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.

Previous phylogenetic analyses of caecilian neuroanatomical data yield results that are difficult to reconcile with those based upon more traditional morphological and molecular data. A review of the literature reveals problems in both the analyses and the data upon which the analyses were based. Revision of the neuroanatomical data resolves some, but not all, of these problems and yields a data set that, based on comparative measures of data quality, appears to represent some improvement over previous treatments. An extended data set of more traditional primarily morphological data is developed to facilitate the evaluation of caecilian relationships and the quality and utility of neuroanatomical and more traditional data. Separate and combined analyses of the neuroanatomical and traditional data produce a variety of results dependent upon character weighting, with little congruence among the results of the separate analyses and little support for relationships among the ‘higher’ caecilians with the combined data. Randomization tests indicate that: (1) there is significantly less incompatibility within each data set than that expected by chance alone; (2) the between-data-set incompatibility is significantly greater than that expected for random partitions of characters so the two data sets are significantly heterogeneous; (3) the neuroanatomical data appear generally of lower quality than the traditional data; (4) the neuroanatomical data are more compatible with the traditional data than are phylogenetically uninformative data. The lower quality of the neuroanatomical data may reflect small sample sizes. In addition, a subset of the neuroanatomical characters supports an unconventional grouping of all those caecilians with the most rudimentary eyes, which may reflect concerted homoplasy. Although the neuroanatomical data may be of lower quality than the traditional data, their compatibility with the traditional data suggests that they cannot be dismissed as phylogenetically meaningless. Conclusions on caecilian relationships are constrained by the conflict between the neuroanatomical and traditional data, the sensitivity of the combined analyses to weighting schemes, and by the limited support for the majority of groups in the majority of the analyses. Those hypotheses that are well supported are uncontroversial, although some have not been tested previously by numerical phylogenetic analyses. However, the data do not justify an hypothesis of ‘higher’ caecilian phylogeny that is both well resolved and well supported.