First Molecular Phylogenetic Analysis of the Lagothrix Taxon Living in Southern Peru and Northern Bolivia: Lagothrix lagothricha tschudii (Atelidae, Primates), a New Subspecies.

We sequenced mitochondrial COI and COII genes (1,377 base pairs) of 166 woolly monkeys (Lagothrix) to determine the phylogenetic relationships of tschudii in reference to the other taxa within the genus Lagothrix, to provide the first genetic diversity level estimates for tschudii, and to reconstruct the historical demographic evolution of this taxon. The sample set included, for the first time, 10 individuals of the elusive tschudii taxon sensu Groves from southern Peru and northern Bolivia. Our phylogenetic analyses showed that these 10 exemplars formed a statistically significant and differentiated (molecularly and morphologically) monophyletic clade relative to other traditional subspecies of Lagothrix lagothricha. Therefore, tschudii should be recognized as a fifth subspecies: Lagothrix lagothricha tschudii. The temporal divergence of the ancestors of tschudii and L. l. cana was estimated to have occurred around 1.8 million years ago (MYA). Additionally, mitochondrial diversification within tschudii started no later than 0.96 MYA (Bayesian Inference) or 0.88 MYA (Median Joining -Network), respectively. In contrast to the phylogenetic trees, the FSTstatistic and the gene flow estimates showed L. l. lugens to be the least differentiated taxon of L. lagothricha from L. l. tschudii. Based on genetic distances, L. l. tschudii had the smallest average genetic distance from the other subspecies of L. lagothricha.It was also the taxon within L. lagothricha that had the smallest genetic distance from L. flavicauda. It should be related to L. l. tschudii as the first original taxon in L. lagothricha. Furthermore, the Andean mountains were extremely important in the original diversification of the Lagothrix genus and in the original diversification of L. lagothricha. Although L. l. tschudii has the smallest geographical range of all the taxa of L. lagothricha, its genetic diversity is even higher than in other taxa with wider geographical ranges, such as L. l. lagothricha and L. l. cana. L. l. tschudii showed a very slight demographic increase during the Pleistocene with a decrease of females in the last 10,000 Y, similar to that found for L. l. lugens in a previous study.

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.

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).

Molecular phylogenetics and phylogeography of all the Saimiri taxa (Cebidae, Primates) inferred from mt COI and COII gene sequences.

Some previous genetic studies have been performed to resolve the molecular phylogenetics of the squirrel monkeys (Saimiri). However, these studies did not show consensus in how many taxa are within this genus and what the relationships among them are. For this reason, we sequenced 2,237 base pairs of the mt COI and COII genes in 218 Saimiri individuals. All, less 12 S. sciureus sciureus from French Guyana, were sampled in the wild. These samples represented all the living Saimiri taxa recognized. There were four main findings of this study. (1) Our analysis detected 17 different Saimiri groups: albigena, cassiquiarensis, five polyphyletic macrodon groups, three polyphyletic ustus groups, sciureus, collinsi, boliviensis, peruviensis, vanzolinii, oerstedii and citrinellus. Four different phylogenetic trees showed the Central American squirrel monkey (S. oerstedii) as the most differentiated taxon. In contrast, albigena was indicated to be the most recent taxon. (2) There was extensive hybridization and/or historical introgression among albigena, different macrodon groups, peruviensis, sciureus and collinsi. (3) Different tests showed that our maximum likelihood tree was consistent with two species of Saimiri: S. oerstedii and S. sciureus. If no cases of hybridization were detected implicating S. vanzolinii, this could be a third recognized species. (4) We also estimated that the first temporal splits within this genus occurred around 1.4-1.6 million years ago, which indicates that the temporal split events within Saimiri were correlated with Pleistocene climatic changes. If the biological species concept is applied because, in this case, it is operative due to observed hybridization in the wild, the number of species within this genus is probably more limited than recently proposed by other authors. The Pleistocene was the fundamental epoch when the mitochondrial Saimiri diversification process occurred.

Genetic characterization and structure of the endemic Colombian silvery brown bare-face tamarin, Saguinus leucopus (Callitrichinae, Cebidae, Primates).

