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1.
Science ; 368(6487): 194-197, 2020 04 10.
Artigo em Inglês | MEDLINE | ID: mdl-32273470

RESUMO

Phylogenetic evidence suggests that platyrrhine (or New World) monkeys and caviomorph rodents of the Western Hemisphere derive from source groups from the Eocene of Afro-Arabia, a landmass that was ~1500 to 2000 kilometers east of South America during the late Paleogene. Here, we report evidence for a third mammalian lineage of African origin in the Paleogene of South America-a newly discovered genus and species of parapithecid anthropoid primate from Santa Rosa in Amazonian Perú. Bayesian clock-based phylogenetic analysis nests this genus (Ucayalipithecus) deep within the otherwise Afro-Arabian clade Parapithecoidea and indicates that transatlantic rafting of the lineage leading to Ucayalipithecus likely took place between ~35 and ~32 million years ago, a dispersal window that includes the major worldwide drop in sea level that occurred near the Eocene-Oligocene boundary.


Assuntos
Filogenia , Platirrinos/classificação , Roedores/classificação , África , Animais , Peru
2.
ISME J ; 14(2): 609-622, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31719654

RESUMO

Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.


Assuntos
Biodiversidade , Microbioma Gastrointestinal , Metagenômica , Primatas/microbiologia , Primatas/parasitologia , Animais , Animais Selvagens/microbiologia , Animais Selvagens/parasitologia , Blastocisto/classificação , Cercopithecidae/microbiologia , Cercopithecidae/parasitologia , Cilióforos/classificação , Cilióforos/genética , Cilióforos/isolamento & purificação , Dieta , Endolimax/classificação , Endolimax/genética , Endolimax/isolamento & purificação , Entamoeba/classificação , Entamoeba/genética , Eucariotos/classificação , Eucariotos/genética , Eucariotos/isolamento & purificação , Fezes/microbiologia , Fezes/parasitologia , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Hominidae/microbiologia , Hominidae/parasitologia , Especificidade de Hospedeiro , Lemur/microbiologia , Lemur/parasitologia , Nematoides/classificação , Nematoides/genética , Nematoides/isolamento & purificação , Filogenia , Platirrinos/microbiologia , Platirrinos/parasitologia
3.
Syst Biol ; 69(2): 234-248, 2020 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-31529071

RESUMO

The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.


Assuntos
Classificação/métodos , Filogenia , Animais , Biodiversidade , Modelos Biológicos , Platirrinos/classificação
4.
Immunogenetics ; 72(3): 165-179, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31838542

RESUMO

Non-human primates have been used as animal models because of their phylogenetic closeness to humans. However, the genetic differences between humans and non-human primates must be considered to select the appropriate animal models. Recently, New World monkeys (Platyrrhines) have generated a higher interest in biomedical research, especially in assessing vaccine safety and immunogenicity. Given the continued and renewed interest in Platyrrhines as biomedical models, it is a necessary to have a better and more complete understanding of their immune system and its implications for research. Immunoglobulins (Ig) are the main proteins that mediate humoral immunity. These proteins have evolved as part of an adaptive immune response system derived from ancient vertebrates. There are at least four Ig classes in Prosimians, whereas five have been reported in Catarrhines. Information on the structure and evolution of the loci containing immunoglobulin heavy chain constant genes (Igh) in Platyrrhines, however, is limited. Here, Igh loci were characterized in 10 Platyrrhines using the available whole genome sequences. Human and Macaca Igh loci were also assessed to compare them with their Platyrrhines counterparts. Differences in Igh locus structure were observed between Platyrrhines and Catarrhines. Noteworthy changes occur in the γ gene, which encodes a key Ig involved in organism defense that would favor protection after vaccination. The remarkable differences between the immunoglobulin proteins of Platyrrhines and Catarrhines warrant a cautionary message to biomedical researchers.


