Phylogenetic relationships among some Ateles species: the use of chromosomic and molecular characters

Exploring the Relationship between Spontaneous Sister Chromatid Exchange and Genome Instability in Two Cryptic Species of Non-Human Primates

There are extensive studies on chromosome morphology and karyotype diversity in primates, yet we still lack insight into genomic instability as a key factor underlying the enormous interspecies chromosomal variability and its potential contribution to evolutionary dynamics. In this sense, the assessment of spontaneous sister chromatid exchange (SCE) frequencies represents a powerful tool for evaluating genome stability. Here, we employed G-banding, fluorescence plus Giemsa (FPG), and chromosome orientation fluorescence in situ hybridization (CO-FISH) methodologies to characterize both chromosome-specific frequencies of spontaneously occurring SCE throughout the genome (G-SCE) and telomere-specific SCE (T-SCE). We analyzed primary fibroblast cultures from two male species of Ateles living in captivity: Ateles paniscus (APA) and Ateles chamek (ACH). High frequencies of G-SCEs were observed in both species. Interestingly, G-SCEs clustered on evolutionary relevant chromosome pairs: ACH chromosomes 1, 2, 3, 4, and 7, and APA chromosomes 1, 2, 3, 4/12, 7, and 10. Furthermore, a statistically significant difference between the observed and expected G-SCE frequencies, not correlated with chromosome size, was also detected. CO-FISH analyses revealed the presence of telomere-specific recombination events in both species, which included T-SCE, as well as interstitial telomere signals and telomere duplications, with APA chromosomes displaying higher frequencies, compared to ACH. Our analyses support the hypothesis that regions of Ateles chromosomes susceptible to recombination events are fragile sites and evolutionary hot spots. Thus, we propose SCE analyses as a valuable indicator of genome instability in non-human primates.

Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification

To investigate the distribution of LINE-1 repeat sequences, a LINE-1 probe was Fluorescence In Situ Hybridized (FISH) on the chromosomes of Ateles geoffroyi and Ateles fusciceps (Atelidae); a LINE-1 probe was also mapped on Cebuella pygmaea (Cebidae) and used as an outgroup for phylogenetic comparison. Ateles spider monkeys have a highly rearranged genome and are an ideal model for testing whether LINE-1 is involved in genome evolution. The LINE-1 probe has been mapped in the two Atelidae species for the first time, revealing a high accumulation of LINE-1 sequences along chromosomal arms, including telomeres, and a scarcity of LINE-1 signals at centromere positions. LINE-1 mapping in C. pygmaea (Cebidae) revealed signals at centromere positions and along chromosome arms, which was consistent with previous published data from other Cebidae species. In a broader sense, the results were analyzed in light of published data on whole-chromosomal human probes mapped in these genomes. This analysis allows us to speculate about the presence of LINE-1 sequences at the junction of human chromosomal syntenies, as well as a possible link between these sequences and chromosomal rearrangements.

Sex chromosome systems in Neotropical Primates: What have we learnt so far from cytogenetics and genomics?

Neotropical Primates (Platyrrhini) show great diversity in their life histories, ecology, behaviour and genetics. This diversity extends to their chromosome complements, both to autosomes and to sex chromosomes. In this contribution, we will review what is currently known about sex chromosomes in this group, both from cytogenetic and from genomic evidence. The X and Y chromosomes in Neotropical Primates, also known as New World Monkeys, have striking structural differences compared with Old World Monkeys when Catarrhini sex chromosomes are considered. The XY bivalent displays a different meiotic behaviour in prophase I, and their Y chromosome shows extensive genomic differences. Even though the most widespread sex chromosome system is the XX/XY and thus considered the ancestral one for Platyrrhini, modifications of this sexual system are observed within this group. Multiple sex chromosome systems originated from Y-autosome translocations were described in several genera (Aotus, Callimico and Alouatta). In the howler monkeys, genus Alouatta, an independent origin of the sexual systems in South American and Mesoamerican species was postulated. All the above-mentioned evidence suggests that the Y chromosome of Platyrrhini has a different evolutionary history compared with the Catarrhini Y. There is still much to understand regarding their sex chromosome systems.

Sperm Morphology in Neotropical Primates

The morphological and morphometric characterization of spermatozoa has been used as a taxonomic and phylogenetic tool for different species of mammals. We evaluated and compared the sperm morphometry of five neotropical primate species: Alouatta caraya, Ateles belzebuth and Ateles chamek of family Atelidae; and Cebus cay (=Sapajus cay) and Cebus nigritus (=Sapajus nigritus) of family Cebidae. After the collection of semen samples, the following parameters were measured on 100 spermatozoa from each specimen: Head Length, Head Width, Acrosome Length, Midpiece Length, Midpiece Width and Tail Length. Considering the available literature on sperm morphometry, we gathered data of 75 individuals, from 20 species, 8 genera and 2 families. These data were superimposed on a phylogeny to infer the possible direction of evolutionary changes. Narrower and shorter spermatozoa seem to be the ancestral form for Cebidae, with a trend toward wider and larger heads in derived groups. The spermatozoa of Atelidae may show an increase in total length and midpiece length. Sperm heads would have become narrower in the more derived groups of Ateles. Sperm length may increase in the more derived species in both families. Our results are discussed in the context of sperm competition and sexual selection.

