bennett, Kevin J. Gaston & Ian P. F. Owens (2008) Sympatric Speciation in Birds Is Rare: Insights from Range Data and Simulations. The American Naturalist, 171, 646-657.
Anacker, B.L. & Strauss, S.Y. (2014) The geography and ecology of plant speciation:
range overlap and niche divergence in sister species. Proceedings of the Royal Society B-Biological Sciences, 281, 20132980.
Balkenhol, N., Waits, L.P. & Dezzani, R.J. (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data.
Ecography, 32, 818-830.
Beaumont, M.A. (2005) Adaptation and speciation: what can Fst tell us? Trends in Ecology & Evolution, 20, 435-440.
Beaumont, M.A. & Nichols, R.A. (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London, Series B: Biological Sciences, 263, 1619-1626.
Bertorelle, G., Benazzo, A. & Mona, S. (2010) ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology, 19, 2609-2625.
Bierne, N., Gagnaire, P.A. & David, P. (2013) The geography of introgression in a patchy environment and the thorn in the side of ecological speciation. Current Zoology, 59, 72-86.
Blair, M.E., Sterling, E.J., Dusch, M., Raxworthy, C.J. & Pearson, R.G. (2013) Ecological divergence and speciation between lemur (Eulemur) sister species in Madagascar. Journal of Evolutionary Biology, 26, 1790-1801.
Camargo, A., Morando, M., Avila, L.J. & Sites, 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, 2834-2849.
Carta, A., Hanson, S. & Muller, J.V. (2016) Plant regeneration from seeds responds to phylogenetic relatedness and local adaptation in Mediterranean Romulea (Iridaceae) species. Ecology and Evolution, 6, 4166-4178.
Chao, C.-T., Huang, B.-H., Chang, J.-T. & Liao, P.-C. (2020) Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data.
PhytoKeys, 140
83
Chen, C.Y., Liang, B.K., Chung, J.D., Chang, C.T., Hsieh, Y.C., Lin, T.C. & Hwang, S.Y. (2014) Demography of the upward-shifting temperate woody species of the Rhododendron pseudochrysanthum complex and ecologically relevant adaptive divergence in its trailing edge populations. Tree Genetics & Genomes, 10, 111-126.
Chen, S.F., Rossiter, S.J., Faulkes, C.G. & Jones, G. (2006) Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros). Molecular Ecology, 15, 1643-1656.
Chi, W.-R., Namson, J. & Suppe, J. (1981) Stratigraphic record of plate interactions in the Coastal Range of eastern Taiwan. Memoir of the Geological Society of China, 4, 155-194.
Chiang, Y.C., Huang, B.H. & Liao, P.C. (2012a) Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA. PLOS ONE, 7, e50844.
Chiang, Y.C., Huang, B.H., Shih, H.C., Hsu, T.W., Chang, C.W. & Liao, P.C. (2012b) Characterization of 24 transferable microsatellite loci in four skullcaps
(Scutellaria, Labiatae). American Journal of Botany, 99, E24-E27.
Coyne, J.A. (2007) Sympatric speciation. Curr Biol, 17, R787-8.
Coyne, J.A. (2011) Speciation in a small space. Proceedings of the National Academy of Sciences of the United States of America, 108, 12975-12976.
Coyne, J.A. & Orr, H.A. (2004) Speciation: a catalogue and critique of species concepts. Speciation, pp. 272-92. Oxford University Press.
Cruzan, M.B. (2001) Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic Scutellaria montana (Lamiaceae). Evolution, 55, 1569-1580.
Csillery, K., Blum, M.G., Gaggiotti, O.E. & Francois, O. (2010) Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol, 25, 410-8.
de Lafontaine, G., Prunier, J., Gérardi, S. & Bousquet, J. (2015) Tracking the
progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana x P. rubens). Molecular Ecology, 24, 5229-5247.
Denda, T. (2002) Cleistogamy in Scutellaria rubropunctata Hayata (Labiatae) from the Ryukyu Archipelago. The Biological magazine, Okinawa, 40, 7-14.
