DOI: 10.5061/dryad.4g42q
title: Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?

description: Paleontological systematics relies heavily on morphological data that have
 undergone decay and fossilization. Here, we apply a heuristic means to
 assess how a fossil's incompleteness detracts from inferring its
 phylogenetic relationships. We compiled a phylogenetic matrix for primates
 and simulated the extinction of living species by deleting an extant
 taxon's molecular data and keeping only those morphological
 characters present in actual fossils. The choice of characters present in
 a given living taxon (the subject) was defined by those present in a given
 fossil (the template). By measuring congruence between a well-corroborated
 phylogeny to those incorporating artificial fossils, and by comparing real
 vs. random character distributions and states, we tested the information
 content of paleontological datasets and determined if extinction of a
 living species leads to bias in phylogeny reconstruction. We found a
 positive correlation between fossil completeness and topological
 congruence. Real fossil templates sampled for 36 or more of the 360
 available morphological characters (including dental) performed
 significantly better than similarly complete templates with random states.
 Templates dominated by only one partition performed worse than templates
 with randomly sampled characters across partitions. The template based on
 the Eocene primate Darwinius masillae performs better than most other
 templates with a similar number of sampled characters, likely due to
 preservation of data across multiple partitions. Our results support the
 interpretation that Darwinius is strepsirhine, not haplorhine, and suggest
 that paleontological datasets are reliable in primate phylogeny
 reconstruction.
description: Dataset S1. Combined
 morphology-DNA data matrix in nexus formatWe compiled a dataset of
 morphological and molecular characters, sampled at genus level for 24
 extant primates and two outgroups. Genera represented in previous studies
 (Seiffert et al. 2009; Springer et al. 2012) by multiple species were
 condensed into single terminals in order to minimize missing data. In
 cases where different species within a genus exhibited different character
 states, we coded the genus as polymorphic for that character. Condensing
 taxa to genus-level also has the advantage of improving the tractability
 of both MP and Bayesian phylogenetic analysis by slightly reducing the
 number of terminals. We used the alignment of Springer et al. (2012;
 Treebase accession #S13451) as our molecular dataset, consisting of 61199
 nucleotide characters distributed across 69 nuclear and 10 mitochondrial
 genes. This alignment comprises part of our morphology-DNA data matrix in
 our supplementary data file S1.S1_combined.nexDataset S2. Morphological data matrix in nexus formatOur morphological dataset was derived primarily from Seiffert et al. (2009), updated by Gladman et al. (2013) and Boyer and Seiffert (2013), and enabled us to sample 85 fossil taxa. In order to improve overlap with the available DNA sequences, several extant taxa were added: Callicebus sp., Cebus sp., Chlorocebus aethiops, Colobus sp., Daubentonia madagascariensis, Hylobates sp., Macaca sp., and a composite Dermoptera consisting of Cynocephalus volans and Galeopithecus variegatus, treated as a single taxon. Characters were coded from direct observations of museum specimens housed at the University Museum of Zoology, Cambridge, based on the descriptions in the matrix of Seiffert et al. (2009), supplemented with images available from www.digimorph.org, and data from Luckett (1976), Wible and Covert (1987), Beard et al. (1988), Dagosto (1990), Yoder (1994), Ross et al. (1998), Gebo (2001), and Pilbeam (2004). Our morphology matrix is available in nexus format as supplementary data (S2) and from http://www.datadryad.org. Postcranial data for Callicebus moloch and Chlorocebus aethiops were derived primarily from Ross et al. (1998) and Yoder (1994), respectively. Alouatta seniculus and Pan troglodytes were added to the matrix using data from Boyer and Seiffert (2013) and Seiffert (pers. comm.). Facial vibrissae (Yoder 1994: character 61) were coded for new taxa according to the presence of vibrissae musculature as reported in Muchlinski et al. (2013). Not all characters have been treated consistently by previous investigators, or were sufficiently described and illustrated so as to enable coding new taxa. Where the anatomical basis for making a particular coding decision was not clear to us, we have left previous codings as-is and added only "?" to our new taxa.S2_morph.nexartExA script to make artificial fossils, which can be used in artificial extinction analyses. Link to artEx in GitHub repository at https://github.com/davipatti/artExTable S1.Table S1: Key linking X-axis of Fig. 8 to taxon names.tableS1_taxonNumbers.xlsFigure S1.Fig S1: Asymmetric means of calculating topological similarity. AFT-ECT represents number of splits in extant combined topology shared with artificial fossil topologies (also given in Fig. 1). ECT-AFT represents splits in artificial fossil topologies shared with extant combined topology. Number of morphological characters (X-axis) corresponds to 0-100% complete (out of 360 total) in 10% intervals.figS1.aiFigure S2. Q accuracyFig. S2: Relationship between Q and topological accuracy. Q quantifies the extent to which a dataset is evenly sampled across partitions; as Q approaches 1 all partitions are evenly sampled; as Q approaches 0 only one partition contains data. Topological accuracy is quantified as the number of splits (i.e., unrooted clades) in the well corroborated, extant combined topology (or ECT, Fig. 1) present in the artificial fossil topology (or AFT). For the 85 fossil templates, there is a statistically significant correlation (Pearson’s R = 0.694, p &lt;&lt;0.01, Rohlf & Sokal 1995: table R) between Q values (X-axis) and ECT splits present in AFTs (Y-axis). “All fossils” (black circles) represent our 85 real fossil templates, with a select few identified with polygons. “Random templates” (open circles) indicate artificial fossils generated using real character state data with missing entries inserted at random across partitions (see Fig. 2a and Methods).FigS2-Qaccuracy.ai