Delimitation of evolutionary units in Cuvier’s dwarf caiman, <Emphasis Type="Italic">Paleosuchus palpebrosus</Emphasis> (Cuvier, 1807): insights from conservation of a broadly distributed species

An important goal of evolutionary and conservation biology is the identification of units below the species level, such as Evolutionarily Significant Units (ESUs), providing objectively delimited units for species conservation and management. In this study we tested the hypothesis that Cuvier’s dwarf caiman (Paleosuchus palpebrosus)—a species broadly distributed across several biomes and watersheds of South America—is comprised of different ESUs. We analyzed mitochondrial cytochrome b sequences of 206 individuals and 532 unlinked ddRAD loci of 20 individuals chosen from amongst the mitochondrial haplogroups. Analysis of the cytochrome b sequences revealed four mitochondrial clusters, while STRUCTURE analysis of ddRAD loci detected three genomic clusters with different levels of mixture between them. Using the Adaptive Evolutionary Conservation (AEC) framework we identified three ESUs: “Amazon”, “Madeira-Bolivia” and “Pantanal”; one of them composed of two different Management Units (MUs), “Madeira” and “Bolivia”. In general, based on the comparisons with other crocodilian species, genetic diversity of each lineage was moderate however, the Madeira MU showed fivefold lower genetic diversity than other geographic groups. Considering the particularities of each Paleosuchus palpebrosus conservation unit, we recommend that the conservation status of each is evaluated separately. Tropical biodiversity is largely underestimated and in this context the broadly distributed species are the most likely candidates to harbor distinct evolutionary lineages. Thus, we suggest that conservation research should not neglect species that are generally considered of Least Concern by IUCN due to the taxon’s broad geographic distribution.     

Phylogeny and phylogeography of squirrel monkeys (genus Saimiri) based on cytochrome b genetic analysis

Squirrel monkeys (genus Saimiri) are distributed over a wide area encompassing the Amazon Basin: French Guiana, Suriname, and Guyana, together with Western Panama and Western Costa Rica. The genus Saimiri includes a complex of species and subspecies displaying considerable morphological variation. Taxonomic and systematic studies have identified, in this genus, one to seven species comprising up to 16 subspecies. The phylogenetic relationships between these taxa are poorly understood. Molecular markers have yielded a consistent framework for the systematics of Central and South American Saimiri, identifying four distinct clades: S. oerstedii, S. sciureus, S. boliviensis, and S. ustus. Here, we reconsider the phylogenetic and biogeographic history of Saimiri on the basis of mitochondrial (mtDNA) sequence data, focusing mostly on individuals originating from the Amazon Basin. We studied 32 monkeys with well‐defined geographic origins and inferred the phylogenetic relationships between them on the basis of full‐length cytochrome b gene nucleotide sequences. The high level of gene diversity observed (0.966) is consistent with the high level of behavioral and morphological variation observed across the geographic range of the genus: 20 mtDNA haplotypes were identified with a maximum divergence of 4.81% between S. b. boliviensis and S. ustus. In addition to confirming the existence of the four clades previously identified on the basis of molecular characters, we suggest several new lineages, including S. s. macrodon, S. s. albigena, S. s. cassiquiarensis, and S. s. collinsi. We also propose new patterns of dispersion and diversification for the genus Saimiri, and discuss the contribution of certain rivers and forest refuges to its structuring. Am. J. Primatol. 72:242–253, 2010. © 2009 Wiley‐Liss, Inc.     

Rapid evaluation of threats to biodiversity: human footprint score and large vertebrate species responses in French Guiana

Although there is an extensive literature demonstrating the impact of human activities on both species extinction risk and local ecological processes, the methodological tools that allow for the visualization and quantification of the intensity of the observed and forthcoming impacts are lacking. Here we propose a Footprint index for French Guiana, (northern Atlantic coast of South America) which sums up the expected and proven disturbances on biodiversity. The index was developed by superimposing geographical and human data, including human population densities, land use, settlements and camps, mining and forest activities, tracks, roads and rivers. The relevance of the index as a general measure of anthropic impact on large terrestrial fauna was estimated by investigating the structure of the large terrestrial vertebrate assemblages, including primates, large frugivorous birds, rodents and ungulates, in relation to the extent of disturbances. The abundance of large terrestrial fauna was assessed using the line-transect sampling method in 34 forest sites facing different disturbance levels, including hunting, logging and fragmentation, and consequently different footprint scores. A Self Organizing Map was used to combine species abundances and disturbance scores. It allowed us to rank species in accordance to their sensitivity towards disturbances, identifying the response of fauna to different concomitant threats. The index provided correct identification of sites with similar threats which proves it is a relevant estimator of human disturbance. In addition, the richness of animal communities and abundances of several seed dispersers and predators were negatively correlated to the index (e.g. large monkeys and frugivorous birds, r ² = 0.49, P < 0.0001 and r ² = 0.48, P < 0.0001, respectively), indicating its reliability in identifying areas where animal communities are disturbed. The index could, therefore, constitute a useful tool to identify areas where ecological processes supported by those species are expected to be disrupted, and where they are already disrupted. Furthermore, the footprint index can deal with lack of field data or with only partially valid information, and so may directly help land managers forecast and, hopefully, mitigate forthcoming impacts resulting from the development of human activities.     