Dormann, C.F. (2007) Promising the future? Global change projections of species distributions. Basic and Applied Ecology, 8, 387-397.
Doyle, J. & Doyle, J. (1987) Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochem Bull, 19, 11-15.
Earl, D.A. & Vonholdt, B.M. (2012) STRUCTURE HARVESTER: a website and
84
program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361.
Ellstrand, N.C. & Elam, D.R. (1993) Population genetic consequences of small population size: Implications for plant conservation. Annual Review of Ecology and Systematics, 24, 217-242.
Endler, J.A. (1977) Geographic variation, speciation, and clines. Princeton University Press.
Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
Excoffier, L. & Lischer, H.E.L. (2010) Arlequin suite ver 3.5: a new series of
programs to perform population genetics analyses under Linux and Windows.
Molecular Ecology Resources, 10, 564-567.
Federman, S., Dornburg, A., Downie, A., Richard, A.F., Daly, D.C. & Donoghue, M.J.
(2015) The biogeographic origin of a radiation of trees in Madagascar:
implications for the assembly of a tropical forest biome. BMC Evolutionary Biology, 15, 216.
Foll, M. & Gaggiotti, O. (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics, 180, 977-993.
Fountain, T., Nieminen, M., Siren, J., Wong, S.C. & Hanski, I. (2016) Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly. Proceedings of the National Academy of Sciences of the United States of America, 113, 2678-2683.
Gavin, D.G. & Hu, F.S. (2006) Spatial variation of climatic and non-climatic controls on species distribution: the range limit of Tsuga heterophylla. Journal of Biogeography, 33, 1384-1396.
Gillespie, R.G., Croom, H.B. & Palumbi, S.R. (1994) Multiple origins of a spider radiation in Hawaii. Proceedings of the National Academy of Sciences, 91, 2290-2294.
Glor, R.E. & Warren, D. (2011) Testing ecological explanations for biogeographic boundaries. Evolution, 65, 673-683.
Gorel, A.-P., Duminil, J., Doucet, J.-L. & Fayolle, A. (2019) Ecological niche divergence associated with species and populations differentiation in
Erythrophleum (Fabaceae, Caesalpinioideae). Plant Ecology and Evolution, 152, 41-52.
Grinnell, J. (1917) The niche relationships of the California thrasher. Auk, 34, 427-433.
85
Grossenbacher, D.L., Veloz, S.D. & Sexton, J.P. (2014) Niche and range size patterns suggest that speciation begins in small, ecologically diverged populations in North American monkeyflowers (Mimulus spp.). Evolution, 68, 1270-1280.
Harter, D.E.V., Thiv, M., Weig, A., Jentsch, A. & Beierkuhnlein, C. (2015) Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width. Ecology and Evolution, 5, 4327-4344.
He, J., Gao, Z., Su, Y., Lin, S. & Jiang, H. (2018) Geographical and temporal origins of terrestrial vertebrates endemic to Taiwan. Journal of Biogeography, 45, 2458-2470.
He, Q., Edwards, D.L. & Knowles, L.L. (2013) Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution, 67, 3386-3402.
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, 4606-4618.
Hey, J. (2006) Recent advances in assessing gene flow between diverging populations and species. Current Opinion in Genetics & Development, 16, 592-596.
Hey, J. (2009) Isolation with Migration Models for More Than Two Populations.
Molecular Biology and Evolution, 27, 905-920.
Hey, J. (2010) Isolation with Migration Models for More Than Two Populations.
Molecular Biology and Evolution, 27, 905-920.
Hey, J., Chung, Y., Sethuraman, A., Lachance, J., Tishkoff, S., Sousa, V.C. & Wang, Y.
(2018) Phylogeny estimation by integration over isolation with migration models. Molecular Biology and Evolution, 35, 2805-2818.
Hijmans, R.J. & van Etten, J. (2014) raster: Geographic data analysis and modeling. R package version, 2, 15.
