Southern African Populations Research Articles

Extensive Population Structure Highlights an Apparent Paradox of Stasis in the Impala (Aepyceros melampus).

Impalas are unusual among bovids because they have remained morphologically similar over millions of years-a phenomenon referred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common (Aepyceros melampus melampus) and black-faced (A. m. petersi) impala. We investigated the evolutionary forces working within the species to explore how they might be associated with its evolutionary stasis as a taxon. Despite being one of the most abundant bovid species, we found low genetic diversity overall, and a phylogeographic signal of spatial expansion from southern to eastern Africa. Contrary to expectations under a scenario of evolutionary stasis, we found pronounced genetic structure between and within the two subspecies with indications of ancient, but not recent, gene flow. Black-faced impala and eastern African common impala populations had more runs of homozygosity than common impala in southern Africa, and, using a proxy for genetic load, we found that natural selection is working less efficiently in these populations compared to the southern African populations. Together with the fossil record, our results are consistent with a fixed-optimum model of evolutionary stasis, in which impalas in the southern African core of the range are able to stay near their evolutionary fitness optimum as a generalist ecotone species, whereas eastern African impalas may struggle to do so due to the effects of genetic drift and reduced adaptation to the local habitat, leading to recurrent local extinction in eastern Africa and re-colonisation from the South.

High Resolution Class I HLA -A, -B, and -C Diversity in Eastern and Southern African Populations.

Africa remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data, despite being one of the most genetically diverse regions in the world. This critical gap in genetic information poses a substantial barrier to HLA-based research on the continent. In this study, Class I HLA data from Eastern and Southern African populations were analysed to assess genetic diversity across the region. We examined allele and haplotype frequency distributions, deviations from Hardy-Weinberg Equilibrium (HWE), linkage disequilibrium (LD), and conducted neutrality tests of homozygosity across various populations. Additionally, the African HLA data were compared to those of Caucasian and African American populations using the Jaccard index and multidimensional scaling (MDS) methods. The study revealed that South African populations exhibited 50.4% more genetic diversity within the Class I HLA region compared to other African populations. Zambia showed an estimated 36.5% genetic diversity, with Kenya, Rwanda and Uganda showing 35.7%, 34.2%, and 31.1%, respectively. Furthermore, an analysis of in-country diversity among different tribes indicated an average Class I HLA diversity of 25.7% in Kenya, 17% in Rwanda, 2.8% in South Africa, 13.6% in Uganda, and 6.5% in Zambia. The study also highlighted the genetic distinctness of Caucasian and African American populations compared to African populations. Notably, the differential frequencies of disease-promoting and disease-preventing HLA alleles across these populations emphasize the urgent need to generate high-quality HLA data for all regions of Africa and its major ethnic groups. Such efforts will be crucial in enhancing healthcare outcomes across the continent.

Links between the Botswana High and drought modes over southern Africa

AbstractDrought is one of the most devastating threats to the livelihoods of the southern African population, who mainly rely on rain‐fed agriculture for income. Previous studies have highlighted that the Botswana High influences drought over the region; however, its influence on the spatial modes of drought remains unknown. This study examines the spatiotemporal structures of drought modes (DMs) over southern Africa and their link with the Botswana High in observation, reanalysis and Model for Prediction Across Scales (MPAS). To characterize droughts, the study uses the 3‐month scale standardized precipitation index (SPI) and the standardized precipitation evapotranspiration index (SPEI). Spatiotemporal characteristics of the DMs are identified using empirical orthogonal function (EOF) analysis on SPI and SPEI. EOF analysis is also used to identify the spatiotemporal characteristics of the Botswana High. The relationship between each DM and the Botswana High is quantified using correlation and R2 analysis. In all the datasets (Climate Research Unit (CRU), European Centre for Medium‐Range Weather Forecasts version 5 (ERA5), 20th Century reanalysis II (20C) and MPAS), the most dominant five DMs (hereafter DM1–DM5) over southern Africa jointly explain more than 60% of the interannual variability in the 3‐month scale summer droughts for SPEI and SPI. CRU, ERA5 and MPAS agree that the Botswana High correlates with the interannual variability of DM1, with a stronger correlation in ERA5 (r = −0.85) compared to MPAS (r = −0.42) and CRU (r = −0.35). Additionally, wet years (+ve SPEI and SPI) are characterized by a weak Botswana High and drought years (−ve SPEI and SPI) by a strong Botswana High. The wet and dry years correspond to the −ve and +ve phases of El Niño–Southern Oscillation (ENSO), respectively. Given this, the results of this study suggest that the Botswana High might be a teleconnection pattern through which ENSO signals influence DM1 over the region.