iDNA screening: Disease vectors as vertebrate samplers

In the current context of global change and human‐induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time‐consuming and skill‐demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood‐fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high‐throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human‐induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large‐scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco‐epidemiology.     

Phylogeographic and conservation genetic analysis of the black caiman (Melanosuchus niger)

We assessed the spatial distribution of the genetic variability of Melanosuchus niger from 11 localities in South America using 1,027 base pairs of the mitochondrial cytochrome b gene. Screening 132 animals, we found 41 haplotypes, high values of genetic diversity, low values of nucleotide diversity and significant deviations from neutral expectation of allelic frequencies in some localities. Mantel test and nested-clade analysis indicated that isolation-by-distance was an important population dynamic for the species as a whole. Wright's fixation indexes analyses showed that hydrogeographically separated populations from French Guiana together with Amapá state population in Brazil are genetically differentiated from all other populations that are found in the Amazon drainage basin. These indexes also disclosed that the population from Ecuador is genetically differentiated in relation to the populations from Brazil, Peru and French Guiana. Within the Amazon Basin little differentiation exists, and genetic and geographic distances are not correlated. Demographic data as well as population genetic data suggest that M. niger is recovering in some protected regions. However, part of this apparent recovery may be owing to the movement of animals into protected regions.     

Assessment of large-vertebrate species richness and relative abundance in Neotropical forest using line-transect censuses: what is the minimal effort required?

Line-transect sampling is a strategy commonly used to assess richness and abundance of large diurnal vertebrates in tropical forests, but the relationships between the sampling effort (measured as transect length in km) and the accuracy of the estimates based on the field data have rarely been investigated. Using data from 17 distinct surveys in French Guiana, we demonstrated that 85 km of transect are sufficient to extrapolate species richness whatever the forest type and the disturbance level of the habitat. Concerning species abundances, reliable estimations were obtained after 40–90 km of transects for large birds, howlers, tamarins, and agoutis. In contrast, relative abundances of capucins, sakis, and ungulates, were still not stabilized after 100 km but can still be reliably assessed with this effort. These species have larger home range than the former, and the accuracy of abundance assessment may be related to use of space. Since species with small area requirements regularly use their entire home range, abundance prediction with a moderate sampling effort may be facilitated. On the contrary, species with large home ranges may exhibit strong seasonal habitat partitioning, therefore decreasing the accuracy of abundance estimation on a low-effort survey. This analysis provides the first evidence of the minimal efforts required to assess large vertebrate richness and relative abundance of some species in a neotropical rainforest. We encourage similar works on other sites, to collect additional information on the influence of forest productivity and species assemblage composition on the minimal required sampling effort. This would permit confident extrapolations of species richness and abundance in other Neotropical forests and may provide efficient guidelines to integrate the predictive analytical tool developed in this work in future biodiversity management plans.     

Novel mammalian herpesviruses and lineages within the Gammaherpesvirinae: cospeciation and interspecies transfer

Novel members of the subfamily Gammaherpesvirinae, hosted by eight mammalian species from six orders (Primates, Artiodactyla, Perissodactyla, Carnivora, Scandentia, and Eulipotyphla), were discovered using PCR with pan-herpesvirus DNA polymerase (DPOL) gene primers and genus-specific glycoprotein B (gB) gene primers. The gB and DPOL sequences of each virus species were connected by long-distance PCR, and contiguous sequences of approximately 3.4 kbp were compiled. Six additional gammaherpesviruses from four mammalian host orders (Artiodactyla, Perissodactyla, Primates, and Proboscidea), for which only short DPOL sequences were known, were analyzed in the same manner. Together with available corresponding sequences for 31 other gammaherpesviruses, alignments of encoded amino acid sequences were made and used for phylogenetic analyses by maximum-likelihood and Bayesian Monte Carlo Markov chain methods to derive a tree which contained two major loci of unresolved branching details. The tree was rooted by parallel analyses that included alpha- and betaherpesvirus sequences. This gammaherpesvirus tree contains 11 major lineages and presents the widest view to date of phylogenetic relationships in any subfamily of the Herpesviridae, as well as the most complex in the number of deep lineages. The tree's branching pattern can be interpreted only in part in terms of the cospeciation of virus and host lineages, and a substantial incidence of the interspecies transfer of viruses must also be invoked.     

