16Specimen-level phylogenetic approaches are widely used in molecular biology for 17 taxonomic and systematic purposes. However, they have been largely ignored in analyses based on 18 morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a 19 number of specimen-level studies have been published in vertebrate paleontology. These studies 20indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at 21 low taxonomic levels. Herein, we review the challenges when working with individual organisms as 22 operational taxonomic units in a paleontological context, and propose guidelines of how best to 23 perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that 24no single methodology appears to be perfectly suited to resolve relationships among individuals, 25and that different taxa probably require different approaches to assess their systematics, we 26advocate the use of a number of methodologies. In particular, we recommend the inclusion of as 27 many specimens and characters as feasible, and analysis of relationships using an extended implied 28 weighting approach with different downweighting functions. Resulting polytomies should be 29 explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between 30 different iterations of the analysis should be evaluated by a combination of support values such as 31 jackknifing and symmetric resampling. Species delimitation should be consistent among the 32 ingroup and based on a reproducible approach. Although time-consuming and methodologically 33 challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific 34 variability and provide the basis for more informed and accurate creation of species-level 35 operational taxonomic units in large-scale systematic studies. It also has the potential to inform us 36 about past speciation processes, morphological trait evolution, and their potential intrinsic and 37 extrinsic drivers in preeminent detail. 38Keywords. character weighting, cladistics, parsimony, species delimitation, vertebrate morphology 39 40 3 41 Specimen-level phylogenetic analysis is becoming increasingly popular in vertebrate 42 paleontology, in particular (but not only) in dinosaur systematics (This kind of phylogenetic analysis includes single specimens instead of species or genera as 46 operational taxonomic units (OTUs), and thus ignores earlier species-and/or genus-level 47 2004; Boyd et al. 2009; Scannella et al. 2014; Longrich 2015; Mounier & Caparros 2015; Tschopp 59 et al. 2015; Campbell et al. 2016). 60 Longrich (2015) and Tschopp et al. (2015) specifically highlighted the ability of specimen-61 level phylogenetic analyses to act as a test for homology of particular morphological features, and 62 thus to assess a trait's phylogenetic informativeness versus its status as intraspecific variation. This 63 issue is particularly important in vertebrate paleontology, where many s...