High conservation importance of range-edge populations of Hooded Vultures (Necrosyrtes monachus)

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 (HO = 0.495) than the Ghanaian population (HO = 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.

African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig’s presence in Madagascar.

Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry.

Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated the analytical performance of the GenoPharm® custom open array platform which evaluates 120 SNPs across 46 pharmacogenes. Using commercially available reference samples (Coriell Biorepository) and in-house extracted DNA, we assessed accuracy, precision, and linearity of GenoPharm®. We then used GenoPharm® on 218 samples from two Southern African black populations and determined allele and genotype frequencies for selected actionable variants. Across all assays, the GenoPharm® panel demonstrated 99.5% concordance with the Coriell reference samples, with 98.9% reproducibility. We observed high frequencies of key genetic variants in people of African ancestry: CYP2B6*6 (0.35), CYP2C9*8, *11 (0.13, 0.03), CYP2D6*17 (0.21) and *29 (0.11). GenoPharm® open array is therefore an accurate, reproducible and sensitive test that can be used for clinical pharmacogenetic testing and is inclusive of variants specific to the people of African ancestry.

Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe

BackgroundWhile the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).ResultsOur results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.ConclusionsTaken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.

Natural selection has driven the recurrent loss of an immunity gene that protects Drosophila against a major natural parasite

Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we have investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. We found that increased expression of the gene lectin-24A after infection by parasitic wasps was associated with a faster cellular immune response and greatly increased rates of killing the parasite. lectin-24A encodes a protein that is strongly up-regulated in the fat body after infection and localizes to the surface of the parasite egg. In certain susceptible lines, a deletion upstream of the lectin-24A has largely abolished expression. Other mutations predicted to abolish the function of this gene have arisen recurrently in this gene, with multiple loss-of-expression alleles and premature stop codons segregating in natural populations. The frequency of these alleles varies greatly geographically, and in some southern African populations, natural selection has driven them near to fixation. We conclude that natural selection has favored the repeated loss of an important component of the immune system, suggesting that in some populations, a pleiotropic cost to lectin-24A expression outweighs the benefits of resistance.

Towards Evidence-Based Implementation of Pharmacogenomics in Southern Africa: Comorbidities and Polypharmacy Profiles across Diseases.

Pharmacogenomics may improve patient care by guiding drug selection and dosing; however, this requires prior knowledge of the pharmacogenomics of drugs commonly used in a specific setting. The aim of this study was to identify a preliminary set of pharmacogenetic variants important in Southern Africa. We describe comorbidities in 3997 patients from Malawi, South Africa, and Zimbabwe. These patient cohorts were included in pharmacogenomic studies of anticoagulation, dyslipidemia, hypertension, HIV and breast cancer. The 20 topmost prescribed drugs in this population were identified. Using the literature, a list of pharmacogenes vital in the response to the top 20 drugs was constructed leading to drug-gene pairs potentially informative in translation of pharmacogenomics. The most reported morbidity was hypertension (58.4%), making antihypertensives the most prescribed drugs, particularly amlodipine. Dyslipidemia occurred in 31.5% of the participants, and statins were the most frequently prescribed as cholesterol-lowering drugs. HIV was reported in 20.3% of the study participants, with lamivudine/stavudine/efavirenz being the most prescribed antiretroviral combination. Based on these data, pharmacogenes of immediate interest in Southern African populations include ABCB1, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, SLC22A1, SLCO1B1 and UGT1A1. Variants in these genes are a good starting point for pharmacogenomic translation programs in Southern Africa.

