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The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

Published online by Cambridge University Press:  06 December 2018

Emanuel TSCHOPP  and
Paul UPCHURCH
Emanuel TSCHOPP*
Affiliation:
Division of Paleontology, American Museum of Natural History, Central Park West @ 79th Street, New York, NY 10024, USA. Email: [email protected] Dipartimento di Scienze della Terra, Università di Torino, Via Valperga Caluso 35, 10125 Torino, Italy. Museu da Lourinhã, Rua João Luís de Moura 95, 2530-157 Lourinhã, Portugal.
Paul UPCHURCH
Affiliation:
Department of Earth Sciences, University College London, Gower Street, London, WC1E 6BT, UK.
*
*Corresponding author
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Abstract

Specimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

Keywords

character weightingcladisticsspecies delimitationvariabilityvertebrate morphology
Type
Articles
Information
Earth and Environmental Science Transactions of The Royal Society of Edinburgh , Volume 109 , Issue 1-2: Fossils, Function and Phylogeny: Papers on Early Vertebrate Evolution in Honour of Professor Jennifer A. Clack , March 2018 , pp. 301 - 323
Copyright
Copyright © The Royal Society of Edinburgh 2018 

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