1,988
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data

References

  • Aplin, K.P. & Archer, M., 1987. Recent advances in marsupial systematics with a new syncretic classification. In Possums and Opossums: Studies in Evolution. Archer, M., ed., Surrey Beatty & Sons, Sydney, xv–lxxi.
  • Archer, M., Binfield, P., Hand, S.J., Black, K.H., Creaser, P., Myers, T.J., Gillespie, A.K., Arena, D.A., Scanlon, J., Pledge, N. & Thurmer, J., 2018. Miminipossum notioplanetes, a Miocene forest-dwelling phalangeridan (Marsupialia; Diprotodontia) from northern and central Australia. Palaeontologia Electronica 21, 1–11.
  • Ascarrunz, E., Claude, J. & Joyce, W.G., 2019. Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods. PeerJ 7, e7476.
  • Asher, R., 2018. Taxonomy, trees, and truth in historical mammalogy. In Mammalian Evolution, Diversity and Systematics. Zachos, F.E. & Asher, R.J., eds, DE Gruyter, Berlin, Germany.
  • Asher, R.J. & Smith, M.R., 2022. Phylogenetic signal and bias in palaeontology. Systematic Biology 71, 986–1008.
  • Asher, R.J., Smith, M.R., Rankin, A. & Emry, R.J., 2019. Congruence, fossils and the evolutionary tree of rodents and lagomorphs. Royal Society Open Science 6, 190387.
  • Baum, B.R., 1992. Combining trees as a way of combining datasets for phylogenetic inference and the desirability of combining gene trees. Taxon 41, 3–10.
  • Baverstock, P.R., Krieg, M. & Birrell, J., 1990. Evolutionary relationships of Australian marsupials as assessed by albumin immunology. Australian Journal of Zoology 37, 273–287.
  • Beck, R., 2008. A dated phylogeny of marsupials using a molecular supermatrix and multiple fossil constraints. Journal of Mammalogy 89, 175–189.
  • Beck, R.M.D. & Baillie, C., 2018. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proceedings of the Royal Society B: Biological Sciences 285, 20181632.
  • Beck, R.M.D., Louys, J., Brewer, P., Archer, M., Black, K.H. & Tedford, R.H., 2020. A new family of diprotodontian marsupials from the latest Oligocene of Australia and the evolution of wombats, koalas, and their relatives (Vombatiformes). Scientific Reports 10, 9741.
  • Beck, R.M., Voss, R.S. & Jansa, S.A., 2022. Craniodental morphology and phylogeny of marsupials. Bulletin of the American Museum of Natural History 457, 1–352.
  • Billet, G. & Bardin, J., 2019. Serial homology and correlated characters in morphological phylogenetics: Modeling the evolution of dental crests in placentals. Systematic Biology 68, 267–280.
  • Celik, M., Cascini, M., Haouchar, D., VAN Ded Burg, C., Dodt, W., Evans, A.R., Prentis, P., Bunce, M., Fruciano, C. & Phillips, M.J., 2019. A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution. Zoological Journal of the Linnean Society 186, 793–812.
  • Celik, M.A. & Phillips, M.J., 2020. Conflict resolution for Mesozoic mammals: reconciling phylogenetic incongruence among anatomical regions. Frontiers in Genetics 11, 0651.
  • Dávalos, L.M., Cirranello, A.L., Geisler, J.H. & Simmons, N.B., 2012. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews 87, 991–1024.
  • Dávalos, L.M., Velazco, P.M., Warsi, O.M., Smits, P.D. & Simmons, N.B., 2014. Integrating incomplete fossils by isolating conflicting signal in saturated and non-independent morphological characters. Systematic Biology 63, 582–600.
  • Doronina, L., Feigin, C.Y. & Schmitz, J., 2022. Reunion of Australasian possums by shared SINE insertions. Systematic Biology 71, 1045–1053.
  • Duchéne, D.A., Bragg, J.G., Duchéne, S., Neaves, L.E., Potter, S., Moritz, C., Johnson, R.N., Ho, S.Y. & Eldridge, M.D., 2018. Analysis of phylogenomic tree space resolves relationships among marsupial families. Systematic Biology 67, 400–412.
  • Gallus, S., Janke, A., Kumar, V. & Nilsson, M.A., 2015. Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. Genome Biology and Evolution 7, 985–992.
  • Gatesy, J., O’Grady, P. & Baker, R.H., 1999. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15, 271–313.
  • Gauthier, J., Kluge, A.G. & Rowe, T., 1988. Amniote phylogeny and the importance of fossils. Cladistics 4, 105–209.
  • Gillespie, A.K., Archer, M. & Hand, S.J., 2016. A tiny new marsupial lion (Marsupialia, Thylacoleonidae) from the early Miocene of Australia. Palaeontologia Electronica 19, 1–25.
  • Goloboff, P.A., Torres, A. & Arias, J.S., 2018. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 34, 407–437.
  • Goswami, A., Weisbecker, V. & Sanchez-Villagra, M.R., 2009. Developmental Modularity and the Marsupial-Placental Dichotomy. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution 312B, 186–195.