Assuntos
Cadeias Pesadas de Imunoglobulinas/genética , Platirrinos/genética , Platirrinos/imunologia , Animais , Evolução Biológica , Evolução Molecular , Genoma/genética , Genômica/métodos , Humanos , Cadeias Pesadas de Imunoglobulinas/imunologia , Região Variável de Imunoglobulina/genética , Filogenia , Primatas/genética , Vertebrados/genética
5.
Immunogenetics ; 72(1-2): 25-36, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31624862

RESUMO

The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology. The Immuno Polymorphism Database (IPD)-MHC NHP Database (IPD-MHC NHP), which curates MHC data of great and small apes, as well as Old and New World monkeys, has been upgraded. The curators of the database are responsible for providing official designations for newly discovered alleles. This nomenclature report updates the 2012 report, and summarizes important nomenclature issues and relevant novel features of the IPD-MHC NHP Database.


Assuntos
Bases de Dados Genéticas , Complexo Principal de Histocompatibilidade/genética , Primatas/genética , Primatas/imunologia , Alelos , Animais , Cercopithecidae/genética , Hominidae/genética , Complexo Principal de Histocompatibilidade/fisiologia , Filogenia , Platirrinos/genética , Polimorfismo Genético , Terminologia como Assunto
6.
BMC Evol Biol ; 19(1): 196, 2019 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-31666001

RESUMO

BACKGROUND: The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates. RESULTS: The results showed that the MIR element had integrated into the genome of our common ancestor, specifically in the BLOC1S2 gene region, before the radiation of all primate lineages and that the AluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR and AluSp sequences provide a 3' splice site (AG) and 5' splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR and AluSp combination. CONCLUSIONS: We show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.


Assuntos
Processamento Alternativo , Elementos de DNA Transponíveis , Evolução Molecular , Primatas/genética , Elementos Alu , Animais , Evolução Biológica , Cercopithecidae/classificação , Cercopithecidae/genética , Éxons , Humanos , Íntrons , MicroRNAs/genética , Especificidade de Órgãos , Platirrinos/classificação , Platirrinos/genética , Primatas/classificação , Proteínas/genética , Transcriptoma
7.
Malar J ; 18(1): 276, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31426810

RESUMO

BACKGROUND: Parasites from the genus Plasmodium, the aetiological agent of malaria in humans, can also infect non-human primates (NHP), increasing the potential risk of zoonotic transmission with its associated global public health concerns. In Colombia, there are no recent studies on Plasmodium spp. infecting free-ranging NHP. Thus, this study aimed to determine the diversity of Plasmodium species circulating in fragmented forests in central Colombia, both in Anopheles mosquitoes and in the four sympatric NHP in the region (Ateles hybridus, Cebus versicolor, Alouatta seniculus and Aotus griseimembra), in order to evaluate the risk of infection to humans associated with the presence of sylvatic hosts and vectors infected with Plasmodium spp. METHODS: Overall, there were collected 166 fecal samples and 25 blood samples from NHP, and 442 individuals of Anopheles spp. DNA extraction, nested PCR using mitochondrial (cox3 gene) and ribosomal (18S rDNA) primers, electrophoresis and sequencing were conducted in order to identify Plasmodium spp. from the samples. RESULTS: Plasmodium falciparum was detected in two fecal samples of Alouatta seniculus, while Plasmodium vivax/simium infected Ateles hybridus, Cebus versicolor and Alouatta seniculus. Co-infections with P. vivax/simium and Plasmodium malariae/brasilianum were found in three individuals. The highest prevalence from blood samples was found for Plasmodium malariae/brasilianum in two Alouatta seniculus while Plasmodium vivax/simium was most prevalent in fecal samples, infecting four individuals of Alouatta seniculus. Seven Anopheles species were identified in the study site: Anopheles (Anopheles) punctimacula, Anopheles (An.) malefactor, Anopheles (Nyssorhynchus) oswaldoi, Anopheles (Nys.) triannulatus, Anopheles (An.) neomaculipalpus, Anopheles (Nys.) braziliensis and Anopheles (Nys.) nuneztovari. Infection with P. vivax/simium was found in An. nuneztovari, An. neomaculipalpus, and An. triannulatus. Furthermore, An. oswaldoi and An. triannulatus were found infected with P. malariae/brasilianum. The effect of fragmentation and distance to the nearest town measured in five forests with different degrees of fragmentation was not statistically significant on the prevalence of Plasmodium in NHP, but forest fragmentation did have an effect on the Minimum Infection Rate (MIR) in Anopheles mosquitoes. CONCLUSIONS: The presence of Plasmodium spp. in NHP and Anopheles spp. in fragmented forests in Colombia has important epidemiological implications in the human-NHP interface and the associated risk of malaria transmission.