We analyzed 115 Saguinus leucopus, from four Colombian departments (Antioquia, Bolivar, Caldas and Tolima ), for 701 bp of the mt COII gene and at 10 microsatellite loci to estimate gene diversity levels, possible molecular subspecies and historical demographic changes in this species. This endemic Colombian species showed an elevated gene diversity in this gene, although its geographical distribution is very restrictive and extremely threatened by habitat fragmentation. The mt COII gene did not show any geographical structure in the distribution of the haplotypes within this species, but it did show a noteworthy population expansion throughout the history of this species. A Bayesian analysis showed that the haplotype diversification of this species began around 1.6 million years ago (MYA), whilst a haplotype network gave the beginning of this diversification at around 0.5-0.6 MYA. Forty-seven individuals out of the 115 were analyzed for 10 DNA microsatellites. The genetic diversity was relatively elevated for this kind of marker too, and comparable to that found in other Neotropical monkeys with a wider geographical distribution. Two gene pools were detected with the microsatellites, one in the northern distribution area (Antioquia) and the other in the southern distribution area (Tolima). No tests detected any bottleneck affecting this population; however, two procedures (k test and Kimmel et al. 1998 test) detected significant population expansion for the microsatellite markers, like that seen with the mt COII gene.

Molecular systematics and phylogeography of Cebus capucinus (Cebidae, Primates) in Colombia and Costa Rica by means of the mitochondrial COII gene.

We propose the first molecular systematic hypothesis for the origin and evolution of Cebus capucinus based on an analysis of 710 base pairs (bp) of the cytochrome c oxidase subunit II (COII) mitochondrial gene in 121 C. capucinus specimens sampled in the wild. The animals came from the borders of Guatemala and Belize, Costa Rica, and eight different departments of Colombia (Antioquia, Chocó, Sucre, Bolivar, Córdoba, Magdalena, Cauca, and Valle del Cauca). Three different and significant haplotype lineages were found in Colombia living sympatrically in the same departments. They all presented high levels of gene diversity but the third Colombian gene pool was determined likely to be the most ancestral lineage. The second Colombian mitochondrial (mt) haplogroup is likely the source of origin of the unique Central America mt haplogroup that was detected. Our molecular population genetics data do not agree with the existence of two well-defined subspecies in Central America (limitaneus and imitator). This Central America mt haplogroup showed significantly less genetic diversity than the Colombian mt haplogroups. All the C. capucinus analyzed showed evidence of historical population expansions. The temporal splits among these four C. capucinus lineages were related to the completion of the Panamanian land bridge as well as to climatic changes during the Quaternary Period.

Métodos genéticos para la reintroducción de monos de los géneros Saguinus, Aotus y Cebus (Primates: Cebidae) decomisados en Bogotá, Colombia

Genetic methods for the reintroduction of primates Saguinus, Aotus and Cebus (Primates: Cebidae) seized in Bogota, Colombia. Primates are one of more confiscated taxa by the environmental authorities in Bogota, Colombia. During 2008, 133 monkeys were confiscated; samples from 115 of them were sequenced by the mitochondrial cythocrome oxidase II gene (mtCOII) and 112 sequences obtained were of high quality. These sequences were compared with those obtained by our research group from individuals directly sampled in the field, with precise geographic origin. So, a more specific geographic area of the Colombian territory could be considered for a correct rehabilitation treatment during the reintroduction of these confiscated animals. The main results with five primate species were: 1- For all the specimens analyzed of Saguinus leucopus, they could be liberated in any geographical area of its distribution range, since only one gene pool was found. 2- For the 14 Aotus sp. individuals sequenced from the SDA (Environmental District Secretariat), one of them (A. vociferans) was coming from the Amazon, seven exemplars belonged to A. griseimembra from the Magdalena Valley and the Colombian Caribbean coasts, four individuals represented to A. brumbacki from the Colombian Eastern Llanos, and two were associated to A. azarae azarae from Northern Argentina and Paraguay (which means that illegal traffic of animals is arriving to Colombia from other South-American countries). 3-Out 14 Cebus albifrons sequenced, two belonged to the geographical area of C. a. versicolor, one to C. a. pleei, 10 to C. a. leucocephalus and one could be not assigned because its sequence yielded a great genetic divergence with respect to the other specimens sequenced of this species. 4- The two Cebus capucinus sequenced showed to be associated to a gene pool found in the Northern of Chocó, Sucre and Córdoba Departments. 5- Out 11 Cebus apella sequenced, 10 showed to belong to the gene pool presented in the Colombian Eastern Llanos and highly related (but differentiable) to Cebus apella apella from the French Guyana. It could be named C. a. fatuellus sensu Groves (2001). One exemplar sequenced could be not related with the other C. apella analyzed, nor the related taxa to the aforementioned species (C. a. paraguayanus =C. cay; C. xanthosternos; C. nigritus). Rev. Biol. Trop. 58 (3): 1049-1067. Epub 2010 September 01.

