Published June 15, 2021 | Version v1
Journal article Open

Total Evidence Phylogenetic Analysis Supports New Morphological Synapomorphies for Bovidae (Mammalia, Artiodactyla)

Description

Calamari, Zachary T. (2021): Total Evidence Phylogenetic Analysis Supports New Morphological Synapomorphies for Bovidae (Mammalia, Artiodactyla). American Museum Novitates 2021 (3970): 1-40, DOI: 10.1206/3970.1, URL: https://bioone.org/journals/american-museum-novitates/volume-2021/issue-3970/3970.1/Total-Evidence-Phylogenetic-Analysis-Supports-New-Morphological-Synapomorphies-for-Bovidae/10.1206/3970.1.full

Files

source.pdf

Files (714.7 kB)

Name Size Download all
md5:fe83bade72e96765da7b79d263ded890
714.7 kB Preview Download

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FF83FFDEFFE96765DA7BFFD2FFDEFF90

Related works

Has part
Figure: 10.5281/zenodo.5355811 (DOI)

References

  • Barbera, P., et al. 2019. EPA-ng: Massively parallel evolutionary placement of genetic sequences. Systematic Biology 68: 365-369.
  • Barido-Sottani, J., et al. 2018. Taming the BEAST-a community teaching material resource for BEAST 2. Systematic Biology 67: 170-174.
  • Barmann, E.V. 2013. Towards a comprehensive phylogeny of Bovidae (Ruminantia, Artiodactyla, Mammalia). Ph.D. dissertation, Zoology, University of Cambridge, 242 pp.
  • Barmann, E.V. 2014. The evolution of body size, horn shape and social behaviour in crown Antilopini - an ancestral character state analysis. Zitteliana B 32: 185-196.
  • Barmann, E.V., and G.E. Rossner. 2011. Dental nomenclature in Ruminantia: towards a standard terminological framework. Mammalian Biology 76: 762-768.
  • Barmann, E.V., and T. Schikora. 2014. The polyphyly of Neotragus - results from genetic and morphometric analyses. Mammalian Biology 79: 283-286.
  • Barmann, E.V., G E. Rossner, and G. Worheide. 2013. A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 67: 484-93.
  • Berger, S.A., and A. Stamatakis. 2011. Aligning short reads to reference alignments and trees. Bioinformatics 27: 2068-2075.
  • Berger, S.A., D. Krompass, and A. Stamatakis. 2011. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology 60: 291-302.
  • Bibi, F. 2007. Origin, paleoecology, and paleobiogeography of early Bovini. Palaeogeography, Palaeoclimatology, Palaeoecology 248: 60-72.
  • Bibi, F. 2013. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evolutionary Biology 13: 166.
  • Bibi, F. 2014. Assembling the ruminant tree: combining morphology, molecules, extant taxa, and fossils. Zitteliana B 32: 197-212.
  • Bibi, F., et al. 2009. The fossil record and evolution of Bovidae: state of the field. Palaeontologia Electronica 12.
  • Bibi, F., E. Vrba, and F. Fack. 2012. A new African fossil caprin and a combined molecular and morphological Bayesian phylogenetic analysis of Caprini (Mammalia: Bovidae). Journal of Evolutionary Biology 25: 1843-1854.
  • Bouckaert, R.R., and A.J. Drummond. 2017. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evolutionary Biology 17.
  • Calamari, Z.T. 2016. Sexual maturity and shape development in cranial appendages of extant ruminants. Ecology and Evolution 6 (21): 7820-7830.
  • Cantalapiedra, J.L., G.M. Alcalde, and M. Hernandez Fernandez. 2014. The contribution of phylogenetics to the study of ruminant evolutionary ecology. Zitteliana B 32: 47-52.
  • Cantalapiedra, J.L., M. Hernandez Fernandez, B. Azanza, and J. Morales. 2015. Congruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by Tertiary abiotic change. Evolution 69: 2941-2953.
  • Chen, L., et al. 2019. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364.
  • Cohen, K.M., S.C. Finney, P.L. Gibbard, and J.-X. Fan. 2013. The ICS International Chronostrategraphic Chart. Episodes 36: 199-204.
  • Davalos, L.M., P.M. Velazco, O.M. Warsi, P.D. Smits, and N.B. Simmons. 2014. Integrating incomplete fossils by isolating conflicting signal in saturated and non-independent morphological characters. Systematic Biology 63: 582-600.
  • Decker, J.E., et al. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 106: 18644-18649.
  • Delsuc, F., et al. 2016. The phylogenetic affinities of the extinct glyptodonts. Current Biology 26: R155-R156.
  • DeMiguel, D., B. Azanza, and J. Morales. 2014. Key innovations in ruminant evolution: a paleontological perspective. Integrative Zoology 9: 412-433.
  • Eernisse, D.J., and A.G. Kluge. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Molecular Biology and Evolution 10: 1170-1195.
