Biology subjects

Key, A.

Publications and source records attributed to Key, A..

3 recordsLinked to original sources

bioRxiv2024

Spatiotemporal dispersion of DENV1 genotype V in western Colombia

Dengue virus (DENV) is a significant public health concern in Colombia, with increased transmission of DENV type 1 (DENV-1) in the departments of Risaralda and Valle del Cauca in the Central-West region of the country following a large outbreak in 2019. However, little is known about the source, genetic diversity, and evolution of circulating viruses. We obtained plasma samples from individuals with acute DENV infection and analyzed DENV-1 genetic diversity, phylodynamics, and phylogeography. We found that most viruses belonged to DENV-1 genotype V, and phylogenetic analysis revealed three distinct clades, each of which was most closely related to viruses from neighboring departments of Colombia sampled over the last 5-10 years. Thus, the 2019 outbreak and subsequent DENV-1 circulation was not due to the introduction of a new lineage but rather reflected local DENV-1V dispersion and evolution. We identified amino acid positions under positive selection in structural proteins and NS1, which may have a role in immune evasion and pathogenesis. Overall, our analysis of DENV1 genotype V diversity, evolution and spread within Colombia highlights the important role of genomic surveillance in understanding virus dynamics during endemic circulation and outbreaks.

evolutionary biology↗

bioRxiv2024

The Acheulean niche: climate and ecology predict handaxe production in Europe

The Acheulean was the most spatially and temporally vast stone tool industry produced by early humans, persisting for >1.6 million years across three continents. Understanding how behavioral and artifactual variation in these populations relates to climate change and ecology is vital to correctly interpreting the archaeological record, especially given the major climatic and cultural fluctuations during the Pleistocene. Bifacially flaked core tools - which technologically define the tradition - are sometimes regionally and periodically absent within the Acheuleans boundaries. Biface presence is broadly associated with, but rarely formally tested against, environmental conditions. Here, we investigate biface presence/absence and climate/ecological variation at a continental scale between 726 and 130ka. Using a comprehensive sample of European sites matched to paleoenvironmental reconstructions, we demonstrate clear associations between Acheulean presence and specific environments. Acheulean habitat suitability was most strongly associated with mean winter temperatures above -5/-10{degrees}C, and precipitation of the driest month above 15 mm. Two major habitats, warm forest/woodland and shrubland, comprised the European Acheulean niche. Acheulean spatial presence was reconstructed through time: during interglacial and glacial periods it covered most of southwestern Europe, but extended along northern coastal routes during interglacials. Central and Eastern Europe always remained unsuitable. The Acheulean was excluded from areas experiencing both low winter temperatures and low summer precipitation, but reached areas including only one of those two climatic extremes, suggesting seasonal migrations to avoid the harshest seasons. These analyses explain current Acheulean site distributions in Europe and suggest strong links between handaxes, specific ecological conditions, and prehistoric demographic patterns.

evolutionary biology↗

bioRxiv2022

Optimal linear estimation models predict 1400-2800 years of co-existence between Neandertals and Homo sapiens in western Europe.

Recent fossil discoveries suggest that Neandertals and Homo sapiens may have co-existed in Europe for as long as five to six thousand years. Yet, evidence for their contemporaneity at any regional scale remains elusive. In France and northern Spain, a region which features some of the latest directly-dated Neandertals in Europe, Protoaurignacian assemblages attributed to Homo sapiens appear to replace Neandertal-associated Chatelperronian assemblages. Using the earliest and latest known occurrences as starting points, Bayesian modelling has provided some indication that these occupations may in fact have been partly contemporaneous. The reality, however, is that we are unlikely to ever identify the first or last appearance of a species or cultural tradition in the archaeological and fossil record. Here, we use optimal linear estimation modelling to estimate the first appearance date of Homo sapiens and the extinction date of Neandertals in France and northern Spain by statistically inferring these missing portions of the Protoaurignacian and Chatelperronian archaeological records. Additionally, we estimate the extinction date of Neandertals in this region using a set of directly-dated Neandertal fossil remains. The results suggest that the onset of the Homo sapiens occupation of this region likely preceded the extinction of Neandertals and the Chatelperronian by up to 1400-2900 years - raising the possibility of an extended co-existence of these groups during the initial Upper Palaeolithic of this region. Whether or not this co-existence featured some form of direct interaction, however, remains to be resolved.

evolutionary biology↗