Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-26T06:57:55.444Z Has data issue: false hasContentIssue false
  • English
  • Français

Exploring the impact of unstable terminals on branch support values in paleontological data

Published online by Cambridge University Press:  15 February 2021

Jorge R. Flores Open the ORCID record for Jorge R. Flores [Opens in a new window] ,
Samuli Lehtonen  and
Jaakko Hyvönen
Jorge R. Flores*
Affiliation:
Finnish Museum of Natural History (Botany), P.O. Box 7, FI-00014, University of Helsinki, Finland. E-mail: [email protected]
Samuli Lehtonen
Affiliation:
Biodiversity Unit, University of Turku, 20014Turku, Finland. E-mail: [email protected]
Jaakko Hyvönen
Affiliation:
Organismal and Evolutionary Biology, Viikki Plant Science Centre, Post Office Box 65, FI-00014, University of Helsinki, Finland; and Finnish Museum of Natural History (Botany), P.O. Box 7, FI-00014, University of Helsinki, Finland. E-mail: [email protected]
*
*Corresponding author.
Get access Rights & Permissions [Opens in a new window]

Abstract

Recent studies have acknowledged the many benefits of including fossils in phylogenetic inference (e.g., reducing long-branch attraction). However, unstable taxa are known to be problematic, as they can reduce either the resolution of the strict consensus or branch support. In this study, we evaluate whether unstable taxa that reduce consensus resolution affect support values, and the extent of such impact, under equal and extended implied weighting. Two sets of analyses were conducted across 30 morphological datasets to evaluate complementary aspects. The first focused on the analytical conditions incrementing the terminal instability, while the second assessed whether pruning wildcards improves support. Changes in support were compared with the “number of nodes collapsed by unstable terminals,” their “distance to the root,” the “proportion of missing data in a dataset,” and the “proportion of sampled characters.” Our results indicate that the proportion of missing entries distributed among closely related taxa (for a given character) might be as detrimental for stability as those distributed among characters (for a given terminal). Unstable terminals that (1) collapse few nodes or (2) are closely located to the root node have more influence on the estimated support values. Weighting characters according to their extra steps while assuming that missing entries contribute to their homoplasy reduced the instability of wildcards. Our results suggest that increasing character sampling and using extended implied weighting decreases the impact of wildcard terminals. This study provides insights for designing future research dealing with unstable terminals, a typical problem of paleontological data.

Type
Articles
Information
Paleobiology , Volume 47 , Issue 3 , August 2021 , pp. 432 - 445
Check for updates
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of The Paleontological Society

