São Paulo is the most populous, developed and industrialized state of Brazil. Despite of intensive human activities, large habitat loss and fragmentation of the native vegetation cover, pumas (Puma concolor) still inhabit remnant habitat fragments in the northeastern area of the state. We investigated the occurrence of genetic structure and levels of genetic variability on pumas to aggregate basic information for conservation efforts to maintain long term viable populations of this top-predator in the region. By analyzing microsatellite loci variation, we corroborated the hypothesis of absence of genetic structure, and estimated high levels of genetic diversity (expected heterozygosity of 0.79 and mean of 10 alleles per locus). In spite of the increasing number of roadkilling and puma-human conflicts in the area, apparently pumas still maintain some level of gene flow between protected areas of the region. The observed excess of heterozygotes suggests a recent bottleneck event in this population, probably a consequence of the profound landscape transformation of the studied area during the last century; another possibility is this may be due to the observed deviation in the population sex ratio, which may be influencing the pumas' mating system. We propose that: (1) landscape management in the study area should be focused on increasing habitat connectivity, creating protected areas and structures to allow highway crossing of pumas;(2) educational actions should be undertaken to change community perception of large carnivores, and possibly the implementation of compensatory actions to ranchers.

DNA molecular analyses were used in a forensic investigation involving illegal wildlife poaching in central Brazil. The Brazilian environmental agency (IBAMA) sent us two samples of confiscated meat from illegal poaching for species and individual identification. Comparative analysis of cytochrome b sequences (1,070 bp) provided incontestable evidence that the meat samples were from the lowland tapir, Tapirus terrestris. The analysis of nine microsatellites indicated that the two seized meat samples shared the same genotypes, implying that meat from only one individual was present. The lowland tapir is the last representative of megamammals in South America and is a vulnerable species, locally extinct in several regions. The present paper reports a successful genetic investigation of an illegal hunting crime, in which DNA-based molecular analyses of seized ground meat samples were the only tool able to identify the species and individual, proving to be highly useful for wildlife crime investigations.

We describe ten microsatellite loci from the lowland tapir (Tapirus terrestris), one of the last members of the Neotropical megafauna and considered a vulnerable species. A total of 74 alleles were detected, ranging from four to thirteen alleles per locus. The expected heterozygosity ranged from 0.34 to 0.88, with a mean of 0.635. All but one locus conformed to the Hardy-Weinberg expectations. These microsatellite loci can be used in population genetic studies of the genus Tapirus, in which all species are threatened globally.

Abstract:Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis), originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars), we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD) and Iguaçu Region (IR). Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883). Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE) revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i) larger effective population size of ocelots (relative to jaguars) in each fragment, implying a slower effect of drift-induced differentiation; and (ii) potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America.