Sun, J. et al. Synchronous turnover of flora, fauna, and climate at the Eocene-Oligocene Boundary in Asia. Sci. Rep. 4, 7463 (2014).
Google Scholar
Tiffney, B. H. Perspectives on the origin of the floristic similarity between eastern Asia and eastern North America. J. Arnold Arbor. Harv. Univ. 66, 73–94 (1985).
Tiffney, B. H. The Eocene North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the Northern Hemisphere. J. Arnold Arbor. Harv. Univ. 66, 243–273 (1985).
Donoghue, M. J. A phylogenetic perspective on the distribution of plant diversity. Proc. Natl Acad. Sci. USA 105, 11549–11555 (2008).
Google Scholar
Edwards, E. J. et al. Convergence, consilience, and the evolution of temperate deciduous forests. Am. Nat. 190, S87–S104 (2017).
Google Scholar
Segovia, R. A. et al. Freezing and water availability structure the evolutionary diversity of trees across the Americas. Sci. Adv. 6, eaaz5373 (2020).
Google Scholar
Tiffney, B. H. & Manchester, S. R. The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Northern Hemisphere Tertiary. Int. J. Plant Sci. 162, S3–S17 (2001).
Tierney, J. E. et al. Past climates inform our future. Science 370, eaay3701 (2020).
Google Scholar
Axelrod, D. I. Biogeography of oaks in the Arcto-Tertiary province. Ann. Mo. Bot. Gard. 70, 629–657 (1983).
Axelrod, D. I., Ai-Shehbaz, I. & Raven, P. H. History of the Modern Flora of China. (Springer, 1996).
Cavender-Bares, J. Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution. N. Phytol. 221, 669–692 (2019).
Delcourt, H. R. & A., D. P. North American Terrestrial Vegetation. (Cambridge University Press, 2000).
Olson, J. S., Watts, J. A. & Allison, L. J. Carbon in Live Vegetation of Major World Ecosystems (1983).
Soepadmo, E. Flora Malesiana Series I. Vol. 7 (Noordhoff International Publishing, 1972).
Vogt, K. A. et al. Review of root dynamics in forest ecosystems grouped by climate, climatic forest type and species. Plant Soil 187, 159–219 (1996).
Google Scholar
Whitmore, T. C. Tropical Rain Forest of the Far East. (Oxford University Press, 1984).
Zhu, H. Ecological and biogeographical studies on the tropical rain forest of south Yunnan, SW China with a special reference to its relation with rain forests of tropical Asia. J. Biogeogr. 24, 647–662 (1997).
Averill, C., Bhatnagar, J. M., Dietze, M. C., Pearse, W. D. & Kivlin, S. N. Global imprint of mycorrhizal fungi on whole-plant nutrient economics. Proc. Natl Acad. Sci. USA 116, 23163–23168 (2019).
Google Scholar
Martin, F., Kohler, A., Murat, C., Veneault-Fourrey, C. & Hibbett, D. S. Unearthing the roots of ectomycorrhizal symbioses. Nat. Rev. Microbiol. 14, 760–773 (2016).
Google Scholar
Smith, S. E. & Read, D. J. Mycorrhizal Symbiosis, 2nd edn. (Academic Press, 1997).
Abrahamson, W. G. & Melika, G. Gall-inducing insects (Cynipinae) provide insights into plant systematic relationships. Am. J. Bot. 85, 111–111 (1998).
Raman, A. Nutritional diversity in gall-inducing insects and their evolutionary relationships with flowering plants. Int. J. Ecol. Environ. Sci. 22, 133–143 (1996).
Stone, G. N. et al. Extreme host plant conservatism during at least 20 million years of host plant pursuit by oak gallwasps. Evolution 63, 854–869 (2009).
Google Scholar
Johnson, W. C. & Webb, T. The role of bluejays (Cyanocitta cristata L.) in the postglacial dispersal of fagaceous trees in eastern North America. J. Biogeogr. 16, 561–571 (1989).
Koenig, W. D. & Haydock, J. Oaks, acorns, and the geographical ecology of acorn woodpeckers. J. Biogeogr. 26, 159–165 (1999).
