Origins of Shared Genetic Variation in African Cichlids

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of 160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.

Herbivores equalize the seedling height growth of three dominant tree species in an African tropical rain forest

Determining the impact of insect herbivores on forest tree seedlings and saplings is difficult without experimentation in the field. Moreover, this impact may be heterogeneous in time and space because of seasonal rainfall and canopy disturbances, or ‘gaps’, which can influence both insect abundance and plant performance. In this study we used fine netting to individually protect seedlings of Microberlinia bisulcata, Tetraberlinia bifoliolata and Tetraberlinia korupensis trees (Fabaceae = Leguminosae) from insects in 41 paired gap-understorey locations across 80 ha of primary rain forest (Korup, Cameroon). For all species, growth in height and leaf numbers was negligible in the understorey, where M. bisulcata had the lowest survival after c. 2 years. In gaps, however, all species responded positively with pronounced above-ground growth across seasons. When exposed to herbivores their seedling height growth was similar, but in the absence of herbivores, M. bisulcata significantly outgrew both Tetraberlinia species and matched their leaf numbers. This result suggests that insect herbivores might play an important role in maintaining species coexistence by mitigating sapling abundance of the more palatable M. bisulcata, which in gaps was eaten the most severely. The higher ratio in static leaf damage of control-to-caged M. bisulcata seedlings in gaps than understorey locations was consistent with the Plant Vigour Hypothesis. This result, however, did not apply to either Tetraberlinia species. For M. bisulcata and T. korupensis, but not T. bifoliolata (the most shade-tolerant species), caging improved relative seedling survival in the understory locations compared to gaps, providing restricted support for the Limiting Resource Model. Approximately 2.25 years after treatments were removed, the caged seedlings were taller and had more leaves than controls in all three species, and the effect remained strongest for M. bisulcata. We conclude that in this community the impact of leaf herbivory on seedling growth in gaps is strong for the dominant M. bisulcata, which coupled to a very low shade-tolerance contributes to limiting its regeneration. However, because gaps are common to most forests, insect herbivores may be having impacts upon functionally similar tree species that are also characterized by low sapling recruitment much more widely than currently appreciated. An implication for the restoration and management of M. bisulcata populations in forests outside of Korup is that physical protection from herbivores of new seedlings where the canopy is opened by gaps, or by harvesting, should substantially increase its subcanopy regeneration, and thus, too, its opportunities for adult recruitment.

The “Out of Africa Tribe” (II): Paleolithic warriors with big canoes and protective weapons

It is generally difficult to establish a timeline for the appearance of different technologies and tools during human cultural evolution. Here I use stochastic character mapping of discrete traits using human mtDNA phylogenies rooted to the Reconstructed Sapiens Reference Sequence (RSRS) as a model to address this question. The analysis reveals that the ancestral state of Homo sapiens was hunting, using material innovations that included bows and arrows, stone axes and spears. However, around 80,000 y before present, a transition occurred, from this ancestral hunting tradition, toward the invention of protective weapons such as shields, the appearance of ritual fighting as a socially accepted behavior and the construction of war canoes for the fast transport of large numbers of warriors. This model suggests a major cultural change, during the Palaeolithic, from hunters to warriors. Moreover, in the light of the recent Out of Africa Theory, it suggests that the “Out of Africa Tribe” was a tribe of warriors that had developed protective weapons such as shields and used big war canoes to travel the sea coast and big rivers in raiding expeditions.

Buffer capacity: capturing a dimension of resilience to climate change in African smallholder agriculture

Building resilience to climate change in agricultural production can ensure the functioning of agricultural-based livelihoods and reduce their vulnerability to climate change impacts. This paper thus explores how buffer capacity, a characteristic feature of resilience, can be conceptualised and used for assessing the resilience of smallholder agriculture to climate change. It uses the case of conservation agriculture farmers in a Kenyan region and examines how their practices contribute to buffer capacity. Surveys were used to collect data from 41 purposely selected conservation agriculture farmers in the Laikipia region of Kenya. Besides descriptive statistics, factor analysis was used to identify the key dimensions that characterise buffer capacity in the study context. The cluster of practices characterising buffer capacity in conservation agriculture include soil protection, adapted crops, intensification/irrigation, mechanisation and livelihood diversification. Various conservation practices increase buffer capacity, evaluated by farmers in economic, social, ecological and other dimensions. Through conservation agriculture, most farmers improved their productivity and incomes despite drought, improved their environment and social relations. Better-off farmers also reduced their need for labour, but this resulted in lesser income-earning opportunities for the poorer farmers, thus reducing the buffer capacity and resilience of the latter.

Testosterone and acute stress are associated with fibrinogen and von Willebrand factor in African men: the SABPA study.

BACKGROUND Low testosterone, acute and chronic stress and hypercoagulation are all associated with hypertension and hypertension-related diseases. The interaction between these factors and future risk for coronary artery disease in Africans has not been fully elucidated. In this study, associations of testosterone, acute cardiovascular and coagulation stress responses with fibrinogen and von Willebrand factor in African and Caucasian men in a South African cohort were investigated. METHODS Cardiovascular variables were studied by means of beat-to-beat and ambulatory blood pressure monitoring. Fasting serum-, salivary testosterone and citrate coagulation markers were obtained from venous blood samples. Acute mental stress responses were evoked with the Stroop test. RESULTS The African group demonstrated a higher cardiovascular risk compared to Caucasian men with elevated blood pressure, low-grade inflammation, chronic hyperglycemia (HbA1c), lower testosterone levels, and elevated von Willebrand factor (VWF) and fibrinogen levels. Blunted testosterone acute mental stress responses were demonstrated in African males. In multiple regression analyses, higher circulating levels of fibrinogen and VWF in Africans were associated with a low T environment (R(2) 0.24-0.28; p≤0.01), but only circulating fibrinogen in Caucasians. Regarding endothelial function, a low testosterone environment and a profile of augmented α-adrenergic acute mental stress responses (diastolic BP, D-dimer and testosterone) were associated with circulating VWF levels in Africans (Adj R(2) 0.24; p<0.05). CONCLUSIONS An interdependence between acute mental stress, salivary testosterone, D-dimer and vascular responses existed in African males in their association with circulating VWF but no interdependence of the independent variables occurred with fibrinogen levels.

