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In the last 300 thousand years, the genus

Evolutionary processes happen gradually over time and are, thus, considered time dependent. In addition, several evolutionary processes are either adaptations to local habitats or changing habitats, otherwise restricted thereby. Since evolutionary processes driving speciation take place within the landscape of environmental and temporal bounds, several published studies have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species. Correct calibration is critical towards attributing evolutionary adaptations and speciation both to the time and paleogeography that contributed to it. Data from more than 4000 studies and nearly 1,50,000 species are available from a central TimeTree resource and provide opportunities of retrieving divergence times, evolutionary timelines, and time trees in various formats for most vertebrates. These data greatly enhance the ability of researchers to investigate evolution. However, there is limited functionality when studying lists of species that require batch retrieval. To overcome this, a PYTHON package termed Python-Automated Retrieval of TimeTree data (PAReTT) was created to facilitate a biologist-friendly interaction with the TimeTree resource. Here, we illustrate the use of the package through three examples that includes the use of timeline data, time tree data, and divergence time data. Furthermore, PAReTT was previously used in a meta-analysis of candidate genes to illustrate the relationship between divergence times and candidate genes of migration. The PAReTT package is available for download from GitHub or as a pre-compiled Windows executable, with extensive documentation on the package available on GitHub wiki pages regarding dependencies, installation, and implementation of the various functions.

Evolutionary processes such as speciation happens gradually over time making such processes time-dependant. Many studies conducted over the past two decades have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species in most lineages of the tree of life, including fish, amphibians, reptiles, birds, and mammals. Data from more than 4 000 of these studies are now publicly available from a central time tree resource and provide opportunities of retrieving divergence times, evolutionary timelines, and time trees in various formats to enhance scientific investigations of evolution. There is, however, still limited functionality when studying large lists of species that would require the batch retrieval of data. To overcome this, a PYTHON package called Python Automated Retrieval of Time Tree data, abbreviated as PAReTT, was created to facilitate the interaction with the time tree resource when working with species lists. This package was recently used in a meta-analysis of candidate genes to study migration genetics and was able to successfully retrieve data for forty or more species to illustrate the relationship between divergence times and genetic data. The PAReTT package is freely available for download from GitHub to implement in PYTHON or as a pre-compiled Windows executable, with extensive documentation on the package available on the PAReTT GitHub wiki pages on dependencies, installation, and implementation of the various functions.

In the last 300 thousand years, the genus Chlorocebus expanded from equatorial Africa into the southernmost latitudes of the continent, where colder climate was a probable driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 ( UCP1 ) gene region—implicated in non-shivering thermogenesis (NST)—in 73 wild savannah monkeys from three taxa representing this southern expansion ( Chlorocebus pygerythrus hilgerti, Chlorocebus cynosuros and Chlorocebus pygerythrus pygerythrus ) ranging from Kenya to South Africa. We found 17 single nucleotide polymorphisms with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant linkage disequilibrium with each other. Phylogenetic generalized least-squares modelling with ecological covariates suggest that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance is demonstrated by a relatively isolated population in the southern coastal belt of South Africa. We suggest that sunbathing behaviours common to savannah monkeys, in combination with the strength of solar irradiance, may mediate adaptations to thermal stress via NST among savannah monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

The genus Chlorocebus is widely distributed throughout sub-Saharan Africa, and in the last 300 thousand years expanded from equatorial Africa into the southernmost latitudes of the continent. In these new environments, colder climate was a likely driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 (UCP1) gene region – implicated in non-shivering thermogenesis within brown/beige adipocytes – in 73 wild savanna monkeys from three taxa representing this southern expansion (C. pygerythrus hilgerti, C. cynosuros, C. p. pygerythrus) ranging from Kenya to South Africa. We found 17 SNPs with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant LD with each other. Phylogenetic generalized least squares modeling with ecological covariates suggest that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance appears to be driven by a population isolate in the southern coastal belt of South Africa. We suggest that sunbathing behaviors common to savanna monkeys, in combination with strength of solar irradiance, may mediate adaptations to thermal stress via non-shivering thermogenesis among savanna monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

