Project description:During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.
Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.
Project description:Cell migration is crucial for many physiological and pathological processes. During embryogenesis, neural crest cells undergo coordinated epithelial to mesenchymal transformations and migrate towards various forming organs. Here we develop a computational model to understand how mutual interactions between migrating neural crest cells (NCs) and the surrounding population of placode cells (PCs) generate coordinated migration. According to experimental findings, we implement a minimal set of hypotheses, based on a coupling between chemotactic movement of NCs in response to a placode-secreted chemoattractant (Sdf1) and repulsion induced from contact inhibition of locomotion (CIL), triggered by heterotypic NC-PC contacts. This basic set of assumptions is able to semi-quantitatively recapitulate experimental observations of the characteristic multispecies phenomenon of "chase-and-run", where the colony of NCs chases an evasive PC aggregate. The model further reproduces a number of in vitro manipulations, including full or partial disruption of NC chemotactic migration and selected mechanisms coordinating the CIL phenomenon. Finally, we provide various predictions based on altering other key components of the model mechanisms.
Project description:The discovery of fall armyworm, a native of the Western Hemisphere, in western Africa in 2016 was rapidly followed by detections throughout sub-Saharan Africa, India, and most recently southeastern Asia. This moth pest has a broad host range that threatens such important crops as corn, rice, millet, and sorghum, creating concern for its potential impact on agriculture in the Eastern Hemisphere. Although genetic data suggest populations sampled in Africa and India originate from a recent common source, it is not known whether this is the case for populations in southeastern Asia, nor whether the subgroup with a preference for rice and millet is present in the region. This study found through comparisons of genetic markers that the fall armyworm from Myanmar and southern China are closely related to those from Africa and India, suggesting a common origin for these geographically distant populations. The results are consistent with a single recent introduction into the Eastern Hemisphere followed by rapid dispersion. The molecular similarities include discrepancies between the genetic markers that brings into question whether the subpopulation most likely to be a threat to rice and millet is present in significant numbers in Asia.
Project description:Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.
Project description:The proliferation of ski run construction is a worldwide trend. The machine-grading of slopes involved during ski run construction changes the physical, chemical and biological properties of the soil, having significant long-term ecological impact on the environment. Establishing and developing plant communities in these affected areas is crucial in rehabilitating the biotic and abiotic soil environment, while also improving slope stability and reducing the risk of natural hazards. This study evaluates changes in plant-soil properties and the long-term effects of machine-grading and subsequent restoration of ski runs so as to contribute to formulating the best practices in future ski run constructions. Study plots were established in 2000 and re-surveyed in 2017 on ski runs, which had been machine-graded and hydroseeded in the 1990s. Vegetation, root trait and soil surveys were carried out on ski run plots and compared to paired, undisturbed control sites off the ski runs. Plant cover remained unchanged on the ski-runs over time but plant richness and diversity considerably increased, reaching similar levels to undisturbed vegetation. Plant composition moved towards more semi-natural stages, showing a reduction in seeded plants with a comparable increase in the cover of colonizing native species. Root trait results were site-specific showing great variations between the mid and long-term after-effects of machine-grading and revegetation when compared to undisturbed sites. Under long-term management, the soil pH was still higher and the organic C content still lower in the ski runs than in the undisturbed sites, as the aggregate stability. The standard actions applied (machine-grading, storage and re-use of topsoil, hydroseeding of commercial seed mixtures, application of manure soon after seeding and low-intensity grazing) allowed the ecosystem to partially recover in three decades, and even if the soil has still a lower chemical and physical fertility than the undisturbed sites, the plant species composition reveals a satisfactory degree of renaturalization.
Project description:Collective cell migration in morphogenesis and cancer progression often involves the coordination of multiple cell types. How reciprocal interactions between adjacent cell populations lead to new emergent behaviours remains unknown. Here we studied the interaction between neural crest (NC) cells, a highly migratory cell population, and placodal cells, an epithelial tissue that contributes to sensory organs. We found that NC cells chase placodal cells by chemotaxis, and placodal cells run when contacted by NC. Chemotaxis to Sdf1 underlies the chase, and repulsion involving PCP and N-cadherin signalling is responsible for the run. This chase-and-run requires the generation of asymmetric forces, which depend on local inhibition of focal adhesions. The cell interactions described here are essential for correct NC migration and for segregation of placodes in vivo and are likely to represent a general mechanism of coordinated migration.