Payne, J. & Francis, C. M. A Field Guide to the Mammals of Borneo. (Sabah Society with World Wildlife Fund Malaysia, 1985).
Steele, M. A. Oak Seed Dispersal. (The Johns Hopkins University Press, 2021).
Vander Wall, S. B. The evolutionary ecology of nut dispersal. Bot. Rev. 67, 74–117 (2001).
Vander Wall, S. B. How plants manipulate the scatter-hoarding behaviour of seed-dispersing animals. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 365, 989–997 (2010).
Barrón, E. et al. in Oaks physiological ecology. Exploring the functional diversity of genus Quercus L. (eds. Eustaquio Gil-Pelegrín, José Javier Peguero-Pina, & Domingo Sancho-Knapik) 39–105 (Springer International Publishing, 2017).
Crepet, W. L. & Nixon, K. C. Earliest megafossil evidence of Fagaceae: Phylogenetic and biogeographic implications. Am. J. Bot. 76, 842–855 (1989).
Denk, T. & Grimm, G. W. Significance of pollen characteristics for infrageneric classification and phylogeny in Quercus (Fagaceae). Int. J. Plant Sci. 170, 926–940 (2009).
Denk, T., Grímsson, F. & Zetter, R. Fagaceae from the early Oligocene of Central Europe: Persisting new world and emerging old world biogeographic links. Rev. Palaeobot. Palynol. 169, 7–20 (2012).
Grímsson, F., Grimm, G. W., Zetter, R. & Denk, T. 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 (2016).
Jones, J. H. Evolution of the Fagaceae: the implications of foliar features. Ann. Mo. Bot. Gard. 73, 228–275 (1986).
Manchester, S. R. Biogeographical relationships of North American Tertiary floras. Ann. Mo. Bot. Gard. 86, 472–522 (1999).
Sadowski, E. M., Schmidt, A. R. & Denk, T. Staminate inflorescences with in situ pollen from Eocene Baltic amber reveal high diversity in Fagaceae (oak family). Willdenowia 50, 405–517 (2020).
Bouchal, J., Zetter, R., Grimsson, F. & Denk, T. Evolutionary trends and ecological differentiation in early Cenozoic Fagaceae of western North America. Am. J. Bot. 101, 1332–1349 (2014).
Google Scholar
Naryshkina, N. N. & Evstigneeva, T. A. Fagaceae in the Eocene palynoflora of the south of primorskii region: New data on taxonomy and morphology. Paleontol. J. 54, 429–439 (2020).
Sadowski, E.-M., Hammel, J. U. & Denk, T. Synchrotron X-ray imaging of a dichasium cupule of Castanopsis from Eocene Baltic amber. Am. J. Bot. 105, 2025–2036 (2018).
Google Scholar
Gandolfo, M. A., Nixon, K. C., Crepet, W. L. & Grimaldi, D. A. A late Cretaceous fagalean inflorescence preserved in amber from New Jersey. Am. J. Bot. 105, 1424–1435 (2018).
Google Scholar
Hipp, A. L. et al. Genomic landscape of the global oak phylogeny. N. Phytol. 226, 1198–1212 (2020).
Google Scholar
Wilf, P., Nixon, K. C., Gandolfo, M. A. & Cuneo, N. R. Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests. Science 364, eaaw5139 (2019).
Google Scholar
Petit, R. J. & Hampe, A. Some evolutionary consequences of being a tree. Annu. Rev. Ecol., Evol. Syst. 37, 187–214 (2006).
Smith, S. A. & Donoghue, M. J. Rates of molecular evolution are linked to life history in flowering plants. Science 322, 86–89 (2008).
Google Scholar
Boucher, F. C., Verboom, G. A., Musker, S. & Ellis, A. G. Plant size: A key determinant of diversification? N. Phytol. 216, 24–31 (2017).
Parins-Fukuchi, C., Stull, G. W. & Smith, S. A. Phylogenomic conflict coincides with rapid morphological innovation. Proc. Natl Acad. Sci. USA 118, e2023058118 (2021).