Assuntos
Anopheles/parasitologia , Malária/veterinária , Doenças dos Macacos/epidemiologia , Mosquitos Vetores/parasitologia , Plasmodium/isolamento & purificação , Platirrinos , Animais , Colômbia/epidemiologia , Meio Ambiente , Florestas , Malária/epidemiologia , Malária/parasitologia , Doenças dos Macacos/parasitologia , Prevalência
8.
Zoonoses Public Health ; 66(7): 798-804, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31293103

RESUMO

The Brazilian Amazon is endemic for malaria and natural infections by Plasmodium spp. have been detected in Neotropical primates. Despite the diversity of primate species in the region, studies on infections by these agents are limited. The aim of the present study was to investigate the frequency of infection by Plasmodium vivax and P. falciparum in free-born primates that were kept in captivity, in the western Amazon, Brazil. Blood samples were collected from 98 Neotropical primates. Detection of P. vivax and P. falciparum DNA was performed using a semi-nested PCR, and the amplified products were sequenced. Plasmodium spp. DNA was detected in 6.12% (6/98) of the primates. P. vivax, and P. falciparum DNA was detected in 2.04% (2/98) and 4.08% (4/98) of these mammals, respectively. Sequencing and phylogenetic analysis confirmed the results obtained from the semi-nested PCR. The presence of infected non-human primates (NHP) can be auxiliary in the maintenance of P. falciparum and P. vivax and may have implications for the malaria surveillance and control in the Brazilian Amazon. It is necessary to structure an efficient surveillance system for the aetiological agents of malaria that infect NHP and humans to reduce the risk of Plasmodium spp. introduction into new areas, to protect all susceptible species.


Assuntos
Malária Falciparum/veterinária , Malária Vivax/veterinária , Doenças dos Macacos/parasitologia , Plasmodium falciparum , Plasmodium vivax , Animais , Brasil/epidemiologia , Feminino , Malária Falciparum/epidemiologia , Malária Falciparum/parasitologia , Malária Vivax/epidemiologia , Malária Vivax/parasitologia , Masculino , Doenças dos Macacos/epidemiologia , Platirrinos
9.
Genes Cells ; 24(7): 473-484, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31099158

RESUMO

Induced pluripotent stem (iPS) cells hold great promise for regenerative medicine and the treatment of various diseases. Before proceeding to clinical trials, it is important to test the efficacy and safety of iPS cell-based treatments using experimental animals. The common marmoset is a new world monkey widely used in biomedical studies. However, efficient methods that could generate iPS cells from a variety of cells have not been established. Here, we report that marmoset cells are efficiently reprogrammed into iPS cells by combining RNA transfection and chemical compounds. Using this novel combination, we generate transgene integration-free marmoset iPS cells from a variety of cells that are difficult to reprogram using conventional RNA transfection method. Furthermore, we show this is similarly effective for human and cynomolgus monkey iPS cell generation. Thus, the addition of chemical compounds during RNA transfection greatly facilitates reprogramming and efficient generation of completely integration-free safe iPS cells in primates, particularly from difficult-to-reprogram cells.