Los primates son uno de los grupos de mamíferos más decomisados por la autoridades ambientales (SDA) en Bogotá, Colombia. Un total de 133 primates fueron confiscados en Bogotá durante el año 2008 y mantenidos en las instalaciones de la SDA. De ellos, 115 fueron secuenciados para el gen mitocondrial citocromo oxidasa II (mtCOII) y en 112 ejemplares, las secuencias obtenidas fueron de alta calidad. Esas secuencias se compararon con las obtenidas para ejemplares muestreados directamente en campo por nuestro grupo de investigación y con origen geográfico conocido. De ese modo, se pudo determinar las áreas geográficas, en el territorio colombiano, donde pueden liberarse esos ejemplares después del tratamiento de rehabilitación oportuno. Los resultados principales para las cinco especies de primates fueron como siguen: 1- Para Saguinus leucopus, los animales analizados pueden ser liberados en cualquier área geográfica dentro del rango de distribución de la especie, ya que solo se detectó un acervo genético sin estructura espacial. 2- Para los 14 Aotus sp. secuenciados procedentes de la SDA, se determinó que: uno de ellos pertenecía a A. vociferans, propio de la Amazonía; siete ejemplares pertenecieron a A. griseimembra, propio del valle del Magdalena hasta la costa Caribe colombiana; cuatro ejemplares representaron a A. brumbacki, de los Llanos Orientales de Colombia; y dos ejemplares se asociaron con A. azarae azarae del norte de Argentina y Paraguay, con lo cual se muestra que en Colombia se está recibiendo fauna ilegal procedente de otros países. 3- De los 14 Cebus albifrons secuenciados, dos pertenecieron al área geográfica de distribución de C. a. versicolor; uno al de C. a. pleei, 10 al de C. a. leucocephalus, y uno no pudo ser asignado ya que su secuencia mostraba gran divergencia respecto a los otros ejemplares secuenciados de esta especie. 4- Los dos Cebus capucinus secuenciados mostraron estar asociados a un acervo genético encontrado en el norte del Chocó, Sucre y Córdoba. 5- De 11 Cebus apella secuenciados, 10 mostraron pertenecer al acervo genético que se encuentra en los Llanos Orientales de Colombia y altamente relacionado a Cebus apella apella de la Guyana Francesa, aunque podrían representar un acervo propio de Colombia, C. a. fatuellus sensu Groves (2001). Un individuo no pudo ser relacionado con ningún grupo de los otros C. apella estudiados, ni con los taxones relacionados a la especie mencionada, pero, probablemente, con su propio estatus taxonómico (C. a. paraguayanus = C. cay, C. xanthosternos, C. nigritus).

[Genetic methods for the reintroduction of primates Saguinus, Aotus and Cebus (Primates: Cebidae) seized in Bogota, Colombia]. / Métodos genéticos para la reintroducción de monos de los géneros Saguinus, Aotus y Cebus (Primates: Cebidae) decomisados en Bogotá, Colombia.

Primates are one of more confiscated taxa by the environmental authorities in Bogota, Colombia. During 2008, 133 monkeys were confiscated; samples from 115 of them were sequenced by the mitochondrial cythocrome oxidase II gene (mtCOII) and 112 sequences obtained were of high quality. These sequences were compared with those obtained by our research group from individuals directly sampled in the field, with precise geographic origin. So, a more specific geographic area of the Colombian territory could be considered for a correct rehabilitation treatment during the reintroduction of these confiscated animals. The main results with five primate species were: 1--For all the specimens analyzed of Saguinus leucopus, they could be liberated in any geographical area of its distribution range, since only one gene pool was found. 2--For the 14 Aotus sp. individuals sequenced from the SDA (Environmental District Secretariat), one of them (A. vociferans) was coming from the Amazon, seven exemplars belonged to A. griseimembra from the Magdalena Valley and the Colombian Caribbean coasts, four individuals represented to A. brumbacki from the Colombian Eastern Llanos, and two were associated to A. azarae azarae from Northern Argentina and Paraguay (which means that illegal traffic of animals is arriving to Colombia from other South-American countries). 3--Out 14 Cebus albifrons sequenced, two belonged to the geographical area of C. a. versicolor, one to C. a. pleei, 10 to C a. leucocephalus and one could be not assigned because its sequence yielded a great genetic divergence with respect to the other specimens sequenced of this species. 4--The two Cebus capucinus sequenced showed to be associated to a gene pool found in the Northern of Chocó, Sucre and Córdoba Departments. 5--Out 11 Cebus apella sequenced, 10 showed to belong to the gene pool presented in the Colombian Eastern Llanos and highly related (but differentiable) to Cebus apella apella from the French Guyana. It could be named C. a. fatuellus sensu Groves (2001). One exemplar sequenced could be not related with the other C. apella analyzed, nor the related taxa to the aforementioned species (C. a. paraguayanus = C. cay; C. xanthosternos; C. nigritus).