Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J., Bierne, N., Boughman, J., Brelsford, A., Buerkle, C. A. & Buggs, R. 2013. Hybridization and speciation. Journal of evolutionary biology 26: 229-246.
Aberer, A. J., Kobert, K. & Stamatakis, A. 2014. ExaBayes: massively parallel Bayesian tree inference for the whole-genome era. Molecular biology and evolution 31: 2553-2556.
Abouheif, E. 1999. A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1: 895-909.
Adam Freedman, N. W. (2020) Best Practices for De Novo Transcriptome Assembly with Trinity. URL: https://informatics.fas.harvard.edu/best-practices-for-de-novo-transcriptome-assembly-with-trinity.html
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: 541-545.
Alejo-Jacuinde, G., González-Morales, S. I., Oropeza-Aburto, A., Simpson, J. & Herrera-Estrella, L. 2020. Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species. BMC Plant Biology 20: 1-18.
Andrews, S. (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom. URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Arcila, D., Ortí, G., Vari, R., Armbruster, J. W., Stiassny, M. L., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J. & Betancur-R, R. 2017. Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nature Ecology & Evolution 1: 0020.
Bai, S.-N. & Xu, Z.-H. 2013. Unisexual cucumber flowers, sex and sex differentiation. International Review of Cell and Molecular Biology 304: 1-55.
Bailey, I. W. & Sinnott, E. W. 1916. The climatic distribution of certain types of angiosperm leaves. American journal of botany: 24-39.
Baker-Brosh, K. F. & Peet, R. K. 1997. The ecological significance of lobed and toothed leaves in temperate forest trees. Ecology 78: 1250-1255.
Baumgartner, A., Donahoo, M., Chitwood, D. H. & Peppe, D. J. 2020. The influences of environmental change and development on leaf shape in Vitis. American Journal of Botany 107: 676-688.
Berardini, T. Z., Reiser, L., Li, D., Mezheritsky, Y., Muller, R., Strait, E. & Huala, E. 2015. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. genesis 53: 474-485.
Betancur-R, R., Arcila, D., Vari, R. P., Hughes, L. C., Oliveira, C., Sabaj, M. H. & Ortí, G. 2019. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 73: 329-345.
Bilsborough, G. D., Runions, A., Barkoulas, M., Jenkins, H. W., Hasson, A., Galinha, C., Laufs, P., Hay, A., Prusinkiewicz, P. & Tsiantis, M. 2011. Model for the regulation of Arabidopsis thaliana leaf margin development. Proceedings of the National Academy of Sciences 108: 3424-3429.
Blomberg, S. P. & Garland Jr, T. 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology 15: 899-910.
Blomberg, S. P., Garland Jr, T. & Ives, A. R. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57: 717-745.
Bolger, A. M., Lohse, M. & Usadel, B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
Borgardt, S. J. & Nixon, K. C. 2003. A comparative flower and fruit anatomical study of Quercus acutissima, a biennial‐fruiting oak from the Cerris group (Fagaceae). American Journal of Botany 90: 1567-1584.
Borges, R., Machado, J. P., Gomes, C., Rocha, A. P. & Antunes, A. 2019. Measuring phylogenetic signal between categorical traits and phylogenies. Bioinformatics 35: 1862-1869.
Boscain, L. 2023. iNaturalist observation: https://www.inaturalist.org/observations/157026905 [Image] https://inaturalist-open-data.s3.amazonaws.com/photos/271569949/original.jpg [Access date: 2024-04-05]
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A. & Drummond, A. J. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS computational biology 10: e1003537.
Brett, D. W. 1964. The inflorescence of Fagus and Castanea, and the evolution of the cupules of the Fagaceae. New Phytologist 63: 96-118.
Byrne, M. E., Barley, R., Curtis, M., Arroyo, J. M., Dunham, M., Hudson, A. & Martienssen, R. A. 2000. Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature 408: 967-971.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. & Madden, T. L. 2009. BLAST+: architecture and applications. BMC bioinformatics 10: 1-9.
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
Carmichael, M. J., Pancost, R. D. & Lunt, D. J. 2018. Changes in the occurrence of extreme precipitation events at the Paleocene–Eocene thermal maximum. Earth and Planetary Science Letters 501: 24-36.
Carstens, B. C. & Knowles, L. L. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology 56: 400-411.
Castoe, T. A., de Koning, A. J., Kim, H.-M., Gu, W., Noonan, B. P., Naylor, G., Jiang, Z. J., Parkinson, C. L. & Pollock, D. D. 2009. Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences 106: 8986-8991.
Cavender‐Bares, J. 2019. Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution. New Phytologist 221: 669-692.
Chabot, B. F. & Hicks, D. J. 1982. The ecology of leaf life spans. Annual review of ecology and systematics 13: 229-259.
Chang, S., Puryear, J. & Cairney, J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant molecular biology reporter 11: 113-116.
Chen, X., Li, C., Wang, H. & Guo, Z. 2019. WRKY transcription factors: evolution, binding, and action. Phytopathology Research 1: 1-15.
Chen, Z., Ding, Z., Yang, S., Zhang, C. & Wang, X. 2016. Increased precipitation and weathering across the Paleocene‐Eocene Thermal Maximum in central China. Geochemistry, Geophysics, Geosystems 17: 2286-2297.
