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Exploring the Relationship between Spontaneous Sister Chromatid Exchange and Genome Instability in Two Cryptic Species of Non-Human Primates. Animals (Basel) 2023; 13:ani13030510. [PMID: 36766399 PMCID: PMC9913470 DOI: 10.3390/ani13030510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
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.
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Assessment of genetic variability in captive capuchin monkeys (Primates: Cebidae). Sci Rep 2021; 11:7306. [PMID: 33790375 PMCID: PMC8012615 DOI: 10.1038/s41598-021-86734-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/19/2021] [Indexed: 11/08/2022] Open
Abstract
Capuchin monkeys (genera Cebus and Sapajus) show a wide range distribution, from Honduras to Argentina. The aim of this work was to evaluate the genetic and phenotypic variability of captive specimens putatively belonging to S. cay (SCY) and S. nigritus (SNI) at their southernmost distribution limit. Forty-four individuals held in five captive centers from Argentina were analyzed based on external morphology, karyology and DNA sequences of mitochondrial control region (mtDNA-CR). Three morphotypes associated with their probable geographical origin in SCY and a single morphotype in SNI were found. For SCY we could associate each morphotype with the most frequent karyotype. SNI showed a single phenotype and a homogenous karyotype. Heterochromatin showed geographical patterns within species. A 515-bp mtDNA-CR fragment was sequenced, defining fourteen haplotypes at 59 polymorphic sites. A network constructed with our 14 haplotypes and other 77 from S. apella, S. macrocephalus, S. cay and S. nigritus from bibliography revealed some phylogeographic signals. Our SCY and SNI samples rendered four groups that differed in multiple mutational steps, with SCY being more similar to S. apella than to S. macrocephalus. Also, we identified two genetic divergent SCY groups: samples from NOA and from NEA with high mitochondrial diversity. Our results highlight the relevance of using complementary genetic tools throughout the distribution ranges of SCY and SNI for a better assessment of their diversity.
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Penedo DM, de Armada JLA, Nieves M, Verona CEDS, de Oliveira AM, Dos Santos EJDS, Nogueira DM. Genetic analysis of an insular population of Sapajus nigritus (Primates: Cebidae) in Rio de Janeiro state, Brazil. Primates 2021; 62:395-406. [PMID: 33459941 DOI: 10.1007/s10329-020-00880-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022]
Abstract
The black-horned capuchin (Sapajus nigritus) is a neotropical primate with wide distribution from southeastern Brazil to northeastern Argentina. Although this species has been described with coat pattern variation, even with intrapopulational differences, and characterized as having the greatest genetic diversity among Sapajus species, there are still few studies on natural populations that contribute to the knowledge of this intraspecific variability. We examined individuals from an as yet unstudied population of Ilha da Marambaia, Rio de Janeiro (RJ) state, Brazil, compared with published data for S. nigritus. We sought to confirm the species through phenotypic and genetic characterization using C-banding and fluorescence in situ hybridization with #11qHe+/21WCP probes for chromosomal constitutive heterochromatin (He+) patterns, and cytochrome c oxidase I and II gene sequences for phylogenetic analysis. The coat presented two color patterns, varying from brown to blackish on the body, yellow to brown on the chest, and white to yellow on the face, besides the presence and shape of the tufts on the head, corresponding to S. nigritus. He+ was identified in pairs 4, 12, 13 and 17, and less consistently in pairs 6, 19 and 21, already described for this species. While most Sapajus species have a large He+ block, here pair 11 was identified without extracentromeric He+, the same as reported for S. nigritus from Argentina. Molecular analysis showed divergence of this population from other S. nigritus sequences, reinforcing a trend already demonstrated when samples from RJ are compared with the rest of the distribution, which may represent an evolutionary deviation.
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Affiliation(s)
- Diego Mattos Penedo
- Programa de Pós-Graduação em Biologia Animal, UFRRJ, Seropédica, RJ, Brazil.