The proximate composition of milk from fifteen free-ranging white rhinoceroses at different lactation stages is reported with detailed analysis of fatty acid composition and minerals. Lactose is the main component at 7.93 ± 0.53%, followed by 0.93 ± 0.19% protein, 1.76 ± 0.39% fat, 0.40 ± 0.18% ash, 0.05 ± 0.01% glucose, and 0.04 ± 0.02% non protein nitrogen The interindividual variation of all the components is high, showing no trend of change over lactation. The K and P content decreased over lactation. The fatty acid composition of rhinoceros milk is characteristic with a high saturated fatty acids content of 62%-84%, of which the medium chain fatty acids form the major portion. The C10:0, C12:0, C16:0, and C18:1c9 are the major fatty acids in the milk fat. The results are compared with the two other Perissodactylae families, the Equidae and Tapiridae. Differences in gross composition are small, but the milk of the Rhinocerotidae have the lowest gross energy, while the milk fats consist of the highest amounts of saturated fatty acids, while the low levels of C16:1c9 and C18:1c9 indicate the lowest mammary Δ9-desaturase activity.

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.

The linebreeding of southern African antelope species, involving selection for specific coat colour phenotypes, is a wide-spread practice in the South African game farming industry. Concerns have been voiced with regards to the genetic status of these line-bred colour variants, due to the high risk of inbreeding. The springbok (Antidorcas marsupialis) is one of the most well-known examples of such linebreeding. Numerous colour variants have been observed, with the most notable the black, copper and white colour phenotypes. To our knowledge, no research has been performed on the genetic basis of these springbok colour variants. In this study, we aimed to 1) assess the level of genetic variation within and among the common, black, copper and white colour variants of springbok, and 2) investigate the possible genetic mechanisms involved in the coat colour of these variants. Portions of the mtDNA control region (CR) and two immune-linked Toll-like receptor (TLR4 and TLR7) genes were sequenced for the genetic diversity estimates. A 50 K Bovine SNP chip was also screened to assess the level of genetic diversity of a subset of samples. The complete melanocortin 1 receptor (MC1R) gene was targeted for the second aim. Comparable levels of diversity were identified across specimens. Pairwise genetic diversity analysis of the SNP data identified the white springbok as a unique group within springbok, with Bayesian clustering analysis supporting this observation. A possible reason for this clustering pattern was linked to the historical occurrence of white springbok in nature. The level of genetic diversity observed for each colour variant was associated with 1) the large historical and extant population sizes of springbok providing a deep genetic pool and/or 2) the management practices of the managers/farmers that are aimed at preventing or minimizing inbreeding and loss of genetic diversity. The MC1R assessment identified a nonsynonymous SNP (c. G902A) unique to white springbok (homozygous AA). A 24 bp deletion was observed in black, copper and king springbok colour variants. This deletion was complete for ∼21 % of black springbok. The heterozygous variant was observed in ∼88 % of copper springbok and ∼5 % of black springbok. This would suggest that additional genetic factors are involved in coat colour determination (due to the incomplete association of the 24 bp deletion). Further research is therefore needed to identify the other possible genetic factors involved.

BackgroundThe microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa.ResultsWe characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated withLactobacillusandEscherichia/ShigellaandHelicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples.ConclusionsThe vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus.

Temminck's ground pangolin (

Anthropogenic landscapes are rapidly replacing natural nonhuman primate habitats. Yet, the access to anthropogenic resources on primate biology, health, and fitness remain poorly studied. Given their ubiquity across a range of human impacted landscapes, from cities to national parks, savanna monkeys (Chlorocebusspp.) provide an excellent study system in which to test these effects. We compared body condition and reproductive maturation in vervets (Chlorocebus pygerythrus) inhabiting a private farm in !Gariep Dam, with ample access to anthropogenic foods, and wild-foraging vervets in Soetdoring Nature Reserve, South Africa. Overall, vervets in !Gariep show significantly thicker skin folds, and higher BMI and body mass, than those in Soetdoring, suggesting increased fat deposition. Males in !Gariep have larger relative testis volumes at peri-pubescent ages compared to those in Soetdoring, suggesting early reproductive maturation associated with age-specific increases in body mass. Females from !Gariep showed evidence of an earlier onset of reproduction than those in Soetdoring, based on parity status as assessed by nipple length and evidence of lactation. Parity status at sub-adult dental ages was also strongly associated with body mass. These results are consistent with a positive effect of anthropogenic food-enhancement on body fat deposition, potentially linked to an earlier onset of reproductive maturation. Further investigation into primate responses to cultivated resources will inform our understanding of the broader effects of food enhancement on developmental plasticity.