A Systematic Review of Indigenous Food Plant Usage in Southern Africa

Indigenous food plants provide various social functions; they are crucial to food supply diversification efforts, and they improve food and nutrition security. Research has shown that indigenous foods’ nutritional potential and advantages have yet to be adequately appreciated and explored. This systematic review discusses the various elements contributing to IF promotion, which may help increase their intake. Therefore, a systematic literature review was conducted to determine the availability, regularity of consumption, utilisation, preparation, harvesting, and preservation of indigenous foods. Additionally, this review details the knowledge, perceptions, and beliefs of IFs under these themes. The findings of this systematic review highlight the importance of promoting IFs through policies, the development of capabilities and skills, in-depth research, and an extensive indigenous food plant composition. The fact that Southern African populations do not value indigenous foods and their potential advantages appears to be a significant barrier. Furthermore, the younger generation has lost access to the older generations’ indigenous food knowledge. Thus, the preservation of indigenous food knowledge in books and continuing education of the younger generation about the importance of consuming indigenous foods and the nutrition content they contain may help with its uptake.

Hybrid breakdown in male reproduction between recently diverged Drosophila melanogaster populations has a complex and variable genetic architecture.

Secondary contact between formerly isolated populations may result in hybrid breakdown, in which untested allelic combinations in hybrids are maladaptive and limit genetic exchange. Studying early-stage reproductive isolation may yield key insights into the genetic architectures and evolutionary forces underlying the first steps toward speciation. Here, we leverage the recent worldwide expansion of Drosophila melanogaster to test for hybrid breakdown between populations that diverged within the last 13,000 years. We found clear evidence for hybrid breakdown in male reproduction, but not female reproduction or viability, supporting the prediction that hybrid breakdown affects the heterogametic sex first. The frequency of non-reproducing F2 males varied among different crosses involving the same southern African and European populations, as did the qualitative effect of cross direction, implying a genetically variable basis of hybrid breakdown and a role for uniparentally inherited factors. The levels of breakdown observed in F2 males were not recapitulated in backcrossed individuals, consistent with the existence of incompatibilities with at least three partners. Thus, some of the very first steps toward reproductive isolation could involve incompatibilities with complex and variable genetic architectures. Collectively, our findings emphasize this system's potential for future studies on the genetic and organismal basis of early-stage reproductive isolation.

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Background and aim: African Greater Cane (ACG) rat populations are widely distributed across Africa but the ancestral origin of populations inhabiting different geographical regions is unknown. There is currently no information available on the genetic differentiation of these populations resulting from long-time geographical isolation, environmental and anthropogenic pressures they face in each region. This limits our ability to understand potential speciation processes in AGC and their implications for their conservation and of other small wild mammals exposed to similar ecological conditions in the savannah biomes in Africa. Methods: We analyzed mitochondrial genes targeting the D-loop region of AGC samples from two blocks of the Eastern Arc Mountains in Tanzania (eastern), three agro-ecological zones in Ghana (western) and four sites in South Africa (southern) to characterize the phylogeographical patterns of the species. Results: AGC populations from Tanzania revealed higher haplotype diversity than those from the two other régions. Analysis of variance (AMOVA) revealed higher genetic variations within than between populations in all geographic regions. Demographic history analysis revealed a negative and significant Tajima’s D for a single southern African population as well as close relatedness with the Eastern Africa populations, suggesting a common ancestral origin. Conclusion: This is the first study to compare maternal lineages of AGC populations from eastern, western and southern Africa and provides a basis for future genetic studies of the species, its evolutionary ecology and the conservation of these populations across their range. Conservation implications: Evidence of recent population size expansion underpinned by high genetic diversity observed in the Uluguru urban (Tanzania) Guinea savannah (Ghana) and Kwazulu Natal (South Africa) populations suggest that the AGC populations are not currently threatened, consistent with the current IUCN status. Also, the distinct haplotypes observed in each region suggest that the populations can be managed as meta-populations, thus providing opportunities for potential local game-farming programs.

The duplicated P450s CYP6P9a/b drive carbamates and pyrethroids cross-resistance in the major African malaria vector Anopheles funestus.