| | | | - Mariela Nieves
- Instituto de Ecología, Genética y Evolución de Buenos Aires-CONICET, FCEyN-UBA, Buenos Aires, Argentina
| | | | - Andréa Maria de Oliveira
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, UERJ, Rio de Janeiro, RJ, Brazil
| | | | - Denise Monnerat Nogueira
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, UFRRJ, Seropédica, RJ, Brazil
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Ruiz-García M, Sánchez-Castillo S, Castillo MI, Luengas K, Ortega JM, Leguizamon N, Bello A, Mark Shostell J. The mystery of the origins of Cebus albifrons malitiosus and Cebus albifrons hypoleucus: mitogenomics and microsatellite analyses revealed an amazing evolutionary history of the Northern Colombian white-fronted capuchins. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:525-547. [PMID: 30822184 DOI: 10.1080/24701394.2019.1570174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Knowledge of the genetic units of species is fundamental to the conservation of biodiversity. This is true for all regions, including the Neotropics where the Earth has its greatest diversity, including roughly 34% of primate species, a group that has almost 60% of its taxa threatened with extinction. The untufted (gracile) capuchins are medium-sized Neotropical primates, traditionally classified in four species: Cebus albifrons, C. capucinus, C. olivaceus, and C. kaapori. They have a very confusing intra-specific systematics with a large number of fragmented and isolated populations throughout their geographical distributions. We sequenced a large sample of gracile capuchins, including all of the recognized species, to offset the paucity of phylogenic and phylogeographic data regarding this group and to try to understand their phylogeny and evolution. A set of 189 gracile and robust capuchins were sequenced for their mitogenomes whereas another set of 394 gracile and robust capuchins were sequenced at two individual mitochondrial genes (mtCOI-COII). Additionally, 41 Colombian gracile capuchins were geno typified at eight nuclear DNA microsatellites. Our main findings are as follows: (1) Nineteen different groups of gracile capuchin were detected with the mitogenomics data set and more than twenty significant groups and sub-groups were identified with the mtCOI-COII genes; (2) The temporal splits of the older gracile capuchin haplogroups expanded between 2 and 4 million years ago (MYA), during the Pliocene; (3) The two most northern taxa of Colombian C. albifrons (malitiosus and hypoleucus) are the same taxon (C. a. hypoleucus) as was claimed by Cabrera. This taxon represents an old colonization event from the Amazon to current northern Colombia. It is intensely hybridized (evidence from both mitochondrial and nuclear genes) with a haplogroup of C. capucinus (H3) and also has an influx of robust capuchins; (4) Three different and independent migrations of C. albifrons from the Amazon arrived to northern Colombia giving rise to C. a. hypoleucus (including malitiosus), C. a versicolor (including leucocephalus, cesarae, and pleei), and C. a. adustus; (5) On the Caribbean island of Trinidad, two different gracile capuchin taxa exist, one autochthonous, which could correspond to a fourth migration into northwestern South America (C. a. trinitatis) and probably another one, introduced more recently (C. olivaceus brunneus); (6) The values of the genetic distance analyses, the inexistence of reciprocal mitochondrial monophylia for many clades of gracile capuchins and the strong hybridization detected with nuclear microsatellites, especially among hypoleucus (malitiosus), C. capucinus-H3, versicolor, and cesarae, support that all the gracile capuchins belong to one unique superspecies: C. capucinus (senior name for all the gracile capuchins).
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Affiliation(s)
- Manuel Ruiz-García
- a Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Sebastián Sánchez-Castillo
- a Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , Colombia
| | - María Ignacia Castillo
- a Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Kelly Luengas
- a Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Juan Manuel Ortega
- a Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , Colombia
| | | | - Aurita Bello
- b Secretaría Distitral del Ambiente (SDA) , Bogotá , Colombia
| | - Joseph Mark Shostell
- c Math, Science and Technology Department , University of Minnesota Crookston 2900 University Ave , Crookston , MN , USA
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How Many Species, Taxa, or Lineages of Cebus albifrons (Platyrrhini, Primates) Inhabit Ecuador? Insights from Mitogenomics. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Puntieri F, Andrioli NB, Nieves M. Association between Genomic Instability and Evolutionary Chromosomal Rearrangements in Neotropical Primates. Genome Biol Evol 2018; 10:1647-1656. [PMID: 29905781 PMCID: PMC6366543 DOI: 10.1093/gbe/evy119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2018] [Indexed: 11/17/2022] Open
Abstract
During the last decades, the mammalian genome has been proposed to have regions prone to
breakage and reorganization concentrated in certain chromosomal bands that seem to
correspond to evolutionary breakpoints. These bands are likely to be involved in
chromosome fragility or instability. In Primates, some biomarkers of genetic damage may be
associated with various degrees of genomic instability. Here, we investigated the
usefulness of Sister Chromatid Exchange as a biomarker of potential sites of frequent
chromosome breakage and rearrangement in Alouatta caraya, Ateles
chamek, Ateles paniscus, and Cebus cay. These Neotropical
species have particular genomic and chromosomal features allowing the analysis of genomic
instability for comparative purposes. We determined the frequency of spontaneous induction
of Sister Chromatid Exchanges and assessed the relationship between these and structural
rearrangements implicated in the evolution of the primates of interest. Overall,
A. caraya and C. cay presented a low proportion of
statistically significant unstable bands, suggesting fairly stable genomes and the
existence of some kind of protection against endogenous damage. In contrast,
Ateles showed a highly significant proportion of unstable bands; these
were mainly found in the rearranged regions, which is consistent with the numerous genomic
reorganizations that might have occurred during the evolution of this genus.
