Inferring large phylogenies: The big tree problem

14 Supertrees are phylogenetic trees whose topologies are derived from a set of 15 partially overlapping, smaller trees. Here we present a supertree for the order Primates, 16 constructed by analyzing source trees we binary-coded using Matrix Representation using 17 Parsimony analysis (MRP). The source trees are derived from previously published 18 studies, and are based on a variety of data types, reconstructed using a variety of 19 methods. In terms of the number of species included in the analysis, the composite 20 estimate presented here is the largest phylogeny of the Primates available to date; it is 21 well-resolved and generally fits with our understanding of the systematics of this order. 22 Areas with few or incongruent data are identified using strength-of-grouping and rQS 23 values. In addition to this updated topology, we present divergence dates estimated using 24 a new method that utilizes overlapping fossil-calibrated clock-like DNA sequence data. 25 For the nodes for which no molecular estimates are available we provide expected ages 26 under a pure birth model. We analyze the divergence date estimates and find that, overall, 27 the Order Primates has diversified at a constant rate of cladogenesis, though looked at in 28 more detail we note, in agreement with earlier studies, a significantly elevated rate in the 29 cercopithecines. 30