Cross-resistance to insecticides in multiple resistant malaria vectors is hampering resistance management. Understanding its underlying molecular basis is critical to implementation of suitable insecticide-based interventions. Here, we established that the tandemly duplicated cytochrome P450s, CYP6P9a/b are driving carbamate and pyrethroid cross-resistance in Southern African populations of the major malaria vector Anopheles funestus. Transcriptome sequencing revealed that cytochrome P450s are the most over-expressed genes in bendiocarb and permethrin-resistant An. funestus. The CYP6P9a and CYP6P9b genes are overexpressed in resistant An. funestus from Southern Africa (Malawi) versus susceptible An. funestus (Fold change (FC) is 53.4 and 17 respectively), while the CYP6P4a and CYP6P4b genes are overexpressed in resistant An. funestus in Ghana, West Africa, (FC is 41.1 and 17.2 respectively). Other up-regulated genes in resistant An. funestus include several additional cytochrome P450s (e.g. CYP9J5, CYP6P2, CYP6P5), glutathione-S transferases, ATP-binding cassette transporters, digestive enzymes, microRNA and transcription factors (FC<7). Targeted enrichment sequencing strongly linked a known major pyrethroid resistance locus (rp1) to carbamate resistance centering around CYP6P9a/b. In bendiocarb resistant An. funestus, this locus exhibits a reduced nucleotide diversity, significant p-values when comparing allele frequencies, and the most non-synonymous substitutions. Recombinant enzyme metabolism assays showed that both CYP6P9a/b metabolize carbamates. Transgenic expression of CYP6P9a/b in Drosophila melanogaster revealed that flies expressing both genes were significantly more resistant to carbamates than controls. Furthermore, a strong correlation was observed between carbamate resistance and CYP6P9a genotypes with homozygote resistant An. funestus (CYP6P9a and the 6.5kb enhancer structural variant) exhibiting a greater ability to withstand bendiocarb/propoxur exposure than homozygote CYP6P9a_susceptible (e.g Odds ratio = 20.8, P<0.0001 for bendiocarb) and heterozygotes (OR = 9.7, P<0.0001). Double homozygote resistant genotype (RR/RR) were even more able to survive than any other genotype combination showing an additive effect. This study highlights the risk that pyrethroid resistance escalation poses to the efficacy of other classes of insecticides. Available metabolic resistance DNA-based diagnostic assays should be used by control programs to monitor cross-resistance between insecticides before implementing new interventions.

Mismatch between conservation needs and actual representation of lions from West and Central Africa in in situ and ex situ conservation

AbstractMismatches between conservation action and conservation needs have been highlighted for diverse species. Lion (Panthera leo) conservation is no exception, raising the question of whether current conservation strategies are always adequate to ensure the long‐term persistence of threatened taxa.To investigate the representation of different lion Evolutionary Significant Units in field research, captive populations, funding allocation, and education, we carried out a literature review and sent an online questionnaire to zoos worldwide. Over 75% of the publications focused on southern and eastern African populations. Uplisting the West African lion to Critically Endangered did not change this result. We received 88 responses from zoos, which reported 346 lions in 83 zoos. Only 14 individuals have West and Central African origins. Over 70% of the respondents reported that they do not include any information on the conservation status or taxonomy of lions from West and Central Africa in their education programs. The minority of zoos funding in situ lion projects did so in Eastern and Southern Africa. We provide recommendations to encourage role‐players involved in lion and other threatened species conservation to address this mismatch by shifting some of their attention and funding to West and Central Africa.

A review of the conservation status of Black Stork Ciconia nigra in South Africa, Lesotho, and Eswatini

