Detection of convergent genome-wide signals of adaptation to tropical forests in humans

Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments without external resources. It is therefore possible that humans have developed recent biological adaptations in response to specific selective pressures to cope with this challenge. To understand such biological adaptations we analyzed genome-wide SNP data under a Bayesian statistics framework, looking for outlier markers with an overly large extent of differentiation between populations living in a tropical forest, as compared to genetically related populations living outside the forest in Africa and the Americas. The most significant positive selection signals were found in genes related to lipid metabolism, the immune system, body development, and RNA Polymerase III transcription initiation. The results are discussed in the light of putative tropical forest selective pressures, namely food scarcity, high prevalence of pathogens, difficulty to move, and inefficient thermoregulation. Agreement between our results and previous studies on the pygmy phenotype, a putative prototype of forest adaptation, were found, suggesting that a few genetic regions previously described as associated with short stature may be evolving under similar positive selection in Africa and the Americas. In general, convergent evolution was less pervasive than local adaptation in one single continent, suggesting that Africans and Amerindians may have followed different routes to adapt to similar environmental selective pressures.

SOCIO-ENVIRONMENTAL FACTORS ASSOCIATED WITH THE DISTRIBUTION OF DRACUNCULUS MEDINENSIS (GUINEA WORM DISEASE) AND SUGGESTED METHODS FOR CONTROL, IBARAPA, NIGERIA, 1982 (AFRICA)

A population-based cross-sectional survey of socio-environmental factors associated with the prevalence of Dracunculus medinensis (guinea worm disease) was conducted in Idere, a rural agricultural community in Ibarapa, Oyo state, Nigeria, during 1982.^ The epidemiologic data were collected by household interview of all 501 households. The environmental data were collected by analysis of water samples collected from all domestic water sources and rainfall records.^ The specific objectives of this research were to: (a) Describe the prevalence of guinea worm disease in Idere during 1982 by age, sex, area of residence, drinking water source, religion and weekly amount of money spent by the household to collect potable drinking water. (b) Compare the characteristics of cases with non-cases of guinea worm in order to identify factors associated with high risk of infection. (c) Investigate domestic water sources for the distribution of Cyclops. (d) Determine the extent of potable water shortage with a view to identifying factors responsible for such shortage in the community. (e) Describe the effects of guinea worm on school attendance during 1980/1982 school years by class and location of school from piped water supply.^ The findings of this research indicate that during 1982, 31.8 percent of Idere's 6,527 residents experienced guinea worm infection, with higher prevalence of infection recorded in males in their most productive years and females in their teenage years. The role of sex and age to risk of higher infection rate was explained in the context of water related exposure and water intake due to dehydration from physical occupational actitives of subgroups.^ Potable water available to residents was considerably below the minimum recommended by WHO for tropical climates, with sixty-eight percent of water needs of the residents coming from unprotected surface water which harbour Cyclops, the obligatory intermediate host of Dracunculus medinensis. An association was found between periods of relative high density of Cyclops in domestic water and rainfall.^ Impact of guinea worm infection on educational activities was considerable and its implications were discussed, including the implications of the research findings in relation to control of guinea worm disease in Ibarapa. ^

Hydrogeological investigations in the upper Ouémé catchment in Benin, West Africa

