Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

Mark S. Springer, Robert Meredith, John Gatesy, Christopher A. Emerling, Jong Park, Daniel L. Rabosky, Tanja Stadler, Cynthia Steiner, Oliver A. Ryder, Jan E. Janečka, Colleen A. Fisher, William J. Murphy

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197 Citations (Scopus)

Abstract

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.

Original languageEnglish
Article numbere49521
JournalPLoS ONE
Volume7
Issue number11
DOIs
StatePublished - 16 Nov 2012

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Primates
biogeography
Phylogeny
phylogeny
fossils
ancestry
Genes
Strepsirhini
Biological Extinction
Dinosaurs
Mammals
Mitochondrial Genes
Nucleic Acid Databases
Molecular Dynamics Simulation
North America
Crowns
Haplorhini
Clocks
extinction
mammals

Cite this

Springer, Mark S. ; Meredith, Robert ; Gatesy, John ; Emerling, Christopher A. ; Park, Jong ; Rabosky, Daniel L. ; Stadler, Tanja ; Steiner, Cynthia ; Ryder, Oliver A. ; Janečka, Jan E. ; Fisher, Colleen A. ; Murphy, William J. / Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix. In: PLoS ONE. 2012 ; Vol. 7, No. 11.
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abstract = "Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ({"}Grande Coupure{"}) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.",
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Springer, MS, Meredith, R, Gatesy, J, Emerling, CA, Park, J, Rabosky, DL, Stadler, T, Steiner, C, Ryder, OA, Janečka, JE, Fisher, CA & Murphy, WJ 2012, 'Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix', PLoS ONE, vol. 7, no. 11, e49521. https://doi.org/10.1371/journal.pone.0049521

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix. / Springer, Mark S.; Meredith, Robert; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia; Ryder, Oliver A.; Janečka, Jan E.; Fisher, Colleen A.; Murphy, William J.

In: PLoS ONE, Vol. 7, No. 11, e49521, 16.11.2012.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Springer, Mark S.

AU - Meredith, Robert

AU - Gatesy, John

AU - Emerling, Christopher A.

AU - Park, Jong

AU - Rabosky, Daniel L.

AU - Stadler, Tanja

AU - Steiner, Cynthia

AU - Ryder, Oliver A.

AU - Janečka, Jan E.

AU - Fisher, Colleen A.

AU - Murphy, William J.

PY - 2012/11/16

Y1 - 2012/11/16

N2 - Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.

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