The ethnoprimatology of the Maijuna of the Peruvian Amazon and implications for primate conservation

BACKGROUND

In Amazonia, primates are not only an important food source but they also hold significant cultural and symbolic value for many indigenous groups. We document the relationship between primates and community members of the Maijuna indigenous community of Sucusari in the Peruvian Amazon and describe how ethnoprimatological studies provide a better understanding of the significance of primates in people's lives. Additionally, we explore how ethnoprimatological studies can help inform and enhance primate conservation initiatives.

METHODS

Semi-structured interviews were conducted with 50 residents of the community of Sucusari to assess the classification, cultural significance and traditional uses, beliefs, ceremonies and stories of primates within the Sucusari River basin.

RESULTS

Primates play an important role in the lives of individuals in the Sucusari community. They are distinguished by their arboreal lifestyle, and among the 11 species reported in the area, seven (Lagothrix lagotricha, Alouatta seniculus, Pithecia monachus, Callicebus spp., Saimiri sciureus, Leontocebus nigricollis) are highly recognized and culturally salient. Primates are used as food, medicine, pets, domestic tools and in the production of handicrafts. They are primarily hunted for local consumption, with larger primates such as L. lagotricha being preferred. Lagothrix lagotricha was also the most commonly reported pet species and the only observed pet primate in the community during surveys. Maijuna traditional beliefs include ancestral dietary taboos for A. seniculus, which are referred to as sorcerer monkeys, but this taboo is no longer fully adhered to. Maijuna traditional stories associated with primates describe the origin of primates found in Sucusari.

CONCLUSION

Primates are embedded in the intricate sociocultural system of the community of Sucusari. Better understanding the relationship between primates and people can help to focus conservation efforts on primate species of particularly high sociocultural importance as well as ecological value, such as L. lagotricha. We highly recommend the inclusion of ethnoprimatological studies into primate conservation initiatives to accomplish more effective conservation planning, ultimately integrating the goals of biodiversity conservation with the cultural and economic needs of indigenous and local communities.

Distribution extension of Ateles chamek (Humboldt 1812) in the southwestern Brazilian Amazon: identification by visual evidence and fecal DNA

One group of Ateles chamek (Humboldt 1812) was observed during 12 days in the Vila Bela da Santíssima Trindade municipality, in the state of Mato Grosso. During that time fecal samples (n=10) were collected and molecular sequencing was used to confirm species identification. The results suggest that the particular pattern of facial hair color observed in this group may be used for differentiation from other sub-populations; however, a deeper study is required for confirmation of these results. This record represents the most southwestern observation of this species, and increases the geographic distribution of A. chamek for about 16 km into the southern Brazilian Amazon. Taking into consideration the threatened status of this species of monkey, and that this region is under constant intensive deforestation, it is important to highlight that ecological studies and conservation activities require urgent development.

Revisiting the phylogenetic relationships, biogeography, and taxonomy of spider monkeys (genus Ateles) in light of new molecular data

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.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification.

Analysis of the heterochromatin of Cebus (Primates, Platyrrhini) by micro-FISH and banding pattern comparisons

The karyotype of the neotropical primate genus Cebus (Platyrrhini: Cebidae), considered the most ancestral one, shows the greatest amount of heterochromatin described among Platyrrhini genera. Banding techniques and restriction enzyme digestion have previously revealed great variability of quantity and composition of heterochromatin in this genus. In this context, we use fluorescence in situ hybridization (FISH) to analyse this genomic region and discuss its possible role in the diversification of Cebus.We used a heterochromatin probe for chromosome 11 of Cebus libidinosus (11qHe+ CLI probe), obtained by chromosome microdissection. Twenty-six specimens belonging to the families Atelidae, Cebidae, Callitrichidae and Pithecidae (Platyrrhini) were studied. Fourteen out of 26 specimens were Cebus (Cebidae) individuals of C. libidinosus, C. xanthosternos, C. apella, C. nigritus, C. albifrons, C. kaapori and C. olivaceus. In Cebus specimens, we found 6 to 22 positive signals located in interstitial and telomeric positions along the different species. No hybridization signal was observed among the remaining Ceboidea species, thus reinforcing the idea of a Cebus-specific heterochromatin composed of a complex system of repetitive sequences.