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Aberer, A. J., and Stamatakis, A.. 2011. A simple and accurate method for rogue taxon identification. Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011:118–122.CrossRefGoogle Scholar
Aberer, A. J., Krompass, D., and Stamatakis, A.. 2013. Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Systematic Biology 62:162–166.CrossRefGoogle ScholarPubMed
Buenaventura, E., Whitmore, D., and Pape, T.. 2017. Molecular phylogeny of the hyperdiverse genus Sarcophaga (Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa. Cladistics 33:109–133.CrossRefGoogle Scholar
Coates, M. I., Gess, R. W., Finarelli, J. A., Criswell, K. E., and Tietjen, K.. 2017. A Symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes. Nature 541:208–211.CrossRefGoogle ScholarPubMed
Cobbett, A., Wilkinson, M., and Wills, M. A.. 2007. Fossils impact as hard as living taxa in parsimony analyses of morphology. Systematic Biology 56:753–766.CrossRefGoogle Scholar
Cong, P., Ma, X., Hou, X., Edgecombe, G. D., and Strausfeld, N. J.. 2014. Brain structure resolves the segmental affinity of anomalocaridid appendages. Nature 513:538–542.CrossRefGoogle ScholarPubMed
Daley, A. C., Budd, G. E., Caron, J. B., Edgecombe, G. D., and Collins, D.. 2009. The Burgess Shale anomalocaridid Hurdia and its significance for early euarthropod evolution. Science 323:1597–1600.CrossRefGoogle ScholarPubMed
Dávalos, L. M., Velazco, P. M., Warsi, O. M., Smits, P. D., and Simmons, N. B.. 2014. Integrating incomplete fossils by isolating conflicting signal in saturated and non-independent morphological characters. Systematic Biology 63:582–600.CrossRefGoogle ScholarPubMed
Davis, S. P., Finarelli, J. A., and Coates, M. I.. 2012. Acanthodes and shark-like conditions in the last common ancestor of modern gnathostomes. Nature 486:247–250.CrossRefGoogle ScholarPubMed
Dececchi, T. A., Larsson, H. C. E., and Hone, D. W. E.. 2012. Yixianosaurus longimanus (Theropoda: Dinosauria) and its bearing on the evolution of Maniraptora and ecology of the Jehol fauna. Vertebrata Palasiatica 50:111–139.Google Scholar
Dragoo, J. W., Honeycutt, R. L., Mammalogy, J., and May, N.. 2007. Systematics of mustelid-like carnivores. Systematics 78:426–443.Google Scholar
Estabrook, G. F. 1992. Evaluating undirected positional congruence of individual taxa between two estimates of the phylogenetic tree for a group of taxa. Systematic Biology 41:172–177.CrossRefGoogle Scholar
Flores, J., Bippus, A., Suárez, G., and Hyvönen, J.. 2020. Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships. Cladistics. doi: 10.1111/cla.12442.Google ScholarPubMed
Fordyce, R. E., and Marx, F. G.. 2018. Gigantism precedes filter feeding in baleen whale evolution. Current Biology 28:1670–1676.e2.CrossRefGoogle ScholarPubMed
Gauthier, J., Kluge, A., and Rowe, T.. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105–209.CrossRefGoogle Scholar
Gernandt, D. S., Holman, G., Campbell, C., Parks, M., Mathews, S., Raubeson, L. A., Liston, A., Stockey, R. A., and Rothwell, G. W.. 2016. Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability. Botany 94:863–884.CrossRefGoogle Scholar
Goloboff, P. 1993. Estimating character weights during tree search. Cladistics 9:83–91.CrossRefGoogle Scholar
Goloboff, P. 1998. Principios básicos de Cladística. Sociedad Argentina de Botánica, Buenos Aires.Google Scholar
Goloboff, P. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15:415–428.CrossRefGoogle Scholar
Goloboff, P. 2014. Extended implied weighting. Cladistics 30:260–272.CrossRefGoogle ScholarPubMed
Goloboff, P., and Arias, J. S.. 2019. Likelihood approximations of implied weights parsimony can be selected over the MK model by the Akaike information criterion. Cladistics 35:695–716.CrossRefGoogle ScholarPubMed
Goloboff, P., and Catalano, S.. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32:221–238.CrossRefGoogle ScholarPubMed
Goloboff, P., and Szumik, C.. 2015. Identifying unstable taxa: efficient implementation of triplet-based measures of stability, and comparison with Phyutility and Roguenarok. Molecular Phylogenetics and Evolution 88:93–104.CrossRefGoogle ScholarPubMed
Goloboff, P., Farris, J., Källersjö, M., and Oxelman, B.. 2003. Improvements to resampling measures of group support. Cladistics 19:324–332.CrossRefGoogle Scholar
Goloboff, P., Carpenter, J., Arias, J., and Esquivel, D.. 2008a. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24:758–773.CrossRefGoogle Scholar