Summary Across South Africa, Lesotho, and Eswatini, long-term citizen science atlas data have suggested concerning declines in the population of Black Stork Ciconia nigra. Unlike the Asian and European populations, the southern African Black Stork population is described as resident and is listed as “Vulnerable” in South Africa, Lesotho, and Eswatini. Here we report on surveys of historical nesting locations across northern South Africa, finding evidence for nest site abandonment and limited evidence of recent breeding. We undertook detailed species distribution modelling within a maximum entropy framework, using occurrence records from the BirdLasser mobile app. We cross-validated the models against information in the Southern African Bird Atlas Project (SABAP2) database, highlighting Lesotho as an important potential breeding area. Additionally, we used SABAP2 to assess population trends by investigating interannual patterns in reporting rate. Comparing current reporting rates with those from SABAP1 (1987–1992), we found that there has been a dramatic decrease. We noted that a large proportion of the population occurs outside the breeding range during the breeding season, suggesting a considerable non-breeding population, especially in the extensive wildlife refuge of the Kruger National Park. The slow declines observed might be indicative of a population which is not losing many adults but is failing to recruit significant numbers of juveniles due to limited breeding. Using densities derived from transect surveys, we used predictive models to derive estimates of breeding range carrying capacity and a population estimate, which suggested declines to numbers around 600 for this subregion. Minimising disturbance at breeding sites of this cliff-nesting species and improving water quality at key population strongholds are pathways to improving the status of the species in the subregion.

Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal.

Intertidal rocky shore surveys along the South African coastline (∼3,000 km) have demonstrated the presence and abundance of the encrusting orange sponge Hymeniacidon perlevis (Montagu, 1814), a well-known globally distributed species. After analysing the southern African populations, we gained a better understanding of the genetic structure of this now-accepted global species. Apart from confirming the presence of a single population of H. perlevis, we also determined its distribution in the southern African intertidal rocky shore ecosystem, compared its genetic diversity to congeners, predict its global distribution via environmental niche modelling, and discussed possible underlying mechanisms controlling the species' global distribution. We surveyed the South African coastline and sampled sponges at 53 rocky shore sites spanning over 3,000 km, from Grosse Bucht south of Lüderitz (Namibia) to Kosi Bay on the east coast of South Africa. DNA sequences of the nuclear rDNA internal transcribed spacer (ITS1) and the COI mitochondrial gene were obtained from 61 samples and compared them to a world-wide sample of other H. perlevis sequences. Using environmental predictor variables from the global dataset BIO-ORACLE, we predicted the probability of global occurrence of the species using an ensemble of eight distribution models. South African specimens were found to be 99-100% identical to other populations of H. perlevis (=H. sinapium) from other world-wide regions. The presence of a single population of H. perlevis in southern Africa is supported by genetic data, extending its distribution to a relatively wide geographical range spanning more than 4,000 km along the temperate southern African coast. The predicted global occurrence by ensemble model matched well with the observed distribution. Surface temperature mean and range were the most important predictor variables. While H. perlevis appears to have been introduced in many parts of the world, its origins in Europe and southern Africa are unclear.

Species distribution models and climatic niche comparisons provide clues on the geographic origin of a spider invasion in the Americas

Identifying the source population of alien species is important to assess the distribution and potential effects in the invaded area. The araneid spider Cyrtophora citricola is widely distributed in Europe, Asia, and Africa; however, in the last 26 years, it has been reported in several countries across the Americas. To date, the geographic origin of the populations established in the Americas remains unclear, but considering the successful colonization after its recent arrival, assessing climatic similarities between the invaded and native geographic ranges could be useful to address this question. In this study, we used a combination of Species Distribution Models and Ordination Methods to assess the climatic match between the invaded region (the Americas) and two potential origins (southern Africa and the Mediterranean) aiming to determine the more likely origin for the populations established in the Americas. We found that the American populations of C. citricola occupy sites with climatic conditions more similar to those occupied by southern African populations, than to those occupied by the Mediterranean populations. Therefore, our results suggest a southern African rather than a Mediterranean origin for the populations established in America. In addition, our results also show that populations in America are spreading into sites that differ in climate conditions from those occupied by native populations. Further studies assessing intrinsic (e.g., physiological tolerances, plasticity, behavior, reproduction) and extrinsic (physical barriers, predator release) factors could provide further information to disentangle the mechanisms behind the geographic and climatic niche expansion of this species.