Chepinoga, V., Stepantsova, N., Seregin, A. 2024. IRKU Herbarium: collections of vascular plants. Version 1.159. Irkutsk State University. Quercus dentata Thunb. [Image] https://plant.depo.msu.ru/open/public/item/IRKU032616/img/0.jpg?gbif accessed via GBIF.org on 2024-03-19. https://www.gbif.org/occurrence/3908973132
Clemente, M., Corigliano, M. G., Pariani, S. A., Sánchez-López, E. F., Sander, V. A. & Ramos-Duarte, V. A. 2019. Plant serine protease inhibitors: biotechnology application in agriculture and molecular farming. International journal of molecular sciences 20: 1345.
Coculo, D. & Lionetti, V. 2022. The plant invertase/pectin methylesterase inhibitor superfamily. Frontiers in Plant science 13: 863892.
Consortium, T. U. 2021. UniProt: the universal protein knowledgebase in 2021. Nucleic acids research 49: D480-D489.
Cook, L. G. & Crisp, M. D. 2005. Not so ancient: the extant crown group of Nothofagus represents a post-Gondwanan radiation. Proceedings of the Royal Society B: Biological Sciences 272: 2535-2544.
Coyne, J. & Orr, H. 2004. Speciation Sinauer Associates Sunderland, MA.
Crepet, W. L. & Nixon, K. C. 1989. Earliest megafossil evidence of Fagaceae: phylogenetic and biogeographic implications. American Journal of Botany 76: 842-855.
Culley, T. M., Weller, S. G. & Sakai, A. K. 2002. The evolution of wind pollination in angiosperms. Trends in Ecology & Evolution 17: 361-369.
Degnan, J. H. & Rosenberg, N. A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in ecology & evolution 24: 332-340.
Djoumad, A., Villette, S., Isayenka, I. & Beaudoin, N. 2018. Involvement of type-f thioredoxins during germination and early seedling development and in response to oxidative stress in Arabidopsis thaliana. Botany 96: 471-484.
Dos Reis, M., Donoghue, P. C. & Yang, Z. 2016. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics 17: 71-80.
Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS biology 4: e88.
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. 2011. Testing for ancient admixture between closely related populations. Molecular biology and evolution 28: 2239-2252.
Eastburn, D., McElrone, A. & Bilgin, D. 2011. Influence of atmospheric and climatic change on plant–pathogen interactions. Plant pathology 60: 54-69.
Edelman, N. B., Frandsen, P. B., Miyagi, M., Clavijo, B., Davey, J., Dikow, R. B., García-Accinelli, G., Van Belleghem, S. M., Patterson, N. & Neafsey, D. E. 2019. Genomic architecture and introgression shape a butterfly radiation. Science 366: 594-599.
Edwards, E. J., Chatelet, D. S., Chen, B.-C., Ong, J. Y., Tagane, S., Kanemitsu, H., Tagawa, K., Teramoto, K., Park, B. & Chung, K.-F. 2017. Convergence, consilience, and the evolution of temperate deciduous forests. The American Naturalist 190: S87-S104.
eFloras (2008) eFloras. Published on the Internet http://www.efloras.org [Access date: 2023-06-29] Missouri Botanical Garden, St. Louis, MO & Harvard University Herbaria, Cambridge, MA.
Elad, Y. & Pertot, I. 2014. Climate change impacts on plant pathogens and plant diseases. Journal of Crop Improvement 28: 99-139.
Ellis, B., Daly, D. C., Hickey, L. J., Johnson, K. R., Mitchell, J. D., Wilf, P. & Wing, S. L. 2009. Manual of leaf architecture.
Emms, D. M. & Kelly, S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology 20: 1-14.
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32: 3047-3048.
Fan, F., Yang, X., Cheng, Y., Kang, Y. & Chai, X. 2017. The DnaJ gene family in pepper (Capsicum annuum L.): comprehensive identification, characterization and expression profiles. Frontiers in plant science 8: 689.
Fay, J. C. & Wu, C.-I. 2003. Sequence divergence, functional constraint, and selection in protein evolution. Annual review of genomics and human genetics 4: 213-235.
Felsenstein, J. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1427-1434.
Fernández-Cruz, J. & Fernández-López, J. 2012. Morphological, molecular and statistical tools to identify Castanea species and their hybrids. Conservation Genetics 13: 1589-1600.
Fernández-Cruz, J. & Fernández-López, J. 2016. Genetic structure of wild sweet chestnut (Castanea sativa Mill.) populations in northwest of Spain and their differences with other European stands. Conservation genetics 17: 949-967.
Ferraro, R. 2023. iNaturalist observation: https://www.inaturalist.org/observations/154041017 [Image] https://inaturalist-open-data.s3.amazonaws.com/photos/266123229/original.jpeg [Access date: 2024-04-05]
Fick, S. E. & Hijmans, R. J. 2017. WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. International journal of climatology 37: 4302-4315.
Finch-Savage, W. 1992. Embryo water status and survival in the recalcitrant species Quercus robur L: evidence for a critical moisture content. Journal of Experimental Botany 43: 663-669.
Finch-Savage, W., Blake, P. & Clay, H. 1996. Desiccation stress in recalcitrant Quercus robur L. seeds results in lipid peroxidation and increased synthesis of jasmonates and abscisic acid. Journal of Experimental Botany 47: 661-667.
Fluhr, R., Lampl, N. & Roberts, T. H. 2012. Serpin protease inhibitors in plant biology. Physiologia plantarum 145: 95-102.
