Harvey, P. H. & Pagel, M. D. The comparative method in evolutionary biology. Vol. 239 (Oxford University Press, 1991).
Oyston, J. W., Hughes, M., Wagner, P. J., Gerber, S. & Wills, M. A. What limits the morphological disparity of clades? Interface Focus 5, 0042 (2015).
Google Scholar
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).
Google Scholar
Webb, C. O. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Naturalist 156, 145–155 (2000).
Google Scholar
Purvis, A., Gittleman, J. L. & Brooks, T. Phylogeny and conservation. (Cambridge University Press, 2005).
Page, R. D. M. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics 10, 155–173 (1994).
Google Scholar
Weaver, S. C. & Vasilakis, N. Molecular evolution of dengue viruses: contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease. Infect., Genet. Evolution 9, 523–540 (2009).
Google Scholar
Tassy, P. Trees before and after Darwin. J. Zool. Syst. Evolut. Res. 49, 89–101 (2011).
Google Scholar
Heather, J. M. & Chain, B. The sequence of sequencers: The history of sequencing DNA. Genomics 107, 1–8 (2016).
Google Scholar
Pyron, R. A. Post-molecular systematics and the future of phylogenetics. Trends Ecol. Evolution 30, 384–389 (2015).
Google Scholar
Sansom, R. S. & Wills, M. A. Differences between hard and soft phylogenetic data. Proc. R. Soc. B: Biol. Sci. 284, 20172150 (2017).
Google Scholar
Scotland, R. W., Olmstead, R. G. & Bennett, J. R. Phylogeny reconstruction: the role of morphology. Syst. Biol. 52, 539–548 (2003).
Google Scholar
Regier, J. C. et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463, 1079–1083 (2010).
Google Scholar
Callender-Crowe, L. M. & Sansom, R. S. Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are. Zool. J. Linn. Soc. 194, 1–13 (2022).
Google Scholar
Wahlberg, N. et al. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. R. Soc. B: Biol. Sci. 272, 1577–1586 (2005).
Google Scholar
He, L. et al. A molecular phylogeny of selligueoid ferns (Polypodiaceae): Implications for a natural delimitation despite homoplasy and rapid radiation. Taxon 67, 237–249 (2018).
Google Scholar
Fernández, R., Edgecombe, G. D. & Giribet, G. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Sci. Rep. 8, 1–7 (2018).
Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).
Google Scholar
Asher, R. J., Bennett, N. & Lehmann, T. The new framework for understanding placental mammal evolution. BioEssays 31, 853–864 (2009).
Google Scholar
Shoshani, J. & McKenna, M. C. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenetics Evolution 9, 572–584 (1998).
Google Scholar
Beck, R. M. D. & Baillie, C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc. R. Soc. B: Biol. Sci. 285, 20181632 (2018).
Google Scholar
Zou, Z. T. & Zhang, J. Z. Morphological and molecular convergences in mammalian phylogenetics. Nat. Commun. 7, 1–9 (2016).
Hillis, D. M. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18, 23–42 (1987).
Google Scholar
Thompson, N. Alfred Russell Wallace Contributions to the theory of Natural Selection, 1870, and Charles Darwin and Alfred Wallace, ‘On the Tendency of Species to form Varieties’ (Papers presented to the Linnean Society 30th June 1858). (Routledge, 2004).
Croizat, L. Panbiogeography; or an introductory synthesis of zoogeography, phytogeography, and geology, with notes on evolution, systematics, ecology, anthropology, etc., Vol. 1, 2a & 2b (Published by the author, Caracas., 1958).
Means, J. C. & Marek, P. E. Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae? PeerJ 5, e3854 (2017).
Google Scholar
Wills, M. A., Barrett, P. M. & Heathcote, J. F. The modified gap excess ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies. Syst. Biol. 57, 891–904 (2008).
Google Scholar
Fisher, D. C. Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annu. Rev. Ecol., Evolution Syst. 39, 365–385 (2008).
Google Scholar
Lazarus, D. B. & Prothero, D. R. The role of stratigraphic and morphologic data in phylogeny. J. Paleontol. 58, 163–172 (1984).
Camerini, J. R. Evolution, biogeography, and maps: an early history of Wallace’s Line. Isis 84, 700–727 (1993).
Google Scholar
Upchurch, P., Hunn, C. A. & Norman, D. B. An analysis of dinosaurian biogeography: evidence for the existence of vicariance and dispersal patterns caused by geological events. Proc. R. Soc. B: Biol. Sci. 269, 613–621 (2002).
Google Scholar
Ferreira, G. S., Bronzati, M., Langer, M. C. & Sterli, J. Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira). R. Soc. Open Sci. 5, 171773 (2018).
Google Scholar
Ronquist, F. & Sanmartín, I. Phylogenetic methods in biogeography. Annu. Rev. Ecol., Evolution, Syst. 42, 441–464 (2011).
Google Scholar
IUCN. The IUCN Red List of Threatened Species. Version 2019-2., https://www.iucnredlist.org (2019).
