J. Paul Grobler

SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104–106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107–108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.

A Novel Trap Design for the Capture and Sedation of Vervet Monkeys (Chlorocebus aethiops)

Studies of population genetics and genomics, morphometrics, endocrinology and immunology of primates often require effective methods of trapping and sedation. In this paper, we describe a progressively refined trap design used by the authors to trap more than 770 vervet monkeys (Chlorocebus aethiops) in southern and eastern Africa between 1973 and 2009. The design offers ease of construction, portability, sensitivity of the trigger mechanism and the ability to restrain animals for sedation. In addition to a detailed description of the trap design, this paper presents notes on strategies for baiting, temporal trends during trapping and possible application to other taxa

Management of hybridization in an endemic species: decision making in the face of imperfect information in the case of the black wildebeest—Connochaetes gnou

Hybridization between introduced and endemic ungulates, resulting from anthropogenic actions, has been reported for several species. Several studies of such events contain the common themes of extralimital movements, problematic phenotypic and genetic detection, and imperfect management. In southern Africa, the endemic black wildebeest (Connochaetes gnou) currently faces a serious threat of hybridization and introgression. This species survived near extinction and consequent genetic bottlenecks in the late 1800s and in the 1930s. Initiatives by private farmers followed by conservation authorities led to a dramatic recovery in numbers of this species. However, in an ironic twist, the very same advances in conservation and commercial utilisation which led to the recovery of numbers are now themselves threatening the species. Injudicious translocation has brought the species into contact with its congener, the blue wildebeest (Connochaetes taurinus), and in recent times, hybridization between the species has occurred at numerous localities in South Africa. Consequently, a significant proportion of the national black wildebeest population potentially carries a proportion of introgressed blue wildebeest genetic material. We discuss completed and ongoing attempts to find molecular markers to detect hybrids and highlight the difficulty of detecting advanced backcrosses. Additional avenues of research, such as work on morphology (cranial and postcranial elements), estimating of the probability of introgression and modelling of diffusion rates are also introduced. In addition to the difficulty in detecting hybrid animals or herds, the lack of consensus on the fate of hybrid herds is discussed. Finally, in an environment of imperfect information, we caution against implementation of management responses that will potentially induce a new genetic bottleneck in C. gnou.

Using the Stable Carbon and Nitrogen Isotope Compositions of Vervet Monkeys (Chlorocebus pygerythrus) to Examine Questions in Ethnoprimatology

This study seeks to understand how humans impact the dietary patterns of eight free-ranging vervet monkey (Chlorocebus pygerythrus) groups in South Africa using stable isotope analysis. Vervets are omnivores that exploit a wide range of habitats including those that have been anthropogenically-disturbed. As humans encroach upon nonhuman primate landscapes, human-nonhuman primate interconnections become increasingly common, which has led to the rise of the field of ethnoprimatology. To date, many ethnoprimatological studies have examined human-nonhuman primate associations largely in qualitative terms. By using stable carbon (δ13C) and nitrogen (δ15N) isotope analysis, we use quantitative data to understand the degree to which humans impact vervet monkey dietary patterns. Based on initial behavioral observations we placed the eight groups into three categories of anthropogenic disturbance (low, mid, and high). Using δ13C and δ15N values we estimated the degree to which each group and each anthropogenically-disturbed category was consuming C4 plants (primarily sugar cane, corn, or processed foods incorporating these crops). δ13C values were significantly different between groups and categories of anthropogenic-disturbance. δ15N values were significantly different at the group level. The two vervet groups with the highest consumption of C4 plants inhabited small nature reserves, appeared to interact with humans only sporadically, and were initially placed in the mid level of anthropogenic-disturbance. However, further behavioral observations revealed that the high δ13C values exhibited by these groups were linked to previously unseen raiding of C4 crops. By revealing these cryptic feeding patterns, this study illustrates the utility of stable isotopes analysis for some ethnoprimatological questions.

The complete mitochondrial genome of Temminck's ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic position of the Pholidota (Weber, 1904)

Temminckis ground pangolin is primarily a nocturnal mammal belonging to the order Pholidota. The body is covered in hard overlapping scales and these animals find refuge in burrows, feeding only on termites and ants. In this study, the whole mtDNA of Temminckis ground pangolin was sequenced and the phylogenetic position of Pholidota determined within Eutheria, using whole mtDNA sequences from various representative species. The results indicate that the whole mtDNA of Temminckis ground pangolin is 16,559 bp long and shared some similarities with the whole mtDNA of the back-bellied tree pangolin and the Chinese pangolin. Phylogenetic analysis indicate that the order Pholidota is closely related and share a recent common ancestor with the order Carnivora rather than with the ant/insect eating order Xenarthra and the group Afrotheria. A time measured phylogeny of Pholidota estimated a split from Carnivora at around 87 mya, followed by a split of the African pangolins from their Asian counterparts such as the Chinese pangolin at around 47 mya. This suggests a Laurasian origin and convergent evolution of the Pholidota with respect to Xenarthra and Afrotheria.

