Genetic structuring, dispersal and taxonomy of the high-alpine populations of the Geranium arabicum/kilimandscharicum complex in tropical eastern Africa.
ABSTRACT: The scattered eastern African high mountains harbor a renowned and highly endemic flora, but the taxonomy and phylogeographic history of many plant groups are still insufficiently known. The high-alpine populations of the Geranium arabicum/kilimandscharicum complex present intricate morphological variation and have recently been suggested to comprise two new endemic taxa. Here we aim to contribute to a clarification of the taxonomy of these populations by analyzing genetic (AFLP) variation in range-wide high-alpine samples, and we address whether hybridization has contributed to taxonomic problems. We identified only two genetic groups. One corresponded to G. kilimandscharicum, which has been reported as exclusively high-alpine and confined to the eastern Rift mountains in East Africa. The other corresponded to G. arabicum, reported from lower altitudes on the same mountains as well as from a wide altitudinal span in Ethiopia and on the western Rift mountains in East Africa. The four populations analyzed of a recently described species from the Bale Mts in Ethiopia were admixed, indicating that they result from recent long-distance dispersal of G. kilimandscharicum from East Africa followed by hybridization with local G. arabicum in naturally disturbed habitats. Some admixture between the two genetic groups was also inferred on other mountains, supporting earlier suggestions of introgression based on morphology. We did not find support for recognition of the recently suggested new subspecies of G. arabicum in Ethiopia. Interestingly, the high-alpine G. kilimandscharicum lacked clear geographic structuring, suggesting a recent history of colonization of the different mountains or extensive intermountain gene flow.
Project description:Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants.Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite).It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms.Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.
Project description:We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.
Project description:Transcriptome profiling of three DDT resistant strains of Anopheles gambiae in Cameroon (Gare, Messa and Nkolondom- 2 M forms and one S form) compared to the susceptible strain Ngousso (M form) and Kisumu (S form). S-form is distributed across sub-Saharan Africa and breeds mostly in association with rain-dependent pools and temporary puddles. M-form distribution overlaps with that of S-form in West and Central Africa, but the former form is apparently absent east of the Great Rift Valley; it is able to exploit relatively more permanent breeding sites, often closely associated with human activities, such those created by irrigation, rice cultivation and urbanization (Santolamazza et al., 2011).
Project description:Continental rift systems form by propagation of isolated rift segments that interact, and eventually evolve into continuous zones of deformation. This process impacts many aspects of rifting including rift morphology at breakup, and eventual ocean-ridge segmentation. Yet, rift segment growth and interaction remain enigmatic. Here we present geological data from the poorly documented Ririba rift (South Ethiopia) that reveals how two major sectors of the East African rift, the Kenyan and Ethiopian rifts, interact. We show that the Ririba rift formed from the southward propagation of the Ethiopian rift during the Pliocene but this propagation was short-lived and aborted close to the Pliocene-Pleistocene boundary. Seismicity data support the abandonment of laterally offset, overlapping tips of the Ethiopian and Kenyan rifts. Integration with new numerical models indicates that rift abandonment resulted from progressive focusing of the tectonic and magmatic activity into an oblique, throughgoing rift zone of near pure extension directly connecting the rift sectors.
Project description:The kinematic evolution of the West Antarctic rift system has important consequences for regional and global geodynamics. However, due to the lack of Neogene seafloor spreading at the plate boundary and despite being poorly resolved, East-West Antarctic motion was assumed to have ended abruptly at 26 million years ago. Here we present marine magnetic data collected near the northern edge of the rift system showing that motion between East and West Antarctica lasted until the middle Neogene (~11 million years ago), long after the cessation of the known mid-Cenozoic pulse of motion. We calculate new rotation parameters for the early Neogene that provide the kinematic framework to understand the varied lithospheric settings of the Transantarctic Mountains and the tectono-volcanic activity within the rift. Incorporation of the Antarctic plate motion into the global plate circuit has major implications for the predicted Neogene motion of the Pacific Plate relative to the rest of the plates.
Project description:East Africa is one of the centres of distribution and diversity for Lobelia L. (Campanulaceae, sub-family Lobelioideae). Lobelia habitats in East Africa have been facing habitat fragmentation and loss, which are recognised as a major threat to biodiversity. However, previous plant conservation studies in East Africa only focused on protected areas and ignored unprotected areas. Future conservation strategies of plants, such as Lobelia, will depend on knowledge of their distribution patterns and habitat preference in East Africa. To understand the distribution pattern and the habitat preference of Lobelia in five countries (Kenya, Uganda, Tanzania, Rwanda and Burundi) of East Africa, we conducted a literature review in the seven major vegetation regions (afro-alpine, afro-montane forest, drier savannah, grasslands, wetter savannah, Zambezian woodland and semi-desert and desert). We also employed meander and patterned searches, which allowed greater opportunities for recording Lobelia species. Our results showed that the genus is distributed in all of the seven regions of the five countries with 54 taxa. The afro-montane forest region, with 41 taxa, is the richest in species diversity, followed by the Zambezian woodland region with 18 taxa. The semi-desert and desert region has the lowest number with only four taxa. The afro-alpine region has 15 taxa, although the region is the smallest by area. The herbaceous type was found in all regions, while the giant type has a clear preference for the afro-alpine and afro-montane forest regions. Future conservation for Lobelia should consider its habitat preference by, for example, focusing on the afro-alpine and afro-montane forest regions. This study will facilitate the setting of future conservation strategies for Lobelia.