Assuntos
Reprogramação Celular , Fibroblastos/citologia , Células-Tronco Pluripotentes Induzidas/citologia , Preparações Farmacêuticas/administração & dosagem , RNA/administração & dosagem , Transfecção/métodos , Idoso , Animais , Diferenciação Celular , Células Cultivadas , Feminino , Fibroblastos/efeitos dos fármacos , Fibroblastos/fisiologia , Humanos , Células-Tronco Pluripotentes Induzidas/efeitos dos fármacos , Células-Tronco Pluripotentes Induzidas/fisiologia , Platirrinos
10.
PLoS One ; 14(5): e0215436, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31042728

RESUMO

Recently, ambient occlusion, quantified through portion de ciel visible (PCV) was introduced as a method for quantifying dental morphological wear resistance and reconstructing diet in mammals. Despite being used to reconstruct diet and investigate the relationship between dental form and function, no rigorous analysis has investigated the correlation between PCV and diet. Using a sample of platyrrhine and prosimians M2s, we show average PCV was significantly different between most dietary groups. In prosimian, insectivores had the lowest PCV, followed by folivores, omnivores, frugivores, and finally hard-object feeders. In platyrrhines, omnivores had the lowest average PCV, followed by folivores, frugivores, and finally hard-object feeders. PCV was correlated to two topographic variables (Dirichlet normal energy, DNE, and relief index, RFI) but uncorrelated to three others (orientation patch count rotated, OPCR, tooth surface area, and tooth size). The OPCR values here differed greatly from previously published values using the same sample, showing how differences in data acquisition (i.e., using 2.5D vs. 3D surfaces) can lead to drastic differences in results. Compared to other popular topographic variables, PCV performed as well or better at predicting diet in these groups, and when combined with a metric for size, the percent of successful dietary classifications reached 90%. Further, using an ontogenetic series of hominin (Paranthropus robustus) M2s, we show that PCV correlates well with probability of wear, with PCV values being higher on the portions of the occlusal surface that experience more wear (e.g., cusps and crest tips, wear facets) than the portions of the tooth that experience less. This relationship is strongest once wear facets have begun to form on the occlusal surface. These results highlight the usefulness of PCV in quantifying morphological wear resistance and predicting diet in mammals.


Assuntos
Resistência à Doença , Platirrinos/fisiologia , Strepsirhini/fisiologia , Dente/anatomia & histologia , Animais , Comportamento Animal , Oclusão Dentária , Dieta , Comportamento Alimentar , Platirrinos/anatomia & histologia , Strepsirhini/anatomia & histologia , Dente/fisiologia , Desgaste dos Dentes
11.
Xenotransplantation ; 26(3): e12498, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30770572

RESUMO

BACKGROUND: Old World non-human primates (OWNHPs) are used for preclinical pig-to-NHP studies. However, like pigs, OWNHPs express Neu5Gc, and therefore do not develop natural anti-Neu5Gc antibodies. New World NHPs (NWNHPs) have been reported not to express Neu5Gc. We investigated the potential of NWNHPs in xenotransplantation research. METHODS: We investigated expression of Gal, Neu5Gc, and Sda antigens on RBCs and PBMCs from humans, selected OWNHPs, and capuchin monkeys (a NWNHP). Serum anti-Gal and anti-Neu5Gc IgM and IgG levels were measured by ELISA. Binding of primate serum IgM and IgG to pig RBCs was measured by flow cytometry. RESULTS: (a) Neither humans, OWNHPs, or capuchin monkeys expressed Gal on their RBCs, but capuchins expressed Gal on PBMCs. Humans and capuchins did not express Neu5Gc on either RBCs or PBMCs, but OWNHPs expressed Neu5Gc on both cells. Sda was not expressed on any RBCs or PBMCs. (b) By ELISA, human and OWNHP, but not capuchin, sera showed IgM and IgG binding to Gal. Human and capuchin, but not OWNHP, sera demonstrated some binding to Neu5Gc. (c) Anti-Sda IgM/IgG antibodies were detected in OWNHP sera. Knockout of Sda on pig RBCs did not significantly reduce human and capuchin antibody binding. CONCLUSION: Capuchin monkeys could be surrogates for humans in experiments using RBCs, islets, neuronal cells, etc, from triple-knockout pigs (but may be too small to be used as recipients of pig organ grafts).