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.

Mapping correlates of parasitism in wild South African vervet monkeys (Chlorocebus aethiops)

A growing focus of nonhuman primate conservation and management planning concerns factors affecting the dynamics of parasite infection and disease transmission. Here, we examine the effects of anthropogenic and environmental components of the landscape on the prevalence, richness, and species diversity of gastrointestinal parasites in wild-caught vervet monkeys (Chlorocebus aethiops) in South Africa. Nematodes of the genus Trichuris and the family Strongylidae and protists of the subclass Coccidia were present in 55.13% of sampled animals (n = 43). Parasitological, geographical, demographic and climatic correlates of infection were assessed in a geographical information systems (GIS) platform. The findings of this study suggest that parasitism in South African vervets may be better predicted by environmental factors than by degree of anthropogenic contact. This research represents one of the first surveys of parasitic infection in a wild monkey species in southern Africa.

Homogeneity at Nuclear Microsatellite Loci Masks Mitochondrial Haplotype Diversity in the Endangered Fanshell Pearlymussel (Cyprogenia stegaria)

We report on multiple patterns of differentiation and connectivity in the fanshell pearlymussel (Cyprogenia stegaria), based on different markers. Knowledge of genetic variation and genetic connectivity among remaining populations of this federally endangered species is needed to initiate implementation of the species recovery plan. We collected tissue samples from 96 specimens from the Green, Rolling Fork, and Licking Rivers, tributaries to the Ohio River, and the Clinch River, a tributary to the Tennessee River, providing broad coverage of the current distributional range of the species. Results from 7 nuclear DNA microsatellite markers suggested minimal population-level differentiation, whereas a mitochondrial DNA (mtDNA) marker (ND1) exhibited significant differentiation between C. stegaria in the Clinch River and the Ohio River populations. The ND1 data also confirm the existence of 2 distinct mtDNA lineages in the genus that transcends species boundaries. Further analyses suggest that the disproportionally strong signal from 2 very divergent ND1 lineages possibly masks finer-grained structure in the Ohio River population, based on one of the mtDNA lineages only. We recommend further sampling to confirm the absence of one lineage from the upper Clinch River drainage and suggest that provisional management guidelines should limit reciprocal exchanges among C. stegaria populations from the Clinch River and those in the Ohio River system.

Localized population divergence of vervet monkeys (Chlorocebus spp.) in South Africa: Evidence from mtDNA

OBJECTIVE Vervet monkeys are common in most tree-rich areas of South Africa, but their absence from grassland and semi-desert areas of the country suggest potentially restricted and mosaic local population patterns that may have relevance to local phenotype patterns and selection. A portion of the mitochondrial DNA control region was sequenced to study patterns of genetic differentiation. METHODS DNA was extracted, and mitochondrial DNA sequences were obtained from 101 vervet monkeys at 15 localities, which represent both an extensive (widely across the distribution range) and intensive (more than one troop at most of the localities) sampling strategy. Analyses utilized Arlequin 3.1, MEGA 6, BEAST v1.5.2, and Network V3.6.1. RESULTS The dataset contained 26 distinct haplotypes, with six populations fixed for single haplotypes. Pairwise P-distance among population pairs showed significant differentiation among most population pairs, but with nonsignificant differences among populations within some regions. Populations were grouped into three broad clusters in a maximum likelihood phylogenetic tree and a haplotype network. These clusters correspond to i) north-western, northern, and north-eastern parts of the distribution range as well as the northern coastal belt; ii) central areas of the country; and iii) southern part of the Indian Ocean coastal belt and adjacent inland areas. CONCLUSIONS Apparent patterns of genetic structure correspond to current and past distribution of suitable habitat, geographic barriers to gene flow, geographic distance, and female philopatry. However, further work on nuclear markers and other genomic data are necessary to confirm these results.

Scale samples from Temminck’s ground pangolin (Smutsia temminckii): a non-invasive source of DNA

Non-invasive sampling aims to obtain suitable samples without causing harm to the study organism, thus making it a more preferred sampling technique. Molecular methods have advanced in such a way that quality DNA can be obtained from less invasive mammal samples. Various PCR enhancing techniques have also been developed to aid in amplification of low quality DNA samples, to produce reliable results that can be used to monitor populations and species or for forensic applications. Temminck’s ground pangolin is one of the few mammals to be covered in scales. In this study, we attempt to identify the most appropriate DNA isolation and PCR methods as well as determine whether PCR additives could be used to improve isolation of DNA and downstream amplification of mitochondrial DNA, from scale samples collected from these pangolins. In this study, it was determined that several different methods are required in order to successfully amplify DNA, and a decision tree rather than a single method should be followed.