Project description:Rift Valley fever (RVF), a mosquito-borne disease affecting ruminants and humans, is one of the most important viral zoonoses in Africa. The objective of the present study was to develop a geographic knowledge-based method to map the areas suitable for RVF amplification and RVF spread in four East African countries, namely, Kenya, Tanzania, Uganda and Ethiopia, and to assess the predictive accuracy of the model using livestock outbreak data from Kenya and Tanzania. Risk factors and their relative importance regarding RVF amplification and spread were identified from a literature review. A numerical weight was calculated for each risk factor using an analytical hierarchy process. The corresponding geographic data were collected, standardized and combined based on a weighted linear combination to produce maps of the suitability for RVF transmission. The accuracy of the resulting maps was assessed using RVF outbreak locations in livestock reported in Kenya and Tanzania between 1998 and 2012 and the ROC curve analysis. Our results confirmed the capacity of the geographic information system-based multi-criteria evaluation method to synthesize available scientific knowledge and to accurately map (AUC = 0.786; 95% CI [0.730-0.842]) the spatial heterogeneity of RVF suitability in East Africa. This approach provides users with a straightforward and easy update of the maps according to data availability or the further development of scientific knowledge.
Project description:Despite uncontested evidence for fossils belonging to the early hominin genus Australopithecus in East Africa from at least 4.2 million years ago (Ma), and from Chad by 3.5 Ma, thus far there has been no convincing evidence of Australopithecus, Paranthropus or early Homo from the western (Albertine) branch of the Rift Valley. Here we report the discovery of an isolated upper molar (#Ish25) from the Western Rift Valley site of Ishango in Central Africa in a derived context, overlying beds dated to between ca. 2.6 to 2.0 Ma. We used µCT imaging to compare its external and internal macro-morphology to upper molars of australopiths, and fossil and recent Homo. We show that the size and shape of the enamel-dentine junction (EDJ) surface discriminate between Plio-Pleistocene and post-Lower Pleistocene hominins, and that the Ishango molar clusters with australopiths and early Homo from East and southern Africa. A reassessment of the archaeological context of the specimen is consistent with the morphological evidence and suggest that early hominins were occupying this region by at least 2 Ma.
Project description:Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical, and cultural traditions1,2. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa, and Asia - in what is termed the Jewish Diaspora3-5. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people6. While many genetic studies have shed light on Jewish diseases and origins, including those focusing on uniparentally- and biparentally-inherited markers7-16, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbors have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities, and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not been previously reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and North Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight sub-cluster that overlies Druze and Cypriot samples, but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Bene Israel Indian Jews cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively; despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant. Overall design: 466 samples are analysed on three different Illumina platforms.
Project description:Sub-Saharan Africa has one of the highest levels of child malnutrition globally. Therefore, a critical look at the distribution of malnutrition within its sub-regions is required to identify the worst affected areas. This study provides a meta-analysis of the prevalence of malnutrition indicators (stunting, wasting and underweight) within four sub-regions of sub-Saharan Africa.Cross-sectional data from the most recent Demographic and Health Surveys (2006-2016) of 32 countries in sub-Saharan Africa were used. The countries were grouped into four sub-regions (East Africa, West Africa, Southern Africa and Central Africa), and a meta-analysis was conducted to estimate the prevalence of each malnutrition indicator within each of the sub-regions. Significant heterogeneity was detected among the various surveys (I2 >50%), hence a random effect model was used, and sensitivity analysis was performed, to examine the effects of outliers. Stunting was defined as HAZ<-2; wasting as WHZ<-2 and underweight as WAZ<-2.Stunting was highest in Burundi (57.7%) and Malawi (47.1%) in East Africa; Niger (43.9%), Mali (38.3%), Sierra Leone (37.9%) and Nigeria (36.8%) in West Africa; Democratic Republic of Congo (42.7%) and Chad (39.9%) in Central Africa. Wasting was highest in Niger (18.0%), Burkina Faso (15.50%) and Mali (12.7%) in West Africa; Comoros (11.1%) and Ethiopia (8.70%) in East Africa; Namibia (6.2%) in Southern Africa; Chad (13.0%) and Sao Tome & Principle (10.5%) in Central Africa. Underweight was highest in Burundi (28.8%) and Ethiopia (25.2%) in East Africa; Niger (36.4%), Nigeria (28.7%), Burkina Faso (25.7%), Mali (25.0%) in West Africa; and Chad (28.8%) in Central Africa.The prevalence of malnutrition was highest within countries in East Africa and West Africa compared to the WHO Millennium development goals target for 2015. Appropriate nutrition interventions need to be prioritised in East Africa and West Africa if sub-Saharan Africa is to meet the WHO global nutrition target of improving maternal, infant and young child nutrition by 2025.