1
|
Ruiz-García M, Pinedo-Castro M, Shostell JM. Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Avenue, Crookston, MN 56716, USA
| |
Collapse
|
2
|
Moreira DA, Lamarca AP, Soares RF, Coelho AMA, Furtado C, Scherer NM, Moreira MAM, Seuánez HN, Boroni M. Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution. Front Genet 2020; 11:831. [PMID: 32849820 PMCID: PMC7412869 DOI: 10.3389/fgene.2020.00831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/09/2020] [Indexed: 12/03/2022] Open
Abstract
The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with significant concern about genes related to the immune system. In the absence of a reference genome, RNA-seq and de novo transcriptome assembly have proved to be valuable genetic procedures for accessing gene sequences and testing evolutionary hypotheses. We present here a first report on the sequencing, assembly, annotation and adaptive selection analysis for thousands of transcripts of B. arachnoides from two different samples, corresponding to 13 different blood cells and fibroblasts. We assembled 284,283 transcripts with N50 of 2,940 bp, with a high rate of complete transcripts, with a median high scoring pair coverage of 88.2%, including low expressed transcripts, accounting for 72.3% of complete BUSCOs. We could predict and extract 81,400 coding sequences with 79.8% of significant BLAST hit against the Euarchontoglires SwissProt dataset. Of these 64,929 sequences, 34,084 were considered homologous to Supraprimate proteins, and of the remaining sequences (30,845), 94% were associated with a protein domain or a KEGG Orthology group, indicating potentially novel or specific protein-coding genes of B. arachnoides. We use the predicted protein sequences to perform a comparative analysis with 10 other primates. This analysis revealed, for the first time in an Atelid species, an expansion of APOBEC3G, extending this knowledge to all NWM families. Using a branch-site model, we searched for evidence of positive selection in 4,533 orthologous sets. This evolutionary analysis revealed 132 amino acid sites in 30 genes potentially evolving under positive selection, shedding light on primate genome evolution. These genes belonged to a wide variety of categories, including those encoding the innate immune system proteins (APOBEC3G, OAS2, and CEACAM1) among others related to the immune response. This work generated a set of thousands of complete sequences that can be used in other studies on molecular evolution and may help to unveil the evolution of primate genes. Still, further functional studies are required to provide an understanding of the underlying evolutionary forces modeling the primate genome.
Collapse
Affiliation(s)
- Daniel A Moreira
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Alessandra P Lamarca
- Laboratory of Bioinformatics and Molecular Evolution, Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rafael Ferreira Soares
- Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ana M A Coelho
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carolina Furtado
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Nicole M Scherer
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Miguel A M Moreira
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| |
Collapse
|
3
|
Spontaneous color preferences in rhesus monkeys: What is the advantage of primate trichromacy? Behav Processes 2020; 174:104084. [PMID: 32061913 DOI: 10.1016/j.beproc.2020.104084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Color perception and color signaling play an important role in various aspects of animal behavior. However, in mammals, trichromatic vision characterized by three retinal photopigments tuned to peak short, middle and long wavelengths is limited only to some primate species. In Old and New World primates a second photopigment has appeared repeatedly during phylogeny, allowing red colors to be distinguished from yellows and greens. Several hypotheses aspire to explain the adaptive benefits of trichromatic vision for primates. The predominant one is foraging adaptation for facilitation visual detection of fruits or young leaves. Alternative explanations are based on the function of red color in aposematic signaling or its role in socio-sexual communication. We tested spontaneous color preference in macaque monkeys (Macaca mulatta) for both food and non-food objects in a laboratory environment. We hypothesized that preference for or avoidance of red color together with the context of such behavior may help us to understand what the adaptive advantage leading to a rapid expansion of a gene for a second pigment in the long-wavelength region was. We found neither preference nor avoidance toward red color in non-food objects, but we found a significant preference for red color in food; therefore, we suggest that the results support the foraging hypothesis in macaque monkeys.
Collapse
|
4
|
Schrago CG, Seuánez HN. Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys. Am J Primatol 2019; 81:e22955. [PMID: 30779198 DOI: 10.1002/ajp.22955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/05/2018] [Accepted: 12/15/2018] [Indexed: 11/07/2022]
Abstract
The phylogenetic position of owl monkeys, grouped in the genus Aotus, has been a controversial issue for understanding Neotropical primate evolution. Explanations of the difficult phylogenetic assignment of owl monkeys have been elusive, frequently relying on insufficient data (stochastic error) or scenarios of rapid speciation (adaptive radiation) events. Using a coalescent-based approach, we explored the population-level mechanisms likely explaining these topological discrepancies. We examined the topological variance of 2,192 orthologous genes shared between representatives of the three major Cebidae lineages and the outgroup. By employing a methodological framework that allows for reticulated tree topologies, our analysis explicitly tested for non-dichotomous evolutionary processes impacting the finding of the position of owl monkeys in the cebid phylogeny. Our findings indicated that Aotus is a sister lineage of the callitrichines. Most gene trees (>50%) failed to recover the species tree topology, although the distribution of gene trees mismatching the true species topology followed the standard expectation of the multispecies coalescent without reticulation. We showed that the large effective population size of the common ancestor of Aotus and callitrichines was the most likely factor responsible for generating phylogenetic uncertainty. On the other hand, fast speciation scenarios or introgression played minor roles. We propose that the difficult phylogenetic placement of Aotus is explained by population-level processes associated with the large ancestral effective size. These results shed light on the biogeography of the early cebid diversification in the Miocene, highlighting the relevance of evaluating phylogenetic relationships employing population-aware approaches.
Collapse
Affiliation(s)
- Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Silvestro D, Tejedor MF, Serrano-Serrano ML, Loiseau O, Rossier V, Rolland J, Zizka A, Höhna S, Antonelli A, Salamin N. Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors. Syst Biol 2018; 68:78-92. [PMID: 29931325 PMCID: PMC6292484 DOI: 10.1093/sysbio/syy046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors contributed equally to this work
| | - Marcelo F Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Instituto Patagónico de Geología y Paleontología (CCT CONICET-CENPAT), Boulevard Almirante Brown 2915, 9120 Puerto Madryn, Chubut, Argentina.,Facultad de Ciencias Naturales, Sede Trelew, Universidad Nacional de la Patagonia 'San Juan Bosco', 9100 Trelew, Chubut, Argentina.,These authors contributed equally to this work
| | | | - Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Zoology, University of British Columbia, 2212 Main Mall, Vancouver, BC Canada
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Munich, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Gothenburg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.,These authors are severs as a co-last authorship
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors are severs as a co-last authorship
| |
Collapse
|
6
|
Woods R, Turvey ST, Brace S, MacPhee RDE, Barnes I. Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation. Proc Natl Acad Sci U S A 2018; 115:12769-12774. [PMID: 30420497 PMCID: PMC6294883 DOI: 10.1073/pnas.1808603115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.
Collapse
Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom;
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| |
Collapse
|
7
|
Wang X, Lim BK, Ting N, Hu J, Liang Y, Roos C, Yu L. Reconstructing the phylogeny of new world monkeys ( platyrrhini): evidence from multiple non-coding loci. Curr Zool 2018; 65:579-588. [PMID: 31616489 PMCID: PMC6784508 DOI: 10.1093/cz/zoy072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/12/2018] [Indexed: 11/27/2022] Open
Abstract
Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.
Collapse
Affiliation(s)
- Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yunpeng Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg, Göttingen, Germany
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| |
Collapse
|
8
|
DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics. J Virol 2018; 92:JVI.00980-18. [PMID: 29976674 DOI: 10.1128/jvi.00980-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 01/22/2023] Open
Abstract
Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.
Collapse
|
9
|
Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin Leontopithecus chrysopygus (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family. G3-GENES GENOMES GENETICS 2018; 8:1985-1991. [PMID: 29650540 PMCID: PMC5982826 DOI: 10.1534/g3.118.200153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe the complete mitochondrial genome sequence of the Black Lion Tamarin, an endangered primate species endemic to the Atlantic Rainforest of Brazil. We assembled the Leontopithecus chrysopygus mitogenome, through analysis of 523M base pairs (bp) of short reads produced by next-generation sequencing (NGS) on the Illumina Platform, and investigated the presence of nuclear mitochondrial pseudogenes and heteroplasmic sites. Additionally, we conducted phylogenetic analyses using all complete mitogenomes available for primates until June 2017. The single circular mitogenome of BLT showed organization and arrangement that are typical for other vertebrate species, with a total of 16618 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region (D-loop region). Our full phylogenetic tree is based on the most comprehensive mitogenomic dataset for Callitrichidae species to date, adding new data for the Leontopithecus genus, and discussing previous studies performed on primates. Moreover, the mitochondrial genome reported here consists of a robust mitogenome with 3000X coverage, which certainly will be useful for further phylogenetic and evolutionary analyses of Callitrichidae and higher taxa.
Collapse
|
10
|
Schrago CG, Mello B, Pereira AG, Furtado C, Seuánez HN. Impact of long-term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages. Ecol Evol 2017; 8:1206-1216. [PMID: 29375791 PMCID: PMC5773316 DOI: 10.1002/ece3.3736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 01/03/2023] Open
Abstract
Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.
Collapse
Affiliation(s)
- Carlos G Schrago
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Beatriz Mello
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Anieli G Pereira
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Carolina Furtado
- Division of Genetics National Cancer Institute Rio de Janeiro Brazil
| | - Hector N Seuánez
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil.,Division of Genetics National Cancer Institute Rio de Janeiro Brazil
| |
Collapse
|
11
|
Garbino GST, Martins-Junior AMG. Phenotypic evolution in marmoset and tamarin monkeys (Cebidae, Callitrichinae) and a revised genus-level classification. Mol Phylogenet Evol 2017; 118:156-171. [PMID: 28989098 DOI: 10.1016/j.ympev.2017.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022]
Abstract
Marmosets and tamarins (Cebidae, Callitrichinae) constitute the most species-rich subfamily of New World monkeys and one of the most diverse phenotypically. Despite the profusion of molecular phylogenies of the group, the evolution of phenotypic characters under the rapidly-emerging consensual phylogeny of the subfamily has been little studied, resulting in taxonomic proposals that have limited support from other datasets. We examined the evolution of 18 phenotypic traits (5 continuous and 13 discrete), including pelage, skull, dentition, postcrania, life-history and vocalization variables in a robust molecular phylogeny of marmoset and tamarin monkeys, quantifying their phylogenetic signal and correlations among some of the traits. At the family level, our resulting topology supports owl monkeys (Aotinae) as sister group of Callitrichinae. The topology of the callitrichine tree was congruent with previous studies except for the position of the midas group of Saguinus tamarins, which placement as sister of the bicolor group did not receive significant statistical support in both Maximum Parsimony and Bayesian Inference analyses. Our results showed that the highest value of phylogenetic signal among continuous traits was displayed by the long call character and the lowest was exhibited in the home range, intermediate values were found in characters related to osteology and skull size. Among discrete traits, pelage and osteology had similar phylogenetic signal. Based on genetic, osteological, pelage and vocalization data, we present an updated genus-level taxonomy of Callitrichinae, which recognizes six genera in the subfamily: Callimico, Callithrix, Cebuella, Mico, Leontopithecus and Saguinus. To reflect their phenotypic distinctiveness and to avoid the use of the informal "species group", we subdivided Saguinus in the subgenera Leontocebus, Saguinus and Tamarinus (revalidated here).
Collapse
Affiliation(s)
- Guilherme S T Garbino
- PPG-Zoologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Antonio M G Martins-Junior
- Laboratório de Genética e Evolução, Instituto Federal do Pará, Campus de Tucuruí, Brazil; Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
| |
Collapse
|
12
|
Dumas F, Mazzoleni S. Neotropical primate evolution and phylogenetic reconstruction using chromosomal data. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/11250003.2016.1260655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- F. Dumas
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
| | - S. Mazzoleni
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
13
|
Vertebrate Bioacoustics: Prospects and Open Problems. VERTEBRATE SOUND PRODUCTION AND ACOUSTIC COMMUNICATION 2016. [DOI: 10.1007/978-3-319-27721-9_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
|
14
|
Defining Genera of New World Monkeys: The Need for a Critical View in a Necessarily Arbitrary Task. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9882-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
15
|
Moraes-Barros N, Arteaga MC. Genetic diversity in Xenarthra and its relevance to patterns of neotropical biodiversity. J Mammal 2015. [DOI: 10.1093/jmammal/gyv077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
16
|
Garbino GST. How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems. Cladistics 2015; 31:652-678. [DOI: 10.1111/cla.12106] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Guilherme S. T. Garbino
- IPÊ - Instituto de Pesquisas Ecológicas; C. Postal 47 12960-000, Nazaré Paulista São Paulo Brazil
- Pós-graduação; Museu de Zoologia; Universidade de São Paulo; Avenida Nazaré 481 04263-000 São Paulo SP Brazil
| |
Collapse
|
17
|
Morales-Jimenez AL, Disotell T, Di Fiore A. Revisiting the phylogenetic relationships, biogeography, and taxonomy of spider monkeys (genus Ateles) in light of new molecular data. Mol Phylogenet Evol 2014; 82 Pt B:467-83. [PMID: 25451801 DOI: 10.1016/j.ympev.2014.09.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 09/10/2014] [Accepted: 09/19/2014] [Indexed: 12/29/2022]
Abstract
Spider monkeys (Ateles) are one of the most endangered groups of primates in the Neotropics. The genus is widely distributed from Mexico to the north of Bolivia and includes many morphologically distinct forms in terms of pelage color and patterning. The taxonomy, phylogenetic relationships, and biogeographic history of the genus have been subject to much debate, making scientific communication difficult and creating challenges for conservation actions. We extracted DNA from samples of all currently recognized species of spider monkeys collected from across the geographic range of the genus, sequenced ∼3.5 kilobases of coding sequence from the mitochondrial genome, and used this large dataset to (a) infer the phylogenetic relationships among the different forms of spider monkeys, (b) evaluate whether currently recognized species of spider monkeys form reciprocally monophyletic groups that are concordant with contemporary classifications, and (c) estimate divergence dates among the different lineages of Ateles. We found that all proposed species of spider monkeys for which we have samples from multiple localities indeed appear to form monophyletic groups. However, in contrast to previous studies, several of our analyses robustly inferred Ateles marginatus from northeast Brazil as the sister taxon to all other spider monkeys. A Bayesian dating analysis suggests that the most recent common ancestor of extant Ateles dates to ∼6.7 Ma, in the late Miocene, and most species-level splits within the genus took place in the late Pliocene, suggesting that the modern diversity in spider monkeys cannot be explained principally by isolation and divergence of populations in forest refugia during the Pleistocene. Based on our new phylogenetic inference and dating analysis, we propose a revised biogeographic scenario for the evolution of this genus.
Collapse
Affiliation(s)
- Alba Lucia Morales-Jimenez
- Center for the Study of Human Origins, New York University, Department of Anthropology, 25 Waverly Place, New York, NY 10003, United States; Fundación Biodiversa Colombia, Cra. 22 # 41 - 80, Apto. 401, Bogotá, D.C., Colombia.
| | - Todd Disotell
- Center for the Study of Human Origins, New York University, Department of Anthropology, 25 Waverly Place, New York, NY 10003, United States
| | - Anthony Di Fiore
- Center for the Study of Human Origins, New York University, Department of Anthropology, 25 Waverly Place, New York, NY 10003, United States; University of Texas at Austin, Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, 2201 Speedway Stop C3200, Austin, TX 78712, United States.
| |
Collapse
|
18
|
Perez SI, Rosenberger AL. The status of platyrrhine phylogeny: A meta-analysis and quantitative appraisal of topological hypotheses. J Hum Evol 2014; 76:177-87. [DOI: 10.1016/j.jhevol.2014.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 08/16/2014] [Accepted: 08/17/2014] [Indexed: 11/27/2022]
|
19
|
|
20
|
Schneider H, Sampaio I. The systematics and evolution of New World primates - A review. Mol Phylogenet Evol 2013; 82 Pt B:348-57. [PMID: 24201058 DOI: 10.1016/j.ympev.2013.10.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 08/22/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022]
Abstract
This paper provides an overview of the taxonomy of New World primates from proposals of the 1980's based on morphology to the great number of studies based on molecular data aiming for the elucidation of the phylogeny of New World monkeys. The innovations of the first molecular phylogeny presented by Schneider et al. (1993) positioned Callimico as a sister group of Callithrix and Cebuella; Callicebus as a member of the pitheciids; Brachyteles as sister to Lagothrix; and the night monkeys (Aotus), capuchins (Cebus) and squirrel monkeys (Saimiri) in the same clade with the small callitrichines. These results were subsequently confirmed by dozens of subsequent studies using data from DNA sequences. Some issues difficult to resolve with the phylogenetic analyses of DNA sequences, such as the diversification of the oldest lineages (pitheciids, atelids and cebids), and the confirmation of Aotus as a member of the Cebinae clade (together with Cebus/Saimiri), were clarified with new molecular approaches based on the presence or absence of Alu insertions as well as through the use of phylogenomics. At this time, all relationships at the intergeneric level had been deciphered, with the exception of the definition of the sister group of callitrichines (whether Aotus or Cebus/Saimiri are sister to callitrichines, or if Aotus, Saimiri and Cebus form a clade together). Future studies should prioritize the alpha taxonomy of most Neotropical primate groups, and the use of phylogenetic and geographic data, combined with reliable estimates of divergence times, to clarify the taxonomic status at species and genus level, as well as to help understand the evolutionary history of this remarkable and highly diversified group.
Collapse
Affiliation(s)
- Horacio Schneider
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro s/n, Bragança, Pará, CEP 68600-000, Brazil.
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro s/n, Bragança, Pará, CEP 68600-000, Brazil.
| |
Collapse
|
21
|
Schrago CG, Mello B, Soares AER. Combining fossil and molecular data to date the diversification of New World Primates. J Evol Biol 2013; 26:2438-46. [PMID: 24016177 DOI: 10.1111/jeb.12237] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/11/2013] [Accepted: 07/31/2013] [Indexed: 11/28/2022]
Abstract
Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total-evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies.
Collapse
Affiliation(s)
- C G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | |
Collapse
|
22
|
Haberthur K, Messaoudi I. Animal models of varicella zoster virus infection. Pathogens 2013; 2:364-82. [PMID: 25437040 PMCID: PMC4235715 DOI: 10.3390/pathogens2020364] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 04/16/2013] [Accepted: 05/01/2013] [Indexed: 11/16/2022] Open
Abstract
Primary infection with varicella zoster virus (VZV) results in varicella (chickenpox) followed by the establishment of latency in sensory ganglia. Declining T cell immunity due to aging or immune suppressive treatments can lead to VZV reactivation and the development of herpes zoster (HZ, shingles). HZ is often associated with significant morbidity and occasionally mortality in elderly and immune compromised patients. There are currently two FDA-approved vaccines for the prevention of VZV: Varivax® (for varicella) and Zostavax® (for HZ). Both vaccines contain the live-attenuated Oka strain of VZV. Although highly immunogenic, a two-dose regimen is required to achieve a 99% seroconversion rate. Zostavax vaccination reduces the incidence of HZ by 51% within a 3-year period, but a significant reduction in vaccine-induced immunity is observed within the first year after vaccination. Developing more efficacious vaccines and therapeutics requires a better understanding of the host response to VZV. These studies have been hampered by the scarcity of animal models that recapitulate all aspects of VZV infections in humans. In this review, we describe different animal models of VZV infection as well as an alternative animal model that leverages the infection of Old World macaques with the highly related simian varicella virus (SVV) and discuss their contributions to our understanding of pathogenesis and immunity during VZV infection.
Collapse
Affiliation(s)
- Kristen Haberthur
- Department of Microbiology and Molecular Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Ilhem Messaoudi
- Department of Microbiology and Molecular Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
| |
Collapse
|
23
|
Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One 2012; 7:e49521. [PMID: 23166696 PMCID: PMC3500307 DOI: 10.1371/journal.pone.0049521] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 10/09/2012] [Indexed: 01/24/2023] Open
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.
Collapse
Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Jong Park
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Rabosky
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanja Stadler
- Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Jan E. Janečka
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Colleen A. Fisher
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| |
Collapse
|
24
|
Bi XX, Huang L, Jing MD, Zhang L, Feng PY, Wang AY. The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella). Genet Mol Biol 2012; 35:545-52. [PMID: 22888306 PMCID: PMC3389545 DOI: 10.1590/s1415-47572012005000034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 03/01/2012] [Indexed: 11/21/2022] Open
Abstract
The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.
Collapse
Affiliation(s)
- Xiao-Xin Bi
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | | | | | | | | | | |
Collapse
|
25
|
Affiliation(s)
- R. D. Martin
- Anthropology Department; The Field Museum; 1400 S. Lake Shore Drive; Chicago; Illinois; 60605; USA
| |
Collapse
|
26
|
Rylands AB, Mittermeier RA, Silva JS. Neotropical primates: taxonomy and recently described species and subspecies. ACTA ACUST UNITED AC 2011. [DOI: 10.1111/j.1748-1090.2011.00152.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. B. Rylands
- Conservation International; 2011 Crystal Drive; Arlington; Virginia; 22202; USA
| | - R. A. Mittermeier
- Conservation International; 2011 Crystal Drive; Arlington; Virginia; 22202; USA
| | - J. S. Silva
- Coordenação de Zoologia; Museu Paraense Emílio Goeldi; Caixa Postal 399; Belém; Pará; 66040-170; Brazil
| |
Collapse
|
27
|
Schneider H, Bernardi JAR, Da Cunha DB, Tagliaro CH, Vallinoto M, Ferrari SF, Sampaio I. A molecular analysis of the evolutionary relationships in the Callitrichinae, with emphasis on the position of the dwarf marmoset. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00502.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
28
|
Youlatos D, Meldrum J. Locomotor diversification in new world monkeys: running, climbing, or clawing along evolutionary branches. Anat Rec (Hoboken) 2011; 294:1991-2012. [PMID: 22042747 DOI: 10.1002/ar.21508] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 11/09/2022]
Abstract
Modern platyrrhines exhibit a remarkable diversity of locomotor and postural adaptations, which evolved along multiple trajectories since the initial immigration to the island continent of South America. We trace this diversification by reviewing the available paleontological and neontological data for postcranial morphology and ecological adaptation. Fossil platyrrhines are notably diverse, from the Oligocene Branisella, to the varied Patagonian early Miocene quadurpedal-leaping and quadrupedal-climbing fossils of disputed affinities, on through the rich middle Miocene Colombian quadurpedal-leaping forms. More recent taxa exhibit even more derived positional patterns, from the largest suspensory atelids in Pleistocene Brazil, to the remarkable Antillean radiation with suspensory forms and also semiterrestrial species, with postcranial morphology convergent on some Old World monkeys. Field studies of positional behavior of modern platyrrhines set the framework for a spectrum of locomotor adaptations. Central within this spectrum is a cluster of medium-sized species with generalized locomotion (quadrupedal-leaping). At opposite poles lie the more derived conditions: large-bodied species exhibiting locomotor specializations for climbing-suspension; small-bodied species exhibiting adaptations for claw climbing and leaping. This behavior-based spectrum of locomotor diversification is similarly evident in a morphology-based pattern, that is, that produced by the shape of the talus. The implications of the record of platyrrhine postcranial evolution for the competing hypotheses of platyrrhine phylogenetic patterns, the "long lineage hypothesis" and the "stem platyrrhine hypothesis," are considered.
Collapse
Affiliation(s)
- Dionisios Youlatos
- Department of Zoology, Aristotle University of Thessaloniki, School of Biology, Greece.
| | | |
Collapse
|
29
|
Organ JM, Muchlinski MN, Deane AS. Mechanoreceptivity of prehensile tail skin varies between ateline and cebine primates. Anat Rec (Hoboken) 2011; 294:2064-72. [PMID: 22042733 DOI: 10.1002/ar.21505] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 11/06/2022]
Abstract
Prehensile tails evolved independently twice in primates: once in the ateline subfamily of platyrrhine primates and once in the genus Cebus. Structurally, the prehensile tails of atelines and Cebus share morphological features distinguishing them from nonprehensile tails (e.g., robust and strong caudal vertebrae, well developed lateral tail musculature, etc.). However, because of their independent evolutionary histories, the prehensile tails of atelines exhibit some differences from the Cebus prehensile tail. Ateline tails are relatively longer than those of Cebus, and they have less well-developed extensor compartment musculature. However, perhaps the most obvious difference is the distinctive hairless friction pad on the ventrodistal surface of the ateline tail; the tail of Cebus is completely covered in hair. This study documents the presence of four epicritic histologic mechanoreceptors in the friction pad of atelines: Meissner's corpuscles, Pacinian corpuscles, Ruffini corpuscles, and Merkel discs. Ruffini corpuscles and Merkel cells were also identified in the ventrodistal skin of the Cebus tail. However, Meissner's and Pacinian corpuscles (not typically associated with hairy skin) were not found in Cebus. Cebus was also compared to its closest living sister taxon, nonprehensile-tailed Saimiri, in which genus only Ruffini corpuscles are observed (no Merkel discs). The differences in mechanoreceptor type and morphology are attributed to the contrasting behavioral and tactile demands of the tail as it is used in posture and locomotion, which also distinguishes atelines from Cebus.
Collapse
Affiliation(s)
- Jason M Organ
- Department of Surgery, Saint Louis University School of Medicine, Missouri, USA.
| | | | | |
Collapse
|
30
|
Morris Goodman (1925–2010). J Hum Evol 2011. [DOI: 10.1016/j.jhevol.2011.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
31
|
Cone photopigment variations in Cebus apella monkeys evidenced by electroretinogram measurements and genetic analysis. Vision Res 2011; 50:99-106. [PMID: 19883678 DOI: 10.1016/j.visres.2009.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 10/27/2009] [Accepted: 10/27/2009] [Indexed: 11/21/2022]
Abstract
We investigated the color vision pattern in Cebus apella monkeys by means of electroretinogram measurements (ERG) and genetic analysis. Based on ERG we could discriminate among three types of dichromatic males. Among females, this classification is more complex and requires additional genetic analysis. We found five among 10 possible different phenotypes, two trichromats and three dichromats. We also found that Cebus present a new allele with spectral peak near 552nm, with the amino acid combination SFT at positions 180, 277 and 285 of the opsin gene, in addition to the previously described SYT, AFT and AFA alleles.
Collapse
|
32
|
Finotelo LFM, Amaral PJS, Pieczarka JC, de Oliveira EHC, Pissinati A, Neusser M, Müller S, Nagamachi CY. Chromosome phylogeny of the subfamily Pitheciinae (Platyrrhini, Primates) by classic cytogenetics and chromosome painting. BMC Evol Biol 2010; 10:189. [PMID: 20565908 PMCID: PMC2905426 DOI: 10.1186/1471-2148-10-189] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 06/20/2010] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The New World monkey (Platyrrhini) subfamily Pitheciinae is represented by the genera Pithecia, Chiropotes and Cacajao. In this work we studied the karyotypes of Pithecia irrorata (2n = 48) and Cacajao calvus rubicundus (2n = 45 in males and 2n = 46 in females) by G- and C-banding, NOR staining and chromosome painting using human and Saguinus oedipus whole chromosome probes. The karyotypes of both species were compared with each other and with Chiropotes utahicki (2n = 54) from the literature. RESULTS Our results show that members of the Pitheciinae have conserved several chromosome forms found in the inferred ancestral Platyrrhini karyotype (associations of human homologous segments 3a/21, 5/7a, 2b/16b, 8a/18, 14/15a and 10a/16a). Further, the monophyly of this subfamily is supported by three chromosomal synapomorphies (2a/10b, an acrocentric 15/14 and an acrocentric human 19 homolog). In addition, each species presents several autapomorphies. From this data set we established a chromosomal phylogeny of Pitheciinae, resulting in a single most parsimonious tree. CONCLUSIONS In our chromosomal phylogeny, the genus Pithecia occurred in a more basal position close to the inferred ancestor of Platyrrhini, while C. c. rubicundus and C. utahicki are closely related and are linked by exclusive synapomorphies.
Collapse
Affiliation(s)
- Liane FM Finotelo
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- FAPESPA Doctorship Scholarship in Neurociences and Celular Biology, Belém, Brazil
| | - Paulo JS Amaral
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- FAPESPA Doctorship Scholarship in Genetics and Molecular Biology, Belém, Brazil
| | - Julio C Pieczarka
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Belém, Brazil
| | - Edivaldo HC de Oliveira
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Michaela Neusser
- Institut für Humangenetik, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Stephan Müller
- Institut für Humangenetik, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Cleusa Y Nagamachi
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Belém, Brazil
| |
Collapse
|
33
|
Biassoni R, Ugolotti E, De Maria A. Comparative analysis of NK-cell receptor expression and function across primate species: Perspective on antiviral defenses. SELF NONSELF 2010; 1:103-113. [PMID: 21487512 DOI: 10.4161/self.1.2.11717] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/06/2010] [Indexed: 01/06/2023]
Abstract
Natural killer (NK) cells are lymphoid effectors that are involved in the innate immune surveillance against infected and/or tumor cells. Their function is under the fine-tuning control of cell surface receptors that display either inhibitory or activating function and in healthy condition, mediate self-tolerance. It is known that inhibitory receptors are characterized by clonal and stochastic distribution and are extremely sensible to any modification, downregulation or loss of MHC class I surface expression that are induced in autologous cells upon viral infection or cancer transformation. This alteration of the MHC class I expression weakens the strength of the inhibitory receptor-induced interaction, thus resulting in a prompt triggering of NK cell function, which ends up in the inhibition of tumor progression and proliferation of pathogen-infected cells. Thus, the inhibitory function of NK cells is only one face of the coin, since NK-cell activation is controlled by different arrays of activating receptors that finally are involved in the induction of cytolysis and/or cytokine release. Interestingly, the inhibitory NK-cell receptors that are involved in dampening NK cell-mediated responses evolved during speciation in different, often structurally unrelated surface-expressed molecules, all using a conserved signaling pathway. In detail, during evolution, the inhibitory receptors that assure the recognition of MHC class I molecules, originate in, at least, three different ways. This ended up in multigene families showing marked structural divergences that coevolved in a convergent way with the availability of appropriate MHC ligand molecules.
Collapse
Affiliation(s)
- Roberto Biassoni
- Molecular Medicine-Istituto Scientifico Giannina Gaslini; Genova, Italy
| | | | | |
Collapse
|
34
|
Lacoste V, Lavergne A, de Thoisy B, Pouliquen JF, Gessain A. Genetic diversity and molecular evolution of human and non-human primate Gammaherpesvirinae. INFECTION GENETICS AND EVOLUTION 2009; 10:1-13. [PMID: 19879975 DOI: 10.1016/j.meegid.2009.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 10/19/2009] [Accepted: 10/21/2009] [Indexed: 12/26/2022]
Abstract
The Gammaherpesvirinae sub-family is divided into two genera: Lymphocryptovirus and Rhadinovirus. Until the middle of the 1990s, the Rhadinovirus genus was only represented by Herpesvirus saimiri and Herpesvirus ateles, which infect New World monkey species. Until the year 2000, Epstein-Barr virus (EBV), the human prototype of the Lymphocryptovirus, and simian homologues had only been detected in humans and Old World non-human primates. It was thought, therefore, that the separation of the continents had resulted in drastic changes in Gammaherpesvirinae evolution. The discovery of Kaposi's sarcoma-associated herpesvirus in humans, belonging to the Rhadinovirus, followed by the identification of CalHV3 (Callitrichine herpesvirus 3), a lymphocryptovirus of the marmoset, challenged this paradigm. The description of numerous viruses belonging to this sub-family from various Old and New World primate species enabled a cospeciation hypothesis for these viruses and their hosts to be developed. This review focuses on the current knowledge of primate Gammaherpesvirinae genetic diversity and molecular evolution. We discuss the various theories based on current genetic data regarding evolutionary relationships between lymphocryptoviruses of Old World primates, the use of these data as a tool to study evolutionary relationships between New World monkey species, and the possible existence of a ninth human herpesvirus belonging to the Rhadinovirus genus.
Collapse
Affiliation(s)
- Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de Guyane, 23 avenue Pasteur, BP6010, 97306 Cayenne Cedex, French Guiana.
| | | | | | | | | |
Collapse
|
35
|
Wildman DE, Jameson NM, Opazo JC, Yi SV. A fully resolved genus level phylogeny of neotropical primates (Platyrrhini). Mol Phylogenet Evol 2009; 53:694-702. [PMID: 19632342 DOI: 10.1016/j.ympev.2009.07.019] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 07/16/2009] [Accepted: 07/20/2009] [Indexed: 12/01/2022]
Abstract
There are more than 125 species of extant New World monkeys (Primates: Platyrrhini) found in approximately 15 genera. The phylogenetic relationships of these neotropical primates have been extensively studied from a molecular perspective. While these studies have been successful at inferring many of the relationships within the platyrrhines, key questions remain. The current study provides a framework for using non-genic, non-coding markers in comparative primate phylogenomic studies in species whose genomes are not yet scheduled for complete sequencing. A random genomic shotgun library was generated from the nocturnal Owl monkey Aotus lemurinus. Eleven unlinked, non-coding, non-genic, non-repetitive, nuclear DNA markers derived from this library were sequenced in at least one representative species of every platyrrhine genus. The combined sequence from these markers yielded a 7.7 kb multiple sequence alignment of 22 taxa. We analyzed these markers independently and combined with a 10 kb dataset consisting of "traditional," previously published markers located within or directly adjacent to genes. Parsimony, maximum likelihood, and Bayesian analysis converged on a single topology for the platyrrhine generic relationships. Notably, we confidently inferred that Pitheciidae is the sister taxon to the other two platyrrhine families (Cebidae, Atelidae). This relationship is supported by high values of branch support as well as topology tests. Additionally, Aotus formed a sister taxon to a clade comprising Cebus and Saimiri. With a fully resolved platyrrhine phylogeny in place it is now possible to design and test hypotheses regarding the evolution and diversification of platyrrhine phenotypes and life histories.
Collapse
Affiliation(s)
- Derek E Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, 540 E. Canfield Ave., Detroit, MI 48201, USA.
| | | | | | | |
Collapse
|
36
|
Steinberg ER, Nieves M, Ascunce MS, Palermo AM, Mudry MD. Morphological and Genetic Characterization of Saimiri boliviensis. INT J PRIMATOL 2009. [DOI: 10.1007/s10764-008-9328-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
37
|
Osterholz M, Walter L, Roos C. Retropositional events consolidate the branching order among New World monkey genera. Mol Phylogenet Evol 2008; 50:507-13. [PMID: 19135536 DOI: 10.1016/j.ympev.2008.12.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 11/10/2008] [Accepted: 12/16/2008] [Indexed: 11/28/2022]
Abstract
Due to contradicting relationships obtained from various morphological and genetic studies, phylogenetic relationships among New World monkey genera are highly disputed. In the present study, we analyzed the presence/absence pattern of 128 SINE integrations in all New World monkey genera. Among them, 70 were specific for only a single genus, whereas another 18 were present in all New World monkey genera. The 40 remaining insertions were informative to elucidate phylogenetic relationships among genera. Several of them confirmed the monophyly of the three families Cebidae, Atelidae and Pitheciidae as well as of the subfamily Callithrichinae. Further markers provided evidence for a sister grouping of Cebidae and Atelidae to the exclusion of Pitheciidae as well as for relationships among genera belonging to Callithrichinae and Atelidae. Although a close affiliation of Saimiri, Aotus and Cebus to Callithrichinae was shown, the relationships among the three genera remained unresolved due to three contradicting insertions.
Collapse
Affiliation(s)
- Martin Osterholz
- Primate Genetics, German Primate Center, Kellnerweg 4, 37077 Goettingen, Germany.
| | | | | |
Collapse
|
38
|
Cadavid LF, Lun CM. Lineage-specific diversification of killer cell Ig-like receptors in the owl monkey, a New World primate. Immunogenetics 2008; 61:27-41. [PMID: 19009288 DOI: 10.1007/s00251-008-0342-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 10/23/2008] [Indexed: 11/25/2022]
Abstract
Killer cell Ig-like receptors (KIRs) modulate the cytotoxic effects of natural killer cells. In primates, the KIRs are highly diverse as a consequence of variation in gene content, alternative domain composition, and loci polymorphism. We analyzed a bacterial artificial chromosome (BAC) clone draft sequence spanning the owl monkey KIR cluster. The draft sequence had seven ordered yet unconnected contigs containing six full-length and two partial gene models, flanked by the LILRB and FcAR framework genes. Gene models were predicted to encode KIRs with inhibitory, activating, or dual functionality. Four gene models encoded three Ig domain receptors, while three others encoded molecules with four Ig domains. The additional domain resulted from an insertion in tandem of a 2,101 bp fragment containing the last 289 bp of intron 2, exon 3, and intron 3, resulting in molecules with two D0 domains. Re-screening of the owl monkey BAC library and sequencing of partial cDNAs from an owl monkey yielded five additional KIRs, four of which encoded receptors with short cytoplasmic domains with premature stop codons due to either a single nucleotide substitution or deletion or the absence of exon 8. Phylogenetic analysis by domains showed that owl monkey KIRs were monophyletic, clustering independently from other primate KIR lineages. Retroelements found in introns, however, were shared by KIRs from different primate lineages. This suggests that the owl monkey inherited a KIR cluster with a rich history of exon shuffling upon which positive selection for ligand binding operated to diversify the receptors in a lineage-specific fashion.
Collapse
Affiliation(s)
- Luis F Cadavid
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Cr. 30 # 4508, Bogotá, Distrito Capital, Colombia.
| | | |
Collapse
|
39
|
Amaral PJS, Finotelo LFM, De Oliveira EHC, Pissinatti A, Nagamachi CY, Pieczarka JC. Phylogenetic studies of the genus Cebus (Cebidae-Primates) using chromosome painting and G-banding. BMC Evol Biol 2008; 8:169. [PMID: 18534011 PMCID: PMC2435554 DOI: 10.1186/1471-2148-8-169] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 06/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosomal painting, using whole chromosome probes from humans and Saguinus oedipus, was used to establish karyotypic divergence among species of the genus Cebus, including C. olivaceus, C. albifrons, C. apella robustus and C. apella paraguayanus. Cytogenetic studies suggested that the species of this genus have conservative karyotypes, with diploid numbers ranging from 2n = 52 to 2n = 54. RESULTS Banding studies revealed morphological divergence among some chromosomes, owing to variations in the size of heterochromatic blocks. This analysis demonstrated that Cebus species have five conserved human associations (i.e., 5/7, 2/16, 10/16, 14/15, 8/18 and 3/21) when compared with the putative ancestral Platyrrhini karyotype. CONCLUSION The autapomorphies 8/15/8 in C. albifrons and 12/15 in C. olivaceus explain the changes in chromosome number from 54 to 52. The association 5/16/7, which has not previously been reported in Platyrrhini, was also found in C. olivaceus. These data corroborate previous FISH results, suggesting that the genus Cebus has a very similar karyotype to the putative ancestral Platyrrhini.
Collapse
Affiliation(s)
- PJS Amaral
- Universidade Federal do Pará. Laboratório de Citogenética, Belém, PA, Brazil
- CAPES Masters Scholarship on Genetics and Molecular Biology, Brazil
| | - LFM Finotelo
- Universidade Federal do Pará. Laboratório de Citogenética, Belém, PA, Brazil
- CNPq Masters Scholarship on Genetics and Molecular Biology, Brazil
| | - EHC De Oliveira
- Universidade Federal do Pará. Laboratório de Citogenética, Belém, PA, Brazil
| | - A Pissinatti
- Centro de Primatologia do Rio de Janeiro – CPRJ/FEEMA, Brazil
| | - CY Nagamachi
- Universidade Federal do Pará. Laboratório de Citogenética, Belém, PA, Brazil
- CNPq Researcher, Brazil
| | - JC Pieczarka
- Universidade Federal do Pará. Laboratório de Citogenética, Belém, PA, Brazil
- CNPq Researcher, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Pará., Campus do Guamá, Av. Perimetral, sn. Guamá, Belém – Pará, Brazil
| |
Collapse
|
40
|
Bauer K, Schreiber A. Double invasion of Tertiary island South America by ancestral New World monkeys? Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1997.tb01480.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
41
|
Schrago CG. On the time scale of New World primate diversification. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:344-54. [PMID: 17133436 DOI: 10.1002/ajpa.20459] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
New World primates comprise a diverse group of neotropical mammals that suddenly appeared in the Late Oligocene deposits of South America at around 26 million years ago (MYA). Platyrrhines seem to have separated from Old World anthropoids ca. 35 MYA, and their subsequent diversfication is not well documented in the fossil record. Therefore, molecular clock studies were conducted to unveil the temporal scenario for the evolution of the group. In this study, divergence times of all splits within platyrrhines until the generic level were investigated, using two different gene data sets under relaxed molecular clocks. Special attention was paid to the basal diversification of living platyrrhines and to the basal split of the modern Cebidae family, since these nodes were reported to be phylogenetically difficult to resolve. The results showed that analyses from various genomic regions are similar to estimates obtained by early single-gene studies. Living New World primates are descendants of ancestors that lived in the Early Miocene, at around 20 MYA, and modern Cebidae and Pitheciidae appeared ca. 16.9 and 15.6 MYA, respectively. The last common ancestor of living Atelidae is 12.4 million years old, making this clade the youngest New World primate family; at approximately the same time, modern Callitrichinae was evolving (11.8 MYA). The gap between the Platyrrhini/Catarrhini separation and the last common ancestor of living Platyrrhini may be as big as 20 million years. Paleontological and geoclimatological evidence corroborates that the sudden appearance of modern families may be a consequence of environmental changes during the Miocene.