Google Scholar
Denk, T., Grimm, G. W., Manos, P. S., Deng, M. & Hipp, A. L. in Oaks Physiological Ecology. Exploring the Functional Diversity of Genus Quercus L. Vol. 7 Tree Physiology (eds. GilPelegrin, E., PegueroPina, J. J., & SanchoKnapik, D.) 13–38 (Springer International Publishing Ag, Gewerbestrasse 11, Cham, Ch-6330, Switzerland, 2017).
Deng, M., Jiang, X. L., Hipp, A. L., Manos, P. S. & Hahn, M. Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Mol. Phylogen. Evol. 119, 170–181 (2018).
Hipp, A. L. et al. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. N. Phytol. 217, 439–452 (2018).
Google Scholar
Crowl, A. A. et al. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). N. Phytol. 226, 1158–1170 (2020).
Google Scholar
Hauser, D. A., Keuter, A., McVay, J. D., Hipp, A. L. & Manos, P. S. The evolution and diversification of the red oaks of the California Floristic Province (Quercus section Lobatae, series Agrifoliae). Am. J. Bot. 104, 1581–1595 (2017).
Google Scholar
McVay, J. D., Hauser, D., Hipp, A. L. & Manos, P. S. Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America. Genome 60, 733–742 (2017).
Google Scholar
McVay, J. D., Hipp, A. L. & Manos, P. S. A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proc. R. Soc. B. 284, 20170300 (2017).
Google Scholar
Manos, P. S., Doyle, J. J. & Nixon, K. C. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Mol. Phylogen. Evol. 12, 333–349 (1999).
Google Scholar
Pham, K. K., Hipp, A. L., Manos, P. S. & Cronn, R. C. A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny. Genome 60, 720–732 (2017).
Google Scholar
Simeone, M. C. et al. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 4, e1897 (2016).
Google Scholar
Oh, S.-H. & Manos, P. S. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57, 434–451 (2008).
Renne, P. R. et al. Time scales of critical events around the Cretaceous-Paleogene boundary. Science 339, 684–687 (2013).
Google Scholar
Koenen, E. J. M. et al. The origin of the Legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous–Paleogene (K–Pg) mass extinction event. Syst. Biol. 70, 508–526 (2021).
Google Scholar
Wang, W. et al. Menispermaceae and the diversification of tropical rainforests near the Cretaceous-Paleogene boundary. N. Phytol. 195, 470–478 (2012).
Suh, A., Smeds, L. & Ellegren, H. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of Neoavian birds. PLoS Biol. 13, e1002224 (2015).
Google Scholar
Feng, Y. J. et al. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary. Proc. Natl Acad. Sci. USA 114, E5864–E5870 (2017).
Google Scholar
Alfaro, M. E. et al. Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary. Nat. Ecol. Evol. 2, 688–696 (2018).
Google Scholar
Meredith, R. W. et al. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334, 521–524 (2011).
Google Scholar
Martinez, I. & Gonzalez-Taboada, F. Seed dispersal patterns in a temperate forest during a mast event: performance of alternative dispersal kernels. Oecologia 159, 389–400 (2009).
Google Scholar
Larson-Johnson, K. Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. N. Phytol. 209, 418–435 (2016).
Google Scholar
Xiang, X. G. et al. Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene. Perspect. Plant Ecol. Evol. Syst. 16, 101–110 (2014).
Casanovas-Vilar, I. et al. Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group. Elife 7, e39270 (2018).
Google Scholar
Huchon, D. et al. Rodent phylogeny and a timescale for the evolution of glires: Evidence from an extensive taxon sampling using three nuclear genes. Mol. Biol. Evol. 19, 1053–1065 (2002).
Google Scholar
Upham, N. S., Esselstyn, J. A. & Jetz, W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol. 17, e3000494 (2019).
Google Scholar
Roth, V. L. & Mercer, J. M. The Effects of Cenozoic Global Change on Squirrel Phylogeny. Science 299, 1568–1572 (2003).
Google Scholar
Jonsson, K. A. et al. A supermatrix phylogeny of corvoid passerine birds (Ayes: Corvides). Mol. Phylogen. Evol. 94, 87–94 (2016).
Prum, R. O. et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573 (2015).
Google Scholar
Benz, B. W., Robbins, M. B. & Peterson, A. T. Evolutionary history of woodpeckers and allies (Aves: Picidae): Placing key taxa on the phylogenetic tree. Mol. Phylogen. Evol. 40, 389–399 (2006).
