Biology subjects

Pless, E.

Publications and source records attributed to Pless, E..

3 recordsLinked to original sources

bioRxiv2024

Sequencing 1206 genomes reveals origin and movement of Aedes aegypti driving increased dengue risk

The number of dengue cases worldwide has increased ten-fold over the past decade as Aedes aegypti, the primary vector of this disease, thrives and expands its distribution, revealing limitations to current control methods. To better understand how Ae. aegypti evolved from a forest dwelling, generalist species to a highly anthropophilic urban species and the impact of contemporary gene flow on the future of dengue control, we sequenced 1,206 genomes from mosquitoes collected at 74 locations around the globe. Here we show that after evolving a preference for humans in the Sahel region of West Africa, the origin of the fully domesticated, anthropophilic subspecies Ae. aegypti aegypti (Aaa) occurred in the Americas during the Atlantic Slave Trade era and was followed by its explosive expansion around the globe. In recent decades, Aaa has invaded coastal Africa, the ancestral home range, introducing insecticide resistance mutations and an affinity for human hosts. Evidence of back-to-Africa migration is found in regions with recent dengue outbreaks, raising concern that global movement of Aaa could increase transmission risk of arboviruses including dengue in urban Africa. These data provide a platform to further study this important mosquito vector species and underscore developing complexity in the fight to limit the spread of dengue, Zika, and chikungunya diseases.

genomics↗

bioRxiv2022

Predicting environmental and ecological drivers of human population structure

Landscape, climate, and culture can all structure human populations, but few methods are designed to disentangle the importance of these many variables. We developed a machine learning method for identifying the variables which best explain migration rates, as measured by the coalescent-based program MAPS that uses shared identical by descent tracts to infer and extrapolate spatial migration across a region of interest. We applied our method to 30 human populations in eastern Africa with high density SNP array data. The remarkable diversity of ethnicities, languages, and environments in this region offers a unique opportunity to explore the variables that shape migration and genetic structure in humans. We explored more than twenty spatial variables relating to landscape, climate, and presence of tsetse flies (an important regional disease vector). The full model explained ~40% of variance in migration rate over the past 56 generations. Precipitation, minimum temperature of the coldest month, and altitude were the most important variables. Among the three groups of tsetse flies, the most important was the fusca group which is a vector for livestock trypanosomiasis. We also performed a selection scan on a subgroup of the populations who live in Ethiopia at relatively high altitudes. We did not identify well-known high-altitude genes, but we did find signatures of positive selection related to metabolism and disease. We conclude that environment has notably shaped the migration and adaptation of human populations in eastern Africa; the remaining variance in structure is likely due to cultural factors not captured in our model.

evolutionary biology↗

bioRxiv2021

The Recombination Landscape of the Khoe-San - the Upper Limits of Recombination Divergence in Humans

Recombination maps are important resources for epidemiological and evolutionary analyses, however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We inferred the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derived a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesized that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. We showed that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we used selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans.

bioinformatics↗