Goloboff, P., Farris, J., and Nixon, K.. 2008b. TNT, a free program for phylogenetic analysis. Cladistics 24:774–786.CrossRefGoogle Scholar
Goloboff, P., Torres, A., and Arias, J.. 2017. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 34:407–437.CrossRefGoogle ScholarPubMed
Goloboff, P., Pittman, M., Pol, D., and Xu, X.. 2019. Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model. Systematic Biology 68:494–504.Google Scholar
Herrera, J. P., and Dávalos, L. M.. 2016. Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree. Systematic Biology 65:772–791.CrossRefGoogle ScholarPubMed
Holroyd, P. A., and Strait, S. G.. 2008. New data on Loveina (Primates: Omomyidae) from the Early Eocene Wasatch Formation and implications for washakiin relationships. Pp. 243–257 in Fleagle, J.G. and Gilbert, C. C., eds. Elwyn Simons: A search for origins. Springer, New York.CrossRefGoogle Scholar
Huelsenbeck, J. 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Biology 40:458–469.CrossRefGoogle Scholar
Jud, N. A., Gandolfo, M. A., Iglesias, A., and Wilf, P.. 2017. Flowering after disaster: early Danian buckthorn (Rhamnaceae). PLoS ONE 12:e0176164.CrossRefGoogle Scholar
Klymiuk, A. A., and Stockey, R. A.. 2012. A lower Cretaceous (Valanginian) seed cone provides the earliest fossil record for Picea (Pinaceae). American Journal of Botany 99:1069–1082.CrossRefGoogle Scholar
Lavin, M., Wojciechowski, M. F., Gasson, P., Hughes, C., and Wheeler, E.. 2003. Phylogeny of robinioid legumes (Fabaceae) revisited: Coursetia and Gliricidia recircumscribed, and a biogeographical appraisal of the Caribbean endemics. Systematic Botany 28:387–409.Google Scholar
Leardi, J. M., Fiorelli, L. E., and Gasparini, Z.. 2015. Redescription and reevaluation of the taxonomical status of Microsuchus schilleri (Crocodyliformes: Mesoeucrocodylia) from the upper Cretaceous of Neuquén, Argentina. Cretaceous Research 52:153–166.CrossRefGoogle Scholar
Legg, D. A., Sutton, M. D., Edgecombe, G. D., and Caron, J. B.. 2012. Cambrian bivalved arthropod reveals origin of arthrodization. Proceedings of the Royal Society of London B 279:4699–4704.Google ScholarPubMed
Lehmann, T. 2009. Phylogeny and systematics of the Orycteropodidae (Mammalia, Tubulidentata). Zoological Journal of the Linnean Society 155:649–702.CrossRefGoogle Scholar
Liu, X., Ren, D., and Yang, D.. 2014. New transitional fossil snakeflies from China illuminate the early evolution of Raphidioptera. BMC Evolutionary Biology 14.CrossRefGoogle ScholarPubMed
Luo, Z. X., Gatesy, S. M., Jenkins, F. A., Amaral, W. W., and Shubin, N. H.. 2015. Mandibular and dental characteristics of Late Triassic mammaliaform Haramiyavia and their ramifications for basal mammal evolution. Proceedings of the National Academy of Sciences USA 112:E7101–E7109.CrossRefGoogle ScholarPubMed
Maidment, S. C. R. 2010. Stegosauria: a historical review of the body fossil record and phylogenetic relationships. Swiss Journal of Geosciences 103:199–210.CrossRefGoogle Scholar
Manos, P. S., Soltis, P. S., Soltis, D. E., Manchester, S. R., Oh, S. H., Bell, C. D., Dilcher, D. L., and Stone, D. E.. 2007. Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets. Systematic Biology 56:412–430.CrossRefGoogle ScholarPubMed
Matthew, W. D. 1909. The Carnivora and Insectivora of the Bridger Basin, middle Eocene. Memoirs of the American Museum of Natural History 9:291–567.Google Scholar
Melo, T. P., Abdala, F., and Soares, M. B.. 2015. The Malagasy cynodont Menadon besairiei (Cynodontia; Traversodontidae) in the middle-upper Triassic of Brazil. Journal of Vertebrate Paleontology 35:e1002562.CrossRefGoogle Scholar
Mulcahy, D. G., Reeder, T. W., Townsend, T., Kuczynski, C. A., Sites, J. W., Wiens, J., Kuczynski, C. A., Townsend, T., Reeder, T. W., Mulcahy, D. G., and Sites, J. W.. 2010. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Systematic Biology 59:674–688.Google Scholar
Musser, G., Ksepka, D. T., and Field, D. J.. 2019. New material of Paleocene–Eocene Pellornis (Aves: Gruiformes) clarifies the pattern and timing of the extant gruiform radiation. Diversity 11.CrossRefGoogle Scholar
Nesbitt, S. J., Smith, N. D., Irmis, R. B., Turner, A. H., Downs, A., and Norell, M. A.. 2009. A complete skeleton of a Late Triassic Saurischian and the early evolution of dinosaurs. Science 326:1530–1533.CrossRefGoogle ScholarPubMed
Novacek, M. J. 1992. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Systematic Biology 41:58–73.CrossRefGoogle Scholar
