Gastrointestinal nematodes in two galliform birds from South Africa: patterns associated with host sex and age.

Parasite ecology has recently focused on elucidating patterns and processes that shape helminth communities in avian hosts. However, helminths parasitizing gamebirds are still poorly understood. Here we describe the gastrointestinal nematode fauna of Swainson's spurfowl, Pternistis swainsonii (Phasianidae) and helmeted guineafowl, Numida meleagris (Numididae), collected at three and four localities, respectively, in South Africa and analyze the prevalence, mean abundance and diversity of their helminth communities. Eleven nematode species were collected from spurfowl, which had a mean number of nematode species per host of 3.01 ± 0.18, whereas guineafowl harboured 15 nematode species, with a mean number of nematode species per host of 3.93 ± 0.12. Focusing on the most prevalent species, we also asked if host sex and/or age were associated with infracommunity structure with regard to nematode counts and species richness, as well as the species and taxonomic composition of infracommunities. While pooling data of nematode species masked the influence of host characteristics on helminth communities, analysis of individual nematode species revealed a number of patterns. In particular, adult female bias was seen in Tetrameres swainsonii in spurfowl and in Allodapa dentigera and Gongylonema congolense in guineafowl; Acuaria gruveli reached higher numbers in adult spurfowl than in juveniles, and helminth infracommunities in juvenile male guineafowl were more species rich than those in adult males. Combined, our results suggest that helminth communities of spurfowl and guineafowl are associated with a complex interplay of numerous factors, including host characteristics, parasite traits and environmental conditions.

Hot days are associated with short-term adrenocortical responses in a southern African arid-zone passerine bird.

Relatively little effort has been directed towards elucidating the role of physiological stress pathways in mediating avian responses to global heating. For free-ranging southern pied babblers, Turdoides bicolor, daily maximum air temperatures (Tmax) between ∼35 and ∼40°C result in reduced foraging efficiency, loss of body mass and compromised breeding success. We tested the hypothesis that very hot days are experienced as stressors by quantifying relationships between Tmax and faecal glucocorticoid metabolite (fGCM) levels in naturally excreted droppings. On days when Tmax<38°C, fGCM levels were independent of Tmax (mean±s.d. 140.25±56.92 ng g-1 dry mass). At Tmax>38°C, however, fGCM levels increased linearly with Tmax and averaged 190.79±70.13 ng g-1 dry mass. The effects of Tmax on fGCM levels did not carry over to the following morning, suggesting that very hot days are experienced as acute stressors.

Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA.

The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations.

Isolation and characterization of 30 STRs in Temminck's ground pangolin (Smutsia temminckii) and potential for cross amplification in other African species.

Temminck's ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck's ground pangolin using next-generation sequencing. The markers were also optimized for crossamplification in other African species. All the markers amplified successfully in Temminck's ground pangolin with allelic polymorphisms observed in 87% of the markers in giant pangolin (S. gigantea) whereas 60% of the markers were amplified polymorphic loci in both whitebellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). Analysis of diversity estimates showed moderate levels of variability in Temminck's ground pangolin (Na = 5; Ho = 0.559), giant pangolin (Na = 4.909; Ho = 0.514) and white-bellied pangolin (Na= 2.686; Ho = 0.541) with lower values being observed in black-bellied pangolin (Na = 3; Ho = 0.242). This study provides data of the first available STR markers which was amplified in all four African pangolin species that can now be used in conservation genetic and evolutionary aspects of population histories.

Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.

Canine parvovirus detected from a serval (Leptailurus serval) in South Africa.

Canine parvovirus first emerged in domestic dogs (Canis familiaris), most likely as a variant of the feline panleucopaenia virus. Relatively recently, canine parvovirus-2a and canine parvovirus-2b infections have been identified in both symptomatic and asymptomatic domestic cats, while canine parvovirus infections have also been demonstrated in wild felids. This report documents the first known case of canine parvovirus-2b detected in unvaccinated serval (Leptailurus serval) from South Africa. The serval presented with clinical signs of vomiting, anorexia and diarrhoea that responded to symptomatic treatment. Two weeks later, severe leucopaenia, thrombocytopenia and death occurred. Typical enteric histological lesions of parvovirus infection were not observed on histopathological examination of the small intestine; however, histological lesions consistent with septicaemia were present. Canine parvovirus was detected in formalin-fixed paraffin-embedded small intestine using polymerase chain reaction. Phylogenetic analysis of the sequence of the canine parvovirus viral capsid protein gene showed similarities between the sample from the serval and canine parvovirus-2b isolates from domestic dogs in Argentina and South Africa. A case of canine parvovirus-2b in a domestic dog from South Africa in 2012 that fell within the same clade as the serval sample appears distantly related because of the long branch length. The significance of these findings is explored. More extensive surveys of canine parvovirus in domestic and wild felids and canids are needed to understand the epidemiology of canine parvovirus in non-domestic felids in South Africa.

