Diaz, J. S. | bioRxiv Science

bioRxiv2024

Incorporating climatic extremes using the GEV distribution improves SDM range edge performance

AimThe changing frequency and intensity of climatic extremes due to climate change can have sudden and adverse impacts on the distribution of species. While species distribution modelling is a vital tool in ecological applications, current approaches fail to fully capture the distribution of climatic extremes, particularly of rare events with the most disruptive potential. Especially at the edges of species ranges, where conditions are already less favourable, predictions might be inaccurate when these extremes are not well represented. LocationEurope TaxonTree species MethodsWe present a novel approach to integrate extreme events into species distribution models based on the generalised extreme value (GEV) distribution. This distribution, following from the extreme value theory has been established as a valuable tool in analysing climatic extremes, both in an ecological context and beyond. The approach relying on the GEV distribution is broadly applicable, readily transferable across species and relies on widely available data. We demonstrate the efficacy of our approach for 28 European tree species, illustrating its superior ability to fully capture the distribution of climatic extremes compared to state-of-the-art methods. ResultsWe found that incorporating parameters on climatic extremes derived from the GEV distribution increased model performance (AICmodel) and characterized range edges more accurately (AUCedge) compared to competing approaches. However, general AUC values were only marginally increased across the species and study period analysed. Overall, the GEV model predicted a narrower niche for the species included in this study. Main conclusionsIncorporating climatic extremes can impact spatial predictions of species distribution models, especially at range margins. We found that using the GEV distribution to characterise extreme variables in SDMs yields the best performance at these distribution edges. Given the importance of range edges for species conservation, a detailed inclusion of extremes in SDMs employed for those applications will help ensure robust conclusions.

ecology↗

bioRxiv2021

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

genetics↗