Successive radiations, not stasis, in the South American primate fauna

Hodgson, Jason A.; Sterner, Kirstin N.; Matthews, Luke J.; Burrell, Andrew S.; Jani, Rachana A.; Raaum, Ryan L.; Stewart, Caro Beth; Disotell, Todd R.

doi:10.1073/pnas.0810346106

Cited by 102 publications

(114 citation statements)

References 40 publications

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“…Table 1 (Ray et al, 2005;Opazo et al, 2006;Schrago, 2007;Hodgson et al, 2009;Osterholz et al, 2009;Wildman et al, 2009). The reconstructed position of Aotus differs from other molecular studies (Schrago, 2007;Perelman et al, 2011;Springer et al, 2012) that place Aotus it at the base of callitrichines rather than cebines.…”

Section: Fossil Platyrrhinesmentioning

confidence: 99%

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Biogeography in deep time – What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Kay

2015

Molecular Phylogenetics and Evolution

111

164

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a b s t r a c tMolecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa.Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium.

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Section: Fossil Platyrrhinesmentioning

confidence: 99%

“…In the first instance, in spite of rapidly accumulating data and methodological progress, branch times remain poorly constrained and subject to substantial variance (Opazo et al, 2006;Schrago, 2007;Hodgson et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Biogeography in deep time – What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Kay

2015

Molecular Phylogenetics and Evolution

111

164

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“…65 Recent sequence-based studies and our research clearly contradict the topology given for other genera such as Callimico and Lophocebus. [72][73] Given its lack of resolution and topological misplacements at the generic level, the continued use of the Purvis phylogeny 27 cannot be recommended.…”

mentioning

confidence: 99%

“…The Bininda-Emonds tree contains an incorrect topology for the basal bifurcations among the platyrrhines given the Alu insertion data and whole mitochondrial genome evidence. 65,72 It also includes apparent anomalies or errors, such as the paraphyletic placement of Callicebus personatus as separate from its congeners and basal to Cebidae. While the Bininda-Emonds tree is useful for mammal-wide comparative analyses, we recommend 10kTrees for studies focused on primates.…”

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confidence: 99%

The 10kTrees website: A new online resource for primate phylogeny

Arnold¹,

Matthews²,

Nunn

2010

Evolutionary Anthropology

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Luke Matthews is an anthropologist and primatologist whose interests include the evolution of primate behavior, primate traditions, and human cultural evolution. He has conducted primatological fieldwork in Ecuador and Argentina. He employs phylogenetics, network analysis, and cluster analysis to study inheritance systems that range from DNA sequences to primate foraging traditions and human material culture. Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes given the dataset.The trees also reflect uncertainty about branch lengths.The comparative method has undergone a revolution in the past 20 years. 2,[14][15][16] Specifically, new phylogenetic methods provide a way to incorporate evolutionary history directly into comparative research. Phylogeny is essential to comparative research because related species tend to resemble one another, resulting in non-independent data points. 2,[17][18] Phylogenetic comparative methods can be used to investigate whether two traits change in tandem through time, while also providing the historical scaffolding to identify independent evolutionary origins of the traits of interest. More recently, phylogenetic methods have provided a toolkit to investigate the tempo and mode of evolution, [19][20] to quantify phylogenetic signal in comparative data, [21][22] and to study the factors that influence diversification rates. [23][24] Computer simulations have revealed that it is usually preferable to conduct comparative tests with some form of phylogenetic method because this reduces false positives (Type I errors) and increases statistical power. [17][18][25][26] This latter point is often under-appreciated, but it is a logical outcome of phylogenetic comparative analyses that reduce error associated with the estimation of statistics and thus enhance the probability of detecting real effects. 26Researchers generally want to include as many species as possible in a comparative analysis. To incorporate phylogeny in comparative studies of primates, previous researchers have used either published primate-wide "supertrees" such as the Purvis phylogeny, 27 or they compiled smaller trees from the literature, often patching these together from among existing phylogenies based on morphology or genetics. 28-29More recently, Bininda-Emonds et al. [30][31] produced a new supertree of mammals, and researchers have begun to use the primate portion of this tree in comparative studies of primates. 32-34The actual tree topology and timing of speciation events is, however, never known with certainty. In addition, phylogenetic relationships should be continually proportion to their posterior probability (see Box 1). The set of trees obtained reflects uncertainty in the phylogeny given the substitution model and data; more certain nodes are found across a greater proportion of the sample of trees, while less certain nodes ...