Hijmans, R.J., Phillips, S., Leathwick, J. & Elith, J. (2013) dismo: Species distribution modeling. R package version 0.8-17,
Hoelzer, G.A., Drewes, R., Meier, J. & Doursat, R. (2008) Isolation-by-distance and outbreeding depression are sufficient to drive parapatric speciation in the absence of environmental influences. PLoS computational biology, 4, e1000126-e1000126.
Holderegger, R., Kamm, U. & Gugerli, F. (2006) Adaptive vs. neutral genetic diversity: implications for landscape genetics. Landscape Ecology, 21, 797-807.
Hsieh, C.F. (2002) Composition, endemism and phytogeographical affinities of the Taiwan flora. Taiwania, 47, 298-310.
Hsieh, T.-H. (2013) Scutellaria hsiehii (Lamiaceae), a New Species from Taiwan.
86
Taiwania, 58
Hsieh, T.-H. & Huang, T.-C. (1995) Notes on the Flora of Taiwan (20)-Scutellaria (Lamiaceae) in Taiwan. Taiwania, 40, 35-56.
Hsieh, T.-H. & Huang, T.-C. (1997) Notes on the Flora of Taiwan (29)-Scutellaria austrotaiwanensis Hsieh & Huang sp. nov.(Lamiaceae) from Taiwan.
Taiwania, 42, 109-116.
Hsiung, H.-Y., Huang, B.-H., Chang, J.-T., Huang, Y.-M., Huang, C.-W. & Liao, P.-C.
(2017) Local climate heterogeneity shapes population genetic structure of two undifferentiated insular Scutellaria species. Frontiers in plant science, 8, 159-159.
Hsu, R. & Wolf, J.H.D. (2009) Diversity and phytogeography of vascular epiphytes in a tropical–subtropical transition island, Taiwan. Flora - Morphology,
Distribution, Functional Ecology of Plants, 204, 612-627.
Hu, Z., Guo, K., Jin, S. & Pan, H. (2019) The influence of climatic changes on
distribution pattern of six typical Kobresia species in Tibetan Plateau based on MaxEnt model and geographic information system. Theoretical and Applied Climatology, 135, 375-390.
Huang, B.-H., Chen, Y.-W., Huang, C.-L., Gao, J. & Liao, P.-C. (2016a) Imbalanced positive selection maintains the functional divergence of duplicated
DIHYDROKAEMPFEROL 4-REDUCTASE genes. Scientific Reports, 6, 39031.
Huang, B.-H., Chen, Y.-W., Huang, C.-L., Gao, J. & Liao, P.-C. (2016b) Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species. BMC Evolutionary Biology, 16, 191.
Huang, B.H., Pang, E.L., Chen, Y.W., Cao, H.F., Ruan, Y. & Liao, P.C. (2015)
Positive Selection and Functional Divergence of R2R3-MYB Paralogous Genes Expressed in Inflorescence Buds of Scutellaria Species (Labiatae).
International Journal of Molecular Sciences, 16, 5900-5921.
Huang, C.-L., Chen, J.-H., Chang, C.-T., Chung, J.-D., Liao, P.-C., Wang, J.-C. &
Hwang, S.-Y. (2016c) Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi. Tree Genetics & Genomes, 12, 53.
Huang, J.P. & Lin, C.P. (2010) Diversification in subtropical mountains:
Phylogeography, Pleistocene demographic expansion, and evolution of polyphenic mandibles in Taiwanese stag beetle, Lucanus formosanus.
Molecular Phylogenetics and Evolution, 57, 1149-1161.
Huang, J.P. & Lin, C.P. (2011) Lineage-specific late pleistocene expansion of an
87
endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan.
BMC Evolutionary Biology, 11, 94.
Huang, Q.Y., Beharav, A., Youchun, U.C., Kirzhner, V. & Nevo, E. (2002) Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel. Genome, 45,
1216-1229.
