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Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severityNARA Subscribed
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the pr...
Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog ( Afrixalus )NARA Subscribed
Restriction site‐associated DNA sequencing (RADseq) has emerged as a useful tool in systematics and population genomics. A common feature of RADseq data sets is that they contain missing data that arise from multiple sources including genealogical sampling bias, assembly methodology and sequencing error. Many RADseq studies have demonstrated that allowing sites (single nucleotide polymorphisms, SNPs) with missing data can incr...
Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome‐wide sequence data for seven amphibiansNARA Subscribed
High‐throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non‐forest habitats. Complex arrangements of...
The 8.2‐ka BP event in north‐eastern North America: first combined oxygen and hydrogen isotopic data from peat in NewfoundlandNARA Subscribed
Finding direct evidence for atmospheric circulation change in terrestrial records of Holocene climate variability remains a fundamental challenge. Here we present the first combined stable oxygen and hydrogen isotopic palaeorecord from a peatland core in Newfoundland, Canada. Sphagnum cellulose samples were isolated from a core from Nordan's Pond Bog, Newfoundland, and analysed for δD values. Combined with existing δ 18 O data...
Peat archives offer a diverse range of physical and chemical proxies from which it is possible to study past environmental and ecological changes. Direct numerical calibration and verification is difficult so process‐based and mechanistic studies are therefore required to establish and quantify links between environmental changes and their associated proxy‐responses. Traditional ‘space‐for‐time’ calibrations provide a solution...
Testate amoebae as a proxy for reconstructing Holocene water table dynamics in southern Patagonian peat bogsNARA Subscribed
Testate amoebae are abundant and diverse in Sphagnum peat bogs and have been used extensively as indicators of past water table depths. Although these unicellular protists are widely dispersed with globally similar hydrological preferences, regional variations in communities demand region‐specific transfer functions. Here we present the first transfer function for southern Patagonian bogs, based on 154 surface samples obtained...
In regions with seasonal temperate climatic regimes, tree growth is rarely controlled by any single environmental factor. As a consequence, the development of robust palaeoclimate reconstructions has proved challenging. Tree‐ring stable carbon isotope ratios (δ 13 C), however, are controlled primarily by photosynthetic rate, not by net growth. Therefore, at sites where climatic controls on tree‐ring growth are not strongly exp...
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