Soltis, P. S., Folk, R. A. & Soltis, D. E. Darwin review: angiosperm phylogeny and evolutionary radiations. Proc. R. Soc. Lond. B 286, 20190099 (2019).
Sauquet, H. & Magallón, S. Key questions and challenges in angiosperm macroevolution. N. Phytol. 219, 1170–1187 (2018).
Morlon, H. Phylogenetic approaches for studying diversification. Ecol. Lett. 17, 508–525 (2014).
Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl Acad. Sci. USA 103, 9130–9135 (2006).
Wang, W. et al. Menispermaceae and the diversification of tropical rainforests near the Cretaceous-Paleogene boundary. N. Phytol. 195, 470–478 (2012).
Cantalapiedra, J. L. et al. Dietary innovations spurred the diversification of ruminants during the Caenozoic. Proc. Biol. Sci. B 281, 20132746 (2014).
Claramunt, S. & Cracraft, J. A new time tree reveals Earth history’s imprint on the evolution of modern birds. Sci. Adv. 1, e1501005 (2015).
Pires, M. M., Rankin, B. D., Silvestro, D. & Quental, T. B. Diversification dynamics of mammalian clades during the K–Pg mass extinction. Biol. Lett. 14, 20180458 (2018).
Stadler, T. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl Acad. Sci. USA 108, 6187–6192 (2011).
Folk, R. A. et al. Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Proc. Natl Acad. Sci. USA 116, 10874–10882 (2019).
Huang, X. C., German, D. A. & Koch, M. A. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. Ann. Bot. 125, 29–47 (2020).
Vieites, D. R., Min, M.-S. & Wake, D. B. Rapid diversification and dispersal during periods of global warming by plethodontid salamanders. Proc. Natl Acad. Sci. USA 104, 19903–19907 (2007).
Rabosky, D. L. et al. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392–395 (2018).
Igea, J. & Tanentzap, A. J. Angiosperm speciation cools down in the tropics. Ecol. Lett. 23, 692–700 (2020).
Cardillo, M., Orme, C. D. L. & Owens, I. P. F. Testing for latitudinal bias in diversification rates: An example using new world birds. Ecology 86, 2278–2287 (2005).
Ricklefs, R. E. Global variation in the diversification rate of passerine birds. Ecology 87, 2468–2478 (2006).
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448 (2012).
Wiens, J. J. & Donoghue, M. J. Historical biogeography, ecology and species richness. Trends Ecol. Evol. 19, 639–644 (2004).
Schluter, D. & Pennell, M. W. Speciation gradients and the distribution of biodiversity. Nature 546, 48–55 (2017).
Economo, E. P., Narula, N., Friedman, N. R., Weiser, M. D. & Guénard, B. Macroecology and macroevolution of the latitudinal diversity gradient in ants. Nat. Commun. 9, 1778 (2018).
Ricklefs, R. E. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 22, 601–610 (2007).
Hinchliff, C. E. et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc. Natl Acad. Sci. USA 112, 12764–12769 (2015).
Govaert, R. How many species of seed plants are there? Taxon 50, 1085–1090 (2001).
Byng, J. W., Christenhusz, M., Fay, M. F. & Chase, M. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. Linn. Soc. 181, 1–20 (2016).
Wang, H. C. et al. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc. Natl Acad. Sci. USA 106, 3853–3858 (2009).
Magallón, S., Gómez-Acevedo, S., Sánchez-Reyes, L. L. & Hernández-Hernández, T. A meta-calibrated timetree documents the early rise of flowering plant phylogenetic diversity. N. Phytol. 207, 437–453 (2015).
Soltis, P. S., Soltis, D. E., Chase, M. W., Endress, P. K. & Crane, P. R. in The Tree of Life (eds Cracraft, J. & Donoghue, M.) 154–167 (Oxford & New York, 2004).
Boyce, C. K., Lee, J. E., Field., T. S., Brodribb, T. J. & Zwieniecki, M. A. Angiosperms helped put the rain in the rainforests: The impact of plant physiological evolution on tropical biodiversity. Ann. Missouri Bot. Gard. 97, 527–540 (2010).
Moreau, C. S. & Bell, C. D. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution 67, 2240–2257 (2013).
Roelants, K. et al. Global patterns of diversification in the history of modern amphibians. Proc. Natl Acad. Sci. USA 104, 887–892 (2007).
Bininda-Emonds, O. R. et al. The delayed rise of present-day mammals. Nature 446, 507–512 (2007).
Feldberg, K. et al. Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci. Rep. 4, 5974 (2014).
