The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km <sup>2</sup> resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km <sup>2</sup> pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

<scp>ReSurveyEurope</scp>: A database of resurveyed vegetation plots in Europe

AbstractAimsWe introduce ReSurveyEurope — a new data source of resurveyed vegetation plots in Europe, compiled by a collaborative network of vegetation scientists. We describe the scope of this initiative, provide an overview of currently available data, governance, data contribution rules, and accessibility. In addition, we outline further steps, including potential research questions.ResultsReSurveyEurope includes resurveyed vegetation plots from all habitats. Version 1.0 of ReSurveyEurope contains 283,135 observations (i.e., individual surveys of each plot) from 79,190 plots sampled in 449 independent resurvey projects. Of these, 62,139 (78%) are permanent plots, that is, marked in situ, or located with GPS, which allow for high spatial accuracy in resurvey. The remaining 17,051 (22%) plots are from studies in which plots from the initial survey could not be exactly relocated. Four data sets, which together account for 28,470 (36%) plots, provide only presence/absence information on plant species, while the remaining 50,720 (64%) plots contain abundance information (e.g., percentage cover or cover–abundance classes such as variants of the Braun‐Blanquet scale). The oldest plots were sampled in 1911 in the Swiss Alps, while most plots were sampled between 1950 and 2020.ConclusionsReSurveyEurope is a new resource to address a wide range of research questions on fine‐scale changes in European vegetation. The initiative is devoted to an inclusive and transparent governance and data usage approach, based on slightly adapted rules of the well‐established European Vegetation Archive (EVA). ReSurveyEurope data are ready for use, and proposals for analyses of the data set can be submitted at any time to the coordinators. Still, further data contributions are highly welcome.</jats:sec

Past surface conditions and speleogenesis as inferred from cave sediments in the Great Cave of Șălitrari Mountain (SW Romania)

Abstract In one of the passages in the Great Cave of Șălitrari Mountain the floor is completely covered by an alluvial deposit at least 6 m in thickness, ranging from boulders, and cobbles, to sand and clay, topped by a layer of dry bat guano. Sediment and mineral samples collected from six profiles underwent broad analyses to determine their petrological and mineralogical makeup, grain-size distribution, and paleoclimatic significance. The complicated facies alternation suggests frequent changes in the former stream’s hydrological parameters, with frequent flooding, leading to the hypothesis that the climate was somewhat wetter than today. Both the mineralogical composition of the sediment (ranging from quartz, mica, gypsum, phosphates, and calcite to garnet, zircon, titanite, olivine, serpentine, tourmaline, sphalerite, pyrite/chalcopyrite, and feldspars) and the petrological composition of the larger clasts (limestone, sandstone, mudstone, granitoids, serpentinite, amphibolite, diorite, gneiss, quartzite, microconglomerate, and schist) ascribe the potential source rocks to an area with contrasting lithologies, such as amphibolites, felsic and basic metaigneous, and metasedimentary rocks, mixed with a variety of detritic rocks. These rock types are not entirely comprised by the catchment area of the modern Presacina Brook, thus implying that due either to hydrological conditions, or to changes in the base level caused by river down cutting or active tectonics, the former source area was much more extensive. Based on morphological and sedimentological criteria, the cave started under pipe-full flow conditions, and further evolved during a prolonged and complex vadose phase. Evidence to support the existence of hypogene conditions is also present. Once the underground stream left the cave and most of the sediment was removed, speleothem precipitation was initiated. In this contribution we put forward evidence that argue for an extra-basinal origin of some of the alluvial sediments, an uncommon fact documented in few cave environments so far

The Romanian Grassland Database (RGD): historical background, current status and future perspectives

This report describes the Romanian Grassland Database (RGD), registered under EU-RO-008 in the Global Index of Vegetation-Plot Databases (GIVD). This collaborative initiative aims at collecting all available vegetation-plot data (relevés) of grasslands and other open habitats from the territory of Romania and providing them for science, nationally and internationally, e.g. via the European Vegetation Archive (EVA) and the global database “sPlot”. It mainly contains data from wet, mesic, dry, saline, alpine and rocky grasslands, but also some other vegetation types like heathlands, mires, ruderal, segetal, aquatic and cryptogam-dominated vegetation. The currently 21,685 relevés have mainly been digitised from literature sources (90%), while the rest comes from individual unpublished sources (10%). We report on the background and history of RGD, explain its “Data Property and Governance Rules” under which data are contributed and retrieved and outline how RGD can contribute to research in the fields of vegetation ecology, macroecology and conservation

ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

International audienc