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Affiliation(s)
- Fiona Puntieri
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Nancy B Andrioli
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariela Nieves
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución de Buenos Aires, CONICET-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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Nieves M, Fantini L, Mudry MD. What do we know about the heterochromatin of capuchin monkeys (Cebus: Platyrrhini)? Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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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
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The 14/15 association as a paradigmatic example of tracing karyotype evolution in New World monkeys. Chromosoma 2015; 125:747-56. [DOI: 10.1007/s00412-015-0565-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Fan X, Supiwong W, Weise A, Mrasek K, Kosyakova N, Tanomtong A, Pinthong K, Trifonov VA, Cioffi MDB, Grothmann P, Liehr T, Oliveira EH. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens. Heliyon 2015; 1:e00042. [PMID: 27441227 PMCID: PMC4945616 DOI: 10.1016/j.heliyon.2015.e00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022] Open
Abstract
Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.
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Key Words
- ACA, Alouatta caraya
- Atelidae
- BACs, bacterial artificial chromosomes
- CAE, Chlorocebus aethiops
- CAP, Cebus apella
- CJA, Callithrix jacchus
- Cebidae
- EC, evolutionary conserved
- ECBs, evolutionary conserved breakpoints
- Evolutionary conserved breakpoints
- Evolutionary genetics
- FISH, fluorescence in situ hybridization
- FS, fragile site
- Fragile sites
- Genetics
- HCM, heterochromatin mix
- HLA, Hylobates lar
- HSA, Homo sapiens
- HSBs, homologous syntenic blocks
- MCB, multicolor banding
- Multicolor banding
- NGS, Next-generation sequencing
- NOR, nucleolus organizer region
- NWMs, New World Monkeys
- New World Monkeys
- OWMs, Old World Monkeys
- Old World Monkeys
- SSC, Saimiri sciureus
- subCTM, sub-centromere/subtelomere-specific multicolor (FISH)
- wcp, whole human chromosome painting
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Affiliation(s)
- Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Weerayuth Supiwong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Alongkoad Tanomtong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Krit Pinthong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Pierre Grothmann
- Serengeti-Park Hodenhagen GmbH, Am Safaripark 1, 29693, Hodenhagen, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Edivaldo H.C.de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, 66075-110 Belém-PA, Brazil
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Lynch Alfaro JW, Izar P, Ferreira RG. Capuchin monkey research priorities and urgent issues. Am J Primatol 2014; 76:705-20. [PMID: 24668460 DOI: 10.1002/ajp.22269] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 01/28/2014] [Accepted: 02/03/2014] [Indexed: 11/09/2022]
Abstract
The "Capuchin research community roundtable: working together towards a comparative biology of Cebus and Sapajus" was held at the International Primatological Society Congress in Cancún, Mexico, August 2012. Goals of the roundtable were to strengthen interactions among the capuchin research community, and to prioritize and coordinate research and training in a more systematic and interactive way in light of increasing conservation urgency. New phylogenetic and biogeographic evidence highlights the distinct evolutionary histories of the two radiations of capuchin monkeys, Cebus (untufted or gracile capuchins) and Sapajus (tufted or robust capuchins), that were formerly lumped under Cebus, and points to a higher number of species, or Evolutionarily Significant Units, in each compared to past capuchin taxonomies. Many of the lesser-known species face increasing fragmentation and destruction of habitat, and most populations of still non-threatened species face encroachment from human settlements. Here, we present capuchin research priorities and urgent issues based on the discussion by capuchin researchers in the roundtable. These include a call for the immediate end to the use of the name Cebus apella and the employment of the term Sapajus spp. instead for captive robust capuchins of unknown origin; for the implementation of rapid assessments for previously unstudied capuchin species or populations in biomes of interest; for the development of standardized methods to allow for comparative analyses across capuchin field sites; and for the creation and maintenance of an open-access website for capuchin monkey data. Finally, we planned the creation of an international Capuchin Action Network, to help disseminate research information; to work as a research community in a more efficient, collaborative manner; to help prioritize research and conservation goals as a community of experts; and to strengthen our political voice.