Huang, T.-C., Hsiao, A. & Wu, M.-J. (2003) Notes on the Flora of Taiwan (35)-Scutellaria taipeiensis TC Huang, A. Hsiao et MJ Wu sp. nov.
(Lamiaceae). Taiwania, 48, 129-137.
Hubisz, M.J., Falush, D., Stephens, M. & Pritchard, J.K. (2009) Inferring weak population structure with the assistance of sample group information.
Molecular Ecology Resources, 9, 1322-1332.
Hutchinson, G.E. (1959) Homage to Santa Rosalia or why are there so many kinds of animals? The American Naturalist, 93, 145-159.
Ito, T., Yu, C.-C., Nakamura, K., Chung, K.-F., Yang, Q.-e., Fu, C.-X., Qi, Z.-C. &
Kokubugata, G. (2017) Unique parallel radiations of high-mountainous
species of the genus Sedum (Crassulaceae) on the continental island of Taiwan.
Molecular Phylogenetics and Evolution, 113, 9-22.
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, 1801-1806.
Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 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, 94.
Jump, A.S. & Penuelas, J. (2005) Running to stand still: adaptation and the response of plants to rapid climate change. Ecology Letters, 8, 1010-1020.
Jump, A.S., Huang, T.-J. & Chou, C.-H. (2012) Rapid altitudinal migration of mountain plants in Taiwan and its implications for high altitude biodiversity.
Ecography, 35, 204-210.
Kawecki, T.J. & Ebert, D. (2004) Conceptual issues in local adaptation. Ecology Letters, 7, 1225-1241.
Kubota, Y., Shiono, T. & Kusumoto, B. (2015) Role of climate and geohistorical factors in driving plant richness patterns and endemicity on the east Asian continental islands. Ecography, 38, 639-648.
Kubota, Y., Hirao, T., Fujii, S.J. & Murakami, M. (2011) Phylogenetic beta diversity reveals historical effects in the assemblage of the tree floras of the Ryukyu
88
Archipelago. Journal of Biogeography, 38, 1006-1008.
Kubota, Y., Hirao, T., Fujii, S., Shiono, T. & Kusumoto, B. (2014) Beta diversity of woody plants in the Japanese archipelago: the roles of geohistorical and ecological processes. Journal of Biogeography, 41, 1267-1276.
Lee, C.-R. & Mitchell-Olds, T. (2011) Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Molecular Ecology, 20, 4631-4642.
Lewin-Koh, N.J., Bivand, R., Pebesma, E., Archer, E., Baddeley, A., Bibiko, H., Dray, S., Forrest, D., Friendly, M. & Giraudoux, P. (2011) maptools: Tools for reading and handling spatial objects. R package version 0.8-10, URL http://CRAN. R-project. org/package= maptools,
Li, Y.C., Fahima, T., Beiles, A., Korol, A.B. & Nevo, E. (1999) Microclimatic stress and adaptive DNA differentiation in wild emmer wheat, Triticum dicoccoides.
Theoretical and Applied Genetics, 98, 873-883.
Liao, P.C., Kuo, D.C., Lin, C.C., Ho, K.C., Lin, T.P. & Hwang, S.Y. (2010) Historical spatial range expansion and a very recent bottleneck of Cinnamomum
kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes. BMC Evolutionary Biology, 10, 124.
Librado, P. & Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
Liebherr, J.K. & Hajek, A.E. (1990) A cladistic test of the taxon cycle and taxon pulse hypotheses. Cladistics, 6, 39-59.
Linder, H.P. (2008) Plant species radiations: where, when, why? Philosophical Transactions of the Royal Society B-Biological Sciences, 363, 3097-3105.
Lopez-Sepulveda, P., Takayama, K., Greimler, J., Penailillo, P., Crawford, D.J., Baeza, M., Ruiz, E., Kohl, G., Tremetsberger, K., Gatica, A., Letelier, L., Novoa, P., Novak, J. & Stuessy, T.F. (2013) Genetic variation (AFLPs and nuclear
microsatellites) in two anagenetically derived endemic species of Myrceugenia (Myrtaceae) on the Juan Fernández Islands, Chile. American Journal of
Botany, 100, 722-734.