Schneider, H., Schuettpelz, E., Pryer, K. M. & Cranfill, R. Ferns diversified in the shadow of angiosperms. Nature 428, 553–557 (2004).
Magallón, S., Crane, P. R. & Herendeen, P. S. Phylogenetic pattern, diversity, and diversification of eudicots. Ann. Mo. Bot. Gard. 86, 297–372 (1999).
Stevens, P. F. Angiosperm phylogeny website. Version 14. http://www.mobot.org/MOBOT/research/APweb/. Accessed 1 January 2018 (2017).
Folk, R. A. et al. Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids. Am. J. Bot. 105, 433–445 (2018).
Töpel, M., Antonelli, A., Yesson, C. & Eriksen, B. Past climate change and plant evolution in western North America: a case study in Rosaceae. PLoS ONE 7, e50358 (2012).
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. 16, 101–110 (2014).
Sun, M. et al. Phylogeny of the Rosidae: a dense taxon sampling analysis. J. Syst. Evol. 54, 363–391 (2016).
Zhao, L. et al. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol. Phylogenet. Evol. 105, 166–176 (2016).
Sun, M. et al. Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank. Preprint at https://www.biorxiv.org/content/10.1101/694950v1 (2019).
Beaulieu, J. M. & O’Meara, B. C. Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms. Am. J. Bot. 105, 417–432 (2018).
Owens, H. L. et al. The latitudinal diversity gradient in New World swallowtail butterflies is caused by contrasting patterns of out-of-and into-the-tropics dispersal. Glob. Ecol. Biogeogr. 26, 1447–1458 (2017).
Chamberlain, S. et al. rgbif: Interface to the Global Biodiversity Information Facility API. R package version 1.3.0. https://CRAN.R-project.org/package=rgbif (2019).
Michonneau, F. & Collins, M. ridigbio: Interface to the iDigBio data API. R package version 0.3.5. https://CRAN.R-project.org/package=ridigbio (2017).
Rabosky, D. L. Extinction rates should not be estimated from molecular phylogenies. Evolution 64, 1816–1824 (2010).
Pyron, R. A. & Burbrink, F. T. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol. Evol. 28, 729–736 (2013).
Revell, J. L. Comparing the rates of speciation and extinction between phylogenetic trees. Ecol. Evol. 8, 5303–5312 (2018).
Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9, e89543 (2014).
Rabosky, D. L. & Huang, H. A robust semi-parametric test for detecting traitdependent diversification. Syst. Biol. 65, 181–193 (2016).
Harvey, M. G. & Rabosky, D. L. Continuous traits and speciation rates: alternatives to state-dependent diversification models. Methods Ecol. Evol. 9, 984–993 (2018).
Revell, J. L. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
Wiens, J. J. et al. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol. Lett. 13, 1310–1324 (2010).
Rabosky, D. L. & Goldberg, E. E. FiSSE: a simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 71, 1432–1442 (2017).
Beaulieu, J. M. & O’Meara, B. C. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65, 583–601 (2016).
Maddison, W. P., Midford, P. E. & Otto, S. P. Estimating a binary character’s effect on speciation and extinction. Syst. Biol. 56, 701–710 (2007).
Akaike, H. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19, 716–723 (1974).
Wagenmakers, E. J. & Farrell, S. AIC model selection using Akaike weights. Psychon. Bull. Rev. 11, 192–196 (2004).
Cramer, B. S., Toggweiler, J. R., Wright, J. D., Katz, M. E. & Miller, K. G. Ocean overturning since the Late Cretaceous: Inferences from a new benthic foraminiferal isotope compilation. Paleoceanography 24, PA4216 (2009).
Morlon, H. et al. RPANDA: an R package for macroevolutionary analyses on phylogenetic trees. Methods Ecol. Evol. 7, 589–597 (2016).
Pound, M. J., Haywood, A. M., Salzmann, U. & Riding, J. B. Global vegetation dynamics and latitudinal temperature gradients during the Mid to Late Miocene (15.97–5.33 Ma). Earth Sci. Rev. 112, 1–22 (2012).
Wang, Q. G. et al. Niche conservatism and elevated diversification shape species diversity in drylands: evidence from Zygophyllaceae. Proc. R. Soc. Lond. B 285, 20181742 (2018).
Rabosky, D. L. & Goldberg, E. E. Model inadequacy and mistaken inferences of trait-dependent speciation. Syst. Biol. 64, 340–355 (2015).
Gamisch, A. Notes on the statistical power of the Binary State Speciation and Extinction (BiSSE) model. Evol. Bioinformatics 12, 165–174 (2016).