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Affiliation(s)
- Jessica W Lynch Alfaro
- Institute for Society and Genetics, University of California, Los Angeles, California; Department of Anthropology, University of California, Los Angeles, California
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Steinberg ER, Nieves M, Mudry MD. Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). COMPARATIVE CYTOGENETICS 2014; 8:43-69. [PMID: 24744833 PMCID: PMC3978242 DOI: 10.3897/compcytogen.v8i1.6716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/25/2014] [Indexed: 05/24/2023]
Abstract
In light of the multiple sex chromosome systems observed in howler monkeys (Alouatta Lacépède, 1799) a combined cladistic analysis using chromosomal and molecular characters was applied to discuss the possible origin of these systems. Mesoamerican and South American howlers were karyologically compared. FISH analysis using the chromosome painting probes for the #3 and #15 human chromosomes was applied to corroborate the homeology of the sexual systems. We found that the HSA3/15 syntenic association, present in the sex chromosome systems of South American Howlers, is not present in those of Mesoamerican ones. The autosomes involved in the translocation that formed the sexual systems in the Mesoamerican and South American species are different, thus suggesting an independent origin. Parsimony analysis resolved the phylogenetic relationships among howler species, demonstrating utility of the combined approach. A hypothesis for the origin of the multiple sex chromosome systems for the genus is proposed.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
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Ruiz-García M, Castillo MI, Lichilín-Ortiz N, Pinedo-Castro M. Molecular relationships and classification of several tufted capuchin lineages (Cebus apella, Cebus xanthosternos and Cebus nigritus, Cebidae), by means of mitochondrial cytochrome oxidase II gene sequences. ACTA ACUST UNITED AC 2012; 83:100-25. [PMID: 23128150 DOI: 10.1159/000342832] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 08/21/2012] [Indexed: 11/19/2022]
Abstract
The morphological systematics of the tufted capuchins is confusing. In an attempt to clarify the complex systematics and phylogeography of this taxon, we provide a first molecular analysis. We obtained mitochondrial cytochrome oxidase II (mtCOII) gene sequences from 49 tufted capuchins that had exact geographic origins from diverse lineages in Colombia, Peru, Bolivia, French Guyana, Brazil, Argentina and Paraguay and that belonged to clearly recognized morphological taxa. This project had 4 main findings: (1) we determined 2 established and related taxa in the northern Amazon River area, which we named C. a. apella and C. a. fatuellus. C. a. apella is distributed from French Guyana until, at least, the Negro River in the northern Brazilian Amazon, whereas C. a. fatuellus is distributed throughout the Colombian Eastern Llanos and the northern Colombian Amazon. We also determined 2 other southern C. apella taxa, which we named C. a. macrodon and C. a. cay. C. a. macrodon has a western and southern Amazon distribution, while C. a. cay has a more southern distribution outside the Amazon basin. (2) In the upper Amazon basin, there is a unique lineage (C. a. macrocephalus) with 1 widely distributed haplotype. The 4 morphological subspecies (C. a. maranonis, C. a. macrocephalus, C. a. peruanus, C. a. pallidus), and maybe a fifth unknown subspecies, described in this area were molecularly undifferentiated at least for the mitochondrial gene analyzed. (3) Our molecular analysis determined that 1 individual of C. robustus fell into the lineage of C. a. macrocephalus. Therefore, this form does not receive any specific name. (4) The animals classified a priori as C. nigritus and C. xanthosternos (because of their morphological phenotypes and by their geographical origins) were clearly differentiated from the other specimens analyzed with the molecular marker employed. Therefore, we consider that these 2 lineages could be assigned the status of full species following the biological species definition. (5) In 2001, Groves described 4 tufted capuchin species (C. apella, C. libidinosus, C. nigritus and C. xanthosternos), while Silva Jr. determined 7 species (C. apella, C. macrocephalus, C. libidinosus, C. cay, C. nigritus, C. robustus and C. xanthosternos). The tests of Swofford-Olsen-Waddell-Hillis, of Shimodaira and Hasegawa and of Templeton did not fit with either of these two classificatory schemes, although Groves' scheme was better with regard to our data than that of Silva Jr. (6) All the temporal splits among the tufted capuchin taxa studied were estimated to have occurred during the last phase of the Pleistocene by using the ρ statistic applied to the median joining haplotype network.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular y Biología Evolutiva, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia.
