Predicting the initial spread of novel Asian origin influenza A viruses in the continental USA by wild waterfowl

Using data on waterfowl band recoveries, we identified spatially explicit hotspots of concentrated waterfowl movement to predict occurrence and spatial spread of a novel influenza A virus (clade 2.3.4.4) introduced from Asia by waterfowl from an initial outbreak in North America in November 2014. In response to the outbreak, the hotspots of waterfowl movement were used to help guide sampling for clade 2.3.4.4 viruses in waterfowl as an early warning for the US poultry industry during the outbreak . After surveillance sampling of waterfowl, we tested whether there was greater detection of clade 2.3.4.4 viruses inside hotspots. We found that hotspots defined using kernel density estimates of waterfowl band recoveries worked well in predicting areas with higher prevalence of the viruses in waterfowl. This approach exemplifies the value of ecological knowledge in predicting risk to agricultural security.     

The spread of modern humans in Europe

The earliest credible evidence of Homo sapiens in Europe is an archaeological proxy in the form of several artifact assemblages (Bohunician) found in South-Central and possibly Eastern Europe, dating to ≤48,000 calibrated radiocarbon years before present (cal BP). They are similar to assemblages probably made by modern humans in the Levant (Emiran) at an earlier date and apparently represent a population movement into the Balkans during a warm climate interval [Greenland Interstadial 12 (GI 12)]. A second population movement may be represented by a diverse set of artifact assemblages (sometimes termed Proto-Aurignacian) found in the Balkans, parts of Southwest Europe, and probably in Eastern Europe, and dating to several brief interstadials (GI 11–GI 9) that preceded the beginning of cold Heinrich Event 4 (HE4) (≈40,000 cal BP). They are similar to contemporaneous assemblages made by modern humans in the Levant (Ahmarian). The earliest known human skeletal remains in Europe that may be unequivocally assigned to H. sapiens (Peçstera cu Oase, Romania) date to this time period (≈42,000 cal BP) but are not associated with artifacts. After the Campanian Ignimbrite volcanic eruption (40,000 cal BP) and the beginning of HE4, artifact assemblages assigned to the classic Aurignacian, an industry associated with modern human skeletal remains that seems to have developed in Europe, spread throughout the continent.     

欧亚地区厕蝇属夏厕蝇种团名录(双翅目:厕蝇科)

本研究采用昆虫分类学原理和方法,对欧亚地区厕蝇科厕蝇属夏厕蝇种团Fannia canicularis-group进行了系统分类研究.欧亚地区夏厕蝇种团昆虫共30种,分别隶属于夏厕蝇亚种团Fannia canicularissubgroup(20种),巨尾厕蝇亚种团Fannia lucidula-subgroup(7种),白纹厕蝇亚种团Fannia leucostictasubgroup(3种),编制了“欧亚地区厕蝇属夏厕蝇种团名录”,详细描述了其国内外分布情况,并对部分外国种类新拟了中文名.     

Historic and geographic surveillance of Pseudogymnoascus destructans possible from collections of bat parasites

Specimens archived in wet collections represent valuable material for scientific research. Here, we show that bat fly (Diptera, Nycteribiidae) samples contain DNA of Pseudogymnoascus destructans , a fungus pathogenic to bats. Using dual‐probe quantitative PCR , we detected P. destructans DNA on bat flies collected in the Samara, Sverdlovsk and Irkutsk regions of Russia between 2005 and 2017. Fungal load was significantly lower on bat flies from wet collections than on freshly collected mites in the Czech Republic. The bat pathogen was present in the Samara region (European part of Russia) in 2005, that is, a year before recognition of white‐nose syndrome in North America. As Samara and Irkutsk regions were identified as new positive locations of P. destructans , our data expand the known geographic distribution of P. destructans . We conclude that ethanol‐stored ectoparasites can be used to identify the presence of pathogens in historic bat populations and understudied geographical regions.     

Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia

The genetic structure of populations of Turnip mosaic virus in Eurasia was assessed by making host range and gene sequence comparisons of 142 isolates. Most isolates collected in West Eurasia infected Brassica plants whereas those from East Eurasia infected both Brassica and Raphanus plants. Analyses of recombination sites (RSs) in five regions of the genome (one third of the full sequence) showed that the protein 1 (P1 gene) had recombined more frequently than the other gene regions in both subpopulations, but that the RSs were located in different parts of the genomes of the subpopulations. Estimates of nucleotide diversity showed that the West Eurasian subpopulation was more diverse than the East Eurasian subpopulation, but the Asian-BR group of the genes from the latter subpopulation had a greater nonsynonymous/synonymous substitution ratio, especially in the P1, viral genome-linked protein (VPg) and nuclear inclusion a proteinase (NIa-Pro) genes. These subpopulations seem to have evolved independently from the ancestral European population, and their genetic structure probably reflects founder effects.     

Simple and cost-effective 14-loci SNP assay designed for differentiation of European,East Asian and African samples

During every criminal investigation, it is vital to extract as much information as possible from every piece of evidence. When it comes to DNA testing, simple short tandem repeat (STR) typing may soon become a relic because it is now possible to genotype more characteristics. Ancestry informative markers are receiving attention from the forensic community because individuals can be assigned to their population or territory of origin based on their analysis. Many panels of this kind have been proposed so far, yet most of them require typing of a large number of loci. In many cases it is crucial to pick a minimal set of the most informative markers due to the limited amount of material available for analysis. In this study, we demonstrate that 14 carefully picked SNPs combined in two multiplex assays are capable of fast, robust and cost effective three-way differentiation of East Asians, Europeans and Africans.     

The landscape of Y chromosome polymorphisms in Russia

Abstract

Background: The pattern of diversity for the Y chromosome provides a view of male-driven processes of dispersal and settlement. By virtue of the broad geographic continuity, the genetic signature of movements from Asia to Europe can be detected in populations of north-eastern Europe.

Aim: To directly test previous hypotheses on the peopling of Russia, by considering a broader spectrum of potential diversity.

Subjects and methods: A total of 636 unrelated males (24 samples) from geographically and ethnically defined populations of Russia, Belarus, Azerbaijan and Georgia were analysed for 16 Y-STR loci. Some of the populations represent more or less distinct isolates.

Results: Microsatellites alone can have the power of detecting Asian contributions to the gene pool of populations now residing in Europe. Within Europe, a greater heterogeneity among populations sharing the same language than between populations sharing the same ethnic affiliation was found. There was low diversity and marked population differentiation in some Altaic speakers. Sympatry eroded inter-ethnic differentiation. No regular decline in genetic similarity with geography was seen.

Conclusion: Two layers of overall diversity represent a main feature of the genetic landscape of the population of the European portion of Russia.