Sandi Willows-Munro

The Cape Parrot Poicephalus robustus and the Grey‐headed Parrot P. fuscicollis suahelicus have recently been recognized as separate species, each with unique habitat requirements; the former a forest species endemic to South Africa, and the latter a woodland and savannah species with a wider distribution in Africa. We tested the hypothesis that stable isotope ratios can be used to identify dietary partitioning in the diet of these two species. We analysed carbon, nitrogen and hydrogen stable isotopes in feathers (three feathers each from seven individuals and one feather from five individuals) from these species at three sites along a north–south gradient; two sites c. 90 km apart where the two species each occur, and a site c. 685 km further south where the Cape Parrot occurs. Carbon and nitrogen isotope values of feathers were similar for the two geographically separated Cape Parrot populations, which were significantly different to values for Grey‐headed Parrot. Low variation within individuals, within each population, and within species reflected unique biome associations for each species. Hydrogen isotope values, on the other hand, reflected location along a north–south hydrogen isotope gradient. Our results support the hypothesis that stable light isotopes are a valuable tool in providing insight into the specialist and biome associated diets of two closely related parrot species.

DNA metabarcoding of zooplankton samples is well suited to surveys of marine pelagic ecosystems; however, consistent amplification across zooplankton groups cannot be assumed when using “universal” miniCOI primers. Under-representation of some groups may result from primer bias or inadequate coverage in barcode reference libraries. We designed taxon-specific mini-barcode primers to improve the representation of copepods, euphausiids, chaetognaths, and hydrozoans in metabarcoding outputs of mixed zooplankton samples from the Southwest (SW) Indian Ocean. In silico analyses of downloaded sequences per group identified the most informative mini-barcode region, and barcode gap analyses confirmed that the selected regions could distinguish among species within each group. In vitro analyses of DNA extracts from individual specimens per group showed that the new mini-barcode primers outperformed the standard and universal miniCOI primers by consistently recovering higher Phred quality scores. Metabarcoding of four in situ mixed zooplankton samples collected with plankton tow nets and processed with a combination of taxon-specific and universal primers identified 220 species. Use of the primer cocktails increased the proportionate representation of the target groups by three- to five-fold compared to a previous study. Read counts were dominated by copepods and euphausiids, implying that they had the highest relative biomass in samples. We conclude that a combination of universal and taxon-specific primers in metabarcoding assays will achieve a more comprehensive assessment of biodiversity by enhancing species richness estimates across different groups.

African lovebirds are popular pet parrots commonly hybridized by breeders leading to genetic admixture. Trade escapees and land use change have now led lovebirds to genetically admix in the wild. Sampling origin is therefore of utmost importance when deriving genetic data from lovebird species to reconstruct phylogeny or historical demographic events as the inclusion of taxa of hybrid origin is a source of spurious results. Here we present complete genomes of all nine currently recognized lovebird species. Each species is represented by an archival geo-referenced individual collected within their natural range.

The global utilisation of Oreochromis spp. in freshwater aquaculture extends to South Africa. Here the native Mozambique tilapia (Oreochromis mossambicus) has been proposed as a priority species for regional aquaculture projects, although it is still not preferred over the non-native O. niloticus. There is limited understanding of the genetic diversity, and genetic differentiation of farmed O. mossambicus in South Africa. Using a suite of 14 microsatellite markers, the present study aimed to determine the origin and genetic diversity of four farmed O. mossambicus populations in KwaZulu-Natal and Mpumalanga provinces. Wild O. mossambicus from rivers surrounding the farms were included to trace the origin of farmed populations. Results revealed lower genetic diversity in farmed populations compared to wild populations. In particular, the University of Zululand population exhibited lower genetic diversity compared to the rest of the farmed populations. While most farmed populations closely resembled their local wild counterparts, the uMphafa ponds exhibited distinct genetic characteristics. Notably, some individuals from uMphafa shared genetic affinities with those from the Thukela River, suggesting that the Thukela River could be the source of this farmed population, or that farmed fish may have been introduced or escaped into the river. The study suggests that select farmed populations may have the potential for use in breeding and broodstock supplementation programs but emphasizes the importance of thorough genetic monitoring. However, before these populations can be considered for broodstock supplementation, further investigation is required to confirm their genetic integrity and rule out potential contamination from invasive species.