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.

Additional file 2 : Supplementary Table 1. Characteristics of microbial samples and individuals used in the studies. Supplementary Table 2. Relative abundances at the phylum and at the genus level within the bacterial communities in four sample type. Showing taxa with > 1% relative abundance in at least one sample type. Supplementary Table 3. Relative abundances of predicted metagenome categorized by function across fecal enterotypes. Only showing genes with significant differential abundance between the enterotypes and at a relative abundance > 0.1%. Data is expressed as relative abundance (%). Supplementary Table 4. Vaginal pH.

Additional file 3 Additional Data 1.

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has devastated health infrastructure around the world. Both ACE2 (an entry receptor) and TMPRSS2 (used by the virus for spike protein priming) are key proteins to SARS-CoV-2 cell entry, enabling progression to COVID-19 in humans. Comparative genomic research into critical ACE2 binding sites, associated with the spike receptor binding domain, has suggested that Old World primates may also be susceptible to disease from SARS-CoV-2 infection. Savanna monkeys (Chlorocebus spp.) are a widespread non-human primate with well-established potential as a bi-directional zoonotic/anthroponotic agent due to high levels of human interaction throughout their range in sub-Saharan Africa and the Caribbean. To characterize potential functional variation in savanna monkey ACE2 and TMPRSS2, we inspected recently published genomic data from 245 savanna monkeys, including 163 wild monkeys from Africa and the Caribbean and 82 captive monkeys from the Vervet Research Colony (VRC). We found several missense variants. One missense variant in ACE2 (X:14,077,550; Asp30Gly), common in Ch. sabaeus, causes a change in amino acid residue that has been inferred to reduce binding efficiency of SARS-CoV-2, suggesting potentially reduced susceptibility. The remaining populations appear as susceptible as humans, based on these criteria for receptor usage. All missense variants observed in wild Ch. sabaeus populations are also present in the VRC, along with two splice acceptor variants (at X:14,065,076) not observed in the wild sample that are potentially disruptive to ACE2 function. The presence of these variants in the VRC suggests a promising model for SARS-CoV-2 infection and vaccine and therapy development. In keeping with a One Health approach, characterizing actual susceptibility and potential for bi-directional zoonotic/anthroponotic transfer in savanna monkey populations may be an important consideration for controlling COVID-19 epidemics in communities with frequent human/non-human primate interactions that, in many cases, may have limited health infrastructure.

Additional file 1 : Supplementary Figure 1. Geographic origins of study animals. Supplementary Figure 2. Maps of sampling sites. The maps were generated using GPS Visualizer [90] with Google Hybrid Map as a background using Map data © 2020 AfriGIS (Pty) Ltd Imagery© 2020 NASA, TerraMetrix. Supplementary Figure 3. Vaginal microbiome in South African vervets in our study compared to Caribbean-origin vervets and other NHPs based on the Yildrim et al. 2014 data [35]. (A) Average community structure in South African vervets (by SIV status), Caribbean origin vervets and other NHPs [35]. Species demarcation: African vervets (SIV Pos and SIV Neg), free-ranging Caribbean vervets (Vw), captive Caribbean-origin vervets (Vc), mangabeys (M), red colobus (Rc), yellow baboon (Bab), olive baboon (Bc), chimpanzee (Chimp), humans (H), lemurs (L), black howler (Bh). (B) Microbial community structure per individual in South African vervets, (C) Community structure per individual in Caribbean-origin vervets [35]. Supplementary Figure 4. A) PCoA of beta-diversity colored by vaginal pH. Acidic pH is a pH 7. B) Chao1 and Shannon Index of vaginal samples pH. C) Genus taxonomic plots of vaginal samples by pH. D) Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples. Supplementary Figure 5. Geography-related microbiome. (A) PCoA for each body site clustering by province. (B) PCoA for each body site clustering by geographic site. (C) Community structure by province. (D) Community structure by geographic site. Differentially abundant taxa between KZN and FS in (E) rectal and (F) fecal microbiome. Supplementary 6. Genus taxonomic plots of D) fecal, E) rectal, F) penile, and G) vaginal samples by the different biomes. Supplementary Figure 7. PCoA of beta-diversity, Chao1 index and Shannon index by different biomes for (A-C) all samples, (D-F) fecal samples, (G-I) rectal samples, (J-L) penile samples, and (M-O) vaginal samples. Supplementary Figure 8. PCoA plots of beta-diversity and alpha diversity metrics of climate variables. PCoA plots of annual mean temperatures in tertiles (Mean Temp Tertile) and minimum temperature of the coldest month in tertiles (Min Temp Tertile) for all samples (A,B), fecal samples (C,D), rectal samples (E,F), penile samples (G,H), and vaginal samples (I,J). Chao1 and shannon index did not differ by any sample type except for Mean Temp Tertile in penile samples (K,L). *Represents p-value 0.5% are shown. Supplementary Figure 16. Comparison of rectal microbiome community structure between vervets from Caribbean populations and Caribbean-origin captive vervets on Western-style diet (based on data from Amato et al. 2015 [34]) and SIV negative and SIV positive vervets from South Africa.

