Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

Studying instances of convergent evolution of novel phenotypes can shed light on the evolutionary constraints that shape morphological diversity. Cichlid fishes from the East African Great Lakes are a prime model to investigate convergent adaptations. However, most studies on cichlid craniofacial morphologies have primarily considered bony structures, while soft tissue adaptations have been less intensely scrutinised. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap. This tissue flap develops from the upper lip and has evolved in only one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap (Labeotropheus trewavasae and Ophthalmotilapia nasuta) to their close relatives without snout flaps (Tropheops tropheops and Ophthalmotilapia ventralis) from Lake Tanganyika and Malawi. Our analysis revealed a greater complexity of differential gene expression patterns underlying the snout flap in the younger adaptive radiation of Lake Malawi than in the older Lake Tanganyika radiation. We identified 201 genes that were repeatedly differentially expressed between species with and without the snout flap in both lakes, suggesting that the pathway that gives rise to snout flaps is evolutionarily constrained, even though the flaps play very different functions in each species. The convergently expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we also found enrichment for transcription factor binding sites upstream of differentially expressed genes such as members of the FOX transcription factor family, especially foxf1 and foxa2, which also showed an increased expression in the flapped snout and are linked to nose morphogenesis in mammals, as well as ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in the development of craniofacial soft tissues. As genes involved in cichlids snout flap development are associated with many human mid-line facial dysmorphologies, our findings imply a conservation of genes involved in mid-line patterning across vastly distant evolutionary lineages of vertebrates.

Bioethics in Kenya: Who is Interested in Certificate Courses

Inadequate training in matters of ethics renders health care providers unprepared for dilemmas faced in public health, research, and clinical practice. Certificate course training offer opportunities to gain more knowledge and skills on all matter ethics. Over the past decade, the increase in research activities in Kenya has not been proportionate to training in ethics. The centre of Biomedical Ethics and Culture (CBEC), Kenya Medical Research Institute (KEMRI) Bioethics training Initiative (CK-BTI) is a Forgaty funded program for building capacity in research ethics for Kenya and Pakistan. This paper evaluates the characteristics of participants that attended the CK-BTI certificate level courses in Kenya between 2017 to 2021. This data was analysed for this paper and utilized information from the training application process. Between November 2017 and July 2021, a total of 1,359 applications were received and 457 (33.6%) trained. The target countries were Kenya and Pakistan but interest was drawn from Tanzania, Uganda, Nigeria, and Zambia. The continued interest in the certificate level ethics courses may imply a need to increase the number of ethics training offered within the East African region.

Some of the geological challenges and opportunities associated with the dynamics of the Cenozoic East African Rift System

The Cenozoic East African Rift System (EARS) is the largest continental rift valley system on Earth. Extending over a total distance of approximately 4,500 km, and with an average width of about 50 km, it is home to some of East Africa's largest urban populations and some of its most important transport, energy and water supply infrastructure. Rifting commenced during the Early Miocene and crustal extension has continued to the present day, posing seismic and volcanic hazards throughout its history of human occupation. Deep-seated landslides also present significant challenges for public safety, land management and infrastructure development on the flanks of rift margins. The rift floor itself poses a range of geohazards to community livelihood and engineering infrastructure, including ground fissuring and cavity collapse, flooding and sedimentation. On the positive side, the development of the EARS has created hydrocarbon and geothermal energy resources, and geomaterials for use as aggregates and cement substitutes in road and building construction. Optimising the use of these resources requires careful planning to ensure sustainability, while land use management and infrastructure development must take full consideration of the hazards posed by the ground and the fragility and dynamism of the human and physical environment.

The principles of helium exploration

Commercial helium systems have been found to date as a serendipitous by-product of petroleum exploration. There are nevertheless significant differences in the source and migration properties of helium compared with petroleum. An understanding of these differences enables prospects for helium gas accumulations to be identified in regions where petroleum exploration would not be tenable. Here we show how the basic petroleum exploration playbook (source, primary migration from the source rock, secondary longer distance migration, trapping) can be modified to identify helium plays. Plays are the areas occupied by a prospective reservoir and overlying seal associated with a mature helium source. This is the first step in identifying the detail of helium prospects (discrete pools of trapped helium). We show how these principles, adapted for helium, can be applied using the Rukwa Basin in the Tanzanian section of the East African Rift as a case study. Thermal hiatus caused by rifting of the continental basement has resulted in a surface expression of deep crustal gas release in the form of high-nitrogen gas seeps containing up to 10% 4He. We calculate the total likely regional source rock helium generative capacity, identify the role of the Rungwe volcanic province in releasing the accumulated crustal helium, and show the spatial control of helium concentration dilution by the associated volcanic CO2. Nitrogen, both dissolved and as a free gas phase, plays a key role in the primary and secondary migration of crustal helium and its accumulation into what might become a commercially viable gas pool. This too is examined. We identify and discuss evidence that structures and seals suitable for trapping hydrocarbon and CO2 gases will likely also be efficient for helium accumulation on the timescale of the Rukwa basin activity.The Rukwa Basin prospective recoverable P50 resources of helium have been independently estimated to be about 138 billion standard cubic feet (2.78 x 109 m3 at STP). If this volume is confirmed it would represent about 25% of the current global helium reserve. Two exploration wells Tai 1 and Tai 2 completed by August 2021 have proved the presence of seal and reservoir horizons with the reservoirs containing significant helium shows.This article is part of the Energy Geoscience Series available at https://www.lyellcollection.org/cc/energy-geoscience-series