Assuntos
Carboidratos/imunologia , Galactosiltransferases/imunologia , Xenoenxertos/imunologia , Transplante Heterólogo , Animais , Animais Geneticamente Modificados , Carboidratos/genética , Cebus , Galactosiltransferases/genética , Técnicas de Inativação de Genes , Rejeição de Enxerto/imunologia , Humanos , Platirrinos , Suínos
12.
Am J Phys Anthropol ; 169(1): 179-185, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30768782

RESUMO

OBJECTIVES: There remain many idiosyncrasies among the values calculated for varying dental topography metrics arising from differences in software preferences among research groups. The aim of this work is to compare and provide potential conversion formulae for dental topography metrics calculated using differing software platforms. METHODS: Three software packages: ArcGIS, Surfer Manipulator, and molaR were used to calculate orientation patch count rotated (OPCR), Dirichlet normal energy (DNE), occlusal relief (OR), slope (m), and angularity (a) on platyrrhine second upper molars. Values derived from the various software packages were compared for distributional consistency and correlation. Where appropriate, formulae for conversion between like measures calculated on different software platforms were developed. RESULTS: When compared with the same measurement across software, OPCR, OR, and slope were all highly correlated. However, only OR demonstrated distributional consistency (i.e., nearly consistent mean, median, max, and min). Slope and OPCR were both higher when calculated by molaR as compared to Surfer Manipulator and ArcGIS calculations, conversion formulae are provided for these measures. DNE is only weakly correlated with angularity; but is correlated with orientation patch count across taxa. DISCUSSION: We explore why there is variation in the dental topography values calculated among the various software packages. The conversion formulae provided in this work will make possible direct comparisons among studies conducted across multiple research groups.


Assuntos
Dente Molar/anatomia & histologia , Odontometria/métodos , Platirrinos/anatomia & histologia , Software , Animais , Antropologia Física , Dieta , Platirrinos/fisiologia
13.
Am J Phys Anthropol ; 169(1): 12-30, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30802306

RESUMO

OBJECTIVES: Fossils have been linked to Alouatta based on shared cranial morphology and small brain size. However, the relationship between endocranial volume and cranial shape is unclear; it is possible that any platyrrhine with a small brain may exhibit "Alouatta-like" features due to being "de-encephalized." We test two hypotheses: (a) there are aspects of cranial shape related to encephalization common to all platyrrhines; (b) it is these cranial traits that unite the small-brained "Alouatta-like" fossils. MATERIALS AND METHODS: Three-dimensional cranial shape and endocranial volume (ECV) were measured on 350+ extant platyrrhine crania, Cartelles, Paralouatta, and Antillothrix. Encephalization quotient (EQ) was calculated using regressions of ECV on cranial centroid size. Multivariate regressions were performed using the shape coordinates and EQ and shape changes associated with EQ were visualized. Cranial shape was predicted for a hypothetical primate with an EQ matching the fossils and this shape was compared to the Alouatta mean. RESULTS: There is a significant proportion of cranial shape variation explained by EQ in some taxa. The aspects of shape that are correlated with EQ are shared by several taxa and some have parallel regression vectors, but there is no overall pattern of shape change common to all platyrrhines. However, all taxa look more similar to Alouatta when their EQ is decreased, particularly Pithecia. DISCUSSION: Given that a decrease in encephalization can cause a more Alouatta-like cranial shape in many extant platyrrhines, it should not be automatically assumed that Alouatta-like cranial traits in a small-brained fossil are evidence of a phylogenetic link to the alouattin clade.