Numbers of Critically Endangered Hooded Vultures ( Necrosyrtes monachus Temminck 1823) are declining across their distribution. The range‐edge population in South Africa is one of the smallest populations with only 100–200 mature individuals. In South Africa, Hooded Vultures nest solitarily in loose colonies (mean distance between nests 0.76 km) along water courses. Basic ecological information, such as breeding behaviour, is still lacking for the species. In this study, we examine the relatedness and nest turnover of nesting individuals along the Olifants River and other locations in the Lowveld of South Africa by sampling nests over five consecutive years. A key hypothesis tested is whether communal roosting sites function as information‐sharing hubs, a phenomenon that has been seen in Cape Vultures ( Gyps coprotheres ) and other cliff‐nesting vultures. Theory suggests that information sharing occurs more frequently between closely related individuals. If true, we expect distance between nests and genetic relatedness to be positively correlated and individuals to use the same nests over multiple years. Naturally moulted feathers ( n = 108) were collected below nests over five consecutive years, and 14 microsatellite loci markers were used to measure genetic relatedness. Mantel tests performed correlating distance between nests to relatedness coefficient estimators TrioML ( r = 0.032, R ² = 0.001, p = 0.224) and LynchRD ( r = 0.007, R ² = 0.00005, p = 0.403), found no statistical correlation. The Mantel test performed using Nei's genetic distance and distance between nests did show a negative correlation ( r = −0.108, R ² = 0.0117, p ‐value = 0.012), indicating that individuals that were more closely related tended to breed further away. No nest reuse was found in this study. We thus believe that these loose colonies do not act as food‐finding hubs, but rather that the Olifants River is an important breeding site for these birds.

Critically endangered Hooded Vultures (Necrosyrtes monachus Temminck, 1823), like many vulture species globally, are experiencing rapid population declines due to anthropogenic factors such as poisonings, human persecution, trading for belief-based use, and habitat loss/degradation. The Hooded Vulture is widespread across sub-Saharan Africa. Although it is considered one of the most abundant vultures in West Africa, this vulture species is less common in East and southern Africa, with the population at the southern-most edge of the distribution (in South Africa and Eswatini) estimated at only 100–200 mature individuals. The distribution of Hooded Vultures has contracted dramatically in southern Africa, with breeding populations largely confined to protected areas such as the Greater Kruger National Park. This study aimed to investigate the genetic diversity of the southern African range-edge population and assess if the recent contraction in the distribution has resulted in the population experiencing a genetic bottleneck. Sixteen microsatellite loci were amplified for samples collected along the Olifants River in the Greater Kruger National Park (n = 30). The genetic diversity in the South African population was compared to samples (n = 30) collected in Ghana, where Hooded Vultures are more abundant. Contrary to expectations, the South African peripheral Hooded Vulture population showed higher levels of heterozygosity (H_O = 0.495) than the Ghanaian population (H_O = 0.315). Neither population showed signs of recent bottleneck events when tested using demographic modelling and Approximate Bayesian computation (ABC). However, both populations showed high levels of inbreeding and relatedness. Our results suggest that despite being a small peripheral population, the South African Hooded Vulture population showed a similar level of genetic diversity as individuals sampled from a core population within the species distribution (in Ghana). This study supports the need for Hooded Vulture conservation efforts in the southern African region and highlights the evolutionary importance of range-edge populations.

DNA metabarcoding requires only a single DNA fragment to detect a species in mixed zooplankton samples, compared to morphology-based methods that rely on the presence of intact specimens. However, metabarcoding protocols have not yet been fully standardised, thus hindering data comparability between studies. To converge on standardised metabarcoding protocols, we used an experimental field-sampling approach to compare the effects of sampling gear (ring-, Manta- and WP2 nets), day and night (DN) sampling and tow duration (5-, 10- and 15-minute tows) on marine zooplankton composition. High-throughput sequencing of the cytochrome c oxidase subunit I (COI) gene region with different primers and taxonomic assignment of amplicon sequence variants at 97% similarity to barcode records were used to identify species. Metabarcoding detected a total of 224 species, of which 92% matched prior occurrence records from the region. Malacostraca (crabs, hermit crabs, lobsters, prawns and shrimps) was the best-represented class (49%), followed by Copepoda (21%), Actinopterygii (ray-finned fishes; 21%), and Gastropoda (9%). Species counts ranged from 9–61 species per tow, with high proportions of unique species in replicate tows. Mean species counts did not differ significantly between net types, DN samples or tow durations, respectively. Proportionate representation amongst taxonomic classes remained within a narrow range, except when sampling deeper habitats with a smaller mesh size. DN samples showed no evidence of daily vertical migration of zooplankton. Consistent inferred species composition across net types, tow duration and DN sampling treatments reflects high detection sensitivity of individual-based sampling, allowing for greater flexibility in planning of zooplankton sampling regimes.

The black‐footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black‐footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black‐footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.

DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D‐loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D‐loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.