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de Oliveira EHC, Neusser M, Müller S. Chromosome evolution in new world monkeys (Platyrrhini). Cytogenet Genome Res 2012; 137:259-72. [PMID: 22699158 DOI: 10.1159/000339296] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During the last decades, New World monkey (NWM, Platyrrhini, Anthropoideae) comparative cytogenetics has shed light on many fundamental aspects of genome organisation and evolution in this fascinating, but also highly endangered group of neotropical primates. In this review, we first provide an overview about the evolutionary origin of the inferred ancestral NWM karyotype of 2n = 54 chromosomes and about the lineage-specific chromosome rearrangements resulting in the highly divergent karyotypes of extant NWM species, ranging from 2n = 16 in a titi monkey to 2n = 62 in a woolly monkey. Next, we discuss the available data on the chromosome phylogeny of NWM in the context of recent molecular phylogenetic analyses. In the last part, we highlight some recent research on the molecular mechanisms responsible for the large-scale evolutionary genomic changes in platyrrhine monkeys.
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Affiliation(s)
- E H C de Oliveira
- Laboratório de Cultura de Tecidos, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
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15
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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.
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Affiliation(s)
- Xiao-Xin Bi
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
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16
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Nieves M, De Oliveira EHC, Amaral PJS, Nagamachi CY, Pieczarka JC, Mühlmann MC, Mudry MD. Analysis of the heterochromatin of Cebus (Primates, Platyrrhini) by micro-FISH and banding pattern comparisons. J Genet 2011; 90:111-7. [PMID: 21677395 DOI: 10.1007/s12041-011-0047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
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.
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Affiliation(s)
- Mariela Nieves
- Grupo de Investigación en Biología Evolutiva, Laboratorio 46, 4° piso, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II - Ciudad Universitaria, Intendente Güiraldes 2160 - C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.
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17
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Mudry MD, Martinez RA, Nieves M, Carballo MA. Biomarkers of genotoxicity and genomic instability in a non-human primate, Cebus libidinosus (Cebidae, Platyrrhini), exposed to nitroimidazole derivatives. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2011; 721:108-13. [DOI: 10.1016/j.mrgentox.2011.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 01/03/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
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18
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Rodrigues LRR, Pieczarka JC, Pissinati A, de Oliveira EHC, das Dores Rissino J, Nagamachi CY. Genomic mapping of human chromosome paints on the threatened masked Titi monkey (Callicebus personatus). Cytogenet Genome Res 2011; 133:1-7. [PMID: 21311179 DOI: 10.1159/000323956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2010] [Indexed: 11/19/2022] Open
Abstract
Callicebus is a complex genus of neotropical primates thought to include 29 or more species. Currently, the genus is divided into 5 species groups: donacophilus, cupreus, moloch, torquatus and personatus. However, the phylogenetic relationships among the species are still poorly understood. This genus is karyotypically diverse and shows extensive variation in diploid number (2n = 16 to 50). To foster a better understanding of the chromosomal diversities and phylogenetic relationships among the species of Callicebus, we performed a chromosome-painting analysis on the Callicebus personatus genome using human probes, and compared the resulting hybridization map to those of previously mapped titi species. We detected 38 hybridization signals per haploid autosomal set of C. personatus. Few ancestral syntenies were conserved without rearrangement, but 4 human associations (HSA20/13, 3c/8b, 1b/1c and 21/3a/15a/14) were demonstrated to be apomorphic traits for C. persona tus. G-banding suggested that these associations are shared with C. nigrifrons and C. coimbrai (personatus group), while C. personatus is linked with C. pallescens (donacophilus group) by 2 synapomorphies: HSA10b/11 (submetacentric) and an inversion of HSA1a.
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Affiliation(s)
- L R R Rodrigues
- Laboratório de Citogenética, ICB, UFPA, Campus Guamá, Belém, Brasil
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19
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Botero S, Rengifo LY, Bueno ML, Stevenson PR. How many species of woolly monkeys inhabit Colombian forests? Am J Primatol 2011; 72:1131-40. [PMID: 20815013 DOI: 10.1002/ajp.20878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
There is a controversy regarding how many species the genus Lagothrix contains, since the Lagothrix lagothricha subspecies have been recently proposed to be actual species. Clarification of species status is of particular importance in the case of L. l. lugens, because it is the most endangered and its distribution is restricted to the Colombian Andes, a highly deforested region. Using cytogenetic and molecular markers, we obtained evidence indicating that the subspecies status is appropriate for the two taxa occurring in this country. We also report high levels of intraspecific variability in the karyotype. We find evidence for a late Pleistocene separation of the subspecies, and we propose it is the limited area of contact between the taxa that allowed for them to partially differentiate.