Forman, L. 1964. Trigonobalanus, a new genus of Fagaceae, with notes on the classification of the family. Kew Bulletin 17: 381-396.
Forman, L. 1966. On the evolution of cupules in the Fagaceae. Kew Bulletin 18: 385-419.
Fritz, M. A., Rosa, S. & Sicard, A. 2018. Mechanisms underlying the environmentally induced plasticity of leaf morphology. Frontiers in genetics 9: 478.
Fritz, S. A. & Purvis, A. 2010. Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conservation Biology 24: 1042-1051.
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28: 3150-3152.
Gambino, G., Perrone, I. & Gribaudo, I. 2008. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochemical Analysis 19: 520-525.
García-Bañuelos, M. L., Vázquez-Moreno, L., Winzerling, J., Orozco, J. A. & Gardea, A. A. 2008. Winter metabolism in deciduous trees: mechanisms, genes and associated proteins. Revista Fitotecnia Mexicana 31: 295-295.
Givnish, T. (1979) On the adaptive significance of leaf form. In: Topics in plant population biology. pp. 375-407. Springer.
González‐Rodríguez, A., Arias, D. M., Valencia, S. & Oyama, K. 2004. Morphological and RAPD analysis of hybridization between Quercus affinis and Q. laurina (Fagaceae), two Mexican red oaks. American Journal of Botany 91: 401-409.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R. & Zeng, Q. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29: 644-652.
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W. & Fritz, M. H.-Y. 2010. A draft sequence of the Neandertal genome. science 328: 710-722.
Greenwood, D. R. 2005. Leaf form and the reconstruction of past climates. New Phytologist: 355-357.
Grímsson, F., Grimm, G. W., Zetter, R. & Denk, T. 2016. Cretaceous and Paleogene Fagaceae from North America and Greenland: evidence for a Late Cretaceous split between Fagus and the remaining Fagaceae. Acta Palaeobotanica 56: 247-305.
Grímsson, F., Zetter, R., Grimm, G. W., Pedersen, G. K., Pedersen, A. K. & Denk, T. 2015. Fagaceae pollen from the early Cenozoic of West Greenland: revisiting Engler’s and Chaney’s Arcto-Tertiary hypotheses. Plant systematics and Evolution 301: 809-832.
Haas, B. J. (2013) TransDecoder. URL: https://github.com/TransDecoder/TransDecoder
Hahn, M. W. & Nakhleh, L. 2016. Irrational exuberance for resolved species trees. Evolution 70: 7-17.
Harder, L. D., Barrett, S. C. & Cole, W. W. 2000. The mating consequences of sexual segregation within inflorescences of flowering plants. Proceedings of the Royal Society of London. Series B: Biological Sciences 267: 315-320.
Harmon, L. 2019. Phylogenetic comparative methods: learning from trees. Doi: https://doi.org/10.32942/osf.io/e3xnr
Harris, B. J., Clark, J. W., Schrempf, D., Szöllősi, G. J., Donoghue, P. C., Hetherington, A. M. & Williams, T. A. 2022. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nature Ecology & Evolution 6: 1634-1643.
Hennon, P. E., Frankel, S. J., Woods, A. J., Worrall, J. J., Norlander, D., Zambino, P. J., Warwell, M. V. & Shaw III, C. G. 2020. A framework to evaluate climate effects on forest tree diseases. Forest Pathology 50: e12649.
Herman, A. B., Spicer, R. A., Aleksandrova, G. N., Yang, J., Kodrul, T. M., Maslova, N. P., Spicer, T. E., Chen, G. & Jin, J.-H. 2017. Eocene–early Oligocene climate and vegetation change in southern China: evidence from the Maoming Basin. Palaeogeography, Palaeoclimatology, Palaeoecology 479: 126-137.
Hill, R. S. & Jordan, G. J. 1993. The evolutionary history of Nothofagus (Nothofagaceae). Australian systematic botany 6: 111-126.
Hipp, A. L., Manos, P. S., González‐Rodríguez, A., Hahn, M., Kaproth, M., McVay, J. D., Avalos, S. V. & Cavender‐Bares, J. 2018. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. New Phytologist 217: 439-452.
Hipp, A. L., Manos, P. S., Hahn, M., Avishai, M., Bodénès, C., Cavender‐Bares, J., Crowl, A. A., Deng, M., Denk, T. & Fitz‐Gibbon, S. 2020. Genomic landscape of the global oak phylogeny. New Phytologist 226: 1198-1212.
Hittinger, C. T., Johnston, M., Tossberg, J. T. & Rokas, A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proceedings of the National Academy of Sciences 107: 1476-1481.
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: 518-522.
Holstein, J. (2001) GBIF: global biodiversity information facility. [Last accessed 20 May 2023]
Huelsenbeck, J. P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
Hundertmark, M. & Hincha, D. K. 2008. LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC genomics 9: 1-22.
Ietswaart, J. & Feij, A. 1989. A multivariate analysis of introgression between Quercus robur and Q. petraea in The Netherlands. Acta botanica neerlandica 38: 313-325.
iNaturalist (2023) iNaturalist Taiwan data set. [Last accessed 27 Jun 2023]
Jamal, F., Pandey, P. K., Singh, D. & Khan, M. 2013. Serine protease inhibitors in plants: nature’s arsenal crafted for insect predators. Phytochemistry Reviews 12: 1-34.