Project description:BACKGROUND:Chikungunya virus (CHIKV) originated in a sylvatic cycle of transmission between non-human animal hosts and vector mosquitoes in the forests of Africa. Subsequently the virus jumped out of this ancestral cycle into a human-endemic transmission cycle vectored by anthropophilic mosquitoes. Sylvatic CHIKV cycles persist in Africa and continue to spill over into humans, creating the potential for new CHIKV strains to enter human-endemic transmission. To mitigate such spillover, it is first necessary to delineate the distributions of the sylvatic mosquito vectors of CHIKV, to identify the environmental factors that shape these distributions, and to determine the association of mosquito presence with key drivers of virus spillover, including mosquito and CHIKV abundance. We therefore modeled the distribution of seven CHIKV mosquito vectors over two sequential rainy seasons in Kédougou, Senegal using Maxent. METHODS:Mosquito data were collected in fifty sites distributed in five land cover classes across the study area. Environmental data representing land cover, topographic, and climatic factors were included in the models. Models were compared and evaluated using area under the receiver operating characteristic curve (AUROC) statistics. The correlation of model outputs with abundance of individual mosquito species as well as CHIKV-positive mosquito pools was tested. RESULTS:Fourteen models were produced and evaluated; the environmental variables most strongly associated with mosquito distributions were distance to large patches of forest, landscape patch size, rainfall, and the normalized difference vegetation index (NDVI). Seven models were positively correlated with mosquito abundance and one (Aedes taylori) was consistently, positively correlated with CHIKV-positive mosquito pools. Eight models predicted high relative occurrence rates of mosquitoes near the villages of Tenkoto and Ngary, the areas with the highest frequency of CHIKV-positive mosquito pools. CONCLUSIONS:Of the environmental factors considered here, landscape fragmentation and configuration had the strongest influence on mosquito distributions. Of the mosquito species modeled, the distribution of Ae. taylori correlated most strongly with abundance of CHIKV, suggesting that presence of this species will be a useful predictor of sylvatic CHIKV presence.
Project description:The aim of this study was to generate an easy to use index to evaluate the ecological state of agricultural land from a sustainability perspective. We selected environmental indicators, such as the use of organic soil amendments (green manure) versus chemical fertilizers, plant biodiversity (including crop associations), variables which characterize soil conservation of conventional agricultural systems, pesticide use, method and frequency of tillage. We monitored the ecological state of 52 agricultural plots to test the performance of the index. The variables were hierarchically aggregated with simple mathematical algorithms, if-then rules, and rule-based fuzzy models, yielding the final multi-criteria index with values from 0 (worst) to 1 (best conditions). We validated the model through independent evaluation by experts, and we obtained a linear regression with an r2 = 0.61 (p = 2.4e-06, d.f. = 49) between index output and the experts' evaluation.
Project description:The emergence of plant-based economies have dominated evolutionary models of Middle and Late Holocene pre-Columbian societies in South America. Comparatively, the use of aquatic resources and the circumstances for intensifying their exploitation have received little attention. Here we reviewed the stable carbon and nitrogen isotope composition of 390 human individuals from Middle and Late Holocene coastal sambaquis, a long-lasting shell mound culture that flourished for nearly 7000 years along the Atlantic Forest coast of Brazil. Using a newly generated faunal isotopic baseline and Bayesian Isotope Mixing Models we quantified the relative contribution of marine resources to the diet of some of these groups. Through the analysis of more than 400 radiocarbon dates we show that fishing sustained large and resilient populations during most of the Late Holocene. A sharp decline was observed in the frequency of sambaqui sites and radiocarbon dates from ca. 2200 years ago, possibly reflecting the dissolution of several nucleated groups into smaller social units, coinciding with substantial changes in coastal environments. The spread of ceramics from ca. 1200 years ago is marked by innovation and intensification of fishing practices, in a context of increasing social and ecological instability in the Late Holocene.