Google Scholar
Lutzoni, F. et al. Contemporaneous radiations of fungi and plants linked to symbiosis. Nat. Commun. 9, 5451 (2018).
Google Scholar
Bonfante, P. & Genre, A. Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nat. Commun. 1, 48 (2010).
Google Scholar
Miyauchi, S. et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat. Commun. 11, 5125 (2020).
Google Scholar
Varga, T. et al. Megaphylogeny resolves global patterns of mushroom evolution. Nat. Ecol. Evol. 3, 668–678 (2019).
Google Scholar
Yang, Y. Y., Qu, X. J., Zhang, R., Stull, G. W. & Yi, T. S. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol. Phylogen. Evol. 163, 107232 (2021).
Whittemore, A. T. & Schaal, B. A. Interspecific gene flow in sympatric oaks. Proc. Natl Acad. Sci. USA 88, 2540–2544 (1991).
Google Scholar
Kremer, A. & Hipp, A. L. Oaks: an evolutionary success story. N. Phytol. 226, 987–1011 (2020).
Petit, R. et al. Chloroplast DNA variation in European white oaks phylogeography and patterns of diversity based on data from over 2600 populations. Ecol. Manag. 176, 595–599 (2003).
Petit, R. et al. Chloroplast DNA footprints of postglacial recolonization by oaks. Proc. Natl Acad. Sci. USA 94, 9996–10001 (1997).
Google Scholar
Petit, R. J. & Excoffier, L. Gene flow and species delimitation. Trends Ecol. Evol. 24, 386–393 (2009).
Google Scholar
Premoli, A. C., Mathiasen, P., Cristina Acosta, M. & Ramos, V. A. Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be? N. Phytol. 193, 261–275 (2012).
Google Scholar
Tsuda, Y., Semerikov, V., Sebastiani, F., Vendramin, G. G. & Lascoux, M. Multispecies genetic structure and hybridization in the Betula genus across Eurasia. Mol. Ecol. 26, 589–605 (2017).
Google Scholar
Zhang, B. W. et al. Phylogenomics reveals an ancient hybrid origin of the persian walnut. Mol. Biol. Evol. 36, 2451–2461 (2019).
Google Scholar
Bock, R. Witnessing genome evolution: experimental reconstruction of endosymbiotic and horizontal gene transfer. Annu. Rev. Genet. 51, 1–22 (2017).
Google Scholar
Hill, W. G. Disequilibrium among several linked neutral genes in finite population: II. Variances and covariances of disequilibria. Theor. Popul. Biol. 6, 184–198 (1974).
Google Scholar
Huerta-Sanchez, E. et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512, 194–197 (2014).
Google Scholar
Huang, Y. et al. Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol. 22, 237 (2021).
Google Scholar
Zhang, X. et al. The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans. Proc. Natl Acad. Sci. USA 118, e2020803118 (2021).
Google Scholar
Cavender-Bares, J., Gonzalez-Rodriguez, A., Pahlich, A., Koehler, K. & Deacon, N. Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone. J. Biogeogr. 38, 962–981 (2011).
Chen, D. et al. Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia: multiple glacial refugia and mainland-migrated island populations. PLoS ONE 7, e47268 (2012).
Google Scholar
Plomion, C. et al. Oak genome reveals facets of long lifespan. Nat. Plants 4, 440–452 (2018).
Google Scholar
Leroy, T. et al. Adaptive introgression as a driver of local adaptation to climate in European white oaks. N. Phytol. 226, 1171–1182 (2020).
O’Donnell, S. T., Fitz-Gibbon, S. T. & Sork, V. L. Ancient introgression between distantly related White Oaks (Quercus sect. Quercus) shows evidence of climate-associated asymmetric gene exchange. J. Hered. 112, 663–670 (2021).
Google Scholar
Nagamitsu, T., Uchiyama, K., Izuno, A., Shimizu, H. & Nakanishi, A. Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan. N. Phytol. 226, 1018–1028 (2020).
Google Scholar
Maxwell, L. M., Walsh, J., Olsen, B. J. & Kovach, A. I. Patterns of introgression vary within an avian hybrid zone. BMC Ecol. Evol. 21, 14 (2021).