O'Connor, P. M., Sertich, J. J. W., Stevens, N. J., Roberts, E. M., Gottfried, M. D., Hieronymus, T. L., Jinnah, Z. A., Ridgely, R., Ngasala, S. E., and Temba, J.. 2010. The evolution of mammal-like crocodyliforms in the Cretaceous period of Gondwana. Nature 466:748–751.CrossRefGoogle ScholarPubMed
O'Reilly, J. E., Puttick, M. N., Parry, L., Tanner, A. R., Tarver, J. E., Fleming, J., Pisani, D., and Donoghue, P.. 2016. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biology Letters 12:20160081.CrossRefGoogle Scholar
Pei, R., Pittman, M., Goloboff, P. A., Dececchi, T. A., Habib, M. B., Kaye, T. G., Larsson, H. C. E. E., Norell, M. A., Brusatte, S. L., and Xu, X.. 2020. Potential for powered flight neared by most close avialan relatives, but few crossed its thresholds. Current Biology. doi: 10.1016/j.cub.2020.06.105.CrossRefGoogle ScholarPubMed
Pol, D., and Escapa, I. H.. 2009. Unstable taxa in cladistic analysis: identification and the assessment of relevant characters. Cladistics 25:515–527.CrossRefGoogle Scholar
Pol, D., and Goloboff, P. A.. 2020. The impact of unstable taxa in coelurosaurian phylogeny and resampling support measures for parsimony analyses. Bulletin of the American Museum of Natural History 440:97–115.Google Scholar
Prevosti, F., and Chemisquy, M.. 2010. The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries. Cladistics 26:326–339.CrossRefGoogle Scholar
Pritchard, A. C., Gauthier, J. A., Hanson, M., Bever, G. S., and Bhullar, B. A. S.. 2018. A tiny Triassic saurian from Connecticut and the early evolution of the diapsid feeding apparatus. Nature Communications 9:1213.CrossRefGoogle ScholarPubMed
Rothwell, G. W., and Stockey, R. A.. 2016. Phylogenetic diversification of Early Cretaceous seed plants: the compound seed cone of Doylea tetrahedrasperma. American Journal of Botany 103:923–937.CrossRefGoogle ScholarPubMed
Rubilar-Rogers, D., Otero, R. A., Yury-Yáñez, R. E., Vargas, A. O., and Gutstein, C. S.. 2012. An overview of the dinosaur fossil record from Chile. Journal of South American Earth Sciences 37:242–255.CrossRefGoogle Scholar
Springer, M. S., Teeling, E. C., Madsen, O., Stanhope, M. J., and De Jong, W. W.. 2001. Integrated fossil and molecular data reconstruct bat echolocation. Proceedings of the National Academy of Sciences USA 98:6241–6246.CrossRefGoogle ScholarPubMed
Stilson, K. T., Hopkins, S. S. B., and Davis, E. B.. 2016. Osteopathology in Rhinocerotidae from 50 million years to the present. PLoS ONE 11(2):e0146221. doi: 10.1371/journal.pone.0146221.Google ScholarPubMed
Tanaka, G., Hou, X., Ma, X., Edgecombe, G. D., and Strausfeld, N. J.. 2013. Chelicerate neural ground pattern in a Cambrian great appendage arthropod. Nature 502:364–367.CrossRefGoogle Scholar
Tavares, V. da C., Warsi, O. M., Balseiro, F., Mancina, C. A., and Dávalos, L. M.. 2018. Out of the Antilles: fossil phylogenies support reverse colonization of bats to South America. Journal of Biogeography 45:859–873.CrossRefGoogle Scholar
Wenzel, J., and Siddall, M.. 1999. Noise. Cladistics 15:51–64.CrossRefGoogle Scholar
Wiens, J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47:625–640.CrossRefGoogle ScholarPubMed
Wiens, J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Systematic Biology 52:528–538.CrossRefGoogle ScholarPubMed
Wiens, J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Systematic Biology 54:731–742.CrossRefGoogle ScholarPubMed
Wiens, J., and Morrill, M. C.. 2011. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Systematic Biology 60:719–731.CrossRefGoogle ScholarPubMed
Wiens, J., and Reeder, T. W.. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Systematic Biology 44:548–558.CrossRefGoogle Scholar
Wilkinson, M. 1996. Majority-rule reduced consensus trees and their use in bootstrapping. Molecular Biology and Evolution 13:437–444.CrossRefGoogle ScholarPubMed
Zhao, Y., Vinther, J., Parry, L. A., Wei, F., Green, E., Pisani, D., Hou, X., Edgecombe, G. D., and Cong, P.. 2019. Cambrian sessile, suspension feeding stem-group ctenophores and evolution of the comb jelly body plan. Current Biology 29:1112–1125.e2.CrossRefGoogle ScholarPubMed
Zhu, M., Yu, X., Lu, J., Qiao, T., Zhao, W., and L, J.. 2012. Earliest known coelacanth skull extends the range of anatomically modern coelacanths to the Early Devonian. Nature Communications 3:722.CrossRefGoogle ScholarPubMed
Zverkov, N. G., and Efimov, V. M.. 2019. Revision of Undorosaurus, a mysterious Late Jurassic ichthyosaur of the boreal realm. Journal of Systematic Palaeontology 17:1183–1213.CrossRefGoogle Scholar