Population structure in African Drosophila melanogaster revealed by microsatellite analysis

Tropical sub-Saharan regions are considered to be the geographical origin of Drosophila melanogaster. Starting from there, the species colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic scenario, African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, limited information is available on the genetic structure of African populations. We used X chromosomal microsatellite variation to study the population structure of D. melanogaster populations using 13 sampling sites in North, West and East Africa. These populations were compared to six European and one North American population. Significant population structure was found among African D. melanogaster populations. Using a Bayesian method for inferring population structure we detected two distinct groups of populations among African D. melanogaster. Interestingly, the comparison to cosmopolitan D. melanogaster populations indicated that one of the divergent African groups is closely related to cosmopolitan flies. Low, but significant levels of differentiation were observed for sub-Saharan D. melanogaster populations from West and East Africa.     

Morphometric and allozyme variation in the African catfishes Clarias gariepinus and C. anguillaris

This study investigated morphological characters and electrophoretic polymorphism at 25 protein loci in nine wild populations of the African clariid catfish Clarias gariepinus and seven wild populations of C. anguillaris. Two other clariid species, Clarias albopunctatus and Heterobranchus longifilis , were used as outgroups in the allozyme study. Morphometric and allozyme data are congruent for the Nilo-Sudanian populations of C. gariepinus and C. anguillaris. Both approaches also distinguished two groups amongst the C. gariepinus populations, one containing Nilo-Sudanian populations and the other including Lake Victoria and southern African populations. However, allozyme data suggest that C. gariepinus is not a monophyletic group and show that C. albopunctatus is more divergent from C. gariepinus and C. anguillaris than it is from H. longifilis , stressing the need for a revision of clariid systematics. The variation observed in C. gariepinus is discussed in terms of palaeogeographical events and its use in aquaculture.     

Microsatellite variation and differentiation in African and non-African populations of Drosophila simulans

Drosophila simulans originated in sub-Saharan Africa or Madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic history, sub-Saharan African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, only limited information is available on the population structure of D. simulans. Here, we analysed X-linked and autosomal microsatellite loci in four sub-Saharan African, one North African, one Israeli, and two European D. simulans populations. Bayesian clustering algorithms combined the North African, Israeli, and European populations into a single cosmopolitan group. The four sub-Saharan populations were split into two separate groups. Pairwise F(ST) analysis, however, indicated significant population differentiation between all eight populations surveyed. A significant signal for population reduction in cosmopolitan populations was found only for X-linked loci.     

Human impact on wildlife populations within a protected Central African forest

This paper addresses the effect of human activities on the density of large mammals in the Dzanga‐Ndoki National Park and the adjacent Dzanga‐Sangha Reserve in the Central African Republic. Between six and eight 20 km long permanent transects were walked on a monthly basis from January 1997 to August 1999 to assess large mammal populations as well as human intrusion. There were no obvious seasonal or monthly trends in elephant, gorilla or non‐human primate densities. Overall, it appears that human activities negatively influence the distribution of most of the large forest animals in Dzanga‐Sangha. Elephants in particular were significantly less common in areas used by humans, but also other species such as non‐human primates showed lower densities closer to the main road and the town of Bayanga. This study confirms the findings of previous studies that roads have a negative impact on wildlife populations. Results of this study stress the need for conservation of large uninterrupted forest blocks to maintain wildlife populations at normal levels. Simply creating roads, even within a protected Central African forest, is likely to have negative impacts on wildlife populations.     

Interdemic variation in the foraging ecology of the African cyprinid, Barbus neumayeri