Health evaluation of translocated free-ranging primates in French Guiana

Among over 40 mammal species threatened by the filling of a hydroelectric dam reservoir in French Guiana, three species of primates have been translocated, comprising 124 red howler monkeys, six white-faced sakis, and 95 golden-handed tamarins. Health status of the animals was evaluated by direct physical examination and by hematological, biochemical, virological, and parasitological surveys of collected blood. The physical condition of the howlers was slightly worse toward the end of the capture period, but that of sakis and tamarins remained satisfactory. Several ectoparasites (ticks, larvae of dipterous insects, fleas, and lice) were collected, and various wounds, apparently nondebilitating, were recorded in howlers. Hematological and biochemical profiles determined for the three species revealed a slight anemia in howlers. Entamoeba, Strongyloides, and Trypanoxyurus were common in fecal samples of howlers. A survey of blood smears from the three species revealed infection by several types of microfilaria, Trypanosoma rangeli-like and Plasmodium brasilianum in all three, and Trypanosoma cruzi-like in howlers. These infections had no significant impact on the health status or the hematological profiles. Serologic investigations revealed occasional reactions against Toxoplasma gondii, a strong anti-Plasmodium response in the two Cebidae species, and a weaker one in tamarins. Attempts to isolate arbovirus failed, but antibody responses to Mayaro and yellow fever viruses were strong, especially in the howlers. A strong correlation between age and serological status led to a better understanding of the epidemic cycles. Our survey indicates French Guianan primates are reservoirs for several anthropozoonoses, including malaria, Chagas disease, and arboviruses.     

A survey of hemoparasite infections in free-ranging mammals and reptiles in French Guiana

Blood smears of 1,353 free-ranging mammals (35 species) and 112 reptiles (31 species) from French Guiana were examined for hemoparasites. Parasites from 3 major groups were recorded: Apicomplexa (including hemogregarines, piroplasms, and Plasmodium spp.), Trypanosomatidae, and Filaroidea. Fifty percent of the individuals (86% of the species) were infected by parasites from at least 1 group. Hemogregarines, identified as Hepatozoon sp., infected numerous snakes with high prevalences (30-100%); infection is reported for the first time in 5 host genera of snakes: Clelia, Oxybelis, Pseustes, Rhinobotryum, and Bothriopsis. Infections were also observed in 4 marsupial species and 1 rodent. Hepatozoon spp. recorded in Didelphis albiventris (Marsupialia) and Coendou prehensilis (Rodentia) may be new species. Plasmodium sp. were observed in 2 snake species, Dipsas indica (Colubridae) and Bothrops atrox (Viperidae). Plasmodium brasilianum was recorded in all 5 primate species examined. Piroplasms were observed in all mammal orders except primates. Large terrestrial rodents were the main hosts of members of the Babesidae; 42% of Myoprocta acouchy, 36% of Dasyprocta agouti, and 44% of Agouti paca were infected. Trypanosomes were common in mammals and were recorded in 70% of the examined genera. Trypanosoma cruzi-like infections were reported in 21 mammal species, including sloths, rodents, carnivores, and primates. Microfilariae were also widespread, with higher prevalences in sloths, anteaters, and porcupines (>40% of the individuals infected) and in tamarins (95% infected). This survey highlights some potential anthropozoonotic risks due to the recent further evidence of Plasmodium brasilianum and P. malariae as a single species and to the increased diversity of hosts for Trypanosoma cruzi.     

Hematological and serum chemistry profiles of free-ranging southern two-toed sloths in French Guiana.

Free-ranging southern two-toed sloths (Choloepus didactylus) were translocated during the flooding of a forest at a hydroelectric dam site in French Guiana. Over an 11 mo period blood samples were collected from 90 sloths (38 males, 52 females) in order to determine hematological and serum chemistry reference values. Mean values and range of values were calculated for 13 hematological and 21 serum chemistry parameters. Variations associated with sex, age and reproductive status were identified. Males had a significantly lower red blood cell count than females. Immature animals had more monocytes while adults had more neutrophils and higher mean corpuscular hemoglobin concentration. Aspartate aminotransferase and triglyceride values were higher in young than in adult sloths but uric acid was lower. Lactating females showed lower red blood cells count and iron levels than non-lactating females. These profiles will help to provide reliable baseline data for medical evaluation of sloths.