  • Gruber, A.R., Lorenz, R., Bernhart, S.H., Neuböck, R. & Hofacker, I.L., 2008. The Vienna RNA websuite. Nucleic Acids Research 36, W70–W74.
  • Gutell, R., Grey, M. & Schnare, M., 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Research 21, 3055–3074.
  • Horovitz, I. & Sánchez-Villagra, M.R., 2003. A morphological analysis of marsupial mammal higher-level phylogenetic relationships. Cladistics 19, 181–212.
  • Huelsenbeck, J.P. & Ronquist, F., 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755.
  • Jenner, R.A., 2004. Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium. Systematic Biology 53, 333–342.
  • Kangas, A.T., Evans, A.R., Thesleff, I. & Jernvall, J., 2004. Nonindependence of mammalian dental characters. Nature 432, 211–214.
  • Kear, B.P., Cooke, B.N., Archer, M. & Flannery, T.F., 2007. Implications of a new species of the Oligo-Miocene kangaroo (Marsupialia: Macropodoidea) Nambaroo, from the Riversleigh World Heratige Area, Queensland, Australia. Journal of Paleontolgy 81, 1147–1167.
  • Kirsch, J.A.W., Lapointe, F.J. & Springer, M.S., 1997. DNA-hybridisation studies of marsupials and their implications for metatherian classification. Australian Journal of Zoology 45, 211–280.
  • Kitching, I.J., Forey, P.L., Humphries, C.J. & Williams, D., 1998. Cladistics: The Theory and Practice of Parsimony Analysis. Oxford University Press, Oxford; New York.
  • Klingenberg, C.P. & Gidaszewski, N.A., 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Systematic Biology 59, 245–261.
  • Lee, M.S.Y., 1998. Convergent evolution and character correlation in burrowing reptiles: towards a resolution of squamate relationships. Biological Journal of the Linnean Society 65, 369–453.
  • Lee, M.S.Y. & Camens, A.B., 2009. Strong morphological support for the molecular evolutionary tree of placental mammals. Journal Evolutionary Biology 22, 2243–2257.
  • Lee, M.S. & Palci, A., 2015. Morphological phylogenetics in the genomic age. Current Biology 25, R922–R929.
  • Lewis, P.O., 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50, 913–925.
  • Lin, Y.H., Mclenachan, P.H., Gore, A.R., Phillips, M.J., Ota, R., Hendy, M. & Penny, D., 2002. Four new mitochondrial genomes, and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology Evolution 19, 2060–2070.
  • Luckett, W.P., 1994. Suprafamilial relationships within Marsupialia: resolution and discordance from multidisciplinary data. Journal of Mammalian Evolution 2, 255–288.
  • Luo, Z.X., Ji, Q., Wible, J.R. & Yuan, C.X., 2003. An early Cretaceous tribosphenic mammal and metatherian evolution. Science 302, 1934–1940.
  • Macleod, N. & Forey, P.L., 2002. Morphology, Shape and Phylogeny. CRC Press, London.
  • Mammal Diversity Database, 2022. Mammal Diversity Database. v1.9.1. Zenodo, Arizona State University, Tempe, AZ, USA.
  • Marshall, L.G., Case, J.A. & Woodburne, M.O., 1990. Phylogenetic relationships of the families of marsupials. In Current Mammalogy Volume 2, Genoways, H.H., ed., Plenum Press, New York, 433–502.
  • Marshall, C.R., 2017. Five palaeobiological laws needed to understand the evolution of the living biota. Nature Ecology & Evolution 1, 0165.
  • Mckenna, M.C. & Bell, S.K., 1997. Classification of Mammals above the Species Level. Columbia University Press, New York.
  • Meredith, R.W., Janecka, J.E., Gatesy, J., Ryder, O.A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simao, T.L., Stadler, T. & Rabosky, D.L., 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521–524.
  • Meredith, R.W., Westerman, M. & Springer, M.S., 2009. A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes. Molecular Phylogenetics and Evolution 51, 554–571.
  • Mitchell, K.J., Pratt, R.C., Watson, L.N., Gibb, G.C., Llamas, B., Kasper, M., Edson, J., Hopwood, B., Male, D., Armstrong, K.N., Meyer, M., Hofreiter, M., Austin, J., Donnellan, S.C., Lee, M.S.Y., Phillips, M.J. & Cooper, A., 2014. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution 31, 2322–2330.
  • Mongiardino Koch, N., Garwood, R.J. & Parry, L.A., 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B: Biological Sciences 288, 20210044.
  • Mongiardino Koch, N. & Parry, L.A., 2020. Death is on our side: Paleontological data drastically modify phylogenetic hypotheses. Systematic Biology 69, 1052–1067.
  • 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.
  • Nilsson, M.A., Churakov, G., Sommer, M., VAN Tran, N., Brosius, J. & Schmitz, J., 2010. Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS Biology 8, e1000436.
  • O’Leary, M.A. & Gatesy, J., 2008. Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils. Cladistics 24, 397–442.