In the African cyprinid, Barbus neumayeri, populations from hypoxic waters have larger gills than populations from well-oxygenated streams. Differences in trophic morphology and feeding performance between these populations suggest a reduction in feeding efficiency in large-gilled fish that may reflect spatial constraints of the gills. However, this variation may also reflect interdemic variation in diets. In this study, we describe patterns of variation in diet, gut morphology, and prey availability for populations of B. neumayeri from swamp (low-oxygen) and stream (high-oxygen) sites in Kibale National Park, Uganda. Our results indicate that B. neumayeri are omnivorous, feeding primarily on benthic prey items; however, diets differed among swamp and stream sites for certain prey types. The observed dietary differences do not provide direct support for predictions based on variation in trophic musculature; hard-bodied prey were more common in low-oxygen sites. Prey availability also differed among sites; in particular, insect abundance and richness was generally lower in the swamp sites. Gut length was longer in one of the four populations, but did not conform to expectations based on diet differences. Condition and growth rates did not differ between populations from hypoxic and well-oxygenated sites, despite observed differences in prey availability and diet, suggesting that B. neumayeri may be distributed in a way that equalizes fitness among populations in different habitats.     

Changes in large herbivore populations across large areas of Tanzania

We collated aerial census data collected during the late 1980s to early 2000s for large herbivore populations in eight large census zones in Tanzania. Of the ungulate populations that showed significant changes in densities at the start versus end of this decade, most declined; very few populations increased significantly. Thomson's gazelle, Grant's gazelle, hartebeest, reedbuck, roan antelope, sable antelope, warthog and zebra, for example, declined in over 50% of the zones where they were surveyed. Interestingly, small‐bodied species fared particularly poorly in many census zones, whereas elephant and giraffe generally fared well across the country. Most populations of all herbivores declined in some portions of the country (e.g. Burigi‐Biharamulo, Katavi, Greater Ruaha and Tarangire census zones). These surveys suggest that, even in a country renowned for its protected areas and conservation commitment, some large herbivore populations need more conservation attention in order to remain stable.     

Melanin and HIV in sub-Saharan Africa

HIV is common in sub-Saharan Africa. Sexually transmitted bacterial and fungal infections increase the chance of HIV infection. Melanin can prevent the penetration of skin and mucus membranes by microorganisms, and soluble melanin can inhibit HIV replication. We suggest that melanin may reduce the incidence of HIV infection through venereally acquired skin lesions, thus reducing the risk of sero-conversion and slow the progress to AIDS. Indigenous sub-Saharan peoples are highly melanized, but there is pigment variation between populations. We show that skin reflectance, a negative correlate of melanin, is positively associated with adult rate of HIV in sub-Saharan countries. There is no such relationship in populations outside sub-Saharan Africa. We suggest that melanin concentration in black people may correlate with resistance to HIV infection.     

Extremely high prevalence of DNASE1*1 allele in African populations

The single nucleotide polymorphism (SNP) at deoxyribonuclease I (DNase I), designated as DNASE1 (NCBI SNP number; 1053874), in exon 8 (A2317G) has been shown to be associated with liver disease, colorectal carcinoma, and gastric carcinoma in Japanese patients. In this study, we investigated the frequency of the DNASE1 polymorphism in Ghanaian (n = 96) and Xhosa (n = 78) populations and compared the results with those of other studies. The single nucleotide polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The frequencies of DNASE1*1 in the Ghanaian and Xhosa populations were 0.90 and 0.88, respectively. These two African populations had an extremely high frequency of DNASE1*1, similar to that of the Ovambos living in Namibia. Caucasians and Asians had a lower frequency of DNASE1*1 than the African groups. This study is the first to reveal an extremely high frequency of DNASE1*1 among African populations.     

Analysis of paternal lineages in Brazilian and African populations

The present-day Brazilian population is a consequence of the admixture of various peoples of very different origins, namely, Amerindians, Europeans and Africans. The proportion of each genetic contribution is known to be very heterogeneous throughout the country. The aim of the present study was to compare the male lineages present in two distinct Brazilian populations, as well as to evaluate the African contribution to their male genetic substrate. Thus, two Brazilian population samples from Manaus (State of Amazon) and Ribeirão Preto (State of São Paulo) and three African samples from Guinea Bissau, Angola and Mozambique were typed for a set of nine Y chromosome specific STRs. The data were compared with those from African, Amerindian and European populations. By using Y-STR haplotype information, low genetic distances were found between the Manaus and Ribeirão Preto populations, as well as between these and others from Iberia. Likewise, no significant distances were observed between any of the African samples from Angola, Mozambique and Guinea Bissau. Highly significant Rst values were found between both Brazilian samples and all the African and Amerindian populations. The absence of a significant Sub-Saharan African male component resulting from the slave trade, and the low frequency in Amerindian ancestry Y-lineages in the Manaus and Ribeirão Preto population samples are in accordance with the accentuated gender asymmetry in admixture processes that has been systematically reported in colonial South American populations.     

Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species

Processes driving and maintaining disjunct genetic populations in marine systems are poorly understood, owing to a lack of evidence of hard barriers that could have shaped patterns of extant population structure. Here, we map two genetically divergent lineages of an obligate rocky shore fish, Clinus cottoides, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.     

mtDNA variation in East Africa unravels the history of afro‐asiatic groups

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long‐term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro‐Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno‐linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model‐based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA‐speaking populations, and shows shared ancestry with Semitic‐speaking groups from Yemen and Egypt and AA‐Chadic‐speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene‐flow (Bantu, Nilo‐Saharan pastoralists), one of them is associated with a more ancient AA‐Cushitic stratum. Most North‐African and Levantine populations (AA‐Berber, AA‐Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Multidimensional scaling and the analysis of human biological diversity in Subsaharan Africa

Much information concerning intergroup variation in Subsaharan Africa has been collected by Hiernaux, who has calculated measures of biological distance (Δg) between pairs of 101 African human populations. The resulting very large matrix of distances is not easily interpreted through simple inspection. Therefore non-metric multidimensional scaling is here applied in order to produce a configuration of 60 selected groups in a space of reduced dimensionality. A three dimensional solution shows acceptable stress, and this map of populations is used to support and extend Hiernaux's earlier conclusions.     

A model for rapid growth evaluation in fishes: the case of the Cyprinids of some large French rivers

Starting from previous work on tropical african fishes (de Merona et al., 1983), we calculate a relationship between Loo and k and between L_OO and the maximum observed length in cyprinid populations of some French great rivers and associated man-made lakes (basins of Garonne and Rhone). 45 populations are used, and they seem to conform to the model well. The growth of both groups of populations differs only by the value of some constants. This follows from differences in the individual growth pattern of fishes, climate, and from differences in food and feeding habits.     

mtDNA variability in two Bantu‐speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub‐Saharan Africa

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu‐speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu‐speaking populations. Moreover, by comparing our data with those from other Niger‐Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub‐Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu‐speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu‐speaking populations, but also between Bantu and non‐Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu‐speakers, with strong interactions between the different lines of Bantu‐speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Founder populations and the current status of exotic parrots in South Africa

Parrots (families Psittacidae and Cacatuidae) are one of the most threatened taxa of birds, with a combination of threats to wild populations, including capture for the cage bird market, habitat modification and destruction, persecution, disease, and threats from introduced species. As a result of the group's popularity as a cage bird, and the transport of vast numbers of individuals across the globe (both legally and illegally), the establishment of populations beyond their natural ranges has likely been enhanced. This review reports on c. 30 parrot species that have been observed outside of their natural ranges in South Africa, most likely derived, and supplemented, from both intentional and unintentional releases. Of these, the Rose-ringed Parakeet Psittacula krameri and at least one Agapornis species have become established as breeding wild populations. Like other invasive species they may pose threats to local biodiversity; however, all are strongly associated with major urban centres where significant changes to natural biota have already occurred.     

Phylogenetic relationships of the Chalcides skink species from the Chafarinas Islands with those from mainland North Africa

Species whose geographical distribution encompasses both mainland and island populations provide ideal systems for examining potential isolation and genetic divergence. This has also interest from a conservationist point of view, as it is important to protect “evolutionarily significant units”. We report a phylogenetic mitochondrial DNA analysis comparing the populations of the three Chalcides skink species from the Chafarinas Islands (NW Africa) with specimens of the same species from the nearest mainland. We tested for the potential genetic distinctiveness of the skink island populations. However, the results of the comparison of the genetic variability of the mitochondrial coding gene cytb were conclusive showing that the genetic divergence between continental and island Chalcides species was either non-existent or extremely low. We discuss how genetic divergence may be lower than expected if separation time of the islands with the mainland has not been long enough or if the island skink populations were currently communicated via ocean rafting with individuals coming from the mainland ones.     

