Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F ST =0.126-0.138), and from DP (F ST =0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.</p

Spatial and seasonal variations of aerosols over China from two decades of multi-satellite observations – Part 2: AOD time series for 1995–2017 combined from ATSR ADV and MODIS C6.1 and AOD tendency estimations

Understanding long-term variations in aerosol loading is essential for evaluating the health and climate effects of airborne particulates as well as the effectiveness of pollution control policies. The expected satellite lifetime is about 10 to 15 years. Therefore, to study the variations of atmospheric constituents over longer periods information from different satellites must be utilized.Here we introduce a method to construct a combined annual and seasonal long time series of AOD at 550 nm using the Along-Track Scanning Radiometers (ATSR: ATSR-2 and AATSR combined) and the MODerate resolution Imaging Spectroradiometer on Terra (MODIS/Terra), which together cover the 1995–2017 period. The long-term (1995–2017) combined AOD time series are presented for all of mainland China, for southeastern (SE) China and for 10 selected regions in China. Linear regression was applied to the combined AOD time series constructed for individual L3 (1°&thinsp; × &thinsp;1°) pixels to estimate the AOD tendencies for two periods: 1995–2006 (P1) and 2011–2017 (P2), with respect to the changes in the emission reduction policies in China.During P1, the annually averaged AOD increased by 0.006 (or 2&thinsp;% of the AOD averaged over the corresponding period) per year across all of mainland China, reflecting increasing emissions due to rapid economic development. In SE China, the annual AOD positive tendency in 1995–2006 was 0.014 (3&thinsp;%) per year, reaching maxima (0.020, or 4&thinsp;%, per year) in Shanghai and the Pearl River Delta regions. After 2011, during P2, AOD tendencies reversed across most of China with the annually averaged AOD decreasing by −0.015 (−6&thinsp;%) per year in response to the effective reduction of the anthropogenic emissions of primary aerosols, SO2 and NOx. The strongest AOD decreases were observed in the Chengdu (−0.045, or −8&thinsp;%, per year) and Zhengzhou (−0.046, or −9&thinsp;%, per year) areas, while over the North China Plain and coastal areas the AOD decrease was lower than −0.03 (approximately −6&thinsp;%) per year. In the less populated areas the AOD decrease was small.The AOD tendency varied by both season and region. The increase in the annually averaged AOD during P1 was mainly due to an increase in summer and autumn in SE China (0.020, or 4&thinsp;%, and 0.016, or 4&thinsp;%, per year, respectively), while during winter and spring the AOD actually decreased over most of China. The AOD negative tendencies during the 2011–2017 period were larger in summer than in other seasons over the whole of China (ca. −0.021, or −7&thinsp;%, per year) and over SE China (ca. −0.048, or −9&thinsp;%, per year).The long-term AOD variations presented here show a gradual decrease in the AOD after 2011 with an average reduction of 30&thinsp;%–50&thinsp;% between 2011 and 2017. The effect is more visible in the highly populated and industrialized regions in SE China, as expected.</p

Spatial and seasonal variations of aerosols over China from two decades of multi-satellite observations – Part 1: ATSR (1995–2011) and MODIS C6.1 (2000–2017)