The scope of this PhD thesis was the hydrogeological conceptualisation of the Upper Ouémé river catchment in Benin. The study area exceeds 14,500 km**2 and is underlain by a crystalline basement. At this setting the typical sequence of aquifers - a regolith aquifer at the top and a fractured bedrock aquifer at the bottom - is encountered, which is found in basement areas all over Africa and elsewhere in the world. The chosen regional approach revealed important information about the hydrochemistry and hydrogeology of this catchment. Based on the regional conceptual model a numerical groundwater flow model was designed. The numerical model was used to estimate the impact of climate change on the regional groundwater resources. This study was realised within the framework of the German interdisciplinary research project IMPETUS (English translation: "Integrated approach to the efficient management of scarce water resources in West Africa"), which is jointly managed by the German universities of Bonn and Cologne. Since the year 2000 the Upper Ouémé catchment was the principal target for investigations into the relevant processes of the regional water cycle. A first study from 2000 to 2003 (Fass, 2004, http://nbn-resolving.de/urn:nbn:de:hbz:5n-03849) focused on the hydrogeology of a small local catchment (~30 km**2). In the course of this thesis five field campaigns were underdone from the year 2004 to 2006. In the beginning of 2004 a groundwater monitoring net was installed based on 12 automatic data loggers. Manual piezometric measurements and the sampling of groundwater and surface water were realised for each campaign throughout the whole study area. Water samples were analysed for major ions, for a choice of heavy metals and for their composition by deuterium, oxygen-18 and tritium. The numerical model was performed with FEFLOW. The hydraulic and hydrochemical characteristics were described for the regolith aquifer and the bedrock aquifer. The regolith aquifer plays the role of the groundwater stock with low conductivity while the fractures of the bedrock may conduct water relatively fast towards extraction points. Flow in fractures of the bedrock depends on the connectivity of the fracture network which might be of local to subregional importance. Stable isotopes in combination with hydrochemistry proved that recharge occurs on catchment scale and exclusively by precipitation. Influx of groundwater from distant areas along dominant structures like the Kandi fault or from the Atacora mountain chain is excluded. The analysis of tritium in groundwater from different depths revealed the interesting fact of the strongly rising groundwater ages. Bedrock groundwater may possibly be much older than 50 years. Equilibrium phases of the silicate weathering products kaolinite and montmorillonite showed that the deeper part of the regolith aquifer and the bedrock aquifer feature either stagnant or less mobile groundwater while the shallow aquifer level is influenced by seasonal groundwater table fluctuations. The hydrochemical data characterised this zone by the progressive change of the hydrochemical facies of recently infiltrated rainwater on its flow path into deeper parts of the aquifers. Surprisingly it was found out that seasonal influences on groundwater hydrochemistry are minor, mainly because they affect only the groundwater levels close to the surface. The transfer of the hydrogeological features of the Upper Ouémé catchment into a regional numerical model demanded a strong simplification. Groundwater tables are a reprint of the general surface morphology. Pumping or other types of groundwater extraction would have only very local impact on the available groundwater resources. It was possible to integrate IMPETUS scenario data into the groundwater model. As a result it was shown that the impact of climate change on the groundwater resources until the year 2025 under the given conditions will be negligible due to the little share of precipitation needed for recharge and the low water needs for domestic use. Reason for concern is the groundwater quality on water points in the vicinity of settlements because of contamination by human activities as shown for the village of Dogué. Nitrate concentrations achieved in many places already alerting levels. Health risks from fluoride or heavy metals were excluded for the Upper Ouémé area.

Discharge data derived from five water level gauges and discharge measurements in the Aguima and Niaou catchment, Benin, West Africa

This paper analyzes the hydrological processes and the impact of soil properties and land use on these processes in tropical headwater catchment in the sub-humid part of Benin (West-Africa), the Aguima catchment. The presented study is integrated in the GLOWA IMPETUS project, which investigates the effects of global change on the water cycle and water availability on a regional scale in Morocco and Benin. The lack of field investigations concerning soil and surface hydrology in the Benin research area necessitates detailed field measurements including measurements of discharge, soil water dynamics, soil physical properties etc. on the local scale in order to understand the dominant runoff generation processes and its influencing factors. This is a pre-requisite to be able to forecast the effects which global change has on hydrological processes and water availability in the region. The paper gives an overview over the hydrologic measuring concept of the IMPETUS-Benin project focusing on measurements concerning the soil saturated conductivity ksat and discharge behaviour of two different sub-catchment of the Aguima catchment. The results of ksat measurements revealed that interflow is the dominant runoff process on the hillslopes of the investigated catchment. Concerning the impact of land use on the hydrological processes infiltration experiments showed that infiltration rates were reduced on cultivated land compared to natural land cover. This results in significant differences in runoff behaviour and runoff ratios while comparing natural and agricultural used catchments.