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Affiliation(s)
- Sergio Botero
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.
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20
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Molecular phylogenetics and phylogeography of the white-fronted capuchin (Cebus albifrons; Cebidae, Primates) by means of mtCOII gene sequences. Mol Phylogenet Evol 2010; 57:1049-61. [DOI: 10.1016/j.ympev.2010.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 07/06/2010] [Accepted: 09/03/2010] [Indexed: 11/23/2022]
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21
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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.
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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
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Nagamachi CY, Pieczarka JC, Milhomem SSR, O'Brien PCM, de Souza ACP, Ferguson-Smith MA. Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes) revealed by chromosome painting. BMC Genet 2010; 11:28. [PMID: 20420709 PMCID: PMC2873553 DOI: 10.1186/1471-2156-11-28] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 04/27/2010] [Indexed: 11/10/2022] Open
Abstract
Background Gymnotus (Gymnotidae, Gymnotiformes) is the Neotropical electric fish genus with the largest geographic distribution and the largest number of species, 33 of which have been validated. The diploid number varies from 2n = 39-40 to 2n = 54. Recently we studied the karyotype of morphologically indistinguishable samples from five populations of G. carapo sensu stricto from the Eastern Amazon of Brazil. We found two cytotypes, 2n = 42 (30 M/SM + 12 ST/A) and 2n = 40 (34 M/SM + 6 ST/A) and we concluded that the differences between the two cryptic species are due to pericentric inversions and one tandem fusion. Results In this study we use for the first time, whole chromosome probes prepared by FACS of the Gymnotus carapo sensu strictu species, cytotype with 2n = 42. Using two color hybridizations we were able to distinguish pairs 1, 2, 3, 7, 9, 14, 16, 18, 19, 20 and 21. It was not possible to separate by FACS and distinguish each of the following chromosome pairs even with dual color FISH: {4,8}; {10,11}; {5,6,17}; {12,13,15}. The FISH probes were then used in chromosome painting experiments on metaphases of the 2n = 40 cytotype. While some chromosomes show conserved synteny, others are rearranged in different chromosomes. Eight syntenic associations were found. Conclusions These results show that the karyotype differences between these cryptic species are greater than assumed by classical cytogenetics. These data reinforce the previous supposition that these two cytotypes are different species, despite the absence of morphological differences. Additionally, the homology of repetitive DNA between the two provides evidence of recent speciation.
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Affiliation(s)
- Cleusa Y Nagamachi
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.
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Garcia-Cruz R, Robles P, Steinberg ER, Camats N, Brieño MA, Garcia-Caldés M, Mudry MD. Pairing and recombination features during meiosis in Cebus paraguayanus (Primates: Platyrrhini). BMC Genet 2009; 10:25. [PMID: 19500368 PMCID: PMC2702343 DOI: 10.1186/1471-2156-10-25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 06/05/2009] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Raquel Garcia-Cruz
- Unitat de Biologia Cellular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
| | - Pedro Robles
- Unitat de Biologia Cellular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
| | - Eliana R Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE), CONICET, Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nuria Camats
- Unitat de Biologia Cellular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
| | - Miguel A Brieño
- Unitat de Biologia Cellular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
| | - Montserrat Garcia-Caldés
- Unitat de Biologia Cellular i Genètica Mèdica, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
- Grupo de Investigación en Biología Evolutiva (GIBE), Departamento de Ecología, Genética y Evolución, FCEyN, UBA, Cdad, Universitaria, Pabellón II, 4to Piso, Lab 46 (1428 EHA), Cdad, Autónoma de Bs As, Buenos Aires, Argentina
| | - Marta D Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE), CONICET, Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires, Buenos Aires, Argentina
- Grupo de Investigación en Biología Evolutiva (GIBE), Departamento de Ecología, Genética y Evolución, FCEyN, UBA, Cdad, Universitaria, Pabellón II, 4to Piso, Lab 46 (1428 EHA), Cdad, Autónoma de Bs As, Buenos Aires, Argentina
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