  • Engel, J. 2004. Morphology and genetics. In T. Gilbert and T. Woodfine (editors), The biology, husbandry and conservation of scimitar-horned oryx (Oryx dammah), 2nd ed.: 3. Marwell Preservation Trust.
  • Fernandez, M.H., and E.S. Vrba. 2005. A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biological Reviews 80: 269-302.
  • Gatesy, J., and P. Arctander. 2000. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes. Systematic Biology 49: 515-538.
  • Gatesy, J., D. Yelon, R. DeSalle, and E.S. Vrba. 1992. Phylogeny of Bovidae (Artiodactyla, mammalia), based on mitochondrial ribosomal DNA sequences. Molecular Biology and Evolution 9: 433-446.
  • Gentry, A.W. 1992. The subfamilies and tribes of the family Bovidae. Mammal Review 22: 1-32.
  • Gentry, A.W. 2000. Caprinae and Hippotragini (Bovidae, Mammalia) in the Upper Miocene. In E.S. Vrba and G.B. Schaller (editors), Antelopes, deer, and relatives: fossil record, behavioral ecology, systematics, and conservation: 65-83. New Haven, CT: Yale University Press.
  • Gentry, A.W. 2011. Bovidae In T. Harrison (editor), Paleontology and geology of Laetoli: human evolution in context. Vol. 2, Fossil hominins and the associated fauna: 363-465. Dordrecht: Springer Netherlands.
  • Geraads, D. 1992. Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla). Zoological Journal of the Linnean Society 104: 193-207.
  • Geraads, D. 2003. Ruminants, other than Giraffidae from the middle Miocene hominoid locality of Candir (Turkey). Courier Forschungsinstitut Senckenberg 240: 181-199.
  • Gilbert, T. 2017. International studbook for the scimitar-horned oryx Oryx Dammah, 12th ed. Winchester, United Kingdom: Marwell Wildlife.
  • Goloboff, P.A. 2014. Extended implied weighting. Cladistics 30: 260-272.
  • Gray, J.E. 1821. On the natural arrangement of vertebrose animals. London Medical Repository 15: 296-310.
  • Guillerme, T., and N. Cooper. 2016. Effects of missing data on topological inference using a total evidence approach. Molecular Phylogenetics and Evolution 94: 146-158.
  • Hagelberg, E., M. Hofreiter, and C. Keyser. 2015. Ancient DNA: the first three decades. Philosophical Transactions of the Royal Society B, Biological Sciences 370: 20130371.
  • Hassanin, A., E. Pasquet, and J.-D. Vigne. 1998. Molecular systematics of the subfamily Caprinae (Artiodactyla, Bovidae) as determined from cytochrome b sequences. Journal of Mammalian Evolution 5: 217-236.
  • Hassanin, A., et al. 2012. Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. Comptes Rendus Biologies 335: 32-50.
  • Hassanin, A., J. An, A. Ropiquet, T.T. Nguyen, and A. Couloux. 2013. Combining multiple autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian mammals: application to the tribe Bovini (Cetartiodactyla, Bovidae). Molecular Phylogenetics and Evolution 66: 766-775.
  • Heath, T.A., J.P. Huelsenbeck, and T. Stadler. 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences of the United States of America 111: E2957-E2966.
  • Hedtke, S.M., T.M. Townsend, and D.M. Hillis. 2006. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Systematic Biology 55: 522-529.
  • Hillis, D.M. 1996. Inferring complex phylogenies. Nature 383: 130-131.
  • Janis, C.M., and K.M. Scott. 1987. The interrelationships of higher ruminant families with a special emphasis on the members of the Cervoidea. American Museum Novitates 2893: 1-85.
  • Janis, C.M., and J.M. Theodor. 2014. Cranial and postcranial morphological data in ruminant phylogenetics. Zitteliana B 32.
  • Johnston, A.R., and N.M. Anthony. 2012. A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene. BMC Evolutionary Biology 12: 120.
  • Katoh, K., K. Misawa, K. Kuma, and T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066.
  • Kozlov, A.M., D. Darriba, T. Flouri, B. Morel, and A. Stamatakis. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35: 4453-4455.
  • Lanfear, R., P.B. Frandsen, A.M. Wright, T. Senfeld, and B. Calcott. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34: 772-773.
  • Lewis, P.O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.
  • Marcot, J.D. 2004. Evolutionary radiations of Ruminantia (Mammalia: Artiodactyla). Ph.D. dissertation, Evolutionary Biology, The University of Chicago, 291 pp.
  • Marcot, J.D. 2007. Molecular phylogeny of terrestrial artiodactyls: conflicts and resolution. In D.R. Prothero and S.E. Foss (editors), The evolution of artiodactyls: 4-18. Baltimore: Johns Hopkins University Press.
  • Mennecart, B., G. Metais, L. Costeur, L. Ginsburg, and G.E. Rossner. 2021. Reassessment of the enigmatic ruminant Miocene genus Amphimoschus Bourgeois, 1873 (Mammalia, Artiodactyla, Pecora). PLOS ONE 16: e0244661.
