Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?


Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Dataset S1. Combined morphology-DNA data matrix in nexus format
Downloaded 84 times
Description We 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.
Download S1_combined.nex (6.925 Mb)
Details View File Details
Title Dataset S2. Morphological data matrix in nexus format
Downloaded 31 times
Description Our 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, 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 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.
Download S2_morph.nex (91.67 Kb)
Details View File Details
Title artEx
Description A script to make artificial fossils, which can be used in artificial extinction analyses. Link to artEx in GitHub repository at
Download // (0 bytes)
Details View File Details
Title Table S1.
Downloaded 43 times
Description Table S1: Key linking X-axis of Fig. 8 to taxon names.
Download tableS1_taxonNumbers.xls (26.11 Kb)
Details View File Details
Title Figure S1.
Downloaded 37 times
Description 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.
Download (1.321 Mb)
Details View File Details
Title Figure S2. Q accuracy
Downloaded 36 times
Description Fig. 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 <<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).
Download (1.299 Mb)
Details View File Details

When using this data, please cite the original publication:

Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ (2015) Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life? Systematic Biology 64(2): 169-186.

Additionally, please cite the Dryad data package:

Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ (2014) Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life? Dryad Digital Repository.
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Search for data

Be part of Dryad

We encourage organizations to: