Evolution of the SEC1 gene in New World monkey lineages (Primates, Platyrrhini)

The structure and evolution of the SEC1 gene were examined for the first time in New World primates of the genera Alouatta, Aotus, Ateles, Brachyteles, Callicebus, Callithrix, Cebus, Chiropotes, Lagothrix, Leontopithecus, Pithecia, Saguinus, and Saimiri. This gene has a high CG content (63.8%) and an estimated heterogeneous size ranging from 795 (Callithrix) to 1041 bp (Pithecia), due to numerous indel events. Similar to other fucosyltransferases, three conserved regions are shared by these primates, except for the callitrichines, Aotus and Pithecia, in which indel events resulted in premature stop codons that are related to the production of a supposedly non-functional protein. Phylogenetic analysis of the SEC1 gene, transition/transversion rates, and nucleotide sequence alignment support the hypothesis that primate SEC1 evolved by divergent evolution, and that the lack of activity in some lineages occurred independently at least twice in New World primates, once in the Aotus-Cebus-Callitrichinae group and again in Pithecia. Likelihood-based inference of ancestral states for the activity of SEC1 leads us to suppose that inactivation of SEC1 in the Callitrichinae was a result of a more complex series of events than in Pithecia.     

Satellite DNA sequences in the New World primateCebus apella (Platyrrhini,Primates)

Two satellite DNAs, designated CapA and CapB, were isolated from the neotropical primate,Cebus apella. The satellites exhibit nonoverlapping distributions onC. apella chromosomes. CapA is a major component of interstitial regions of constitutive heterochromatin, a very large block of heterochromatin comprising most of the long arm of chromosome 11, and some telomeres. The CapA monomer has a length of about 1500 bp and appears recently to have undergone an amplification episode in theC. apella genome. CapA-like sequences are probably present in members of the family Cebidae (to whichC. apella belongs), but not in members of the family Callitrichidae (marmosets). CapB sequences can be detected at the centromeres of manyC. apella chromosomes, and similar sequences are present in all neotropical primates. The 342 bp CapB monomer shares 60%–64% sequence identity with several alpha satellite sequences of human origin. Because of its structure, sequence, and location, it appears that CapB is the New World primate homolog of Old World primate alpha satellite DNA.     

Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates)

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.     

Microsatellite markers for woolly monkeys (Lagothrix lagotricha) and their amplification in other New World primates (Primates: Platyrrhini)

Seven polymorphic microsatellite loci were identified for woolly monkeys (Lagothrix lagotricha) from an ‘enriched’ genomic library. For a wild population of 66 animals, these markers averaged over 10 alleles per locus and provided a combined probability for excluding a random individual from parentage of over 98%. These loci were screened in up to 13 other genera of New World monkeys, and many were variable in multiple taxa. Few other platyrrhine‐specific microsatellite markers have been identified; thus, these loci should prove valuable for studying the population genetic structure and mating system not just of Lagothrix but also of other neotropical primates.     

Chromosomal localization of the telomeric (TTAGGG)n sequence in eight species of New World Primates (Neotropical Primates, Platyrrhini)

Chromosomal localization of the telomeric sequence (TTAGGG)(n) in eight New World Primates (Platyrrhini) (Alouatta caraya, Alouatta palliata, Alouatta guariba clamitans, Aotus azarae, Ateles chamek, Cebus nigritus, Cebus paraguayanus, and Saimiri boliviensis) using Fluorescence In Situ Hybridization (FISH) with a peptide nucleic acid (PNA) pantelomeric probe and their possible relationship with the C-banding pattern were analyzed. FISH showed telomeric signals only at the terminal regions of chromosomes from all the species analyzed. Although all of them showed centromeric C+ bands and different size and location of extracentromeric C+ bands, none, except Aotus azarae exhibited (peri)centromeric interstitial telomere-like sequences (ITS). The presence of ITS in Aotus azarae was limited to one pair of submetacentric chromosomes and very likely represents telomeric sequences remaining after a fusion event of ancestral chromosomes during karyotype evolution. Therefore, our data indicate that the distribution of heterochromatin blocks do not correlate with the presence of ITS. However, we cannot rule out the possibility that simple ITS arrays with a few copies of the (TTAGGG)(n) sequence, not detectable by conventional FISH, might play a role in the karyotypic evolution of Ceboidea. Further FISH and molecular studies will be needed to confirm this hypothesis.     

Molecular phylogenetics of large-bodied tamarins, Saguinus spp. (Primates, Platyrrhini)

With 33 recognized taxa, the tamarins, Saguinus spp., constitute the most diverse genus of New World monkeys (Platyrrhini), and are found almost exclusively within the Amazon basin. This diversity can be subdivided into three main morphological groups, based primarily on pelage characteristics, although there is also an ecologically important division between the small- and large-bodied forms (adult body weight ± 300 g vs. > 450 g, respectively). In the present study, the phylogenetic relationships among the large-bodied forms were analysed using the sequences of a fragment of the mitochondrial rRNA16S gene, from which 58 informative sites were identified. The analysis revealed the existence of four main lineages, three of which coincided with geographical and/or morphological patterns. However, Saguinus leucopus formed a highly distinct clade, contradicting expectations based on its morphology and distribution, but corroborating a previous study of the NADH dehydrogenase subunit I (ND1) gene. Whereas genetic differences between some closely related species were relatively small (< 1%), that observed between the two specimens of S. imperator was twice higher (± 2%), indicating the possible presence of distinct species within this taxon. Previous molecular clock analysis suggested that the earliest radiation event of the large-bodied tamarins occurred sometime in the lower Miocene, whereas the most recent events, such as the division of the closely related S. midas and S. niger would have occurred during the Pleistocene. Most of these events would thus have taken place before the formation of the present-day river system, which now constitutes a considerable barrier to gene flow among many populations.     

Molecular Variation in AVP and AVPR1a in New World Monkeys (Primates,Platyrrhini): Evolution and Implications for Social Monogamy

The neurohypophysial hormone arginine vasopressin (AVP) plays important roles in fluid regulation and vascular resistance. Differences in AVP receptor expression, particularly mediated through variation in the noncoding promoter region of the primary receptor for AVP (AVPR1a), may play a role in social phenotypes, particularly social monogamy, in rodents and humans. Among primates, social monogamy is rare, but is common among New World monkeys (NWM). AVP is a nonapeptide and generally conserved among eutherian mammals, although a recent paper demonstrated that some NWM species possess a novel form of the related neuropeptide hormone, oxytocin. We therefore characterized variation in the AVP and AVPR1a genes in 22 species representing every genus in the three major platyrrhine families (Cebidae, Atelidae and Pitheciidae). For AVP, a total of 16 synonymous substitutions were detected in 15 NWM species. No non-synonymous substitutions were noted, hence, AVP is conserved in NWM. By contrast, relative to the human AVPR1a, 66 predicted amino acids (AA) substitutions were identified in NWM. The AVPR1a N-terminus (ligand binding domain), third intracellular (G-protein binding domain), and C-terminus were variable among species. Complex evolution of AVPR1a is also apparent in NWM. A molecular phylogenetic tree inferred from AVPR1a coding sequences revealed some consensus taxonomic separation by families, but also a mixed group composed of genera from all three families. The overall dN/dS ratio of AVPR1a was 0.11, but signals of positive selection in distinct AVPR1a regions were observed, including the N-terminus, in which we identified six potential positive selection sites. AA substitutions at positions 241, 319, 399 and 409 occurred uniquely in marmosets and tamarins. Our results enhance the appreciation of genetic diversity in the mammalian AVP/AVPR1a system, and set the stage for molecular modeling of the neurohypophyseal hormones and social behavior in primates.     

COII: a useful tool for inferring phylogenetic relationships among New World monkeys (Primates, Platyrrhini)

In this study we evaluated the performance of the cytochrome c oxidase subunit II (COII) mitochondrial gene as a tool for inferring phylogenetic relationships among platyrrhines. Twenty-nine COII sequences were examined in seven platyrrhine genera ( Alouatta , Ateles , Lagothrix , Brachyteles , Cebus , Saimiri , and Aotus ) employing parsimony and distance methods. Phylogenetic signal (g₁) was present in all codon positions, despite the transitional saturation detected at the third position. In tree reconstructions bootstrap support values decreased abruptly above the generic level. Parsimony trees based on weighted transversions (tv : ts, 10 : 1) at the third position showed similar topologies. The utility of COII in phylogenetic studies among platyrrhines seems to be limited, due to its low rate of replacement substitutions and a relatively fast saturation of silent substitutions at third codon positions. Our data suggest that its main utility in platyrrhine systematics lies at the intrageneric level.     

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini,Primates): An Analysis of Fossil and Molecular Data

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27–31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21–29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade.     

Chromosome phylogeny of the subfamily Pitheciinae (Platyrrhini,Primates) by classic cytogenetics and chromosome painting

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.     

Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini)

The estimation of a robust phylogeny is a necessary first step in understanding the biological diversification of the platyrrhines. Although the most recent phylogenies are generally robust, they differ from one another in the relationship between Aotus and other genera as well as in the relationship between Pitheciidae and other families. Here, we used coding and non-coding sequences to infer the species tree and embedded gene trees of the platyrrhine genera using the Bayesian Markov chain Monte Carlo method for the multispecies coalescent (?BEAST) for the first time and to compared the results with those of a Bayesian concatenated phylogenetic analysis. Our species tree, based on all available sequences, shows a closer phylogenetic relationship between Atelidae and Cebidae and a closer relationship between Aotus and the Cebidae clade. The posterior probabilities are lower for these conflictive tree nodes compared to those in the concatenated analysis; this finding could be explained by some gene trees showing no concordant topologies between Aotus and the other genera. Moreover, the topology of our species tree also differs from the findings of previous molecular and morphological studies regarding the position of Aotus. The existence of discrepancies between morphological data, gene trees and the species tree is widely reported and can be related to processes such as incomplete lineage sorting or selection. Although these processes are common in species trees with low divergence, they can also occur in species trees with deep and rapid divergence. The sources of the inconsistency of morphological and molecular traits with the species tree could be a main focus of further research on platyrrhines.     

Phylogeographic analyses of Callicebus lugens (Platyrrhini, Primates)

A phylogeographic study of Callicebus lugens was carried out based on cytochrome b DNA sequence data. Here, we report, for the first time, the distribution of C. lugens south of the Rio Negro, in Barcelos municipality (Amazonas State, Brazil), indicating that this river is not the southern boundary of the distribution of this species as previously proposed. Specimens from the north and south banks showed the same diploid number (2n = 16), while phylogenetic reconstructions based on maximum parsimony, distance, and maximum likelihood analyses grouped all specimens in a strongly supported clade comprising 2 separate lineages, in coincidence with their geographic distribution along riverbanks. Median-joining analysis showed a similar separation, with 22 transitions between the 2 groups, whereas time of divergence estimates indicated that the splitting of the C. lugens lineages occurred some 2.2 million years before present. Conservation strategies should take into consideration that this species might be sympatric with Callicebus torquatus at the south bank of Rio Negro.     

SRY evolution in Cebidae (Platyrrhini: Primates)

Sex determination in mammals is dependent on the presence of SRY, which codes for a protein with a DNA binding motif (the HMG-box domain). Here we analyze the evolution of SRY among seven genera of New World monkeys belonging to the family Cebidae. Estimates of the number of synonymous and nonsynonymous substitutions indicated the absence of positive selection acting on SRY evolution. The presence of indels at the C-terminus coding region in different genera and species maintained an open reading frame, indicating a selective pressure constraining the evolution of this coding region. Available data on the fertility of natural and captive interspecific hybrids failed to show any relationship between SRY evolution and speciation for the genera herein studied. Our phylogenetic arrangement for Cebidae genera was similar to previous topologies based on mitochondrial and autosomal DNA sequences. This arrangement also corroborated the division of Cebus into two species groups. However, for Callithrix the differences among SRY topology and those derived from autosomal and mitochondrial genes suggested a Y-chromosome ancestral polymorphism.     

Climatic Niche Evolution in New World Monkeys (Platyrrhini)

Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.     

Patterns of cranial shape diversification during the phylogenetic branching process of New World monkeys (Primates: Platyrrhini)

One of the central topics in evolutionary biology is understanding the processes responsible for phenotypic diversification related to ecological factors. New World monkeys are an excellent reference system to investigate processes of diversification at macroevolutionary scales. Here, we investigate the cranial shape diversification related to body size and ecology during the phylogenetic branching process of platyrrhines. To investigate this diversification, we used geometric morphometric techniques, a molecular phylogenetic tree, ecological data and phylogenetic comparative methods. Our statistical analyses demonstrated that the phylogenetic branching process is the most important dimension to understand cranial shape variation among extant platyrrhines and suggested that the main shape divergence among the four principal platyrrhine clades probably occurred during the initial branching process. The phylogenetic conservatism, which is the retention of ancestral traits over time within the four principal platyrrhine clades, could be the most important characteristic of platyrrhine cranial shape diversification. Different factors might have driven early shape divergence and posterior relative conservatism, including genetic drift, stabilizing selection, genetic constraints owing to pleiotropy, developmental or functional constraint, lack of genetic variation, among others. Understanding the processes driving the diversification among platyrrhines will probably require further palaeontological, phylogenetic and comparative studies.     

Electrophoretic Polymorphisms and Their Taxonomic Implications in Callitrichini (Primates, Platyrrhini)

Five hundred forty-three blood samples from 15populations of the four genera of callitrichin primateswere studied electrophoretically. Polymorphism andgenetic distances were estimated for 20 loci, 13 of which were polymorphic. The lion tamarin(Leontopithecus) studied here exhibited theleast variability for these loci, while the monospecificCebuella showed the most. The genetic distancesobserved between Callithrix andCebuella genera support previous evidenceindicating a close taxonomic relationship between them.Genetic distance values obtained in this study alsosupport the synonimization of the kuhli form with Callithrix jacchuspenicillata.     