Genetic assessment of an isolated endemic Samango monkey (Cercopithecus albogularis labiatus) population in the Amathole Mountains, Eastern Cape Province, South Africa.

The endemic Samango monkey subspecies (Cercopithecus albogularis labiatus) inhabits small discontinuous Afromontane forest patches in the Eastern Cape, KwaZulu-Natal midlands and southern Mpumalanga Provinces in South Africa. The subspecies is affected by restricted migration between forest patches which may impact on gene flow resulting in inbreeding and possible localized extinction. Current consensus, based on habitat quality, is that C. a. labiatus can be considered as endangered as the small forest patches they inhabit may not be large enough to sustain them. The aim of this study was to conduct a molecular genetic investigation to determine if the observed isolation has affected the genetic variability of the subspecies. A total of 65 Samango monkeys (including juveniles, subadults and adults) were sampled from two localities within the Hogsback area in the Amathole Mountains. Nuclear and mitochondrial DNA variation was assessed using 17 microsatellite markers and by sequencing the hypervariable 1 region (HVR1). Microsatellite data generated was used to determine population structure, genetic diversity and the extent of inbreeding. Sequences of the HVR1 were used to infer individual origins, haplotype sharing and haplotype diversity. No negative genetic factors associated with isolation such as inbreeding were detected in the two groups and gene flow between groups can be regarded as fairly high primarily as a result of male migration. This was in contrast to the low nuclear genetic diversity observed (H o = 0.45). A further reduction in heterozygosity may lead to inbreeding and reduced offspring fitness. Translocations and establishment of habitat corridors between forest patches are some of the recommendations that have emerged from this study which will increase long-term population viability of the subspecies.

Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae.

BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species. CONCLUSIONS: The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.

Forensic application of DNA barcoding for identification of illegally traded African pangolin scales.

The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048-0.188) among genes. However, only three of four African species (Phataginus tricuspis, Phataginus tetradactyla, and Smutsia gigantea, originating from West and Central Africa) and one of four Asian species (Manis javanica from Southeast Asia) were identified among scales. Although the assignment of unknown scales to specific species was reliable, additional genetic tools and representative reference material are required to determine geographic origins of confiscated pangolin specimens.

Mercury concentrations in eggshells of the Southern Ground-Hornbill (Bucorvus leadbeateri) and Wattled Crane (Bugeranus carunculatus) in South Africa.

In this study, wild hatched eggshells were collected from the nests of threatened Wattled Crane and South Ground-Hornbill in an attempt to determine their total Hg concentrations. A total of fourteen eggshell samples from both bird species were collected from different study areas in the Mpumlanga and KwaZulu-Natal Provinces of South Africa. The eggshells were acid digested under reflux and their total Hg concentrations were determined using cold-vapour atomic absorption spectrophotometry (CV-AAS). The observed total Hg levels for the South Ground-Hornbill samples ranged from 1.31 to 8.88 µg g(-1) dry weight (dw), except for one outlier which had an elevated 75.0 µg g(-1) dw. The levels obtained for the Wattled Crane samples were relatively high and these ranged from 14.84 to 36.37 µg g(-1) dw. Generally, all the measured total Hg concentrations for the Wattled Crane samples exceeded the estimated total Hg levels derived for eggshell which were known to cause adverse reproductive effects in avian species from previous studies. Based on these findings, it is, therefore, possible that the exposure of these birds to elevated Hg may have contributed to their present population decline.

Knowledge and uses of African pangolins as a source of traditional medicine in Ghana.