Google Scholar
Hewitt, G. M. Hybrid zones-natural laboratories for evolutionary studies. Trends Ecol. Evol. 3, 158–167 (1988).
Google Scholar
Gernandt, D. S., Resendiz Arias, C., Terrazas, T., Aguirre Dugua, X. & Willyard, A. Incorporating fossils into the Pinaceae tree of life. Am. J. Bot. 105, 1329–1344 (2018).
Google Scholar
Rose, J. P., Toledo, C. A. P., Lemmon, E. M., Lemmon, A. R. & Sytsma, K. J. Out of sight, out of mind: Widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal. Syst. Biol. 70, 162–180 (2021).
Google Scholar
Truffaut, L. et al. Fine-scale species distribution changes in a mixed oak stand over two successive generations. N. Phytol. 215, 126–139 (2017).
Google Scholar
Petit, R. J., Bodénès, C., Ducousso, A., Roussel, G. & Kremer, A. Hybridization as a mechanism of invasion in oaks. N. Phytol. 161, 151–164 (2003).
Sork, V. L. et al. Phylogeny and introgression of California scrub White Oaks (Quercus section Quercus). Int. Oaks J. 27, 61–74 (2016).
Quang, N. D., Ikeda, S. & Harada, K. Nucleotide variation in Quercus crispula Blume. Heredity (Edinb.) 101, 166–174 (2008).
Google Scholar
Graham, A. The role of land bridges, ancient environments, and migrations in the assembly of the North American flora. J. Syst. Evol. 56, 405–429 (2018).
Suarez-Gonzalez, A., Lexer, C. & Cronk, Q. C. B. Adaptive introgression: a plant perspective. Biol. Lett. 14, e47268 (2018).
Abbott, R. J., Barton, N. H. & Good, J. M. Genomics of hybridization and its evolutionary consequences. Mol. Ecol. 25, 2325–2332 (2016).
Google Scholar
Goulet, B. E., Roda, F. & Hopkins, R. Hybridization in plants: Old ideas, new techniques. Plant Physiol. 173, 65–78 (2017).
Google Scholar
Mitchell, N. et al. Correlates of hybridization in plants. Evol. Lett. 3, 570–585 (2019).
Google Scholar
Payseur, B. A. & Rieseberg, L. H. A genomic perspective on hybridization and speciation. Mol. Ecol. 25, 2337–2360 (2016).
Google Scholar
Bodenes, C. et al. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC Plant Biol. 12, 153 (2012).
Google Scholar
Cannon, C. H. & Petit, R. J. The oak syngameon: More than the sum of its parts. N. Phytol. 226, 978–983 (2020).
Chen, S. C., Cannon, C. H., Kua, C. S., Liu, J. J. & Galbraith, D. W. Genome size variation in the Fagaceae and its implications for trees. Tree Genet. Genom. 10, 977–988 (2014).
Kremer, A. et al. Genomics of Fagaceae. Tree Genet. Genom. 8, 583–610 (2012).
Neale, D. B., Martinez-Garcia, P. J., De La Torre, A. R., Montanari, S. & Wei, X. X. Novel insights into tree biology and genome evolution as revealed through genomics. Annu. Rev. Plant Biol. 68, 457–483 (2017).
Google Scholar
Staton, M. et al. Substantial genome synteny preservation among woody angiosperm species: Comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics 16, 744 (2015).
Google Scholar
Manos, P. S. & Stanford, A. M. The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. Int. J. Plant Sci. 162, S77–S93 (2001).
Salojarvi, J. et al. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat. Genet. 49, 904–912 (2017).
Google Scholar
Mishra, B. et al. A reference genome of the European beech (Fagus sylvatica L.). Gigascience 7, giy063 (2018).
Google Scholar
Xing, Y. et al. Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). Gigascience 8, giz112 (2019).
Google Scholar
Sork, V. L. et al. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Preprint at bioRxiv https://doi.org/10.1101/2021.04.09.439191 (2021).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Google Scholar
Camacho, C. et al. BLAST plus: architecture and applications. BMC Bioinforma. 10, 421 (2009).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at http://arxiv.org/abs/1303.3997v2 (2013).