Jiang, L., Bao, Q., He, W., Fan, D. M., Cheng, S. M., López‐Pujol, J., Chung, M. G., Sakaguchi, S., Sánchez‐González, A. & Gedik, A. 2022. Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci. Journal of Systematics and Evolution 60: 759-772.
Joët, T., Ourcival, J.-M. & Dussert, S. 2013. Ecological significance of seed desiccation sensitivity in Quercus ilex. Annals of Botany 111: 693-701.
Jones, J. H. 1986. Evolution of the Fagaceae: the implications of foliar features. Annals of the Missouri Botanical Garden: 228-275.
Jones, T. D., Lunt, D. J., Schmidt, D. N., Ridgwell, A., Sluijs, A., Valdes, P. J. & Maslin, M. 2013. Climate model and proxy data constraints on ocean warming across the Paleocene–Eocene Thermal Maximum. Earth-Science Reviews 125: 123-145.
JSTOR (2000) JSTOR Global Plants. [Last accessed 19 Jun 2023]
Jump, A. S., Marchant, R. & Peñuelas, J. 2009. Environmental change and the option value of genetic diversity. Trends in plant science 14: 51-58.
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: 587-589.
Kamilar, J. M. & Cooper, N. 2013. Phylogenetic signal in primate behaviour, ecology and life history. Philosophical Transactions of the Royal Society B: Biological Sciences 368: 20120341.
Kapli, P., Yang, Z. & Telford, M. J. 2020. Phylogenetic tree building in the genomic age. Nature Reviews Genetics 21: 428-444.
Kawamura, E., Horiguchi, G. & Tsukaya, H. 2010. Mechanisms of leaf tooth formation in Arabidopsis. The Plant Journal 62: 429-441.
Kimura, M. 1968. Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genetics research 11: 247-270.
Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press.
Kishino, H., Miyata, T. & Hasegawa, M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. Journal of Molecular Evolution 31: 151-160.
Kishino, H., Thorne, J. L. & Bruno, W. J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular biology and evolution 18: 352-361.
Kremer, A., Abbott, A. G., Carlson, J. E., Manos, P. S., Plomion, C., Sisco, P., Staton, M. E., Ueno, S. & Vendramin, G. G. 2012. Genomics of fagaceae. Tree Genetics & Genomes 8: 583-610.
Kremer, A., Casasoli, M., Barreneche, T., Bodénès, C., Sisco, P., Kubisiak, T., Scalfi, M., Leonardi, S., Bakker, E. & Buiteveld, J. 2007. Fagaceae trees. Forest trees: 161-187.
Kubatko, L. S. & Degnan, J. H. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic biology 56: 17-24.
Kubitzki, K. (1993) Fagaceae. In: Flowering Plants· Dicotyledons: Magnoliid, Hamamelid and Caryophyllid Families. pp. 301-309. Springer.
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. 2016. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular biology and evolution 34: 772-773.
Lang, P., Dane, F., Kubisiak, T. L. & Huang, H. 2007. Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America. Molecular phylogenetics and evolution 43: 49-59.
Langmead, B. & Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nature methods 9: 357-359.
Langmead, B., Wilks, C., Antonescu, V. & Charles, R. 2019. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics 35: 421-432.
Larson‐Johnson, K. 2016. Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. New Phytologist 209: 418-435.
Leprince, O., Hendry, G. & McKersie, B. 1993. The mechanisms of desiccation tolerance in developing seeds. Seed Science Research 3: 231-246.
Leroy, T., Louvet, J. M., Lalanne, C., Le Provost, G., Labadie, K., Aury, J. M., Delzon, S., Plomion, C. & Kremer, A. 2020. Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytologist 226: 1171-1182.
Li, R.-Q., Chen, Z.-D., Lu, A.-M., Soltis, D. E., Soltis, P. S. & Manos §, P. S. 2004. Phylogenetic relationships in Fagales based on DNA sequences from three genomes. International Journal of Plant Sciences 165: 311-324.
Li, W. & Godzik, A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
Liao, S., Wang, L., Li, J. & Ruan, Y.-L. 2020. Cell wall invertase is essential for ovule development through sugar signaling rather than provision of carbon nutrients. Plant Physiology 183: 1126-1144.
Lin, H.-C. 2019. Oak family in Taiwan. My House Publishing Co., Ltd., Taipei City.
Lodhi, M. A., Ye, G.-N., Weeden, N. F. & Reisch, B. I. 1994. A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Molecular Biology Reporter 12: 6-13.
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.
Ma, X. G., Ren, Y. B. & Sun, H. 2024. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics.
Macdonald, A. D. 1979. Inception of the cupule of Quercus macrocarpa and Fagus grandifolia. Canadian Journal of Botany 57: 1777-1782.
Maddison, W. P. 1997. Gene trees in species trees. Systematic biology 46: 523-536.
Mallet, J., Besansky, N. & Hahn, M. W. 2016. How reticulated are species? BioEssays 38: 140-149.
Manchester, S. R. 1994. Fruits and seeds of the Middle Eocene nut beds flora, Clarno Formation, Oregon. Paleoutographica Americana 58: 1-205.
Manchester, S. R. & Dillhoff, R. M. 2004. Fagus (Fagaceae) fruits, foliage, and pollen from the Middle Eocene of Pacific northwestern North America. Canadian Journal of Botany 82: 1509-1517.