Aerosol optical depth (AOD) patterns and interannual and seasonal variations over China are discussed based on the AOD retrieved from the Along-Track Scanning Radiometer (ATSR-2, 1995–2002), the Advanced ATSR (AATSR, 2002–2012) (together ATSR) and the MODerate resolution Imaging Spectroradiometer (MODIS) aboard the Terra satellite (2000–2017). The AOD products used were the ATSR Dual View (ADV) v2.31 AOD and the MODIS/Terra Collection 6.1 (C6.1) merged dark target (DT) and deep blue (DB) AOD product. Together these datasets provide an AOD time series for 23 years, from 1995 to 2017. The difference between the AOD values retrieved from ATSR-2 and AATSR is small, as shown by pixel-by-pixel and monthly aggregate comparisons as well as validation results. This allows for the combination of the ATSR-2 and AATSR AOD time series into one dataset without offset correction.ADV and MODIS AOD validation results show similar high correlations with the Aerosol Robotic Network (AERONET) AOD (0.88 and 0.92, respectively), while the corresponding bias is positive for MODIS (0.06) and negative for ADV (−0.07). Validation of the AOD products in similar conditions, when ATSR and MODIS/Terra overpasses are within 90&thinsp;min of each other and when both ADV and MODIS retrieve AOD around AERONET locations, show that ADV performs better than MODIS in autumn, while MODIS performs slightly better in spring and summer. In winter, both ADV and MODIS underestimate the AERONET AOD.Similar AOD patterns are observed by ADV and MODIS in annual and seasonal aggregates as well as in time series. ADV–MODIS difference maps show that MODIS AOD is generally higher than that from ADV. Both ADV and MODIS show similar seasonal AOD behavior. The AOD maxima shift from spring in the south to summer along the eastern coast further north.The agreement between sensors regarding year-to-year AOD changes is quite good. During the period from 1995 to 2006 AOD increased in the southeast (SE) of China. Between 2006 and 2011 AOD did not change much, showing minor minima in 2008–2009. From 2011 onward AOD decreased in the SE of China. Similar patterns exist in year-to-year ADV and MODIS annual AOD tendencies in the overlapping period. However, regional differences between the ATSR and MODIS AODs are quite large. The consistency between ATSR and MODIS with regards to the AOD tendencies in the overlapping period is rather strong in summer, autumn and overall for the yearly average; however, in winter and spring, when there is a difference in coverage between the two instruments, the agreement between ATSR and MODIS is lower.AOD tendencies in China during the 1995–2017 period will be discussed in more detail in Part 2 (a following paper: Sogacheva et al., 2018), where a method to combine AOD time series from ADV and MODIS is introduced, and combined AOD time series are analyzed.</p

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies

Expansion cone for the 3-inch PMTs of the KM3NeT optical modules

[EN] Detection of high-energy neutrinos from distant astrophysical sources will open a new window on the Universe. The detection principle exploits the measurement of Cherenkov light emitted by charged particles resulting from neutrino interactions in the matter containing the telescope. A novel multi-PMT digital optical module (DOM) was developed to contain 31 3-inch photomultiplier tubes (PMTs). In order to maximize the detector sensitivity, each PMT will be surrounded by an expansion cone which collects photons that would otherwise miss the photocathode. Results for various angles of incidence with respect to the PMT surface indicate an increase in collection efficiency by 30% on average for angles up to 45 degrees with respect to the perpendicular. Ray-tracing calculations could reproduce the measurements, allowing to estimate an increase in the overall photocathode sensitivity, integrated over all angles of incidence, by 27% (for a single PMT). Prototype DOMs, being built by the KM3NeT consortium, will be equipped with these expansion cones.This work is supported through the EU, FP6 Contract no. 011937, FP7 grant agreement no. 212252, and the Dutch Ministry of Education, Culture and Science.Adrián Martínez, S.; Ageron, M.; Aguilar, JA.; Aharonian, F.; Aiello, S.; Albert, A.; Alexandri, M.... (2013). Expansion cone for the 3-inch PMTs of the KM3NeT optical modules. Journal of Instrumentation. 8(3):1-19. https://doi.org/10.1088/1748-0221/8/03/T03006S1198

Assessing the Potential of Regulating Ecosystem Services as Nature-Based Solutions in Urban Areas

Mounting research assesses the provision of regulating ecosystem services by green infrastructure in urban areas, but the extent to which these services can offer effective nature-based solutions for addressing urban climate change-related challenges is rarely considered. In this chapter, we synthesize knowledge from assessments of urban green infrastructure carried out in Europe and beyond to evaluate the potential contribution of regulating ecosystem services to offset carbon emissions, reduce heat stress and abate air pollution at the metropolitan, city and site scales. Results from this review indicate that the potential of regulating ecosystem services provided by urban green infrastructure to counteract these three climate change-related pressures is often limited and/or uncertain, especially at the city and metropolitan levels. However, their contribution can have a substantially higher impact at site scales such as in street canyons and around green spaces. We note that if regulating ecosystem services are to offer effective nature-based solutions in urban areas, it is critically important that green infrastructure policies target the relevant implementation scale. This calls for a coordination between authorities dealing with urban and environmental policy and for the harmonization of planning and management instruments in a multilevel governance approach. Regulating ecosystem services • Urban green infrastructure • Global climate regulation • Local climate regulation • Air quality regulation • Multi-scale assessmentpublishedVersio

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process