  • Parins-Fukuchi, C., 2018. Use of continuous traits can improve morphological phylogenetics. Systematic Biology 67, 328–339.
  • Phillips, M.J., Haouchar, D., Pratt, R.C., Gibb, G.C. & Bunce, M., 2013. Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS One 8, e57745.
  • Phillips, M.J., Lin, Y.-H., Harrison, G.L. & Penny, D., 2001. Mitochondrial genomes of a bandicoot and a Brushtail possum confirm the monophyly of Australiadelphian marsupials. Proceedings of the Royal Society B 268, 1533–1538.
  • Phillips, M.J. & Pratt, R.C., 2008. Family-level relationships among the Australasian marsupial "herbivores" (Diprotodontia: Koala, wombats, kangaroos and possums). Molecular Phylogenetics and Evolution 46, 594–605.
  • Phillips, M.J., Cascini, M. & Celik, M., 2022. Identifying complex DNA contamination in pig-footed bandicoots helps to clarify an anomalous ecological transition. Diversity 14, 352.
  • Prideaux, G.J. & Warburton, N.M., 2010. An osteology-based appraisal of the phylogeny and evolution of kangaroos and wallabies (Macropodidae: Marsupialia). Zoological Journal of the Linnean Society 159, 954–987.
  • Rabosky, D.L. & Alfaro, M.E., 2010. Evolutionary bangs and whimpers: methodological advances and conceptual frameworks. Systematic Biology 59, 615–618.
  • Rambaut, A. & Grassly, N.C., 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 13, 235–238.
  • Rambaut, A., 1996. Se-Al: Sequence Alignment Editor (online). http://evolve.zoo.ox.ac.uk/.
  • Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A., 2018. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67, 901–904.
  • Ronquist, F., Teslenko, M., VAN DER Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P., 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61, 539–542.
  • Rosa, B.B., Melo, G.A.R. & Barbeitos, M.S., 2019. Homoplasy-based partitioning outperforms alternatives in Bayesian analysis of discrete morphological data. Systematic Biology 68, 657–671.
  • Sánchez-Villagra, M.R., 2001. The phylogenetic relationships of argyrolagid marsupials. Zoological Journal of the Linnean Society 131, 481–496.
  • Scotland, R.W., Olmstead, R.G. & Benett, J.R., 2003. Phylogeny reconstruction: The role of morphology. Systematic Biology 52, 539–548.
  • Slater, G.J., Harmon, L.J. & Alfaro, M.E., 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution; International Journal of Organic Evolution 66, 3931–3944.
  • Springer, M.S., Burk-Herrick, A., Meredith, R., Eizirik, E., Teeling, E., O'Brien, S.J. & Murphy, W.J., 2007. The adequacy of morphology for reconstructing the early history of placental mammals. Systematic Biology 56, 673–684.
  • Springer, M.S. & Douzery, E., 1996. Secondary structure and patterns of evolution among mammalian 12S rRNA molecules. Journal of Molecular Evolution 43, 357–373.
  • Springer, M.S., Kirsch, J.A.W. & Case, J.A., 1997. The chronicle of marsupial evolution. In Molecular Evolution and Adaptive Radiations. Givnish, T. & Systma, K., eds, Cambridge University Press, Cambridge, 129–157.
  • Springer, M.S., Stanhope, M.J., Madsen, O. & DE Jong, W.W., 2004. Molecules consolidate the placental mammal tree. Trends in Ecology & Evolution 19, 430–438.
  • Springer, M.S., Meredith, R.W., Teeling, E.C. & Murphy, W.J., 2013. Technical comment on “The placental mammal ancestor and the post-K-Pg radiation of placentals.” Science 341, 613.
  • Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10. Sinauer Associates, Sunderland.
  • Szalay, F.S., 1993. Metatherian taxon phylogeny: evidence and interpretation from the cranioskeletal system. In Mammal Phylogeny: Mesozoic Differentiation, Multituberculates, Monotremes, Early Therians, and Marsupials. Szalay, F.S., Novacek, M.J. & Mckenna, M.C., eds, Springer-Verlag, New York, 216–242.
  • Szalay, F.S., 1994. Evolutionary History of the Marsupials and an Analysis of Osteological Characters. Cambridge University Press, Cambridge.
  • Szalay, F.S., 2000. Function and adaptation in paleontology and phylogenetics: why do we omit Darwin? Palaeontologia Electronica 3, 1–25.
  • Szalay, F.S. & Sargis, E.J., 2001. Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaborai (Brazil) and the phylogenetics and biogeography of Metatheria. Geodiversitas 23, 139–302.
  • Wang, J., Wible, J.R., Guo, B., Shelley, S.L., Hu, H. & Bi, S., 2021. A monotreme-like auditory apparatus in a Middle Jurassic haramiyidan. Nature 590, 279–283.
  • Wiens, J.J., 2004. The role of morphological data in phylogeny reconstruction. Systematic Biology 53, 653–661.
  • Wiens, J.J., 2000. Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington, DC.
  • Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum-likelihood Criterion. PhD thesis, University of Texas at Austin.