The blue wildebeest (Connochaetes taurinus) is distributed throughout southern and east Africa while the black wildebeest (Connochaetes gnou) is endemic to South Africa and was driven to near extinction in the early 1900s due to hunting pressure and disease outbreaks. Extensive translocation of both species throughout South Africa is threatening the genetic integrity of blue and black wildebeest. To effectively manage these species, genetic tools that can be used to detect hybrid individuals, identify genetically unique subpopulations and determine the levels of genetic diversity are required. In this study, 11 microsatellite markers were developed for wildebeest through next-generation sequencing. The microsatellite loci displayed 2.00–4.14 alleles, unbiased heterozygosity values ranged from 0.32 to 0.60 and observed heterozygosity values ranged from 0.26 to 0.52. The comparatively high level of polymorphism observed in the microsatellite markers indicates that these markers can contribute significantly to our knowledge of population genetic structure, relatedness, genetic diversity and hybridization in these species.

We report the characterization of 23 single nucleotide polymorphism (SNP) markers for the blue (Connochaetes taurinus) and black wildebeest (C. gnou) based on a targeted gene approach. The polymorphisms of these SNP loci were assessed using a captive population of blue and black wildebeest comprising 30 individuals. The minor allele frequency per SNP ranged from 0.000 to 0.458 and the observed and expected heterozygosity ranged from 0.000 to 0.636 and from 0.000 to 0.496, respectively. An understanding of genetic population structure is required to effectively formulate strategies for conservation and/or management. These SNP markers could be employed to provide estimates of parameters such as population structure, relatedness, hybridisation and current and historical gene flow.

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.

The aim of this study was to gain molecular insights into patterns of genetic diversity in indigenous and introduced land snails in Cameroon. These species, Archachatina marginata and Achatina fulica, form an important source of protein in Cameroon, but widespread utilization may possibly impact natural patterns of genetic diversity of the indigenous species, while the introduced species may display signs of genetic drift. The evolutionary relationship between the indigenous and introduced species was also studied. Specimens were collected from seven sites in Cameroon. Genetic analyses using COI mitochondrial DNA data suggest that gene flow among the Ar. marginata populations screened follows a model of isolation by distance, and genetic diversity estimates for this species did not provide support for the hypothesis of loss of genetic diversity in areas of intense harvesting. Diversity in the introduced species was much lower, which is likely the signature of an introduction involving limited numbers.

The impala (Aepyceros melampus ssp.) is a widespread antelope species occurring in sub-Saharan Africa. The two recognized subspecies have non-overlapping distribution ranges, with no known natural mixture of these subspecies until human interference. A number of common impala individuals (A. m. melampus) displaying phenotypic characteristics commonly observed in the black-faced impala (A. m. petersi), namely black facial markings, were seen on a farm in the Limpopo Province, South Africa. This farm falls outside the natural distribution range of A. m. petersi. We therefore aimed to identify the taxonomic placement of these individuals (i.e. A. m. melampus or A. m. petersi) through phylogenetic and molecular clock analyses using D-loop and cytochrome subunit b sequence data. Our results showed that these black-nosed impala from Limpopo are in fact A. m. melampus individuals. The existence of the black-nose phenotype in common impala could be more widespread than previously estimated. The occurrence of introgression between the two subspecies in this region could, however, not be fully excluded, and can only be fully assessed through the use of nuclear DNA analysis.

