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Cited by 211Evolution and Paleontology StudiesGenomics and Phylogenetic StudiesPlant Diversity and Evolution

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

Fabre, P-.H., Rodrigues, A., Douzery, E.J.P.·2009·Molecular Phylogenetics and Evolution
DOI 10.1016/j.ympev.2009.08.004
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Abstract

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.

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  • Efforts to overcome the deficiency using a supermatrix approach with published sequences culled from prior studies are inherently flawed by a prohibitively large proportion of missing data for each taxon (e.g. 59-85%).

    “Efforts to overcome this deficiency using a supermatrix approach [4], [5] with published sequences culled from these prior studies are inherently flawed by a prohibitively large proportion of missing data for each taxon (e.g. 59–85% see [5]).”

    From A molecular phylogeny of living primates (2011) · cites this paper as [5]

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Authors
Fabre, P. H., Rodrigues, A., & Douzery, E. J. P.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Fabre, P-.H.
ORCID
Venue
Molecular Phylogenetics and Evolution
Publisher
Elsevier BV
Published
2009-12
Volume
53
Issue
3
Pages
808-825
ISSN
1055-7903 (ISSN-L)
DOI
10.1016/j.ympev.2009.08.004
OpenAlex
W2075152177
Cited by
211
References
113
Citations by year
2026: 2 · 2025: 5 · 2024: 4 · 2023: 4 · 2022: 7 · 2021: 6 · 2020: 46 · 2019: 3 · 2018: 4 · 2017: 11 · 2016: 14 · 2015: 12 · 2014: 21 · 2013: 26 · 2012: 18
FWCI
11.65
Type
journal article
Language
en
Open access
closed
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • Molecular Phylogenetics and Evolution (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
primate phylogeny, macroevolution, diversification rate shifts, divergence time estimation, relaxed molecular clock, birth-death processes, lemurs, Anthropoidea, Old World monkeys, Macaca, Lemuridae, Galagidae, Callithrix, fossil calibration, primate extinction
MeSH terms
Animals, Cell Nucleus, DNA, Mitochondrial, Fossils, Models, Genetic, Phylogeny, Primates, Sequence Analysis, DNA, Evolution, Molecular, Genetic Speciation

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