Chromosome painting in two genera of South American monkeys: species identification, conservation, and management

Cytogenetic studies showed that a number of New World primate taxa, particularly the genera Alouatta, Aotus, and Callicebus, have highly derived karyotypes. Cytogenetics in these primates, at every level of analysis, has contributed to the recognition of species and revealed that their number was certainly underestimated by researchers relying solely on traditional morphological data. Further attention was drawn to Alouatta and Aotus because they are characterized by translocations of the Y chromosome to autosomes, generating multiple sex chromosome systems. Here we present a report on the hybridization of human chromosome-specific paints on metaphases from 4 individuals originally assigned to Alouatta caraya and 1 individual of Aotuslemurinus. This is only the third karyotype studied with chromosome painting out of more than 10 known karyomorphs in Aotus. The banded chromosomes matched those of karyotype II as defined by Ma et al. [1976a], and we were able to more precisely assign the origin of the sample to A. l. griseimembra. Our results on the Argentinean Alouatta caraya samples were generally comparable to the banding and hybridization pattern of previous studies of A. caraya including the presence of an X(1)X(1)X(2)X(2)/X(1)X(2)Y(1)Y(2) sex chromosome system. The karyotype of the Brazilian Alouatta sample labeled as A. caraya differs from the 3 Argentinean samples by at least 10 chromosome rearrangements. The diploid number, G banding, and hybridization pattern of this female cell line was almost identical to previous painting results on Alouatta guariba guariba. Therefore we must conclude that this cell line is actually from an A. guariba guariba individual. The contribution of cytogenetic tools in identifying species or in this case assigning individuals or cell lines to their precise taxonomic allocation is stressed. Gathering further molecular cytogenetic data on New World primates should be conservation and management priorities.

Pairing and recombination features during meiosis in Cebus paraguayanus (Primates: Platyrrhini)

BACKGROUND

Among neotropical Primates, the Cai monkey Cebus paraguayanus (CPA) presents long, conserved chromosome syntenies with the human karyotype (HSA) as well as numerous C+ blocks in different chromosome pairs.In this study, immunofluorescence (IF) against two proteins of the Synaptonemal Complex (SC), namely REC8 and SYCP1, two recombination protein markers (RPA and MLH1), and one protein involved in the pachytene checkpoint machinery (BRCA1) was performed in CPA spermatocytes in order to analyze chromosome meiotic behavior in detail.

RESULTS

Although in the vast majority of pachytene cells all autosomes were paired and synapsed, in a small number of nuclei the heterochromatic C-positive terminal region of bivalent 11 remained unpaired. The analysis of 75 CPA cells at pachytene revealed a mean of 43.22 MLH1 foci per nucleus and 1.07 MLH1 foci in each CPA bivalent 11, always positioned in the region homologous to HSA chromosome 21.

CONCLUSION

Our results suggest that C blocks undergo delayed pairing and synapsis, although they do not interfere with the general progress of pairing and synapsis.

Population genetic studies of Alouatta caraya (Alouattinae, Primates): inferences on geographic distribution and ecology

Cytochrome b DNA sequence data (ca. 1,140 bp) of 44 Alouatta caraya, including 42 specimens from three localities of Brazil and two from Bolivia, were used for phylogenetic reconstructions and population studies. Seventeen haplotypes were identified, eight of which were present in more than one individual. Seven of these eight haplotypes were shared by individuals from a same locality and one by individuals from two localities. We found 26 variable sites along the entire gene, consisting of 18 transitions and eight transversions; most replacements occurring at the third codon position (65.39%) in contrast to first and second positions (26.92 and 7.69%, respectively). In the sample collected at Chapada dos Guimarães (Brazil), nucleotide and haplotype diversity estimates were pi=0.002325 and h=0.8772, respectively. Maximum parsimony analysis grouped all haplotypes in two clades, separating Bolivian haplotypes from Brazilian haplotypes, the grouping of which did not show a straightforward correspondence with geographic distribution. Median-joining and TCS network pointed to haplotypes 11 or 12 as the most likely ancestral ones. Mismatch distribution and the goodness-of-fit test (SSD estimate=0.0027; P=0.6999) indicated that the population from Chapada dos Guimarães experienced a demographic expansion, in agreement with the median-joining star-like pattern, although this finding could not be confirmed by Fu's F(s) test.

Meiotic characterization and sex determination system of neotropical primates: Bolivian squirrel monkey Saimiri boliviensis (primates: Cebidae)

The chromosomal sex determination system differs among platyrrhine monkeys more than any other group of primates. Although a number of studies have investigated mitotic chromosomes across platyrrhine species, the meiotic chromosomes of many genera have not yet been described. The goal of this study was to characterize the sex determination system of Saimiri boliviensis. We described for the first time the meiotic cycle, confirming the sexual system in germ cells from testicular biopsies of four adult male S. boliviensis. All specimens were weighed and testicular volume was measured. We observed 22 bivalents corresponding to 2N = 44, and a "human-like" XY bivalent was found in diakinesis/metaphase I. In addition, mitotic studies from blood samples of both sexes were performed and G- and C-banding patterns agreed with previously reported karylogy of S. boliviensis boliviensis. Further meiotic studies should be performed in New World primates based on the great value of those studies for systematic evolutionary biology and conservation programs.