McKenna, A. et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Google Scholar
Bertels, F., Silander, O. K., Pachkov, M., Rainey, P. B. & van Nimwegen, E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol. Biol. Evol. 31, 1077–1088 (2014).
Google Scholar
Haudry, A. et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898 (2013).
Google Scholar
Hupalo, D. & Kern, A. D. Conservation and functional element discovery in 20 angiosperm plant genomes. Mol. Biol. Evol. 30, 1729–1744 (2013).
Google Scholar
Dierckxsens, N., Mardulyn, P. & Smits, G. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45, e18 (2017).
Google Scholar
Qu, X. J., Moore, M. J., Li, D. Z. & Yi, T. S. PGA: A software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods 15, 50 (2019).
Google Scholar
Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).
Google Scholar
Katoh, K. & Standley, D. M. Mafft multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Ronquist, F. et al. Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Google Scholar
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. Partitionfinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).
Google Scholar
Akaike, H. New look at statistical-model identification. Ieee Trans. Autom. Control AC19, 716–723 (1974).
Google Scholar
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinforma. 19, 153 (2018).
Chifman, J. & Kubatko, L. Quartet inference from SNP data under the coalescent model. Bioinformatics 30, 3317–3324 (2014).
Google Scholar
PAUP*. Phylogenetic analysis using parsimony (* and other methods). v. Version 4. (Sinauer Associates, Sunderland, 2003).
Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Google Scholar
dos Reis, M. & Yang, Z. Approximate likelihood calculation on a phylogeny for bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).
Google Scholar
Chen, D. et al. Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements. BMC Ecol. Evol. 21, 209 (2021).
Google Scholar
Smith, S. A., Brown, J. W. & Walker, J. F. So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. PLoS ONE 13, e0197433 (2018).
Google Scholar
Johns, C. A., Toussaint, E. F. A., Breinholt, J. W. & Kawahara, A. Y. Origin and macroevolution of micro-moths on sunken Hawaiian Islands. Proc. R. Soc. B. 285, 20181047 (2018).
Google Scholar
Rabosky, D. L. et al. BAMMtools: An R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014).
Salichos, L., Stamatakis, A. & Rokas, A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31, 1261–1271 (2014).
Google Scholar
Smith, S. A., Moore, M. J., Brown, J. W. & Yang, Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150 (2015).
Google Scholar
Xia, X. H., Xie, Z., Salemi, M., Chen, L. & Wang, Y. An index of substitution saturation and its application. Mol. Phylogen. Evol. 26, 1–7 (2003).
Google Scholar
Xia, X. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol. Biol. Evol. 35, 1550–1552 (2018).
Google Scholar
McInerney, J. O. GCUA: general codon usage analysis. Bioinformatics 14, 372–373 (1998).
Google Scholar
Folk, R. A., Mandel, J. R. & Freudenstein, J. V. Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms. Syst. Biol. 66, 320–337 (2017).
Google Scholar
Sukumaran, J. & Holder, M. T. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26, 1569–1571 (2010).
Google Scholar
Olave, M., Avila, L. J., Sites, J. W., Morando, M. & Freckleton, R. Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models. Methods Ecol. Evol. 9, 121–133 (2017).
Than, C. & Nakhleh, L. Species tree inference by minimizing deep coalescences. PLoS Comp. Biol. 5, e1000501 (2009).
Google Scholar
Malinsky, M., Matschiner, M. & Svardal, H. Dsuite – Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).
Google Scholar
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
Google Scholar
Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57, 289–300 (1995).
Google Scholar
Solis-Lemus, C. & Ane, C. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genet. 12, e1005896 (2016).
Google Scholar
Solis-Lemus, C., Bastide, P. & Ane, C. Phylonetworks: A package for phylogenetic networks. Mol. Biol. Evol. 34, 3292–3298 (2017).
Google Scholar
Hejase, H. A. & Liu, K. J. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. BMC Bioinforma. 17, 422 (2016).
Shen, X. X., Hittinger, C. T. & Rokas, A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat. Ecol. Evol. 1, 126 (2017).
Google Scholar
Browning, B. L. & Browning, S. R. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194, 459–471 (2013).
Google Scholar
Source: Ecology - nature.com