Traditional medicine has been practised in Ghana for centuries with the majority of Ghanaians still patronising the services of traditional healers. Throughout Africa a large number of people use pangolins as a source of traditional medicine, however, there is a dearth of information on the use of animals in folk medicine in Ghana, in particular the use of pangolins. The aim of this study was to determine the prevalent use of pangolins and the level of knowledge of pangolin use among traditional healers in Ghana for the treatment of human ailments. Data was gathered from 48 traditional healers using semi-structured interviews on the traditional medicinal use of pangolin body parts in the Kumasi metropolis of Ghana. The cultural importance index, relative frequency of citation, informant agreement ratio and use agreement values were calculated to ascertain the most culturally important pangolin body part as well as the level of knowledge dissemination among traditional healers with regards pangolin body parts. Our study revealed that 13 body parts of pangolins are used to treat various medicinal ailments. Pangolin scales and bones were the most prevalent prescribed body parts and indicated the highest cultural significance among traditional healing practices primarily for the treatment of spiritual protection, rheumatism, financial rituals and convulsions. Despite being classified under Schedule 1 of Ghana's Wildlife Conservation Act of 1971 (LI 685), that prohibits anyone from hunting or being in possession of a pangolin, our results indicated that the use of pangolins for traditional medicinal purposes is widespread among traditional healers in Ghana. A study on the population status and ecology of the three species of African pangolins occurring in Ghana is urgently required in order to determine the impact this harvest for traditional medical purposes has on their respective populations as current levels appear to be unmonitored and unsustainable.

Polybrominated diphenyl ethers (PBDEs) in eggshells of the Southern Ground-Hornbill (Bucorvus leadbeateri) and Wattled Crane (Bugeranus carunculatus) in South Africa.

This study was undertaken to assess the levels of eight PBDE congeners, namely: PBDE-17, 47, 100, 99, 154, 153, 183 and 209 in eggshells of Southern Ground-Hornbill (SGH) Bucorvus leadbeateri and Wattled Crane (WC) Bugeranus carunculatus obtained from different nesting sites within the eastern savanna of Limpopo Province and the midlands of KwaZulu-Natal, respectively. Analyses were performed using gas chromatography­mass spectrometry employing the electron impact ionization technique. The results obtained indicated that the lower brominated congeners were predominant in both species. The total PBDEs ranged between not detected (ND) to 264 µg g−1 lipid weight and 5.98­7146 µg g−1 lipid weight in the SGH and WC samples, respectively. More so, the mean recoveries of the 13C-labelled surrogate standards ranged between 40% (PBDE-100) and 136% (PBDE-99). The potential hazards to these birds via PBDEs exposure were evaluated by determining the hazard quotients (HQs) by employing the established Lowest Observed Effect Level (LOEL) values associated with impaired pipping and hatching success as well as that associated with impaired reproduction. HQs values varying from 0.58 to 0.94 and 27.71 to 45.27, respectively were obtained for SGH and WC species. This implies that the SGH populations are exposed to low to moderate hazards, while the WC populations are susceptible to high hazards. Considering the potential threats posed by PBDEs, particularly to the WC species, it is likely that exposure to the current environmental levels of PBDEs by these birds may contribute to their reduced breeding success and declining population trends.

Ethnomedicinal use of African pangolins by traditional medical practitioners in Sierra Leone.

BACKGROUND: Pangolins (Manidae) have long been used for traditional medicinal purposes in most parts of sub-Saharan Africa. However, very little is known about the extent of this use, the body parts that are used and the ailments these practices are attempting to cure or alleviate. Pangolin body parts are used extensively and frequently by traditional medical practitioners in Sierra Leone. METHODS: A total of 63 traditional medical practitioners consented and were interviewed using semi-structured questionnaires on the traditional medicinal use of pangolin body parts. The use value, informant agreement ratio and use agreement value for each pangolin part was calculated to ascertain the most sought after body part, the level of knowledge dissemination among traditional medical practitioners about body parts and the most culturally significant body part. RESULTS: It was found that 22 pangolin parts are used to treat various ailments and conditions under 17 international categories of diseases. The highest use value was recorded for scales while eyes had the highest level of consensus among the traditional medical practitioners. The highest use value and informant agreement ratio for scales were recorded for spiritual ailments. Scales were the most culturally significant body part according to the use agreement value. CONCLUSION: This study indicates a high importance value for pangolins as part of these communities' spiritual, cultural and medicinal beliefs. However, the numbers of individuals harvested from the wild remains unknown and unregulated even though pangolins have been listed under Schedule 2 of the Wildlife Conservation Act, 1972, of Sierra Leone, which prohibits any person from hunting or being in possession of pangolins. It is likely that this unregulated harvesting and poaching of this threatened species, for medicinal purposes, is unsustainable and there is an urgent need to determine pangolin population abundance within this region to ensure their sustainable harvesting for cultural use and conservation.

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

Temmincki's 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 Temmincki's 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 Temmincki's 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.