Reanalysis of the biogeographical hypothesis of range expansion between robust and gracile capuchin monkeys

Nascimento, Fabrícia F.; Lazar, Ana; Seuánez, Héctor N.; Bonvicino, Cibele Rodrigues

doi:10.1111/jbi.12448

Cited by 14 publications

(16 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…A Set of Calibrations for Mitogenomic Phylogenetic Analysis –. Mitogenomic markers are widely used to construct phylogenies of closely related primate species with examples seen in phylogeographic studies of diversification of primates in the Amazon (Nascimento, et al 2014) and in the timing of human diversification (Rieux, et al 2014). The posterior distributions obtained here for the 10-species genomic data are useful calibrations for mitogenomic studies.…”

Section: Resultsmentioning

confidence: 99%

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Reis

Gunnell

Barba-Montoya

et al. 2017

Preprint

View full text Add to dashboard Cite

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

show abstract

Section: Resultsmentioning

confidence: 99%

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Reis

Gunnell

Barba-Montoya

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Interestingly, the monophyly of Cebus and Sapajus could not be significantly recovered by all reconstruction analyses; while the BI and MP analyses recovered it, the ML analyzes did not. This can be explained by possible past introgression across these two lineages along their evolution, as shown in the mitochondrial markers used ( Nascimento et al , 2015 ; Ruiz-García et al. , 2016 ; Lima et al , 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…These authors interpret the current sympatry of the two genera as the result of the recent reinvasion of the Amazon basin by Sapajus from central Brazil, explained by their “Reinvasion of the Amazon (ROA)” hypothesis. Nascimento et al (2015) challenged this interpretation based on the re-analysis of the data of Lynch Alfaro et al (2012) , concluding that the capuchins originated in the northern Atlantic Forest. And recently, Lima et al (2017) using three mitochondrial markers (Cyt b , Control Region and a fragment of the Cytochrome Oxidase subunit I – COI), provided support the ROA hypothesis of the origin and distribution of the capuchin monkeys in South and Central America.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic relationships among Capuchin (Cebidae, Platyrrhini) lineages: An old event of sympatry explains the current distribution of Cebus and Sapajus

et al. 2018

View full text Add to dashboard Cite

Capuchin monkeys are currently represented by four species of Cebus and eight of Sapajus. This group is taxonomically complex and several questions still need to be clarified. In the current study, using mtDNA markers and a larger sample representation than in previous studies, we seek to understand the phylogenetic relationships among the capuchin lineages and their historical biogeography. All 12 species of capuchins were analyzed for the mitochondrial Control Region and Cytochrome b to test two biogeographical hypotheses: “Reinvasion of the Amazon (ROA)” and “Sympatric Evolution (SEV)”. The phylogenetic relationships among distinct lineages within genera is consistent with an evolutionary diversification pattern probably resulting from an explosive process of diversification and dispersal between 2.0 Ma and 3.0 Ma. Also, the analyses show that the ancestral capuchins were distributed in a wide area encompassing the Amazon and Atlantic Forest. Our results support the SEV hypothesis, showing that the current syntopic distribution of Cebus and Sapajus can be explained by a sympatric speciation event in the Amazon. We also indicate that the recently proposed species taxonomy of Cebus is not supported, and that S. cay and S. macrocephalus are a junior synonym of S. apella.

show abstract

“…In agreement with this, Cummings et al [1995] showed that mitochondrial genomes have higher information content per base than nuclear DNA. However, some care should be taken when using mitochondrial genes for resolving taxonomic problems because gene trees do not necessarily correspond well with species trees [Nascimento et al, 2015]. Furthermore, mitochondrial data show only the evolution of the female lineages, and this could miss hybridization events between close taxa when males are the gene flow vectors ["mitochondrial capture";Burrell et al, 2009].…”

Section: Introductionmentioning

confidence: 99%

First Molecular Phylogenetic Analysis of the Lagothrix Taxon Living in Southern Peru and Northern Bolivia: Lagothrix lagothricha tschudii (Atelidae, Primates), a New Subspecies

Ruiz‐García

Albino

Pinedo-Castro

et al. 2019

IJFP

View full text Add to dashboard Cite

We sequenced mitochondrial COI and COII genes (1,377 base pairs) of 166 woolly monkeys (Lagothrix) to determine the phylogenetic relationships of tschudii in reference to the other taxa within the genus Lagothrix, to provide the first genetic diversity level estimates for tschudii, and to reconstruct the historical demographic evolution of this taxon. The sample set included, for the first time, 10 individuals of the elusive tschudii taxon sensu Groves from southern Peru and northern Bolivia. Our phylogenetic analyses showed that these 10 exemplars formed a statistically significant and differentiated (molecularly and morphologically) monophyletic clade relative to other traditional subspecies of Lagothrix lagothricha. Therefore, tschudii should be recognized as a fifth subspecies: Lagothrix lagothricha tschudii. The temporal divergence of the ancestors of tschudii and L. l. cana was estimated to have occurred around 1.8 million years ago (MYA). Additionally, mitochondrial diversification within tschudii started no later than 0.96 MYA (Bayesian Inference) or 0.88 MYA (Median Joining Network), respectively. In contrast to the phylogenetic trees, the F_STstatistic and the gene flow estimates showed L. l. lugens to be the least differentiated taxon of L. lagothricha from L. l. tschudii. Based on genetic distances, L. l. tschudii had the smallest average genetic distance from the other subspecies of L. lagothricha.It was also the taxon within L. lagothricha that had the smallest genetic distance from L. flavicauda. It should be related to L. l. tschudii as the first original taxon in L. lagothricha. Furthermore, the Andean mountains were extremely important in the original diversification of the Lagothrix genus and in the original diversification of L. lagothricha. Although L. l. tschudii has the smallest geographical range of all the taxa of L. lagothricha, its genetic diversity is even higher than in other taxa with wider geographical ranges, such as L. l. lagothricha and L. l. cana. L. l. tschudii showed a very slight demographic increase during the Pleistocene with a decrease of females in the last 10,000 Y, similar to that found for L. l. lugens in a previous study.

show abstract

Reanalysis of the biogeographical hypothesis of range expansion between robust and gracile capuchin monkeys

Abstract: Figure 5 Posterior probability of root states (y-axis) for root of gene tree using Dataset 3, and for root of each Cebus and Sapajus clades. AR, Argentina; PY, Paraguay; VE, Venezuela.

Cited by 14 publications

References 52 publications

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Phylogenetic relationships among Capuchin (Cebidae, Platyrrhini) lineages: An old event of sympatry explains the current distribution of Cebus and Sapajus

First Molecular Phylogenetic Analysis of the Lagothrix Taxon Living in Southern Peru and Northern Bolivia: Lagothrix lagothricha tschudii (Atelidae, Primates), a New Subspecies

Contact Info

Product

Resources

About