Manos, P. S., Cannon, C. H. & Oh, S.-H. 2008. Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of western North America: recognition of a new genus, Notholithocarpus. Madroño 55: 181-190.
Manos, P. S. & Stanford, A. M. 2001. The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. International Journal of Plant Sciences 162: S77-S93.
Manos, P. S. & Steele, K. P. 1997. Phylogenetic analyses of “higher” Hamamelididae based on plastid sequence data. American Journal of Botany 84: 1407-1419.
Manos, P. S., Zhou, Z.-K. & Cannon, C. H. 2001. Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences 162: 1361-1379.
McCormack, J. E., Hird, S. M., Zellmer, A. J., Carstens, B. C. & Brumfield, R. T. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular phylogenetics and evolution 66: 526-538.
McInerney, F. A. & Wing, S. L. 2011. The Paleocene-Eocene Thermal Maximum: A perturbation of carbon cycle, climate, and biosphere with implications for the future. Annual Review of Earth and Planetary Sciences 39: 489-516.
McKay, J. W. (1942) Self-sterility in the Chinese chestnut (Castanea mollissima). In: Proc. Amer. Soc. Hort. Sci., Vol. 41. pp. 156-160.
McVay, J. D., Hipp, A. L. & Manos, P. S. 2017. A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proceedings of the Royal Society B: Biological Sciences 284: 20170300.
Meise Botanic Garden. 2023. Meise Botanic Garden Herbarium (BR). Version 1.29. Meise Botanic Garden. Lithocarpus glaber (Thunb.) Nakai [Image] https://oxalis.br.fgov.be/images/BR0/000/030/521/209/BR0000030521209.jpg accessed via GBIF.org on 2024-03-20. https://www.gbif.org/occurrence/4072767246
Meleshko, O., Martin, M. D., Korneliussen, T. S., Schröck, C., Lamkowski, P., Schmutz, J., Healey, A., Piatkowski, B. T., Shaw, A. J. & Weston, D. J. 2021. Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus. Molecular biology and evolution 38: 2750-2766.
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: 1530-1534.
Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S. & Warnow, T. 2014. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30: i541-i548.
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L., Tosatto, S. C., Paladin, L., Raj, S. & Richardson, L. J. 2021. Pfam: The protein families database in 2021. Nucleic acids research 49: D412-D419.
MNHN, Chagnoux, S. 2024. The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris). Version 69.354. MNHN - Museum national d'Histoire naturelle. Quercus acutissima Carruth. [Image] https://mediaphoto.mnhn.fr/media/1441448266529SZkdDHMFrs1AiwWZ accessed via GBIF.org on 2024-03-20. https://www.gbif.org/occurrence/731714903
Moran, P. A. 1950. Notes on continuous stochastic phenomena. Biometrika 37: 17-23.
Müller, K., Levesque-Tremblay, G., Fernandes, A., Wormit, A., Bartels, S., Usadel, B. & Kermode, A. 2013. Overexpression of a pectin methylesterase inhibitor in Arabidopsis thaliana leads to altered growth morphology of the stem and defective organ separation. Plant signaling & behavior 8: e26464.
Müller, M. & Gailing, O. 2019. Abiotic genetic adaptation in the Fagaceae. Plant Biology 21: 783-795.
Nakhleh, L. 2013. Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in ecology & evolution 28: 719-728.
Nei, M. & Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford University Press, USA.
Network, U. N. P. (2022) Plant and Animal Phenology Data. USA-NPN, Tucson, Arizona, USA. [Last accessed 10 Jun 2022]
Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution 32: 268-274.
Nichols, R. 2001. Gene trees and species trees are not the same. Trends in Ecology & Evolution 16: 358-364.
Niklaus, M. & Kelly, S. 2019. The molecular evolution of C4 photosynthesis: opportunities for understanding and improving the world’s most productive plants. Journal of Experimental Botany 70: 795-804.
Nixon, K. C. (1984) A biosystematic study of Quercus series Virentes (the live oaks) with phylogenetic analyses of Fagales, Fagaceae and Quercus. PhD thesis. University of Texas at Austin.
Nixon, K. C. & Crepet, W. L. 1989. Trigonobalanus (Fagaceae): taxonomic status and phylogenetic relationships. American Journal of Botany 76: 828-841.
Oh, S.-H. & Manos, P. S. 2008. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57: 434-451.
Okamoto, M. 1989. A comparative study of the ontogenetic development of the cupules in Castanea and Lithocarpus (Fagaceae). Plant systematics and evolution 168: 7-18.
Oliver, J. C. 2013. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution 67: 1823-1830.
Olvera-Carrillo, Y., Luis Reyes, J. & Covarrubias, A. A. 2011. Late embryogenesis abundant proteins: versatile players in the plant adaptation to water limiting environments. Plant signaling & behavior 6: 586-589.
Ori, N., Eshed, Y., Chuck, G., Bowman, J. L. & Hake, S. 2000. Mechanisms that control knox gene expression in the Arabidopsis shoot. Development 127: 5523-5532.
Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.
Pandey, S. P. & Somssich, I. E. 2009. The role of WRKY transcription factors in plant immunity. Plant physiology 150: 1648-1655.
Pavlyutkin, B. 2015. The genus Quercus (Fagaceae) in the early Oligocene flora of Kraskino, Primorskii Region. Paleontological Journal 49: 668-676.
