Data from: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Here, we present a new primate phylogeny inferred from molecular
supermatrix analyses of size 42 kb containing 70% of missing data, and
representing 75% of primate species diversity. The supermatrix was
analysed using a gene-partitioned maximum likelihood approach to obtain an
exhaustive molecular phylogenetic framework. All clades recovered from
recent molecular works were upheld in our analyses demonstrating that the
presence of missing data did not bias our supermatrix inference. The
resulting phylogenetic tree was subsequently dated with a molecular dating
method to provide a timescale for speciation events. Results obtained from
our relaxed molecular clock analyses concurred with previous works based
on the same fossil constraints. The resulting dated tree allowed to infer
of macroevolutionary processes among the primates. Shifts in
diversification rate and speciation rates were determined using the
SymmeTREE method and a birthdeath process. No significant asymmetry was
detected for the primate clade, but significant shifts in diversification
rate were identified for seven clades: Anthropoidea, Lemuriformes,
Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian
Macaca. Comparisons with previous primate supertree results reveal that
(i) there was a diversification event at the root of the Lemuriformes,
(ii) a higher diversification rate is detected for Cercopithecidae and
Anthropoidea and (iii) a shift in diversification is always recovered for
Macaca genus. Macroevolutionary inferences and primate divergence dates
show that major primate diversification events occurred after the
Paleogene, suggesting the extinction of ancient primate lineages.