Detailed paleoecological evidence from Arctic Alaska’s past megafauna can help reconstruct paleoenvironmental conditions and can illustrate ecological adaptation to varying environments. We examined a rare, largely articulated and almost complete skeleton of a steppe bison (Bison priscus) recently unearthed in Northern Alaska. We used a multi-proxy paleoecological approach to reconstruct the past ecology of an individual representing a key ancient taxon. Radiocarbon dating of horn keratin revealed that the specimen has a finite radiocarbon age ∼46,000 ± 1000 cal yr BP, very close to the limit of radiocarbon dating. We also employed Bayesian age modeling of the mitochondrial genome, which estimated an age of ∼33,000–87,000 cal yr BP. Our taphonomic investigations show that the bison was scavenged post-mortem and infested by blowflies before burial. Stable carbon and oxygen isotope (δ13C and δ15N) analyses of sequentially sampled horn keratin reveal a seasonal cycle; furthermore, high δ15N values during its first few years of life are consistent with patterns observed in modern bison that undertook dispersal. We compared sequential analyses of tooth enamel for strontium isotope ratios (87Sr/86Sr) to a spatial model of 87Sr/86Sr values providing evidence for dispersal across the landscape. Synthesis of the paleoecological findings indicates the specimen lived during interstadial conditions. Our multi-proxy, paleoecological approach, combining light and heavy isotope ratios along with genetic information, adds to the broader understanding of ancient bison ecology during the Late Pleistocene, indicating that ancient bison adopted different degrees of paleo-mobility according to the prevailing paleoecological conditions and climate.
Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide “lockdown” (8 March–3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.
Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.
In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – array-based hybridization capture and in-solution capture using either RNA or DNA baits – have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits. , METHOD SUMMARY We compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity and reproducibility for ancient and modern Mycobacterium leprae and Treponema pallidum samples. The three methods – array-based capture and in-solution capture with RNA and DNA baits – were all tested in three independent replicates.
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