Lake-level rise in the late Pleistocene and active subaquatic volcanism since the Holocene in Lake Kivu; East African Rift

The history of Lake Kivu is strongly linked to the activity of the Virunga volcanoes. Subaerial and subaquatic volcanoes, in addition to lake-level changes, shape the subaquatic morphologic and structural features in Lake Kivu's Main Basin. Previous studies revealed that volcanic eruptions blocked the former outlet of the lake to the north in the late Pleistocene, leading to a substantial rise in the lake level and subsequently the present- day thermohaline stratification. Additional studies have speculated that volcanic and seismic activities threaten to trigger a catastrophic release of the large amount of gases dissolved in the lake. The current study presents a bathymetric mapping and seismic profiling survey that covers the volcanically active area of the Main Basin at a resolution that is unprecedented for Lake Kivu. New geomorphologic features identified on the lake floor can accurately describe related lake-floor processes for the first time. The late Pleistocene lowstand is observed at 425 m depth, and volcanic cones, tuff rings, and lava flows observed above this level indicate both subaerial and subaquatic volcanic activities during the Holocene. The geomorphologic analysis yields new implications on the geologic processes that have shaped Lake Kivu's basin, and the presence of young volcanic features can be linked to the possibility of a lake overturn.

Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent

There is established clinical evidence for differences in drug response, cure rates and survival outcomes between different ethnic populations, but the causes are poorly understood. Differences in frequencies of functional genetic variants in key drug response and metabolism genes may significantly influence drug response differences in different populations. To assess this, we genotyped 1330 individuals of African (n=372) and European (n=958) descent for 4535 single-nucleotide polymorphisms in 350 key drug absorption, distribution, metabolism, elimination and toxicity genes. Important and remarkable differences in the distribution of genetic variants were observed between Africans and Europeans and among the African populations. These could translate into significant differences in drug efficacy and safety profiles, and also in the required dose to achieve the desired therapeutic effect in different populations. Our data points to the need for population-specific genetic variation in personalizing medicine and care.

How does the taxonomic status of allopatric populations influence species richness within African cichlid fish assemblages?

Aim  Current estimates of species richness within rapidly evolving species flocks are often highly dependent on the species status of allopatric populations that differ in phenotypic traits. These traits may be unreliable indicators of biological species status and systematists may have inconsistently assigned species among lineages or locations on the basis of these traits, thus hampering comparative studies of regional species richness and speciation rates. Our aim was to develop a method of generating standardized estimates of regional species richness suitable for comparative analysis, and to use these estimates to examine the extent and consistency of species assignment of allopatric populations within rapidly evolving cichlid fish flocks present in three east African lakes. Location  Lakes Malawi, Victoria and Tanganyika. Methods  Using published taxon co-occurrence data, a novel approach was employed to calculate standardized ‘minimum’ estimates of regional species richness for hard substrate associated complexes of cichlids within each of the lakes. Minimum estimates were based on an explicit assumption that if taxa present on equivalent habitats have disjunct distributions, then they are allopatric forms of the same species. These estimates were compared with current observed ‘high-end’ regional species richness estimates for those complexes to determine the consistency of species assignment of allopatric populations between lineages within a lake. A ‘sympatry’ index was developed to enable comparisons of levels of species assignment of allopatric populations between-lakes to be made. Results  Within each lake, the minimum and high-end estimates for species richness were significantly correlated across complexes, indicating that the complexes that contain more recognized species contain the most genuine biological species. However, comparisons of complexes among lakes revealed considerable differences. For equivalent geographical areas, substantially higher proportions of recognized species were totally allopatric within the studied Lake Malawi and Lake Victoria complexes, than those of Lake Tanganyika. Main Conclusions  Among African lakes, levels of assignment to species status of allopatric populations were found to be distinctly different. It is unclear whether the discrepancies are a consequence of differences between the lake faunas in degrees of phenotypic divergence among allopatric populations, or are simply the result of inconsistent taxonomic practices. In either case, these results have considerable wider relevance for they emphasize that quantitative measures of regional and beta diversity are critically dependent on the species status of allopatric populations, an issue usually neglected in comparative studies of species richness. The technique introduced here can be used to standardize measures of regional diversity of lineages for comparative analyses, potentially enabling more accurate identification of processes influencing rates of speciation.

How fit turns into misfit and back: institutional transformations of pastoral commons in African floodplains

We enlarge the notion of institutional fit using theoretical approaches from New Institutionalism, including rational choice and strategic action, political ecology and constructivist approaches. These approaches are combined with ecological approaches (system and evolutionary ecology) focusing on feedback loops and change. We offer results drawn from a comparison of fit and misfit cases of institutional change in pastoral commons in four African floodplain contexts (Zambia, Cameroon, Tanzania (two cases). Cases of precolonial fit and misfit in the postcolonial past, as well as a case of institutional fit in the postcolonial phase, highlight important features, specifically, flexible institutions, leadership, and mutual economic benefit under specific relations of bargaining power of actors. We argue that only by combining otherwise conflicting approaches can we come to understand why institutional fit develops into misfit and back again. Key Words: African floodplains; governance; institutional change; institutional fit; New Institutionalism; pastoral commons