Parameters of the near-bottom nepheloid layer off the northwestern Africa coast

Vertical profiles of light scattering at a right angle and turbidity profiles in seawater indicating suspended matter concentration in the near-bottom nepheloid layer (NNL) were measured simultaneously with temperature, salinity, and density profiles at the continental slope off the northwestern Africa. About 100 stations 5' apart in latitude and longitude were carried out over an ocean area of 6100 sq. km. Special features of the NNL variability in the area were analyzed. It was found that some structural parameters of the NNL (maximum transparency depth, that is the upper boundary of NNL; NNL thickness; maximum and total turbidity) correlate with ocean depth. On the average, thickness of the NNL in the area is 20-40% of the ocean depth. At most stations the NNL is fairly strong. In the shelf region NNL turbidity was influenced by the intensive near-shore upwelling. Formation of ''high-energy near-bottom layers'' in the shelf region resulted from passing of a mesoscale cyclonic eddy that caused redistribution of measured quantities within the entire water column.

(Table 1) Primary production and chlorophyll a concentration in the Northeastern Tropical Atlantic

Results of simultaneous determinations of chlorophyll "a" concentrations and primary production in the northeastern part of the Tropical Atlantic in spring 1977 are discussed. Primary production was low (250-350 mg C/m**2/day in the open parts of the ocean and high (600-1500 mg C/m**2/day) mainly in zones of current divergences and coastal region of the West Africa. Chlorophyll "a" concentration throughout the euphotic zone varied from 6 to 36 mg/m**3 and in the surface layer from 0.05 to 0.60 mg/m**3. Uneven distribution of primary production is due to physiological condition of phytoplankton.

Palynology of the Middle to Late Miocene from ODP Hole 175-1085A off the west coast of South Africa

Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine-driven climate change. Location Middle to Late Miocene in the south-east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south-east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south-western African coast are the disappearance of Podocarpus-dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi-arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre-date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine-driven climate change in south-western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae.

Planktonic foraminiferas in bottom sediments and Late Quaternary paleotemperatures of surface waters in the North Tropical Atlantic

Distribution of planktonic foraminiferal tests was studied in 15 Upper Quaternary sediment cores from the continental slope of Africa, the Canary and Cape Verde basins, and slopes of the Mid-Atlantic Ridge. In all the cores substantial variations were found in relationship between foraminiferal planktonic species reflecting fluctuations of mean annual temperatures of surface waters. Temperature difference in temperatures between present time and that of the maximum of the stadial of the last continental glaciation glacial stadial (about 18,000 yrs ago) ranges from 8.5°C in the Canary upwelling region to minimum values of 2.0°C in the central part of the ocean, i.e. the southern part of the subtropical gyre. Temperature difference the Holocene optimum and 18,000 yrs ago ranges from 10°C to 3°C. Age estimates are supported by radiocarbon dates.

Benthic foraminifera of surface sediments from the continental slope off Sierra Leone, North-West Africa