Pease, J. B., Haak, D. C., Hahn, M. W. & Moyle, L. C. 2016. Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS biology 14: e1002379.
Pease, J. B. & Hahn, M. W. 2015. Detection and polarization of introgression in a five-taxon phylogeny. Systematic biology 64: 651-662.
Peaucelle, A., Louvet, R., Johansen, J. N., Höfte, H., Laufs, P., Pelloux, J. & Mouille, G. 2008. Arabidopsis phyllotaxis is controlled by the methyl-esterification status of cell-wall pectins. Current Biology 18: 1943-1948.
Petel, A. (2017) Gotranseq. URL: https://github.com/feliixx/gotranseq
Piatkowski, D., Schneider, K., Salamini, F. & Bartels, D. 1990. Characterization of five abscisic acid-responsive cDNA clones isolated from the desiccation-tolerant plant Craterostigma plantagineum and their relationship to other water-stress genes. Plant Physiology 94: 1682-1688.
Pollard, D. A., Iyer, V. N., Moses, A. M. & Eisen, M. B. 2006. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS genetics 2: e173.
Potter, K. M., Jetton, R. M., Bower, A., Jacobs, D. F., Man, G., Hipkins, V. D. & Westwood, M. 2017. Banking on the future: progress, challenges and opportunities for the genetic conservation of forest trees. New Forests 48: 153-180.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. & Glöckner, F. O. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596.
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: 901-904.
Ramirez, J., Watson, K., McMillin, L., Gjieli, E., Sessa, E. 2024. The New York Botanical Garden Herbarium (NY). Version 1.66. The New York Botanical Garden. Castanea pumila (L.) Mill. [Image] https://sweetgum.nybg.org/images3/522/742/01459508.jpg accessed via GBIF.org on 2024-04-05. https://www.gbif.org/occurrence/1927992249
Rannala, B. & Yang, Z. 2007. Inferring speciation times under an episodic molecular clock. Systematic biology 56: 453-466.
Ranwez, V., Harispe, S., Delsuc, F. & Douzery, E. J. 2011. MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PloS one 6: e22594.
Rausch, T. & Greiner, S. 2004. Plant protein inhibitors of invertases. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1696: 253-261.
Rauscher, M. (2018) Topology of genealogical trees - theory and application. In: Faculty of Mathematics and Natural Sciences, PhD thesis. Universität zu Köln.
Rawson, H., Begg, J. & Woodward, R. 1977. The effect of atmospheric humidity on photosynthesis, transpiration and water use efficiency of leaves of several plant species. Planta 134: 5-10.
Reis, M. D., Gunnell, G. F., Barba-Montoya, J., Wilkins, A., Yang, Z. & Yoder, A. D. 2018. Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case. Systematic Biology 67: 594-615.
Reis, M. d. & Yang, Z. 2011. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Molecular biology and evolution 28: 2161-2172.
Renner, S., Grimm, G. W., Kapli, P. & Denk, T. 2016. Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150135.
Revell, L. J., Harmon, L. J. & Collar, D. C. 2008. Phylogenetic signal, evolutionary process, and rate. Systematic biology 57: 591-601.
Ripley, B., Venables, W. & Ripley, M. B. 2016. Package ‘nnet’. R package version 7: 700.
Roberts, T. H., Ahn, J.-W., Lampl, N. & Fluhr, R. 2011 Plants and the study of serpin biology. Methods in Enzymology 499: 347-366.
Rokas, A., Williams, B. L., King, N. & Carroll, S. B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
Royer, D. L. & Wilf, P. 2006. Why do toothed leaves correlate with cold climates? Gas exchange at leaf margins provides new insights into a classic paleotemperature proxy. International Journal of Plant Sciences 167: 11-18.
Royer, D. L., Wilf, P., Janesko, D. A., Kowalski, E. A. & Dilcher, D. L. 2005. Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil record. American journal of botany 92: 1141-1151.
Rush, W. D., Kiehl, J. T., Shields, C. A. & Zachos, J. C. 2021. Increased frequency of extreme precipitation events in the North Atlantic during the PETM: Observations and theory. Palaeogeography, Palaeoclimatology, Palaeoecology 568: 110289.
Sackton, T. B. & Clark, N. (2019) Convergent evolution in the genomics era: new insights and directions. Vol. 374. pp. 20190102. The Royal Society.
Sage, R. F. 2004. The evolution of C4 photosynthesis. New phytologist 161: 341-370.
Sanderson, M. J., Thorne, J. L., Wikström, N. & Bremer, K. 2004. Molecular evidence on plant divergence times. American journal of botany 91: 1656-1665.
Satake, A. & Kelly, D. 2021. Delayed fertilization facilitates flowering time diversity in Fagaceae. Philosophical Transactions of the Royal Society B 376: 20210115.
Sauquet, H. 2013. A practical guide to molecular dating. Comptes Rendus Palevol 12: 355-367.
Serrato, A. J., Fernández-Trijueque, J., Barajas-López, J.-d.-D., Chueca, A. & Sahrawy, M. 2013. Plastid thioredoxins: a “one-for-all” redox-signaling system in plants. Frontiers in plant science 4: 463.
Sharma, A., Kumar, V., Shahzad, B., Ramakrishnan, M., Singh Sidhu, G. P., Bali, A. S., Handa, N., Kapoor, D., Yadav, P. & Khanna, K. 2020. Photosynthetic response of plants under different abiotic stresses: a review. Journal of Plant Growth Regulation 39: 509-531.
Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic biology 51: 492-508.
Slocum, R. D. 2005. Genes, enzymes and regulation of arginine biosynthesis in plants. Plant Physiology and Biochemistry 43: 729-745.
Smith, S. A., Brown, J. W. & Walker, J. F. 2018. So many genes, so little time: a practical approach to divergence-time estimation in the genomic era. PloS one 13: e0197433.
Smith, S. D., Pennell, M. W., Dunn, C. W. & Edwards, S. V. 2020. Phylogenetics is the new genetics (for most of biodiversity). Trends in Ecology & Evolution 35: 415-425.
Sobral, R. & Costa, M. M. R. 2017. Role of floral organ identity genes in the development of unisexual flowers of Quercus suber L. Scientific reports 7: 10368.
Soepadmo, E. 1968. A Revision of the Genus Quercus L. Subgen Cyclobalanopsis (Oersted) Schneider in Malesia. US Government Printing Office.
Soepadmo, E. & Van Steenis, C. 1972. Fagaceae. Flora Malesiana-Series 1, Spermatophyta 7: 265-403.
Song, L. & Florea, L. 2015. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. GigaScience 4: s13742-015-0089-y.
Sousa, V. & Hey, J. 2013. Understanding the origin of species with genome-scale data: modelling gene flow. Nature Reviews Genetics 14: 404-414.
Stebbins Jr, G., Matzke, E. B. & Epling, C. 1947. Hybridization in a population of Quercus marilandica and Quercus ilicifolia. Evolution: 79-88.
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X. & Rokas, A. 2023. Incongruence in the phylogenomics era. Nature Reviews Genetics: 1-17.
Suarez-Gonzalez, A., Lexer, C. & Cronk, Q. C. 2018. Adaptive introgression: a plant perspective. Biology letters 14: 20170688.
Sun, Y. & Wen, X. 2020. Demographic Inference of Divergence and Gene Exchange Between Castanopsis fabri and Castanopsis lamontii. Frontiers in Plant Science 11: 198.
Suzuki, R. 2023. iNaturalist observation: https://www.inaturalist.org/observations/164111561 [Image] https://inaturalist-open-data.s3.amazonaws.com/photos/283915423/original.jpeg [Access date: 2024-04-05]
Tagane, S. 2024a. Herbarium Specimens of The Kagoshima University Museum (KAG). Version 1.3. National Museum of Nature and Science, Japan. Quercus glauca var. amamiana [Image] https://dbs.kaum.kagoshima-u.ac.jp/musedb/s_plant/picture/KAG019657/KAG019657.jpg accessed via GBIF.org on 2024-03-20. https://www.gbif.org/occurrence/4054305408
Tagane, S. 2024b. Herbarium Specimens of The Kagoshima University Museum (KAG). Version 1.3. National Museum of Nature and Science, Japan. Quercus repandifolia J.C.Liao [Image] https://dbs.kaum.kagoshima-u.ac.jp/musedb/s_plant/picture/KAG014168/KAG014168.jpg accessed via GBIF.org on 2024-03-20. https://www.gbif.org/occurrence/4054289823
Tauzin, A. S. & Giardina, T. 2014. Sucrose and invertases, a part of the plant defense response to the biotic stresses. Frontiers in plant science 5: 293.
Thorne, J. L., Kishino, H. & Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular biology and evolution 15: 1647-1657.
Tierney, J. E., Poulsen, C. J., Montañez, I. P., Bhattacharya, T., Feng, R., Ford, H. L., Hönisch, B., Inglis, G. N., Petersen, S. V. & Sagoo, N. 2020. Past climates inform our future. Science 370: eaay3701.
Tigano, A. & Friesen, V. L. 2016. Genomics of local adaptation with gene flow. Molecular ecology 25: 2144-2164.
Tomoko, O. 1995. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. Journal of molecular evolution 40: 56-63.
Tung Ho, L. s. & Ané, C. 2014. A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic biology 63: 397-408.
Uhrig, R. G., Ng, K. K. & Moorhead, G. B. 2009. PII in higher plants: a modern role for an ancient protein. Trends in plant science 14: 505-511.
Vanderpool, D., Minh, B. Q., Lanfear, R., Hughes, D., Murali, S., Harris, R. A., Raveendran, M., Muzny, D. M., Hibbins, M. S. & Williamson, R. J. 2020. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS biology 18: e3000954.
Varela, M. C. & Valdiviesso, T. 1996. Phenological phases of Quercus suber L. flowering. International Journal of Forest Genetics.
Wang, L. & Stegemann, J. P. 2010. Extraction of high quality RNA from polysaccharide matrices using cetlytrimethylammonium bromide. Biomaterials 31: 1612-1618.
Wang, Z., Wu, X., Sun, B., Yin, S., Quan, C. & Shi, G. 2022. First fossil record of Castanopsis (Fagaceae) from the middle Miocene Fotan Group of Fujian, southeastern China. Review of Palaeobotany and Palynology 305: 104729.
Wen, J., Xiong, Z., Nie, Z.-L., Mao, L., Zhu, Y., Kan, X.-Z., Ickert-Bond, S. M., Gerrath, J., Zimmer, E. A. & Fang, X.-D. 2013. Transcriptome sequences resolve deep relationships of the grape family. PloS one 8: e74394.