Discerning the global phylogeographic distribution of Phyllosticta citricarpa by means of whole genome sequencing

Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathogen, including 71 isolates from eight countries, Argentina, Australia, Brazil, China, Cuba, Eswatini, South Africa and the United States of America.We assembled draft genomes and used a pairwise read mapping approach for the detection and enumeration of variants between isolates. We performed SSR marker discovery based on the assembled genome with the best assembly statistics, and generated genotype profiles for all isolates with 1987 SSR markers in silico. Furthermore, we identified 32,560 SNPs relative to a reference sequence followed by population genetic analyses based on the three datasets; pairwise variant counts, SSR genotypes and SNP genotypes. All three analysis approaches gave similar overall results. Possible pathways of dissemination among the populations from China, Australia, southern Africa and the Americas are postulated. The Chinese population is the most diverse, and is genetically the furthest removed from all other populations, and is therefore considered the closest to the origin of the pathogen. Isolates from Australia, Eswatini and the South African province Mpumalanga are closely associated and clustered together with those from Argentina and Brazil. The Eastern Cape, North West, and KwaZulu-Natal populations in South Africa grouped in another cluster, while isolates from Limpopo are distributed between the two aforementioned clusters. Southern African populations showed a close relationship to populations in North America, and could be a possible source of P. citricarpa populations that are now found in North America.This study represents the largest whole genome sequencing survey of P. citricarpa to date and provides a more comprehensive assessment of the population genetic diversity and connectivity of P. citricarpa from different geographic origins. This information could further assist in a better understanding of the epidemiology of the CBS pathogen, its long-distance dispersal and dissemination pathways, and can be used to refine phytosanitary regulations and management programmes for the disease.

Genetic and morphological variation of Woodland Kingfisher Halcyon senegalensis reveals cryptic mitochondrial lineages and patterns of mitochondrial–nuclear discordance

The Woodland Kingfisher Halcyon senegalensis is widely distributed throughout sub-Saharan Africa and occupies a wide variety of woodland and savannah habitat. Thus far, three subspecies have been described based on morphological variation. In the present study, using western, eastern and southern African populations, we examined the relationship between morphological and genetic divergence among two named subspecies, H. s. cyanoleuca and H. s. senegalensis, using three mitochondrial markers (CO1, Cytb, 16S) and two nuclear markers (FIB5 and RAG1). Southern birds showed clear evidence for morphological divergence, with a longer wing and tail length, when compared with eastern and western birds. Phylogenetic analyses using Bayesian methods identified two well-characterised genetic clusters, representing the two subspecies. We determined that H. s. senegalensis and H. s. cyanoleuca are closely related subspecies that split recently, approximately 0.66–1.31 MYA in the Pleistocene. Furthermore, genetic substructure was evident within H. s. senegalensis, with three distinct genetic clusters in each region. The separation between the Ghana+Gabon and Uganda lineages of H. s. senegalensis occurred approximately 0.12–0.57 MYA. Nuclear–mitochondrial discordance was detected, however, wherein the pattern of divergence was not detected in the RAG1 and FIB5 sequences. Our results suggest that climate change, biogeographic barriers and local adaptation has played a role in the diversification of Woodland Kingfishers in Africa.

Revealing different migration strategies in a Baltic Common Tern (Sterna hirundo) population with light-level geolocators

The Common Tern (Sterna hirundo) is one of Germany’s farthest migrating bird species. Ringing studies have shown the use of the East Atlantic flyway, and according to their main wintering areas at the western and southern African coasts, German and European Common Tern populations have been divided into two allohiemic groups. However, first ring recoveries of German Common Terns in Israel indicated that some of the birds breeding in eastern Germany cross central Europe and migrate along the eastern African coast. To investigate the migratory behavior of Common Terns from East Germany, we fitted 40 Common Terns breeding in a colony at the German Baltic coast with light-level geolocators. Twenty-four loggers with analyzable datasets could be retrieved, revealing two different migratory strategies within one population. Seventeen individuals (70.83%) used the eastern Atlantic flyway and spent the winter at the western African coast, the Gulf of Guinea and the southern African coast, while the other individuals (n = 7; 29.17%) crossed central Europe, migrated along the eastern African coast and overwintered in the Mozambique Channel and South African coast. We, therefore, suggest to add a third allohiemic group to complement the picture of European Common Tern migration. Moreover, our results provide new knowledge and open new questions, which can be used for future studies regarding the evolution of different migratory strategies and its consequences in relation to climate change.