  • Morales, J., D. Soria, M. Pickford, and M. Nieto. 2003. A new genus and species of Bovidae (Artiodactyla, Mammalia) from the early Middle Miocene of Arrisdrift, Namibia, and the origins of the family Bovidae. Memoir of the Geological Survey of Namibia 19: 371-384.
  • Morales, J., D. Soria, and M. Pickford. 2008. Pecoran ruminants from the early Miocene of the Sperrgebiet, Namibia. Memoir of the Geological Survey of Namibia 20: 397-464.
  • Pattinson, D.J., R.S. Thompson, A.K. Piotrowski, and R.J. Asher. 2015. Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life? Systematic Biology 64: 169-186.
  • Pilgrim, G.E. 1946. The evolution of the buffaloes, oxen, sheep and goats. Journal of the Linnean Society of London, Zoology 41: 272-286.
  • Queiroz, A. de, and J. Gatesy. 2007. The supermatrix approach to systematics. Trends in Ecology and Evolution 22: 34-41.
  • Queiroz, A. de, M.J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657-681.
  • Robinson, T.J., et al. 2014. Phylogeny and vicariant speciation of the grey rhebok, Pelea capreolus. Heredity 112: 325-332.
  • Ropiquet, A. 2017. Two new genera of Bovidae (Mammalia). Dumerilia 7: 78-81.
  • Ropiquet, A., and A. Hassanin. 2005. Molecular evidence for the polyphyly of the genus Hemitragus (Mammalia, Bovidae). Molecular Phylogenetics and Evolution 36: 154-168.
  • Sansom, R.S., and M.A. Wills. 2013. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Scientific Reports 3: 2545.
  • Sansom, R.S., and M.A. Wills. 2017. Differences between hard and soft phylogenetic data. Proceedings of the Royal Society B: Biological Sciences 284: 20172150.
  • Sansom, R.S., M.A. Wills, and T. Williams. 2017. Dental data perform relatively poorly in reconstructing mammal phylogenies: morphological partitions evaluated with molecular benchmarks. Systematic Biology 66: 813-822.
  • Solounias, N., J.C. Barry, R.L. Bernor, E.H. Lindsay, and S.M. Raza. 1995. The oldest bovid from the Siwaliks, Pakistan. Journal of Vertebrate Paleontology 15: 806-814.
  • Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
  • Stamatakis, A. 2016. The RAxML v8.2.X manual. Online resource (available at https://cme.h-its.org/ exelixis/resource/download/NewManual.pdf).
  • Streicher, J.W., J.A. Schulte II, and J J. Wiens. 2016. How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Systematic Biology 65: 128-145.
  • Thomas, H. 1994. Anatomie cranienne et relations phylogenetiques du nouveau bovide (Pseudoryx nghetinhensis) decouvert dans la cordillere annamitique au Vietnam. Mammalia 58: 453-482.
  • Troy, C S., et al. 2001. Genetic evidence for Near-Eastern origins of European cattle. Nature 410: 1088- 1091.
  • Verkaar, E.L.C., I.J. Nijman, M. Beeke, E. Hanekamp, and J.A. Lenstra. 2004. Maternal and paternal lineages in cross-breeding bovine species. Has wisent a hybrid origin? Molecular Biology and Evolution 21: 1165-1170.
  • Vrba, E.S. 2006. A possible ancestor of the living waterbuck and lechwes: Kobus basilcookei sp. nov. (Reduncini, Bovidae, Artiodactyla) from the Early Pliocene of the Middle Awash, Ethiopia. Transactions of the Royal Society of South Africa 61: 63-74.
  • Vrba, E.S. and Y. Haile-Selassie. 2006. A new antelope, Zephyreduncinus oundagaisus (Reduncini, Artiodactyla, Bovidae), from the Late Miocene of the Middle Awash, Afar Rift, Ethiopia. Journal of Vertebrate Paleontology 26: 213-218.
  • Vrba, E.S., J.R. Vaisnys, J.E. Gatesy, R. DeSalle, and K.-Y. Wei. 1994. Analysis of paedomorphosis using allometric characters: the example of Reduncini antelopes (Bovidae, Mammalia). Systematic Biology 43: 92-116.
  • West, A.R. 2016. Mitogenome of the extinct helmeted musk ox, Bootherium bombifrons. Mitochondrial DNA Part B 1: 862-863.
  • Wiens, J.J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Systematic Biology 52: 528- 538.
  • Wiens, J.J., and D.S. Moen. 2008. Missing data and the accuracy of Bayesian phylogenetics. Journal of Systematics and Evolution 46: 307-314.
  • Wiens, J.J., and M.C. Morrill. 2011. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Systematic Biology 60: 719-731.
  • Wu, D.-D., et al. 2018. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nature Ecology & Evolution 2: 1139-1145.
  • Xiaoming, W., Z. Qiu, and N.D. Opdyke. 2003. Litho-, bio-, and magnetostratigraphy and paleoenvironment of Tunggur Formation (Middle Miocene) in Central Inner Mongolia, China. American Museum Novitates 3411: 1-31.
  • Zwickl, D.J., and D.M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51: 588-598.