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The dataset presents a 43 year-long reanalysis of pollen seasons for three major allergenic genera of trees in Europe: alder (Alnus), birch (Betula), and olive (Olea). Driven by the meteorological reanalysis ERA5, the atmospheric composition model SILAM predicted the flowering period and calculated the Europe-wide dispersion pattern of pollen for the years 1980-2022. The model applied an extended 4-dimensional variational data assimilation of in-situ observations of aerobiological networks in 34 European countries to reproduce the inter-annual variability and trends of pollen production and distribution. The control variable of the assimilation procedure was the total pollen release during each flowering season, implemented as an annual correction factor to the mean pollen production. The dataset was designed as an input to studies on climate-induced and anthropogenically driven changes in the European vegetation, biodiversity monitoring, bioaerosol modelling and assessment, as well as, in combination with intra-seasonal observations, for health-related applications., (© 2024. The Author(s).)

With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts., (© 2024. The Author(s).)

The study is aimed at determining the potential spatiotemporal risk of the co-occurrence of airborne pollen and fungal spores high concentrations in different bio-climatic zones in Europe. Birch, grass, mugwort, ragweed, olive pollen and Alternaria and Cladosporium fungal spores were investigated at 16 sites in Europe, in 2005-2019. In Central and northern Europe, pollen and fungal spore seasons mainly overlap in June and July, while in South Europe, the highest pollen concentrations occur frequently outside of the spore seasons. In the coldest climate, no allergy thresholds were exceeded simultaneously by two spore or pollen taxa, while in the warmest climate most of the days with at least two pollen taxa exceeding threshold values were observed. The annual air temperature amplitude seems to be the main bioclimatic factor influencing the accumulation of days in which Alternaria and Cladosporium spores simultaneously exceed allergy thresholds. The phenomenon of co-occurrence of airborne allergen concentrations gets increasingly common in Europe and is proposed to be present on other continents, especially in temperate climate., Competing Interests: Declaration of competing interest All authors declare that they have no competing interests., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River., (© 2023. The Author(s).)

Apex predators are good indicators of environmental pollution since they are relatively long-lived and their high trophic position and spatiotemporal exposure to chemicals provides insights into the persistent, bioaccumulative and toxic (PBT) properties of chemicals. Although monitoring data from apex predators can considerably support chemicals' management, there is a lack of pan-European studies, and longer-term monitoring of chemicals in organisms from higher trophic levels. The present study investigated the occurrence of contaminants of emerging concern (CECs) in 67 freshwater, marine and terrestrial apex predators and in freshwater and marine prey, gathered from four European countries. Generic sample preparation protocols for the extraction of CECs with a broad range of physicochemical properties and the purification of the extracts were used. The analysis was performed utilizing liquid (LC) chromatography coupled to high resolution mass spectrometry (HRMS), while the acquired chromatograms were screened for the presence of more than 2,200 CECs through wide-scope target analysis. In total, 145 CECs were determined in the apex predator and their prey samples belonging in different categories, such as pharmaceuticals, plant protection products, per- and polyfluoroalkyl substances, their metabolites and transformation products. Higher concentration levels were measured in predators compared to prey, suggesting that biomagnification of chemicals through the food chain occurs. The compounds were prioritized for further regulatory risk assessment based on their frequency of detection and their concentration levels. The majority of the prioritized CECs were lipophilic, although the presence of more polar contaminants should not be neglected. This indicates that holistic analytical approaches are required to fully characterize the chemical universe of biota samples. Therefore, the present survey is an attempt to systematically investigate the presence of thousands of chemicals at a European level, aiming to use these data for better chemicals management and contribute to EU Zero Pollution Ambition., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived 1-8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located., (© 2022. The Author(s).)