Translocation of animals in fragmented habitats is an important means of dispersal and gene flow, however, the movement of animals has led to the spread of various diseases globally and wildlife are often the reservoirs of these diseases. Currently, Cape mountain zebra are translocated within South Africa as a management method for augmentation of isolated and fragmented populations. The movement of pathogens due to translocations in local regions have gone largely unchecked, particularly where there may still be isolated regions that can be negatively affected. Equine piroplasmosis is a tick-borne disease caused by Theilaria equi and/or Babesia caballi reported to occur in equids (Bhoora et al., 2010; Zweygarth et al., 2002). Here, the presence of T. equi and B. caballi was detected in 137 clinically healthy Cape mountain zebra from three South African reserves, Mountain Zebra National Park (MZNP), De Hoop Nature Reserve (DHNR) and Karoo National Park (KNP) using the multiplex EP real-time PCR (qPCR) assay. We observed 100% prevalence for T. equi and identified only one animal from MZNP with B. caballi. These results affirm that precautions should be taken prior to founding new populations of Cape mountain zebra and that potential farms and properties adjacent to prospective reserves should be screened for the presence of the organisms in order to mitigate risks of infection to domestic animals. Keywords: Cape mountain zebra, Equus zebra zebra, Translocation, Piroplasm, Babesia caballi, Theilaria equi

The Cape mountain zebra (Equus zebra zebra) is a subspecies of mountain zebra endemic to South Africa. The Cape mountain zebra experienced near extinction in the early 1900's and their numbers have since recovered to more than 4,800 individuals. However, there are still threats to their long-term persistence. A previous study reported that Cape mountain zebra had low genetic diversity in three relict populations and that urgent conservation management actions were needed to mitigate the risk of further loss. As these suggestions went largely unheeded, we undertook the present study, fifteen years later to determine the impact of management on genetic diversity in three key populations. Our results show a substantial loss of heterozygosity across the Cape mountain zebra populations studied. The most severe losses occurred at De Hoop Nature Reserve where expected heterozygosity reduced by 22.85% from 0.385 to 0.297. This is alarming, as the De Hoop Nature Reserve was previously identified as the most genetically diverse population owing to its founders originating from two of the three remaining relict stocks. Furthermore, we observed a complete loss of multiple private alleles from all populations, and a related reduction in genetic structure across the subspecies. These losses could lead to inbreeding depression and reduce the evolutionary potential of the Cape mountain zebra. We recommend immediate implementation of evidence-based genetic management and monitoring to prevent further losses, which could jeopardise the long term survival of Cape mountain zebra, especially in the face of habitat and climate change and emerging diseases.

The bluewildebeest (

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.

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds ...

Toll-like receptors (TLR) are a family of proteins that signal activation of the innate immune response through the recognition of a variety of pathogen molecular compounds. Here, we characterized the complete TLR9 gene in Cape mountain zebra (Equus zebra zebra) from three populations in South Africa and compared sequences to a variety of horse and donkey breeds. Overall, we identified six single nucleotide polymorpHisms (SNPs). A single SNP (G586S) was non-synonymous, whereas the remaining SNPs were synonymous. The G586S alteration was detected in Cape mountain zebra populations with varying frequency. In addition, adaptive diversity was found to be discordant with variation based on neutral markers. The mutation is unique to the Cape mountain zebra when compared to other equid species. The structure of TLR9 is relatively conserved and the resulting amino acid substitution was found to have minimal interaction with active sites in the protein. Future studies can explore the effects of this potentially functional mutation which will contribute to our understanding of genetic diversity within adaptive sites of the Cape mountain zebra genome.

Male reproductive strategies have been well studied in primate species where the ability of males to monopolize reproductive access is high. Less is known about species where males cannot monopolize mating access. Vervet monkeys (Chlorocebus pygerythrus) are interesting in this regard as female codominance reduces the potential for male monopolization. Under this condition, we assessed whether male dominance rank still influences male mating and reproductive success, by assigning paternities to infants in a population of wild vervets in the Eastern Cape, South Africa. To determine paternity, we established microsatellite markers from noninvasive fecal samples via cross-species amplification. In addition, we evaluated male mating and reproductive success for 3 groups over 4 mating seasons. We identified 21 highly polymorphic microsatellites (number of alleles = 7.5 ± 3.1 [mean ± SD], observed heterozygosity = 0.691 ± 0.138 [mean ± SD]) and assigned paternity to 94 of 97 sampled infants (96.9%) with high confidence. Matings pooled over 4 seasons were significantly skewed across 3 groups, although skew indices were low (B index = 0.023-0.030) and mating success did not correlate with male dominance. Paternities pooled over 4 seasons were not consistently significantly skewed (B index = 0.005-0.062), with high-ranking males siring more offspring than subordinates only in some seasons. We detected 6 cases of extra-group paternity (6.4%) and 4 cases of natal breeding (4.3%). Our results suggest that alternative reproductive strategies besides priority of access for dominant males are likely to affect paternity success, warranting further investigation into the determinants of paternity among species with limited male monopolization potential.