Assuntos
Evolução Biológica , Fósseis , Platirrinos/anatomia & histologia , Crânio/anatomia & histologia , Animais , Antropologia Física , Encéfalo/anatomia & histologia , Cefalometria , Feminino , Masculino
14.
Proc Natl Acad Sci U S A ; 116(6): 2306-2311, 2019 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-30674668

RESUMO

The macaque dorsal occipital cortex is generally thought to contain an elongated third visual area, V3d, extending along most of the rostral border of area V2. In contrast, our submillimeter retinotopic fMRI maps (0.6-mm isotropic voxels, achieved by implanted phased-array receive coils) consistently show three sectors anterior to V2d. The dorsal (mirror image) sector complies with the traditional V3d definition, and the middle (nonmirror image) sector with V3A. The ventral (mirror image) sector bends away from V2d, as does the ventrolateral posterior area (VLP) in marmosets and the dorsolateral posterior area (DLP) in owl monkeys, and represents the entire contralateral hemifield as V3A does. Its population-receptive field size, however, suggests that this ventral sector is another area at the same hierarchical level as V4d. Hence, contrary to prevailing views, the retinotopic organization of cortex rostral to V2d differs substantially from widely accepted models. Instead, it is evolutionarily largely conserved in Old and New World monkeys given its surprisingly similar overall visuotopic organization.


Assuntos
Mapeamento Encefálico , Imagem por Ressonância Magnética , Córtex Visual/diagnóstico por imagem , Córtex Visual/fisiologia , Animais , Processamento de Imagem Assistida por Computador , Macaca , Platirrinos , Especificidade da Espécie
15.
Syst Biol ; 68(1): 93-116, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-29931145

RESUMO

Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and because some computational complications occur when $p $ exceeds $n$. Alternative phylogenetic comparative methods have recently been proposed to deal with the large $p $ small $n $ scenario but their use and performances are limited. Herein, we develop a penalized likelihood (PL) framework to deal with high-dimensional comparative data sets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian motion (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU), and Pagel's lambda models. We show using simulations that our PL approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when $p$ approaches $n$, and allows for their accurate estimation when $p$ equals or exceeds $n$. In addition, we show that PL models can be efficiently compared using generalized information criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic principal component analysis in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3D data set of brain shape in the New World monkeys. We find a clear support for an EB model suggesting an early diversification of brain morphology during the ecological radiation of the clade. PL offers an efficient way to deal with high-dimensional multivariate comparative data.


Assuntos
Evolução Biológica , Encéfalo/anatomia & histologia , Classificação/métodos , Modelos Biológicos , Filogenia , Platirrinos/anatomia & histologia , Platirrinos/classificação , Animais
16.
Syst Biol ; 68(1): 78-92, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-29931325

RESUMO

New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5-10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small-weighing 0.4 kg-and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.


Assuntos
Clima , Fósseis , Filogenia , Platirrinos/classificação , África , Animais , Platirrinos/anatomia & histologia
17.
Front Immunol ; 9: 2862, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30568659

RESUMO

Viral infections trigger robust secretion of interferons and other antiviral cytokines by infected and bystander cells, which in turn can tune the immune response and may lead to viral clearance or immune suppression. However, aberrant or unrestricted cytokine responses can damage host tissues, leading to organ dysfunction, and even death. To understand the cytokine milieu and immune responses in infected host tissues, non-human primate (NHP) models have emerged as important tools. NHP have been used for decades to study human infections and have played significant roles in the development of vaccines, drug therapies and other immune treatment modalities, aided by an ability to control disease parameters, and unrestricted tissue access. In addition to the genetic and physiological similarities with humans, NHP have conserved immunologic properties with over 90% amino acid similarity for most cytokines. For example, human-like symptomology and acute respiratory syndrome is found in cynomolgus macaques infected with highly pathogenic avian influenza virus, antibody enhanced dengue disease is common in neotropical primates, and in NHP models of viral hepatitis cytokine-induced inflammation induces severe liver damage, fibrosis, and hepatocellular carcinoma recapitulates human disease. To regulate inflammation, anti-cytokine therapy studies in NHP are underway and will provide important insights for future human interventions. This review will provide a comprehensive outline of the cytokine-mediated exacerbation of disease and tissue damage in NHP models of viral infections and therapeutic strategies that can aid in prevention/treatment of the disease syndromes.