Grundler, M. C. & Rabosky, D. L. Macroevolutionary analysis of discrete traits with rate heterogeneity. Preprint at https://www.biorxiv.org/content/10.1101/2020.01.07.897777v1.full (2020).
Weir, J. T. & Schluter, D. The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574–1576 (2007).
Buzas, M. A., Collins, L. S. & Culver, S. J. Latitudinal difference in biodiversity caused by higher tropical rate of increase. Proc. Natl Acad. Sci. USA 99, 7841–7843 (2002).
Donoghue, M. J. A phylogenetic perspective on the distribution of plant diversity. Proc. Natl Acad. Sci. USA 105, 11549–11555 (2008).
Nürk, N. M., Uribe-Convers, S., Gehrke, B., Tank, D. C. & Blattner, F. R. Oligocene niche shift, Miocene diversification–Cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae). BMC Evol. Biol. 15, 80 (2015).
Xing, Y. & Ree, R. H. Uplift-driven diversification in the Hengduan mountains, a temperate biodiversity hotspot. Proc. Natl Acad. Sci. USA 114, E3444–E3451 (2017).
Lu, L. M. et al. Evolutionary history of the angiosperm flora of China. Nature 554, 234–238 (2018).
Dunn, R. R. et al. Climatic drivers of hemispheric asymmetry in global patterns of ant species richness. Ecol. Lett. 12, 324–333 (2009).
Jablonski, D. Extinction and the spatial dynamics of biodiversity. Proc. Natl Acad. Sci. USA 105(Suppl 1), 11528–11535 (2008).
Schluter, D. Speciation, ecological opportunity, and latitude (American Society of Naturalists Address). Am. Nat. 187, 1–18 (2016).
Arakaki, M. et al. Contemporaneous and recent radiations of the world’s major succulent plant lineages. Proc. Natl Acad. Sci. USA 108, 8379–8384 (2011).
Zanne, A. E. et al. Functional biogeography of angiosperms: life at the extremes. N. Phytol. 218, 1697–1709 (2018).
Díaz, S. et al. The global spectrum of plant form and function. Nature 529, 167–171 (2016).
Zanne, A. E. et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).
Ricklef, R. E. & Renner, S. S. Species richness within families of flowering plants. Evolution 48, 1619–1636 (1994).
Preston, J. C. & Sandve, S. R. Adaptation to seasonality and the winter freeze. Front. Plant Sci. 4, 167 (2013).
Pender, J. E. et al. How sensitive are climatic niche inferences to distribution data sampling? A comparison of biota of North America Program (BONAP) and Global Biodiversity Information Facility (GBIF) datasets. Ecol. Informatics 54, 100991 (2019).
Rabosky, D. L. No substitute for real data: a cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses. Evolution 69, 3207–3216 (2015).
Sun, M. et al. Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids. Am. J. Bot. 107, 1–15 (2020).
Smith, S. A., Beaulieu, J. M. & Donoghue, M. J. Mega-phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches. BMC Evol. Biol. 9, 37 (2009).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Pattengale, N. D. et al. (eds) ISBRA Vol. 6053, 128–139 (Springer, 2010).
Smith, S. A. & O’Meara, B. C. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 689–2690 (2012).
Barnes, R. dggridR: discrete global grids for R. R package version 0.1.12. https://github.com/r-barnes/dggridR/ (2017).
Jablonski, D., Roy, K. & Valentine, J. W. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 06, 102–106 (2006).
Kozak, K. H. & Wiens, J. J. Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecol. Lett. 13, 1378–1389 (2010).
Mullen, S. P., Savage, W. K., Wahlberg, N. & Willmott, K. R. Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies. Proc. R. Soc. Lond. B 278, 1777–1785 (2011).
Rabosky, D. L. Ecological limits on clade diversification in higher taxa. Am. Nat. 173, 662–674 (2009).
Pennell, M. W. et al. Geiger v2.0: An expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30, 2216–2218 (2014).
Losos, J. B. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11, 995–1003 (2008).
P. O. & Rabosky, D. L. Tip rates, phylogenies and diversification: what are we estimating, and how good are the estimates? Methods Ecol. Evol. 10, 821–834 (2019).
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).
Hochberg, Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75, 800–803 (1988).
Meyer, C., Kreft, H., Guralnick, R. & Jetz, W. Global priorities for an effective information basis of biodiversity distributions. Nat. Commun. 6, 8221 (2015).
Sun, M. & Folk, R. A. Code and data for rosid_NCOMMS-19-37964. Zenodo. https://doi.org/10.5281/zenodo.3843441 (2020).
Source: Ecology - nature.com