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“…These genes were selected because we are doing a mitogenomics project with different mammals. Many mitogenomic analyses have shown to be extremely useful in determining phylogenetic relationships and in estimating divergence times in many different groups of organisms, such as birds [34,35] and mammals [36][37][38][39][40][41][42][43][44][45]. Mitochondrial gene trees are more precise in reconstructing the divergence history among species than other molecular markers [46].…”

Section: Molecular Markers Employedmentioning

confidence: 99%

Continuous Miocene, Pliocene and Pleistocene Influences on Mitochondrial Diversification of the Capybara (Hydrochoerus Hydrochoeris; Hydrochoeridae, Rodentia): Incapacity to Determine Exclusive Hypotheses on the Origins of the Amazon and Orinoco Diversity for This Species

Ruiz‐García¹,

Luengas-Villamil²,

Pinedo-Castro³

et al. 2016

J Phylogenetics Evol Biol

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The capybara (Hydrochoerus hydrochoeris) is the largest rodent on the world and it is strongly linked to the river systems of a large fraction of South America and part of Central America (Panama). Thus, it is an interesting species to test hypotheses about the origin of the high biodiversity within the Amazon Basin and in a sizeable fraction of the Neotropics. To test these hypotheses, we sequenced two mitochondrial genes (control region and Cytochrome b) of 78 wild capybaras sampled in Colombia, Peru, Ecuador and Brazil. At least, five different "populations" or ESUs were detected in well delimited geographical areas. However, our results do not support the more recent view that two different species of capybara are present (H. hydrochoeris and H. isthmus), unless chromosomal speciation (stasipatric or parapatric) can be demonstrated between these two groups. A Bayesian tree with the aforementioned two mitochondrial genes, and another Bayesian tree with a subset of 25 capybaras for 10 mitochondrial genes, showed that the initial diversification of the mitochondrial haplotype in capybaras was initiated in the Late Miocene. The trees also showed that the other haplotype diversification processes extended into the Pliocene and Pleistocene. We also detected population expansion events during different moments of the Pleistocene. Although some authors strongly suggest that the Miocene diversification explains the extreme biodiversity in the Amazon Basin and in surroundings areas (for instance, the Paleogeography hypothesis), others consider it the result of available forest refugia (Refuge hypothesis) during the Pleistocene. However, our results suggest that both hypotheses (and others, such as the Riverrefuge, the Recent Lagoon and the Hydrogeological Recent Change hypotheses) could have affected the evolution of the capybara to generate the current mitochondrial diversity. Thus, it is difficult to generalize a unique Amazon biota diversification hypothesis because each species or taxon could be affected by different processes and because the temporal antiquity of each taxon in South America is also different. Many mammalian taxa, and others, migrated into South America during the Great American Biotic Interchange (GABI) and their diversification processes in South America were mainly driven by Pleistocene events as those proposed by the Refuge hypothesis. Older taxa within this continent could have begun their current genetics diversification processes earlier, such as in the case of the capybara.

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Successive radiations, not stasis, in the South American primate fauna

Cited by 102 publications

References 40 publications

Biogeography in deep time – What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Biogeography in deep time – What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

The 10kTrees website: A new online resource for primate phylogeny

Continuous Miocene, Pliocene and Pleistocene Influences on Mitochondrial Diversification of the Capybara (Hydrochoerus Hydrochoeris; Hydrochoeridae, Rodentia): Incapacity to Determine Exclusive Hypotheses on the Origins of the Amazon and Orinoco Diversity for This Species

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