GBIF.org. GBIF Home Page, https://www.gbif.org/ (2019).
Uetz, P., Freed, P., Aguilar, R. & Hošek, J. The reptile database., http://www.reptiledatabase.org (2019).
Archie, J. W. Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst. Zool. 38, 253–269 (1989).
Google Scholar
Wilkinson, M. On phylogenetic relationships within Dendrotriton (Amphibia: Caudata: Plethodontidae) is there sufficient evidence? Herpetological J. 7, 55–65 (1997).
O’Connor, A. & Wills, M. A. Measuring stratigraphic congruence across trees, higher taxa, and time. Syst. Biol. 65, 792–811 (2016).
Google Scholar
Colless, D. H. Review of phylogenetics: the theory and practice of phylogenetic systematics. Syst. Zool. 31, 100–104 (1982).
Google Scholar
Lartillot, N. & Philippe, H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos. Trans. R. Soc. B: Biol. Sci. 363, 1463–1472 (2008).
Google Scholar
Sansom, R. S., Choate, P. G., Keating, J. N. & Randle, E. Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees. Biol. Lett. 14, 20180263 (2018).
Google Scholar
Rosa, B. B., Melo, G. A. & Barbeitos, M. S. Homoplasy-based partitioning outperforms alternatives in Bayesian analysis of discrete morphological data. Syst. Biol. 68, 657–671 (2019).
Google Scholar
Lucena, D. A. & Almeida, E. A. Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae). Zool. J. Linn. Soc. 194, 36–79 (2022).
Google Scholar
O’Reilly, J. E. et al. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biol. Lett. 12, 20160081 (2016).
Google Scholar
Smith, M. R. Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biol. Lett. 15, 20180632 (2019).
Google Scholar
Wiens, J. The role of morphological data in phylogeny reconstruction. Syst. Biol. 53, 653–661 (2004).
Google Scholar
O’Leary, M. A. & Kaufman, S. G. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy., http://www.morphobank.org (2012).
de Queiroz, A. & Gatesy, J. The supermatrix approach to systematics. Trends Ecol. Evolution 22, 34–41 (2007).
Google Scholar
Wilkinson, M. A comparison of two methods of character construction. Cladistics 11, 297–308 (1995).
Google Scholar
Brazeau, M. D. Problematic character coding methods in morphology and their effects. Biol. J. Linn. Soc. 104, 489–498 (2011).
Google Scholar
Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).
Google Scholar
O’Reilly, J. E., Puttick, M. N., Pisani, D. & Donoghue, P. C. Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data. Palaeontology 61, 105–118 (2018).
Google Scholar
Keating, J. N., Sansom, R. S., Sutton, M. D., Knight, C. G. & Garwood, R. J. Morphological phylogenetics evaluated using novel evolutionary simulations. Syst. Biol. 69, 897–912 (2020).
Google Scholar
Makarenkov, V. et al. Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees. BMC Evolut. Biol. 10, 1–16 (2010).
Google Scholar
Stayton, C. T. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence. Evolution 69, 2140–2153 (2015).
Google Scholar
Sattler, R. Homology – a continuing challenge. Syst. Bot. 9, 382–394 (1984).
Google Scholar
Jenner, R. A. & Schram, F. R. The grand game of metazoan phylogeny: rules and strategies. Biol. Rev. 74, 121–142 (1999).
Google Scholar
Pisani, D. & Wilkinson, M. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 51, 151–155 (2002).
Google Scholar
Arcila, D. et al. Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Syst. Biol. 70, 1123–1144 (2021).
Google Scholar
Felsenstein, J. Phylogenies and the comparative method. Am. Naturalist 125, 1–15 (1985).
Google Scholar
Bremer, K. Branch support and tree stability. Cladistics 10, 295–304 (1994).
Google Scholar
Johnson, W. E. et al. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311, 73–77 (2006).
Google Scholar
Van der Made, J. Biogeography and climatic change as a context to human dispersal out of Africa and within Eurasia. Quat. Sci. Rev. 30, 1353–1367 (2011).
Google Scholar
May, F., Rosenbaum, B., Schurr, F. M. & Chase, J. M. The geometry of habitat fragmentation: Effects of species distribution patterns on extinction risk due to habitat conversion. Ecol. Evolution 9, 2775–2790 (2019).
Google Scholar
Swofford, D. L. et al. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525–539 (2001).
Google Scholar
Jaeger, J. J. & Martin, M. African marsupials – vicariance or dispersion? Nature 312, 379–379 (1984).
Google Scholar
Smith, B. T. et al. The drivers of tropical speciation. Nature 515, 406–409 (2014).
Google Scholar
Simkanin, C. et al. Exploring potential establishment of marine rafting species after transoceanic long-distance dispersal. Glob. Ecol. Biogeogr. 28, 588–600 (2019).
Google Scholar
Raxworthy, C. J., Forstner, M. R. J. & Nussbaum, R. A. Chameleon radiation by oceanic dispersal. Nature 415, 784–787 (2002).