Preliminary Seismic Hazard Analyses for the Ugandan Region

Uganda is situated between the two seismically active branches of the East African Rift Valley System, which are characterized by high levels of seismicity. A probabilistic approach has been used to assess the seismic hazard for Uganda and the surrounding areas. A probabilistic seismic hazard analysis requires the availability of an earthquake catalog, relevant ground motion prediction equations, and an outline of how the hazard calculations will be conducted. Using online sources, an earthquake catalog for Uganda and the immediate areas around Uganda was compiled spanning 108 years, from 1912 to 2020. This catalog was homogenized to moment magnitude to match with the selected ground motion prediction equations from Toro and Idriss. A logic tree accounting for the two ground motion prediction equations and dividing the study region into four seismic zones was used for calculating the seismic hazard. As an example, the seismic hazard results at two sites close to each other showed how different seismic hazards can be. Results from the probabilistic seismic hazard analyses was expressed through seismic hazard maps for peak ground acceleration at 10% probability of exceedance in 5, 10, 20, 50, 100 and 500 years, corresponding to return periods of 50, 100, 200, 500, 1000 and 5000 years, respectively. The seismic hazard map for 10% probability of exceedance in 5 years calculated PGAs from 0.02 to 0.10 g and 0.10 to 0.27 g outside of and within the western branch of the East African Rift Valley System, respectively. The estimated PGAs from previous studies at a similar probability of exceedance level are within the range of these findings, although the ranges calculated herein are wider.

Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes

Rapid ecological speciation along depth gradients has taken place independently and repeatedly in freshwater fishes. While the extent of genomic divergence between ecomorphs is often well understood, the molecular mechanisms facilitating such rapid diversification are typically unclear. In Lake Masoko, an East African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow littoral and deep benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data from jaw tissue, we explore two major regulatory transcriptional mechanisms, expression and splicing QTL variants and examine their contribution to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 4.2% were regulated by cis-regulatory expression QTLs, and 6.4% were regulated by cis-regulatory splicing QTLs. There were also strong signals of divergent selection of differentially expressed genes that showed divergent regulation from expression, splicing or both QTL variants, including genes associated with major jaw plasticity and adaptation networks, adaptive immune system response, and oxidoreductase processes. These results suggest that transcriptome plasticity and modification have important roles during early-stage ecological speciation and demonstrate the role of regulatory-variants as important targets of selection driving ecologically-relevant divergence in gene expression that is associated with adaptive diversification.

What Farm Size Sustains a Living? Exploring Future Options to Attain a Living Income From Smallholder Farming in the East African Highlands

Smallholder farming in sub-Saharan Africa keeps many rural households trapped in a cycle of poor productivity and low incomes. Two options to reach a decent income include intensification of production and expansion of farm areas per household. In this study, we explore what is a “viable farm size,” i.e., the farm area that is required to attain a “living income,” which sustains a nutritious diet, housing, education and health care. We used survey data from three contrasting sites in the East African highlands—Nyando (Kenya), Rakai (Uganda), and Lushoto (Tanzania) to explore viable farm sizes in six scenarios. Starting from the baseline cropping system, we built scenarios by incrementally including intensified and re-configured cropping systems, income from livestock and off-farm sources. In the most conservative scenario (baseline cropping patterns and yields, minus basic input costs), viable farm areas were 3.6, 2.4, and 2.1 ha, for Nyando, Rakai, and Lushoto, respectively—whereas current median farm areas were just 0.8, 1.8, and 0.8 ha. Given the skewed distribution of current farm areas, only few of the households in the study sites (0, 27, and 4% for Nyando, Rakai, and Lushoto, respectively) were able to attain a living income. Raising baseline yields to 50% of the water-limited yields strongly reduced the land area needed to achieve a viable farm size, and thereby enabled 92% of the households in Rakai and 70% of the households in Lushoto to attain a living income on their existing farm areas. By contrast, intensification of crop production alone was insufficient in Nyando, although including income from livestock enabled the majority of households (73%) to attain a living income with current farm areas. These scenarios show that increasing farm area and/or intensifying production is required for smallholder farmers to attain a living income from farming. Obviously such changes would require considerable capital and labor investment, as well as land reform and alternative off-farm employment options for those who exit farming.