Collapse
Affiliation(s)
- Carlos G Schrago
- Laboratório de Biodiversidade Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil.
| |
Collapse
|
42
|
de Lima MMC, Sampaio I, Vieira RDS, Schneider H. Spider monkey, Muriqui and Woolly monkey relationships revisited. Primates 2006; 48:55-63. [PMID: 17006741 DOI: 10.1007/s10329-006-0012-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 07/06/2006] [Indexed: 10/24/2022]
Abstract
The taxonomic relationships among the four genera of the Atelidae family, Alouatta (Howler), Ateles (Spider), Lagothrix (Woolly) and Brachyteles (Muriqui), have been the subject of great debate. In general, almost all authors agree with the assignment of Howler monkeys as the basal genus, either in its own tribe Alouattini or in the subfamily Alouattinae, but they disagree on the associations among the other members of the family. Muriquis have been grouped with Spider monkeys based on the fact that they share various behavioral and morphological characteristics. Cladistic analyses using morphological, biochemical, karyotype and behavioral characteristics depicted a phylogenetic tree that places Howler as the basal genus and the remaining genera in an unresolved politomy. More recent studies using molecular data have suggested that Muriqui and Woolly monkeys are sister groups. However, a recent study based on nuclear and mtDNA argued that politomy is what best represents the relationships among Spider, Woolly and Muriqui. To contribute to this debate we have added new data from two nuclear genes, Transferrin and von Willebrand Factor, and using an alignment of 17,997 bp we demonstrate that a total analysis strongly supports the Muriqui-Woolly clade. A gene-to-gene approach showed that four of the eight nuclear genes provide support for the Muriqui-Woolly clade, two strongly and two moderately, while none of the eight genes provide support for any alternative arrangement. The mitochondrial genes were not able to resolve the politomy. A possible reason for the difficulty in resolving atelid relationships may be the short period of time separating each cladogenetic event in the evolutionary process that shaped this family.
Collapse
|
43
|
Isbell LA. Snakes as agents of evolutionary change in primate brains. J Hum Evol 2006; 51:1-35. [PMID: 16545427 DOI: 10.1016/j.jhevol.2005.12.012] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2004] [Revised: 10/04/2005] [Accepted: 12/28/2005] [Indexed: 10/24/2022]
Abstract
Current hypotheses that use visually guided reaching and grasping to explain orbital convergence, visual specialization, and brain expansion in primates are open to question now that neurological evidence reveals no correlation between orbital convergence and the visual pathway in the brain that is associated with reaching and grasping. An alternative hypothesis proposed here posits that snakes were ultimately responsible for these defining primate characteristics. Snakes have a long, shared evolutionary existence with crown-group placental mammals and were likely to have been their first predators. Mammals are conservative in the structures of the brain that are involved in vigilance, fear, and learning and memory associated with fearful stimuli, e.g., predators. Some of these areas have expanded in primates and are more strongly connected to visual systems. However, primates vary in the extent of brain expansion. This variation is coincident with variation in evolutionary co-existence with the more recently evolved venomous snakes. Malagasy prosimians have never co-existed with venomous snakes, New World monkeys (platyrrhines) have had interrupted co-existence with venomous snakes, and Old World monkeys and apes (catarrhines) have had continuous co-existence with venomous snakes. The koniocellular visual pathway, arising from the retina and connecting to the lateral geniculate nucleus, the superior colliculus, and the pulvinar, has expanded along with the parvocellular pathway, a visual pathway that is involved with color and object recognition. I suggest that expansion of these pathways co-occurred, with the koniocellular pathway being crucially involved (among other tasks) in pre-attentional visual detection of fearful stimuli, including snakes, and the parvocellular pathway being involved (among other tasks) in protecting the brain from increasingly greater metabolic demands to evolve the neural capacity to detect such stimuli quickly. A diet that included fruits or nectar (though not to the exclusion of arthropods), which provided sugars as a neuroprotectant, may have been a required preadaptation for the expansion of such metabolically active brains. Taxonomic differences in evolutionary exposure to venomous snakes are associated with similar taxonomic differences in rates of evolution in cytochrome oxidase genes and in the metabolic activity of cytochrome oxidase proteins in at least some visual areas in the brains of primates. Raptors that specialize in eating snakes have larger eyes and greater binocularity than more generalized raptors, and provide non-mammalian models for snakes as a selective pressure on primate visual systems. These models, along with evidence from paleobiogeography, neuroscience, ecology, behavior, and immunology, suggest that the evolutionary arms race begun by constrictors early in mammalian evolution continued with venomous snakes. Whereas other mammals responded by evolving physiological resistance to snake venoms, anthropoids responded by enhancing their ability to detect snakes visually before the strike.
Collapse
Affiliation(s)
- Lynne A Isbell
- Department of Anthropology, University of California, Davis, 95616, USA.
| |
Collapse
|
44
|
Kay RF, Cozzuol MA. New platyrrhine monkeys from the Solimões Formation (late Miocene, Acre State, Brazil). J Hum Evol 2006; 50:673-86. [PMID: 16530809 DOI: 10.1016/j.jhevol.2006.01.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 01/06/2006] [Accepted: 01/16/2006] [Indexed: 11/25/2022]
Abstract
We report here a new fossil primate from the late Miocene of Brazil. The material consists of a lower first molar and a maxilla with P3-4. The fossils were collected in the Solimões Formation at the locality of Patos, upper Acre River, Acre State, Brazil. The locality is assigned to the Huayquerian South American Land Mammal Age based on faunal content (late Miocene; dated to between 9 and 6 Ma). The new material is the oldest known occurrence of fossil primates in Brazil and is recognized as a new genus and species, Solimoea acrensis. Solimoea is the oldest known member of the ateline subfamily, which includes the living genera Ateles, Lagothrix, and Brachyteles. By analogy with the molar structures and diets of extant platyrrhines, Solimoea primarily had a diet of fruit, perhaps similar to that of the spider monkey, Ateles. Two other primate teeth described previously from the same formation in Bolivia document the occurrence of alouattines and cebines. One of those specimens is a late Miocene representative of the middle Miocene Colombian genus Stirtonia. The other represents one of the largest known platyrrhine primates, for which is erected a new primate genus, Acrecebus fraileyi.