Assuntos
Cercopithecidae/imunologia , Citocinas/metabolismo , Hominidae/imunologia , Platirrinos/imunologia , Viroses/imunologia , Animais , Citocinas/imunologia , Modelos Animais de Doenças , Progressão da Doença , Avaliação Pré-Clínica de Medicamentos/métodos , Humanos , Imunoterapia/métodos , Viroses/patologia , Viroses/terapia , Viroses/virologia
18.
Evolution ; 72(12): 2828-2829, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30370653

RESUMO

Adaptive radiations depend critically on ecological opportunity as a driver. Aristide et al. (2018) found that a model incorporating the multivariate niche explains the morphological divergence in New World monkeys better than models with a single ecological axis. This raises the question of whether other continental radiations would show signals of adaptive radiation if the niche is more accurately described.


Assuntos
Evolução Biológica , Platirrinos , Animais , Ecologia , Filogenia , Crânio
19.
J R Soc Interface ; 15(146)2018 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-30257926

RESUMO

The talus is one of the most commonly preserved post-cranial elements in the platyrrhine fossil record. Talar morphology can provide information about postural adaptations because it is the anatomical structure responsible for transmitting body mass forces from the leg to the foot. The aim of this study is to test whether the locomotor behaviour of fossil Miocene platyrrhines could be inferred from their talus morphology. The extant sample was classified into three different locomotor categories and then talar strength was compared using finite-element analysis. Geometric morphometrics were used to quantify talar shape and to assess its association with biomechanical strength. Finally, several machine-learning (ML) algorithms were trained using both the biomechanical and morphometric data from the extant taxa to infer the possible locomotor behaviour of the Miocene fossil sample. The obtained results show that the different locomotor categories are distinguishable using either biomechanical or morphometric data. The ML algorithms categorized most of the fossil sample as arboreal quadrupeds. This study has shown that a combined approach can contribute to the understanding of platyrrhine talar morphology and its relationship with locomotion. This approach is likely to be beneficial for determining the locomotor habits in other fossil taxa.


Assuntos
Fósseis , Locomoção , Aprendizado de Máquina , Platirrinos/fisiologia , Tálus/fisiologia , Algoritmos , Animais , Evolução Biológica , Fenômenos Biomecânicos , Análise de Elementos Finitos , Matemática , Modelos Anatômicos , Filogenia , Crânio/anatomia & histologia
20.
Evolution ; 72(12): 2697-2711, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30246282

RESUMO

Understanding the origin of diversity is a fundamental problem in evolutionary biology. The null expectation for the evolutionary diversification is that all changes in biological diversity are the result of random processes. Adaptive radiations depart from this expectation as ecological factors and natural selection are supposed to play a central role in driving exceptional diversification. However, it is not well understood how large-scale continental radiations, given their characteristics, fit to these opposing theoretical models. Here, we used phylogenetic comparative methods and geometric morphometrics to study the evolutionary process of cranial diversification in the continental radiation of New World monkeys. Particularly, we tested several alternative evolutionary scenarios for morphological evolution in the clade. Results indicated that despite the platyrrhine radiation being old and geographically widespread, the formative patterns arising from the initial stages of diversification probably associated with an adaptive radiation can still be recognized today. We also show that no single explored factor (e.g., ecological or allometric) can be invoked as a complete explanation for the observed phenotypic diversity patterns in the clade and, moreover, that different cranial regions exhibit particular macroevolutionary patterns. Together, our results highlight the evident complexity behind large-scale evolutionary radiations.


Assuntos
Filogenia , Platirrinos/anatomia & histologia , Platirrinos/genética , Crânio/anatomia & histologia , Adaptação Fisiológica , Animais , Modelos Genéticos , Platirrinos/fisiologia
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