Google Scholar
Stehli, F. G. & Webb, S. D. The great American biotic interchange., Vol. 4 (Springer Science & Business Media, 2013).
Ronquist, F. Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Syst. Biol. 46, 195–203 (1997).
Google Scholar
Ricklefs, R. E. & Bermingham, E. The concept of the taxon cycle in biogeography. Glob. Ecol. Biogeogr. 11, 353–361 (2002).
Google Scholar
Ma, H. An analysis of the equilibrium of migration models for biogeography-based optimization. Inf. Sci. 180, 3444–3464 (2010).
Google Scholar
Yiming, L., Niemelä, J. & Dianmo, L. Nested distribution of amphibians in the Zhoushan archipelago, China: can selective extinction cause nested subsets of species? Oecologia 113, 557–564 (1998).
Google Scholar
Crisci, J. V., Katinas, L. & Posadas, P. Historical Biogeography: An Introduction. (Harvard University Press, 2003).
Chen, R. et al. Adaptive innovation of green plants by horizontal gene transfer. Biotechnol. Adv. 46, 107671 (2021).
Google Scholar
Schönknecht, G., Weber, A. P. & Lercher, M. J. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. BioEssays 36, 9–20 (2014).
Google Scholar
Smith, A. B. Echinoderm phylogeny: morphology and molecules approach accord. Trends Ecol. Evolution 7, 224–229 (1992).
Google Scholar
Bateman, R. M., Hilton, J. & Rudall, P. J. Morphological and molecular phylogenetic context of the angiosperms: contrasting the ‘top-down’ and ‘bottom-up’ approaches used to infer the likely characteristics of the first flowers. J. Exp. Bot. 57, 3471–3503 (2006).
Google Scholar
Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl Acad. Sci. 115, E2274–E2283 (2018).
Google Scholar
Richter, S. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Diversity Evolution 2, 217–237 (2002).
Google Scholar
Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008).
Google Scholar
Caravas, J. & Friedrich, M. Of mites and millipedes: recent progress in resolving the base of the arthropod tree. BioEssays 32, 488–495 (2010).
Google Scholar
Howard, R. J. et al. The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. J. Geol. Soc. https://doi.org/10.1144/jgs2021-107 (2022).
Newman, M. E. J. A model of mass extinction. J. Theor. Biol. 189, 235–252 (1997).
Google Scholar
Cobbett, A., Wilkinson, M. & Wills, M. A. Fossils impact as hard as living taxa in parsimony analyses of morphology. Syst. Biol. 56, 753–766 (2007).
Google Scholar
Ruta, M., Krieger, J., Angielczyk, K. & Wills, M. A. The evolution of the tetrapod humerus: morphometrics, disparity, and evolutionary rates. Earth Environ. Sci. Trans. R. Soc. Edinb. 109, 351–369 (2018).
Puttick, M. N., Thomas, G. H. & Benton, M. J. High rates of evolution preceded the origins of birds. Evolution 68, 1497–1510 (2014).
Google Scholar
Sansom, R. S. & Wills, M. A. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci. Rep. 3, 1–5 (2013).
Google Scholar
Brinkworth, A., Sansom, R. & Wills, M. A. Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best. Zool. J. Linn. Soc. 187, 100–116 (2019).
Google Scholar
Brown, J. W. & Smith, S. A. The past sure is tense: on interpreting phylogenetic divergence time estimates. Syst. Biol. 67, 340–353 (2018).
Google Scholar
Barba-Montoya, J., Dos Reis, M. & Yang, Z. H. Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol. Phylogenetics Evolution 114, 386–400 (2017).
Google Scholar
Sanderson, M. J. & Donoghue, M. J. Patterns of variation in levels of homoplasy. Evolution 43, 1781–1795 (1989).
Google Scholar
Alroy, J. Fossilworks: Gateway to the Paleobiology Database, http://fossilworks.org (2019).
Benton, M. J. The Fossil Record 2. (Chapman & Hall, 1993).
Cohen, K. M., Harper, D. A. T. & Gibbard, P. L. ICS International Chronostratigraphic Chart 2021/02, http://www.stratigraphy.org/ (2021).
Gradstein, F. & Ogg, J. Geologic time scale 2004–why, how, and where next! Lethaia 37, 175–181 (2004).
Google Scholar
Rohde, R. A. The GeoWhen Database, (2005).
O’Leary, M. A. et al. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science 339, 662–667 (2013).
Google Scholar
Kluge, A. G. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Biol. 38, 7–25 (1989).
Google Scholar
Tolson, P. J. Phylogenetics of the boid snake genus Epicrates and Caribbean vicariance theory. Occasional Pap. Mus. Zool., Univ. Mich. 715, 1–68 (1987).
Clopper, C. J. & Pearson, E. S. The use of confidence or fiducial limits illustrated in the case of the binomial. Biometrika 26, 404–413 (1934).
Google Scholar
Source: Ecology - nature.com