Collapse
Affiliation(s)
- Richard F Kay
- Department of Biological Anthropology and Anatomy, Duke University, Durham, NC 27710, USA.
| | | |
Collapse
|
45
|
Opazo JC, Wildman DE, Prychitko T, Johnson RM, Goodman M. Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates). Mol Phylogenet Evol 2006; 40:274-80. [PMID: 16698289 DOI: 10.1016/j.ympev.2005.11.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 11/07/2005] [Accepted: 11/09/2005] [Indexed: 11/25/2022]
Abstract
Orthologous sequences of six nuclear genes were obtained for all recognized genera of New World monkeys (Primates: Platyrrhini) and outgroups to evaluate the phylogenetic relationships and to estimate divergence times. Phylogenetic relationships were reconstructed by maximum parsimony, maximum likelihood, and Bayesian approaches. All methods resolved with 100% branch support genus-level relationships, except for the grouping of Aotus as a sister taxa of Cebus and Saimiri, which was supported by low bootstrap percentages and posterior probability. All approaches depict three monophyletic New World monkey families: Atelidae, Cebidae, and Pitheciidae; also within each family, all approaches depict the same branching topology. However, the approaches differ in depicting the relationships of the three families to one another. Maximum parsimony depicts the Atelidae and Cebidae as sister families next joined by the Pitheciidae. Conversely, likelihood and Bayesian phylogenetic trees group families Atelidae and Pitheciidae together to the exclusion of Cebidae. Divergence time estimations using both local molecular clock and Bayesian approaches suggest the families diverged from one another over a short period of geological time in the late Oligocene-early Miocene.
Collapse
Affiliation(s)
- Juan C Opazo
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | | | | | | | | |
Collapse
|
46
|
Gregorin R. Taxonomia e variação geográfica das espécies do gênero Alouatta Lacépède (Primates, Atelidae) no Brasil. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s0101-81752006000100005] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Neste estudo analisou-se a variação geográfica e não-geográfica de táxons de bugios, gênero Alouatta Lacépède, 1799, que ocorrem no Brasil, com o objetivo de esclarecer a taxonomia do grupo. Para a análise morfológica, examinou-se um total de 1.286 espécimes mantidos em cinco museus brasileiros e dois norte-americanos. O material consistiu basicamente de peles, crânios e ossos hióides; esqueletos e espécimes preservados em via úmida foram escassos. O estudo se baseou na análise qualitativa dos complexos morfológicos em adição a 18 morfométicos do crânio e osso hióide. Antes das decisões taxonômicas, elaborou-se um estudo de variação geográfica, sexual, ontogenética e individual. Reconheceu-se 10 espécies de Alouatta ocorrendo no Brasil, sendo a maioria definida por caracteres discretos, porém diagnósticos. São elas: Alouatta caraya (Humboldt, 1812), A. fusca (Geoffroy Saint-Hilaire, 1812), A. clamitans Cabrera, 1940, A. belzebul (Linnaeus, 1766), A. discolor (Spix, 1823), A. ululata Elliot, 1912; A. juara (Linnaeus, 1766), A. macconnelli (Humboldt, 1812), A. puruensis Lönnberg, 1941 e A. nigerrima Lönnberg, 1941. Alouatta macconnelli e A. clamitans mostraram notável variação geográfica na coloração da pelagem e algumas variáveis morfométricas (polimorfismo) o que dificultou as definições e limites dos táxons. Alouatta belzebul apresentou variação em mosaico na coloração da pelagem. Alouatta ululata e A. puruensis foram definidas pela presença de dicromatismo sexual na pelagem, mas este caráter pode ser um artefato e necessita estudos adicionais para corroborar sua validade. Sinonimizou-se Alouatta belzebul mexianae Hagmann, 1908 com A. discolor; e a validade de Alouatta seniculus amazonica Lönnberg 1941, não foi considerada.
Collapse
|
47
|
Vallinoto M, Araripe J, Rego PSD, Tagliaro CH, Sampaio I, Schneider H. [NO TITLE AVAILABLE]. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000200005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
48
|
Nishimura TD, Takai M, Tsubamoto T, Egi N, Shigehara N. Variation in maxillary sinus anatomy among platyrrhine monkeys. J Hum Evol 2005; 49:370-89. [PMID: 16009397 DOI: 10.1016/j.jhevol.2005.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Accepted: 05/07/2005] [Indexed: 10/25/2022]
Abstract
Variations in the maxillary sinus anatomy of extant and fossil catarrhine primates have been extensively examined using computed tomography (CT), and have potential utility for phylogenetic analyses. This approach has also been used to demonstrate its anatomical variation in eight of the 16 extant genera of platyrrhines and the absence of the sinus in Saimiri and Cacajao. We used this approach to evaluate the three-dimensional anatomy of the maxillary sinus in all extant platyrrhine genera, and here argue the phylogenic implications of this variation. This study confirms, for the most part, previous CT studies and augments them with the six genera not studied previously: Ateles, Lagothrix, Callithrix, Cebuella, Pithecia and Chiropotes. The entire maxilla is pneumatized by the sinus in the atelines, Cebus, and Callicebus, whereas the sinus pneumatizes only the medial part of the maxilla in the callitrichines and Aotus. Pithecia has a unique conformation in which the maxillary sinus and the expanded inferior meatus pneumatize the posteromedial and anterolateral parts of the entire maxilla, respectively. Chiropotes has no sinus, and the inferior meatus possibly expands into the area between the middle meatus and medial surface of the maxilla to disturb sinus formation, as in the case of its close relative Cacajao. Finally, we argue that the sinus that pneumatizes the entire maxilla is a primitive feature in extant platyrrhines and was probably shared by the last common ancestor of the anthropoids.
Collapse
Affiliation(s)
- Takeshi D Nishimura
- Laboratory of Physical Anthropology, Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo, Kyoto 606-8502, Japan.
| | | | | | | | | |
Collapse
|
49
|
Tan Y, Yoder AD, Yamashita N, Li WH. Evidence from opsin genes rejects nocturnality in ancestral primates. Proc Natl Acad Sci U S A 2005; 102:14712-6. [PMID: 16192351 PMCID: PMC1253590 DOI: 10.1073/pnas.0507042102] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is firmly believed that ancestral primates were nocturnal, with nocturnality having been maintained in most prosimian lineages. Under this traditional view, the opsin genes in all nocturnal prosimians should have undergone similar degrees of functional relaxation and accumulated similar extents of deleterious mutations. This expectation is rejected by the short-wavelength (S) opsin gene sequences from 14 representative prosimians. We found severe defects of the S opsin gene only in lorisiforms, but no defect in five nocturnal and two diurnal lemur species and only minor defects in two tarsiers and two nocturnal lemurs. Further, the nonsynonymous-to-synonymous rate ratio of the S opsin gene is highest in the lorisiforms and varies among the other prosimian branches, indicating different time periods of functional relaxation among lineages. These observations suggest that the ancestral primates were diurnal or cathemeral and that nocturnality has evolved several times in the prosimians, first in the lorisiforms but much later in other lineages. This view is further supported by the distribution pattern of the middle-wavelength (M) and long-wavelength (L) opsin genes among prosimians.
Collapse
Affiliation(s)
- Ying Tan
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
50
|
Abstract
Background Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates. Results Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.
Collapse
Affiliation(s)
- David A Ray
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA, 70803, USA
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Mark A Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA, 70803, USA
| |
Collapse
|