On "Meteor" cruise 30 (1973) 22 piston-cores were collected off Sierra Leone from water-depths between about 5000 m (Sierra Leone Basin) and 500 m (upper continental slope) with the objective to study the sediment composition and age as well as processes of sedimentation on the continental slope in a tropical humid region. Granulometric analysis and determinations of the carbonate contents of the sediment samples were carried out, as well as qualitative and quantitative analysis of the components of the grain size fractions > 63 µm and of the planktonic and benthonic foraminifera > 160 µm. Presently, the cold Canary Current influences the composition of the planktonic foraminifera within the northwestern area of investigation (profile A), whereas the planktonic fauna of the eastern area (profile C) seems to be truly tropical. In all Quaternary sediments from the continental slope off Sierra Leone, species of Globorotalia are less abundant than in truly pelagic sediments. For that reason, the zonation of the Pleistocene sediments based on the presence or absence of Globorotalia cultrata does not always agree with the climatic changes reflected in the sediments. Concerning past climates better results can be obtained by using the changes in percentage abundances of Globigerina sp. sp. and Globigerinoides sp. sp. as indicators for cool and warm temperatures. The Tertiary sediments contain a pelagic foraminiferal assemblage. In the Holocene sediments the benthonic foraminifera do not only serve as good paleodepth indicators, but their communities are also restricted to defined water masses, which change their positions in accordance with climatic changes. Thus, Cassidulina carinata in the area of investigation is an excellent indicator for sediments deposited during times, which were cooler than today; this is true for all cores from the continental slope off Sierra Leone independent of water-depth although this species presently abounds at water-depths around 600 m. The cores from the continental rise and from the Sierra Leone Basin (M30-261, M30-146, M30-147) were deposited below the calcium carbonate compensation depth. Only small sections of the cores consist of the original carbonate-free sediments, whereas the main part of the sediment column is redeposited material, rich in foraminifera, which normally live on the upper continental slope, or even on the shelf. From these cores only M30-261 can be subdivided into biostratigraphic zones ranging from zone V to zone Y. In all cores from the middle and upper continental slope of the eastern area of investigation (profile C; KL 230, 209-204) and in cores KL 183 and KL 184 from the northwestern area (profile A) we observed an undisturbed succession of sediments from the biostratigraphic zones X (partly), Y and Z. All cores from the central area (M30-181, M30-182, M30-262 to 264) and M30-187 from the upper slope of profile A show variable hiatuses in the sedimentary record. Locally, high velocity bottom currents were probably responsible for erosion, nondeposition or minimal sedimentation rates. These currents might have been initiated partly by the somewhat exposed position of this part of the continental slope, where the shelf edge bends from a northwest towards an eastern direction, and partly by very young tectonic movements. Fracture zones with vertically displaced fault blocs are frequent at Sierra Leone continental margin. According to seismic measurements by McMaster et al. (1975) the sites of the central area are located on an uplifted fault bloc explaining the reduced sediment rates or erosion. Unlike the central area, the eastern area (profile C) is situated on a downfaulted bloc with high sediment rates. The sediments from the cores of profile B as well as the turbiditic deep-sea sediments were deposited under a higher flow regime; therefore they are coarser than the extremely fine-grained sediments of the cores from profile C. Since the sand fraction (> 63 µm) is mainly composed of foraminifera, besides pteropods and light-colored fecal pellets, the carbonate content increases with the increasing percentage of the coarse grain fraction. Higher concentrations of quartz were only observed in core sections with considerable carbonate dissolution (mainly in the X-Zone), and, in general, in all sediments from the eastern area with higher terrigenous input including larger concentration of mica. Especially during times transitional between glacials and interglacials (or interstadials) the bottom currents were intensified. The percentages of coarse fraction and carbonate increase with increasing current velocities. Calcium carbonate dissolution becomes important in water depths > 3500 m. During cooler times the lysokline is depressed. Light-colored fecal pellets were redeposited from Late Neogene sediments (M30-187, M30-181). In the area of investigation they occur in the Holocene and mainly the Pleistocene sediments of the cores from the northwestern and central area because only here Tertiary sediments have been eroded at the uppermost continental slope. In the central area there are at least two periods of non-sedimentation and/or erosion which can be confined as being (1) not older than middle Pliocene and not younger than zone V and (2) younger than zone W. The local character of the erosion is documented by the fact that a complete Late Quaternary section is present in the cores of the northwestern and eastern area, each within less than 100 km from incomplete cores from the central area.

Sedimentology and geochemistry of the sand fraction in surface sediments off West Africa

