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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.

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.

A first step in protecting groups of similarly structured organisms is to place them into discrete taxa. Molecular genetics and phylogeny allow us to rebuild the evolutionary history of these taxa. The Neotropics has roughly 34% of Earth's primate diversity. However, the systematics of Neotropical primates is complex and controversial. The untufted (gracile) capuchins are traditionally classified as four species: Cebus albifrons, C. capucinus, C. olivaceus, and C. kaapori. Of these, Cebus albifrons has confusing intraspecific systematics with a large number of fragmented and isolated populations throughout its geographical distribution, and up to 13 morphological subspecies. The number of taxa of this species in Ecuador, some areas of northern and eastern Colombia, and Trinidad Island is particularly debated. Primatologists have defined two taxa of C. albifrons in Ecuador: a trans-Andean population: C. a. aequatorialis (or C. aequatorialis) and a cis-Andean population: C. a. yuracus (or C. yuracus). To better understand the systematics of this species, we sequenced the mitogenomes of 136 Cebus albifrons, two Cebus olivaceus, and one Cebus kaapori. Our phylogenetic analyses revealed at least nine significantly different haplogroups of C. albifrons in Ecuador, four of which contained exemplars from both the trans-Andean Pacific Ecuador and the cis-Andean Ecuadorian Amazon. The splits of these Ecuadorian haplogroups, and the initial diversification within them, occurred during the Middle to Late Pliocene and the beginning of the Pleistocene. Individuals we analyzed from Vichada Department in eastern Colombia were genetically distinct from other groups of C. albifrons, agreeing with morphological studies which consider it a full subspecies (C. a. albifrons). Phylogenetic analyses showed two different gracile capuchin taxa on Trinidad Island: C. a. trininatis and C. o. brunneus. We conclude that a large portion of the gracile capuchin taxa form a unique species with a complex of populations and subspecies. The species has conserved its reproductive integrity by repeated episodes of reticulation and high levels of gene flow.

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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.

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Titulo en ingles: Study of 14 platyrrhine primate species (cebus, saimiri, aotus, saguinus, lagothrix, alouatta, and ateles) using 10 DNA microsatellites: gene diversity and bottleneck event analyses with conservation propouses.RESUMEN:  Se utilizaron 10  loci microsatélites  para estudiar  varios aspectos  de la composición genética de 14  especies  de Primates Platirrinos Neotropicales (Cebus albifrons, Cebus apella, Cebus capucinus, Aotus nancymae, Saguinus oedipus, Saguinus  leocopus,  Saguinus   geoffroyi, Saimiri  sciureus, Saimiri  boliviensis,  Alouatta  seniculus,  Lagothrix lagotricha,  Ateles fusciceps, Ateles hybridus  y Ateles belzebuth) en cuatro zoológicos colombianos (zoológico de Cali, de Medellín, de  Barranquilla y Jaime  Duque de Bogotá) y de una institución  primatológica  peruana  (IVITA) (Iquitos), al igual que de especimenes  muestreados directamente en la naturaleza.  Diversos aspectos de la composición  genética  de  las  poblaciones  de  esas  especies  fueron analizados  con propósitos conservacionistas: (1)  Se determinó la variabilidad genética (heterocigosis esperada y número de alelos) de las respectivas colecciones de Primates de cada una de esas instituciones, al igual que de los animales capturados en la naturaleza, analizando, así, la variabilidad genética en cada una de las especies seleccionadas. (2)  Se determinó si las poblaciones  en cautiverio, al igual que las especies  como un todo, estaban  en equilibrio Hardy-Weinberg. Para ello se utilizaron diferentes estrategias  analíticas,  en función del tamaño  de las muestras  utilizadas:  F de Wright, f de Robertson & Hill y estimación de valores de probabilidades  exactas con cadenas de Markov.  Esto es importante desde una perspectiva conservacionista para conocer qué colecciones poseen mayor variabilidad genética y, por lo tanto, ser fuente de parentales en programas de reproducción en cautiverio, o para la reintroducción de animales en la naturaleza. Igualmente, se determinó qué especies poseen menor variabilidad genética y si existe coincidencia con el estatus  de peligro, o vulnerabilidad, registradas  por la UICN para esas especies de Primates. (3)   Teniendo  en consideración  el número  de alelos  por marcador,  la heterocigosis  esperada observada  y la heterocigosis esperada a partir del número de alelos observados,  y mediante  los modelos mutacionales de alelos infinitos y “step-wise”, se determinó qué colecciones de Primates en cautiverio han pasado por un cuello de botella reciente, y cuáles no. Estos estudios son muy importantes  desde el punto de vista de la conservación biológica de especies de mamíferos neotropicales.Palabras Claves: Primates Platirrinos; Cebus, Saimiri, Aotus, Saguinus, Alouatta, Lagothrix, Ateles, marcadores microsatélites (STRPs), diversidad génica, equilibrio Hardy-Weinberg, cuello de botella, Colombia, Perú.ABSTRACT: Ten microsatellite DNA loci (STRP) were employed to study several traits in the genetic composition of 14 Platyrrhini Neotropical Primate species (Cebus albifrons, Cebus apella,  Cebus capucinus, Aotus nancymae, Saguinus  oedi- pus, Saguinus leocopus, Saguinus geoffroyi, Saimiri sciureus, Saimiri boliviensis, Alouatta seniculus, Lagothrix lagotricha, Ateles fusciceps, Ateles hybridus and Ateles belzebuth) in four Colombian institutions (Cali, Medellín, Barranquilla and Jaime Duque Zoos) and in one Peruvian Primatologist institution (IVITA, Iquitos), as well as from individuals directly surveyed in the wild. Several aims related to the genetic composition of the populations of these species  were analyzed from a conservation  standpoint: (1) The genetic variability (expected  heterozygosity and number of alleles) were determined in the respective Primate collections of each one of the quoted institutions, as well as for the overall species selected. (2)  In these species and in their respective captive populations, the Hardy- Weinberg equilibrium was estimated. For this aim, different analytical procedures were employed in function of the sample sizes employed:  Wright´s F and Robertson and Hill´s f  statistics and estimations of the exact probability values with Markov´s chains.  This is important from a conservation perspective to know what collections have a greater genetic variability and, therefore, to be sources of parental in captive reproduction programs, or to reintro- duce animals in the wild.  In addition, there was determined  which species have a lower genetic variability and whether  it was in agreement  with the danger,  or vulnerability, status  registered by the UICN for these  Primate species.  (3)  Taking into account the number of alleles, the expected heterozygosity obtained from allele frequen- cies and the expected heterozygosity throughout the observed number of alleles by coalescent simulations, as well as the infinite allele and the step-wise mutation models, it was determined which Primate captive collections have suffered a recent bottleneck and which not.  This kind of studies is very important from a biological conservation point of view for a great number of Neotropical mammal  species.Key Words: Platyrrhini Primates, Cebus, Saimiri, Aotus, Saguinus, Alouatta, Lagothrix, Ateles, SRTPs (micosatellite loci), genetic diversity, Hardy-Weinberg equilibrium, bottleneck events, Colombia, Perú.