Losos, J.B. (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters, 11, 995-1003.
Lynch, M. & Sethuraman, A. (2019) The effects of gene flow from unsampled ‘ghost’
populations on the estimation of evolutionary history under the Isolation with Migration model. bioRxiv, 733600.
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
89
small oceanic island. PLOS ONE, 9, e87469.
Manel, S., Gaggiotti, O.E. & Waples, R.S. (2005) Assignment methods: matching biological questions techniques with appropriate. Trends in Ecology &
Evolution, 20, 136-142.
Martin, N.H. & Willis, J.H. (2007) Ecological divergence associated with mating system causes nearly complete reproductive isolation between sympatric Mimulus species. Evolution, 61, 68-82.
Martinez-Cabrera, H.I., Schlichting, C.D., Silander, J.A. & Jones, C.S. (2012) Low levels of climate niche conservatism may explain clade diversity patterns in the South African genus Pelargonium (Geraniaceae). American Journal of Botany, 99, 954-960.
Middleton, B. (2000) Hydrochory, seed banks, and regeneration dynamics along the landscape boundaries of a forested wetland. Plant Ecology, 146, 169-184.
Minder, A.M. & Widmer, A. (2008) A population genomic analysis of species
boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species. Molecular Ecology, 17, 1552-1563.
Nagl, S., Tichy, H., Mayer, W.E., Takahata, N. & Klein, J. (1998) Persistence of neutral polymorphisms in Lake Victoria cichlid fish. Proceedings of the National Academy of Sciences of the United States of America, 95, 14238-14243.
Nei, M. (1977) F-statistics and analysis of gene diversity in subdivided populations.
Annals of Human Genetics, 41, 225-233.
Nelson, A.D. & Goetze, J.R. (2010) Hydroballochory in two Texas species of Skullcap (Scutellaria drummodii, S. wrightii; Lamiaceae). Texas Journal of Science, 62, 263-270.
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, 2258-2275.
Nino, H. & Emery, K.O. (1961) Sediments of shallow portions of East China Sea and South China Sea. Geological Society of America Bulletin, 72, 731–762.
Nosil, P. & Feder, J.L. (2012) Genomic divergence during speciation: causes and consequences. Philosophical Transactions of the Royal Society B: Biological Sciences, 367, 332-342.
Nosil, P., Funk, D.J. & Ortiz-Barrientos, D. (2009a) Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18, 375-402.
Nosil, P., Harmon, L.J. & Seehausen, O. (2009b) Ecological explanations for (incomplete) speciation. Trends in Ecology & Evolution, 24, 145-156.
Owuor, E.D., Fahima, T., Beiles, A., Korol, A. & Nevo, E. (1997) Population genetic
90
response to microsite ecological stress in wild barley, Hordeum spontaneum.
Molecular Ecology, 6, 1177-1187.
Palumbi, S.R. (2009) Speciation and the evolution of gamete recognition genes:
pattern and process. Heredity, 102, 66-76.
Papadopulos, A.S., Kaye, M., Devaux, C., Hipperson, H., Lighten, J., Dunning, L.T., Hutton, I., Baker, W.J., Butlin, R.K. & Savolainen, V. (2014) Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 369, 20130342.
Papadopulos, A.S.T., Baker, W.J., Crayn, D., Butlin, R.K., Kynast, R.G., Hutton, I. &
Savolainen, V. (2011) Speciation with gene flow on Lord Howe Island.
Proceedings of the National Academy of Sciences, 108, 13188-13193.
Paulay, G. (1994) Biodiversity on oceanic islands: Its origin and extinction1. American Zoologist, 34, 134-144.
Peakall, R. & Smouse, P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537-2539.
Pearson, R.G. & Dawson, T.P. (2003) Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful? Global
Ecology and Biogeography, 12, 361-371.
Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new
Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new