Surface sediments from 5 profiles between 30 and 3000 m water depth off W Africa (12-19° N) have been studied for their sand fraction composition and their total calcium carbonate and organic matter contents to evaluate the effect of climatic and hydrographic factors on actual sedimentation. On the shelf and upper slope (< 500 m), currents prevent the deposition of significant amounts of fine-grained material. The sediments forming here are characterized by high sand contents (> 60 %; in most samples > 89 %), low organic carbon contents (in most samples < 0.8 %), high median diameters of the sand fraction (120-500 µm), and by a predominance of quartz and biogenic relict shells (most abundant: molluscs and bryozoans) in the sand fraction. Median diameters of total sand fraction and of major biogenic sand fraction components (biogenic relict material, benthonic molluscs, benthonic and planktonic foraminifers) co-vary to some extent and show maximum values in 100-300 m water depth, reflectingthe sorting effect of currents (perhaps the northward flowing undercurrent). In this water depth, biogenic relict material is considerably enriched relative to wuartz, the second dominating sand fraction component on the shelf and upper slope, resulting in distinct calcium carbonate maxima of the bulk sediments. The influence of the undercurrent is also reflected in a northward transport of fine grained river load and perhaps in the distribution of the red stained, coarse silt and sand-size clay aggregates, which show maxima in 300-500 m water depth. They probably originate from tropical soils. Abundant coarse red-stained quartz on the shelf off Cape Roxo (12-130° N) suggests a southward extension of last glacial dune fields to this latitude. Below about 500 m water depth, current influence becomes negligible - as indicated by a strong decrease in sand content, a concomitant increase in sedimentary organic carbon contents (up to 2.5-3.5 %), and the occurence of high mica/quartz ratios in the sand fraction. Downslope transport, presumably due to the bioturbation mechanism, is indicated by the presence of coarse shelf-borne particles (glauconite, relict shells) down to about 1000 m water depth. The fine/coarse ratio (clay + silt/sand) of the sediments from water deoth > 500 m never exceed a value of 11 in northern latitudes (19° - 26° N), but shows distinct maxima, ranging from 50 to 120, at latitudes 18°, 17° 15°30', and 14° N in about 2000 m water depth. This distribution is attributed to the deposition of fine-grained river load at the continental slope between 18° and 14° N, brought into the sea by the Senegal and souther rivers and transported northward ny the undercurrent. Strong calcium carbonate dissolution is indicated by the complete disappearance of pteropodes (aragonite) and high fragmentation of the planktoic foraminifers (calcite) in sediments from water depth > 300-600 m. Fragmentation ratios of planktonic foraminifers were found to depend on the organic carbon/carbonate ratios of the sediment suggesting that calcite dissolution at the sea bottom may also be significant in shelf and continental slope water depths if the organic matter/carbonate ratio of the surface sediment is high and the test remain long enough within the oxidizing layer on the top of the sulfate reduction zone. The fact that in the region under study intensity and anual duration of upwelling decrease from north to south is neither reflected in the composition on the sand fraction (i.e. radiolarian and fish debris contents, radiolarian/planktonic foraminiferal ratios, benthos/plankton ratios of foraminifers), nor in the sedimentary organic carbon distribution. On the contrary, these parameters even show in comparable water depths a tendency for highest values in the south, partly because primary production rates remain high in the whole region, particularly on the shelf, due to the nutrient input by rivers in the south. In addition, several hydrographic, sedimentological and climatic factors severely affect their distribution - for example currents, dissolution, grain size composition, deposition of river load, and bulk sedimentation rats.

A 31,000-year high-resolution record from two sediment cores off northwest Africa

Benthic foraminiferal assemblage compositions and sedimentary geochemical parameters were analyzed in two radiocarbon dated sediment cores from the upwelling area off NW Africa at 12°N, to reconstruct productivity changes during the last 31 kyr. High-latitude cold events and variations in low-latitude summer insolation influenced humidity, wind systems, and the position of the tropical rain belt over this time period. This in turn caused changes in intensity and seasonality of primary productivity off the southern Northwest African continental margin. High accumulation rates of benthic foraminifera, carbonate, and organic carbon during times of north Atlantic melt water events Heinrich 2 (25.4 to 24.3 kyr BP) and 1 (16.8 to 15.8 kyr BP) indicate high productivity. Dominance of infaunal benthic foraminiferal species and high numbers of deep infaunal specimens during that time indicate a strong and sustained supply of refractory organic matter reworked from the upper slope and shelf. A more southerly position of the tropical rainbelt and the Northeast trade wind belt during Heinrich 2 and 1 may have enhanced wind intensity and almost permanent upwelling, driving this scenario. A phytodetritus-related benthic fauna indicates seasonally pulsed input of labile organic matter but generally low year-round productivity during the Last Glacial Maximum (23 to 18 kyr BP). The tropical rainbelt is more expanded to the North than during Heinrich Events, and relatively weak NE trade winds resulted in seasonal and weak upwelling, thus lower productivity. High productivity characterized by a seasonally high input of labile organic matter, is indicated for times of orbital forced warming, such as the African Humid Period (9.8 to 7 kyr BP). An intensified African monsoon during boreal summer and the northernmost position of the tropical rainbelt within the last 31 kyr resulted in enhanced river discharge from the northward-extended drainage area (or river basin) initiating intense phytoplankton blooms. In the late Holocene (4 to 0 kyr BP) strong carbonate dissolution may have been caused by even more enhanced organic matter fluxes to the sea floor. Increasing aridity on the continent and stronger NE trade winds induced intensive, seasonal coastal upwelling.