Chromosomal similarities and differences between tamarins,Leontopithecusand Saguinus (Platyrrhini,Primates)

The karyotypes of two taxa of genus Leontopithecus(rosalia and chrysomelas) are studied. Their G-, C- and NOR-banding patterns are compared with those of representatives of the genus Saguinus to determine chromosomal similarities and differences between the two genera and thus contribute to explaining phylogenetic relations between the tamarins. Leontopithecus, like the Saguinus, presents 2n = 46, 14 autosomes plus the Y acrocentric and 30 autosomes plus the X biarmed. No chromosomal rearrangement distinguishes the karyotypes of the representatives of genus Leontopithecus or genus Saguinus. The two genera are distinguished from each other by a paracentric inversion and pericentric inversions on at least four pairs of acrocentric autosomes, displacing the NORs of the small short arms in Leontopithecus to the proximal region of the long arms in Saguinus or vice versa. The tamarins are also distinguished by the distribution of noncentromeric constitutive heterochromatin. The data obtained indicate that the two tamarin genera are closely related chromosomally, suggesting that they probably originated from the same ancestral branch. Am. J. Primatol. 43:265–276, 1997. © 1997 Wiley-Liss, Inc.     

Comparative karyology and evolution of the Amazonian Callithrix (Platyrrhini,Primates)

Chromosomal studies in three species of Amazonian Callithrix (2n=44) and data in the literature show that this group is karyomonotypic. Moreover, it is characterized by the presence of abundant heterochromatic regions, unlike the situation in congeneric forms of Callithrix of the Atlantic coast with 2n=46, and by the presence of a highly repetitive, exclusive DNA component, with a basic repeat motif of 1528 bp. Karyotypic comparisons with other Callitrichids and an outgroup species showed that Callitrichids are karyologically conserved and explained several rearrangements that had presumably occurred during their phyletic radiation. Analyses of karyologic data enabled the construction of two alternative phylogenetic topologies. The lack of derived homoeologies, common to all members of the genus Callithrix grouped at present, and the fact that Amazonian species were more similar to Cebuella pygmaea (2n=44) than to their congeneric forms with 2n=46 suggested that species at present included in the Amazonian Callithrix should be grouped with C. pygmaea.     

Satellite DNA sequences in the neotropical marmoset Callimico goeldii (Primates,Platyrrhini)

Two families of tandemly repeated satellite DNAs were isolated from the neotropical primate Callimico goeldii (Goeldi's marmoset). One satellite, CgoA, is over 70% A+T and has a monomer length of 338 bp. The other satellite, CgoB, is 50% A+T and has a monomer length of 916 bp. Both CgoA and CgoB hybridize strongly with Callimico DNA, but not with the DNA of other new and old world primates. Based upon a neutral substitution rate of 1.5×10^–9/site per year for primates, sequence data from 15 CgoA monomers indicate that the tandem array is at least 30 million years old. Since no other neotropical primate has amplified CgoA sequences, the data suggest that the ancestor of Callimico separated from the other neotropical primates at least 30 million years ago. This value is about fourfold larger than the value of 7–9 million years derived from immunological data by Sarich and Cronin (1980). Possible reasons for this discrepancy are discussed. On leave from: Genetics Section, Instituto Nacional do Cancer, Rio de Janeiro/Department of Genetics, Universidade Federal do Rio de Janeiro, Brazil     

ABO Blood groups in cebidae (Platyrrhini,Primates) from the Rio Jamari Region

Blood and saliva samples were collected from 84Aotus azarae boliviensis, 31Ateles paniscus chamek, 130Callicebus brunneus, 130Cebus apella, 117Pithecia irrorata irrorata, and 117Saimiri ustus. Saliva samples were investigated for human ABH antigens by the standard hemagglutination inhibition test. Two species,P. irrorata andC. brunneus showed monomorphism, presenting only the A blood group. Among the polymorphic species,A. paniscus andC. apella presented theO (30 and 3) and A (1 and 127) phenotypes, and the B (80) and AB (4) phenotypes were detected inA. azarae. S. ustus was the only species that presented all the four phenotypes. The observed distribution was as expected assuming Hardy-Weinberg equilibrium to be present in those species that could be tested. The ABH substances were titrated and a comparison among species was made. Serum samples were used to detect natural antibodies and the results showed some disagreement between serum and saliva phenotypes.