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G. & Gitzendanner, M. A. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences 111: E4859-E4868.
Wilf, P. 1997. When are leaves good thermometers? A new case for leaf margin analysis. Paleobiology 23: 373-390.
Wilf, P., Nixon, K. C., Gandolfo, M. A. & Cúneo, N. R. 2019. Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests. Science 364: eaaw5139.
Wilson, T., Canny, M. & McCully, M. 1991. Leaf teeth, transpiration and the retrieval of apoplastic solutes in balsam poplar. Physiologia Plantarum 83: 225-232.
Wise, M. J. & Tunnacliffe, A. 2004. POPP the question: what do LEA proteins do? Trends in plant science 9: 13-17.
Wolfe, J. A. 1979. Temperature parameters of humid to mesic forests of eastern Asia and relation to forests of other regions of the Northern Hemisphere and Australasia. USGS Prof. Papers: 37p.
Wolfe, J. A. 1993. A method of obtaining climatic parameters from leaf assemblages. US Government Printing Office.
Wormit, A. & Usadel, B. 2018. The multifaceted role of pectin methylesterase inhibitors (PMEIs). International journal of molecular sciences 19: 2878.
Wu, J.-Y., Ding, S.-T., Li, Q.-J., Zhao, Z.-R., Dong, C. & Sun, B.-N. 2014. A new species of Castanopsis (Fagaceae) from the upper Pliocene of West Yunnan, China and its biogeographical implications. Palaeoworld 23: 370-382.
Wu, M., Kostyun, J. L., Hahn, M. W. & Moyle, L. C. 2018. Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance. Molecular ecology 27: 3301-3316.
Wu, Q., Tong, W., Zhao, H., Ge, R., Li, R., Huang, J., Li, F., Wang, Y., Mallano, A. I. & Deng, W. 2022. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. The Plant Journal 111: 406-421.
Xiang, X.-G., Wang, W., Li, R.-Q., Lin, L., Liu, Y., Zhou, Z.-K., Li, Z.-Y. & Chen, Z.-D. 2014. Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene. Perspectives in Plant Ecology, Evolution and Systematics 16: 101-110.
Xie, F., Vahldick, H., Lin, Z. & Nowack, M. K. 2022. Killing me softly-programmed cell death in plant reproduction from sporogenesis to fertilization. Current opinion in plant biology 69: 102271.
Xing, Y., Onstein, R. E., Carter, R. J., Stadler, T. & Peter Linder, H. 2014. Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected. Evolution 68: 2821-2832.
Xiong, H., Zou, F., Guo, S., Yuan, D. & Niu, G. 2019. Self-sterility may be due to prezygotic late-acting self-incompatibility and early-acting inbreeding depression in Chinese chestnut. Journal of the American Society for Horticultural Science 144: 172-181.
Xu, F., Guo, W., Xu, W. & Wang, R. 2008. Habitat effects on leaf morphological plasticity. Acta Biol Cracoviensia Ser Bot 50: 19-26.
Xue, J. H., Dong, W. P., Cheng, T. & Zhou, S. L. 2012. Nelumbonaceae: systematic position and species diversification revealed by the complete chloroplast genome. Journal of Systematics and Evolution 50: 477-487.
Yamori, W., Evans, J. R. & Von Caemmerer, S. 2010. Effects of growth and measurement light intensities on temperature dependence of CO2 assimilation rate in tobacco leaves. Plant, Cell & Environment 33: 332-343.
Yang, C.-K. (2019) Taxonomy of Fagaceae in Taiwan. In: Department of life science, PhD thesis. National Taiwan Normal University.
Yang, C.-K., Huang, B.-H., Ho, S.-W., Huang, M.-Y., Wang, J.-C., Gao, J. & Liao, P.-C. 2018a. Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae). BMC plant biology 18: 1-15.
Yang, J., Guo, Y.-F., Chen, X.-D., Zhang, X., Ju, M.-M., Bai, G.-Q., Liu, Z.-L. & Zhao, G.-F. 2020. Framework phylogeny, evolution and complex diversification of Chinese oaks. Plants 9: 1024.
Yang, Y., Zhu, J., Feng, L., Zhou, T., Bai, G., Yang, J. & Zhao, G. 2018b. Plastid genome comparative and phylogenetic analyses of the key genera in Fagaceae: Highlighting the effect of codon composition bias in phylogenetic inference. Frontiers in plant science 9: 82.
Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution 24: 1586-1591.
Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A.-M. K. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
Yang, Z. & Rannala, B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular biology and evolution 23: 212-226.
Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W. & Glöckner, F. O. 2014. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic acids research 42: D643-D648.
Zeng, Y.-C. 2023. iNaturalist observation: https://www.inaturalist.org/observations/189120203 [Image] https://inaturalist-open-data.s3.amazonaws.com/photos/331206235/original.jpeg [Access date: 2024-04-05]
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC bioinformatics 19: 15-30.
Zhou, B.-F., Yuan, S., Crowl, A. A., Liang, Y.-Y., Shi, Y., Chen, X.-Y., An, Q.-Q., Kang, M., Manos, P. S. & Wang, B. 2022. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nature Communications 13: 1320.
Zhou, Y., Duvaux, L., Ren, G., Zhang, L., Savolainen, O. & Liu, J. 2017. Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity 118: 211-220.