BCS 0938969 - NSF; R01RR0163009 - NIH; The Fulbright Foundation; The University of Limpopo; The University of the Free State, South Africa

Sexual traits vary tremendously in static allometry. This variation may be explained in part by body size-related differences in the strength of selection. We tested this hypothesis with in two populations of vervet monkeys, using estimates of the level of condition dependence for different morphological traits as a proxy for body size-related variation in the strength of selection. In support of the hypothesis, we found that the steepness of allometric slopes increased with the level of condition dependence. One trait of particular interest, the penis, had shallow allometric slopes and low levels of condition dependence, in agreement with one of the most consistent patterns yet detected in the study of allometry, that of genitalia exhibitting shallow allometries.

OBJECTIVES:Direct comparative work in morphology and growth on widely dispersed wild primate taxa is rarely accomplished, yet critical to understanding ecogeographic variation, plastic local variation in response to human impacts, and variation in patterns of growth and sexual dimorphism. We investigated population variation in morphology and growth in response to geographic variables (i.e., latitude, altitude), climatic variables (i.e., temperature and rainfall), and human impacts in the vervet monkey (Chlorocebus spp.). METHODS:We trapped over 1,600 wild vervets from across Sub-Saharan Africa and the Caribbean, and compared measurements of body mass, body length, and relative thigh, leg, and foot length in four well-represented geographic samples: Ethiopia, Kenya, South Africa, and St. Kitts & Nevis. RESULTS:We found significant variation in body mass and length consistent with Bergmann's Rule in adult females, and in adult males when excluding the St. Kitts & Nevis population, which was more sexually dimorphic. Contrary to Rensch's Rule, although the South African population had the largest average body size, it was the least dimorphic. There was significant, although very small, variation in all limb segments in support for Allen's Rule. Females in high human impact areas were heavier than those with moderate exposures, while those in low human impact areas were lighter; human impacts had no effect on males. CONCLUSIONS:Vervet monkeys appear to have adapted to local climate as predicted by Bergmann's and, less consistently, Allen's Rule, while also responding in predicted ways to human impacts. To better understand deviations from predicted patterns will require further comparative work in vervets.

The Afrikaner is an indigenous South African breed of "Sanga" type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.

The information in this submission is supplemental data for the paper by Woogeng et al entitled: Current patterns of genetic diversity in indigenous and introduced species of land snails in Cameroon reflect isolation by distance, limited founder size and known evolutionary relationships

Bayesian mitogenome phylogenetic tree of all available pangolin mitogenomes. Posterior probabilities are indicated on the respective branches. A. jubatus was selected as an outgroup as pangolins are more closely related to the order Carnivora. Asterisks indicate the misidentified mitogenomes. Figure S2. Principal Component Analysis (PCA) of Relative Synonymous Codon Usage values (RSCU) for six pangolin species. Three distinct genera is present (Manis, Phataginus and Smutsia) in the (a) CoxII; (b) NadI, (c) NadIII genes. The two sub-families (Smutsiinae and Maninae) are distinguished in the (d) AtpVIII; (e) NadIV; (f) NadVI genes. Table S1. List of nucleotide percentages and its 3rd codon position percentage (%) (PDF 426 kb)

The information in this submission is supplemental data for the paper by Woogeng et al entitled: Current patterns of genetic diversity in indigenous and introduced species of land snails in Cameroon reflect isolation by distance, limited founder size and known evolutionary relationships

The information in this submission is supplemental data for the paper by Woogeng et al entitled: Current patterns of genetic diversity in indigenous and introduced species of land snails in Cameroon reflect isolation by distance, limited founder size and known evolutionary relationships