Activity patterns in the Sahara Desert: an interpretation based on cross-sectional geometric properties

The Garamantian civilization flourished in modern Fezzan, Libya, between 900 BC and 500 AD, during which the aridification of the Sahara was well established. Study of the archaeological remains suggests a population successful at coping with a harsh environment of high and fluctuating temperatures and reduced water and food resources. This study explores the activity patterns of the Garamantes by means of cross-sectional geometric properties. Long bone diaphyseal shape and rigidity are compared between the Garamantes and populations from Egypt and Sudan, namely from the sites of Kerma, el-Badari, and Jebel Moya, to determine whether the Garamantian daily activities were more strenuous than those of other North African populations. Moreover, sexual dimorphism and bilateral asymmetry are assessed at an intra- and inter-population level. The inter-population comparisons showed the Garamantes not to be more robust than the comparative populations, suggesting that the daily Garamantian activities necessary for survival in the Sahara Desert did not generally impose greater loads than those of other North African populations. Sexual dimorphism and bilateral asymmetry in almost all geometric properties of the long limbs were comparatively low among the Garamantes. Only the lower limbs were significantly stronger among males than females, possibly due to higher levels of mobility associated with herding. The lack of systematic bilateral asymmetry in cross-sectional geometric properties may relate to the involvement of the population in bilaterally intensive activities or the lack of regular repetition of unilateral activities.     

Microsatellite diversities and gene flow in the tsetse fly,Glossina morsitans s.l

Tsetse flies occupy discontinuous habitats and gene flow among them needs to be investigated in anticipation of area-wide control programs. Genetic diversities were estimated at six microsatellite loci in seven Glossina morsitans submorsitans Newstead (Diptera: Glossinidae) populations and five microsatellite loci in six G. m. morsitans Westwood populations. Nei's unbiased diversities were 0.808 and 76 alleles in G. m. submorsitans and 0.727 and 55 alleles in G. m. morsitans. Diversities were less in three laboratory cultures. Matings were random within populations. Populations were highly differentiated genetically. Populations were strongly subdivided, as indicated by fixation indices (F(ST)) of 0.18 in G. m. morsitans and 0.17 in G. m. submorsitans. 35% of the genetic variance in G. m. submorsitans was attributed to differences between populations from The Gambia and Ethiopia. All available genetic evidence suggests that genetic drift is much greater than gene flow among G. morsitans s.l. populations.     

Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa

A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R(2) statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.     

Genetic diversity of Diaphorina citri (Hemiptera: Liviidae) unravels phylogeographic structure and invasion history of eastern African populations

The Asian citrus psyllid (Diaphorina citri Kuwayama) is a key pest of Citrus sp. worldwide, as it acts as a vector for Candidatus Liberibacter asiaticus, the bacterial pathogen that causes citrus Huanglongbing. Diaphorina citri has been reported in Kenya, Tanzania, and more recently in Ethiopia. This study assessed the genetic diversity and phylogeographic structure of the pest to gain insights into the potential sources of its introduction into Africa. Population structure and differentiation of D. citri populations from China, Ethiopia, Kenya, Tanzania, and the USA were assessed using 10 microsatellite loci. Additionally, five new complete mitogenomes of D. citri collected in China, Ethiopia, Kenya, Tanzania, and the USA were analyzed in the context of publicly available sequences. Genotype data grouped the D. citri populations from Kenya and Tanzania in one cluster, and those from Ethiopia formed a separate cluster. The two genetic clusters inferred from genotype data were congruent with mitochondrial sequence data. The mitogenomes from Kenya/Tanzania/China had 99.0% similarity, and the Ethiopia/USA had 99.9% similarity. In conclusion, D. citri populations in eastern Africa have different sources, as the Kenyan and Tanzanian populations probably originated from southeastern Asia, while the Ethiopian population most probably originated from the Americas.