The COST Action 'European Raptor Biomonitoring Facility' (ERBFacility) aims to develop pan-European raptor biomonitoring in support of better chemicals management in Europe, using raptors as sentinel species. This presents a significant challenge involving a range of constraints that must be identified and addressed. The aims of this study were to: (1) carry out a comprehensive review of the constraints that may limit the gathering in the field of raptor samples and contextual data, and assess their relative importance across Europe; and (2) identify and discuss possible solutions to the key constraints that were identified. We applied a participatory approach to identify constraints and to discuss feasible solutions. Thirty-one constraints were identified, which were divided into four categories: legal, methodological, spatial coverage, and skills constraints. To assess the importance of the constraints and their possible solutions, we collected information through scientific workshops and by distributing a questionnaire to stakeholders in all the countries involved in ERBFacility. We obtained 74 answers to the questionnaire, from 24 of the 39 COST participating countries. The most important constraints identified were related to the collection of complex contextual data about sources of contamination, and the low number of existing raptor population national/regional monitoring schemes and ecological studies that could provide raptor samples. Legal constraints, such as permits to allow the collection of invasive samples, and skills constraints, such as the lack of expertise to practice necropsies, were also highlighted. Here, we present solutions for all the constraints identified, thus suggesting the feasibility of establishing a long-term European Raptor Sampling Programme as a key element of the planned European Raptor Biomonitoring Facility., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2021 The Author(s). Published by Elsevier B.V. All rights reserved.)

Wildlife conservation policies directed at common and widespread, but declining, species are difficult to design and implement effectively, as multiple environmental changes are likely to contribute to population declines. Conservation actions ultimately aim to influence demographic rates, but targeting actions towards feasible improvements in these is challenging in widespread species with ranges that encompass a wide range of environmental conditions. Across Europe, sharp declines in the abundance of migratory landbirds have driven international calls for action, but actions that could feasibly contribute to population recovery have yet to be identified. Targeted actions to improve conditions on poor-quality sites could be an effective approach, but only if local conditions consistently influence local demography and hence population trends. Using long-term measures of abundance and demography of breeding birds at survey sites across Europe, we show that co-occurring species with differing migration behaviours have similar directions of local population trends and magnitudes of productivity, but not survival rates. Targeted actions to boost local productivity within Europe, alongside large-scale (non-targeted) environmental protection across non-breeding ranges, could therefore help address the urgent need to halt migrant landbird declines. Such demographic routes to recovery are likely to be increasingly needed to address global wildlife declines.

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe. 1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes 2 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry. , 3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry. 4-8 This transition is documented through extensive ancient genomic data from present-day Britain, 9 , 10 Ireland, 11 with the exception of one Late Neolithic genome sequenced at 0.05× coverage. , This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.12 Iberia, 13 Mediterranean islands, 14 , 15 and Germany. 8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63), 8 , 9 , 16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage. 16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale 1 , the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago 2 . Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

How environmental factors influence population dynamics in long-distance migrants is complicated by the spatiotemporal diversity of the environment the individuals experience during the annual cycle. The effects of weather on several different aspects of life history have been well studied, but a better understanding is needed on how weather affects population dynamics through the different associated traits. We utilise 77 years of data from pied flycatcher (Ficedula hypoleuca), to identify the most relevant climate signals associated with population growth rate. The strongest signals on population growth were observed from climate during periods when the birds were not present in the focal location. The population decline was associated with increasing precipitation in the African non-breeding quarters in the autumn (near the arrival of migrants) and with increasing winter temperature along the migration route (before migration). The number of fledglings was associated positively with increasing winter temperature in non-breeding area and negatively with increasing winter temperature in Europe. These possible carry-over effects did not arise via timing of breeding or clutch size but the exact mechanism remains to be revealed in future studies. High population density and low fledgling production were the intrinsic factors reducing the breeding population. We conclude that weather during all seasons has the potential to affect the reproductive success or population growth rate of this species. Our results show how weather can influence the population dynamics of a migratory species through multiple pathways, even at times of the annual cycle when the birds are in a different location than the climate signal.

Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America., Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines., Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Characterizing functional trait variation and covariation, and its drivers, is critical to understand the response of species to changing environmental conditions. Evolutionary and environmental factors determine how traits vary among and within species at multiple scales. However, disentangling their relative contribution is challenging and a comprehensive trait-environment framework addressing such questions is missing in lichens. We investigated the variation in nine traits related to photosynthetic performance, water use and nutrient acquisition applying phylogenetic comparative analyses in lichen epiphytic communities on beech across Europe. These poikilohydric organisms offer a valuable model owing to their inherent limitations to buffer contrasting environmental conditions. Photobiont type and growth form captured differences in certain physiological traits whose variation was largely determined by evolutionary processes (i.e. phylogenetic history), although the intraspecific component was non-negligible. Seasonal temperature fluctuations also had an impact on trait variation, while nitrogen content depended on photobiont type rather than nitrogen deposition. The inconsistency of trait covariation among and within species prevented establishing major resource use strategies in lichens. However, we did identify a general pattern related to the water-use strategy. Thus, to robustly unveil lichen responses under different climatic scenarios, it is necessary to incorporate both among and within-species trait variation and covariation.

Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish insect fauna, thought to represent roughly half of the diversity of multicellular life in one of the largest European countries. Our results are based on more than a decade of data from the Swedish Taxonomy Initiative and its massive inventory of the country's insect fauna, the Swedish Malaise Trap Project The fauna is considered one of the best known in the world, but the initiative has nevertheless revealed a surprising amount of hidden diversity: more than 3,000 new species (301 new to science) have been documented so far. Here, we use three independent methods to analyze the true size and composition of the fauna at the family or subfamily level: (1) assessments by experts who have been working on the most poorly known groups in the fauna; (2) estimates based on the proportion of new species discovered in the Malaise trap inventory; and (3) extrapolations based on species abundance and incidence data from the inventory. For the last method, we develop a new estimator, the combined non-parametric estimator, which we show is less sensitive to poor coverage of the species pool than other popular estimators. The three methods converge on similar estimates of the size and composition of the fauna, suggesting that it comprises around 33,000 species. Of those, 8,600 (26%) were unknown at the start of the inventory and 5,000 (15%) still await discovery. We analyze the taxonomic and ecological composition of the estimated fauna, and show that most of the new species belong to Hymenoptera and Diptera groups that are decomposers or parasitoids. Thus, current knowledge of the Swedish insect fauna is strongly biased taxonomically and ecologically, and we show that similar but even stronger biases have distorted our understanding of the fauna in the past. We analyze latitudinal gradients in the size and composition of known European insect faunas and show that several of the patterns contradict the Swedish data, presumably due to similar knowledge biases. Addressing these biases is critical in understanding insect biomes and the ecosystem services they provide. Our results emphasize the need to broaden the taxonomic scope of current insect monitoring efforts, a task that is all the more urgent as recent studies indicate a possible worldwide decline in insect faunas., Competing Interests: The authors have declared that no competing interests exist.

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

Unlabelled: Influenza A viruses are major pathogens for humans, domestic animals, and wildlife, and these viruses occasionally cross the species barrier. In spring 2014, increased mortality of harbor seals (Phoca vitulina), associated with infection with an influenza A(H10N7) virus, was reported in Sweden and Denmark. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided a unique opportunity to follow the adaptation of the avian virus to its new seal host. Sequence data for samples collected from 41 different seals from four different countries between April 2014 and January 2015 were obtained by Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded to amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in HA may occur rapidly and are important for virus adaptation to its new mammalian host., Importance: Influenza A viruses are major pathogens for humans, domestic animals, and wildlife. In addition to the continuous circulation of influenza A viruses among various host species, cross-species transmission of influenza A viruses occurs occasionally. Wild waterfowl and shorebirds are the main reservoir for most influenza A virus subtypes, and spillover of influenza A viruses from birds to humans or other mammalian species may result in major outbreaks. In the present study, various sequencing methods were used to elucidate the genetic changes that occurred after the introduction and subsequent spread of an avian influenza A(H10N7) virus among harbor seals of northwestern Europe by use of various samples collected during the outbreak. Such detailed knowledge of genetic changes necessary for introduction and adaptation of avian influenza A viruses to mammalian hosts is important for a rapid risk assessment of such viruses soon after they cross the species barrier., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

The genus Lathrolestes Förster (Hymenoptera: Ichneumonidae) from Northern Europe is reviewed. A new species, L. oelandinus sp. n. from Öland (Southern Sweden) is described. Illustrated diagnoses for 23 Northern European species are provided. Lathrolestes soperi Reshchikov, 2010 is recorded for the first time in the Palaearctic region (from the UK) and L. bipunctatus (Bridgman, 1886), L. citreus (Brischke, 1878), L. clypeatus (Zetterstedt, 1838) are new records for Denmark, and L. moravicus Habermehl, 1923 is a new record for Finland, France and Russia. Additionally L. ensator recorded newly from Belorus, L. erythrocephalus from Azerbaijan, L. macropygus and L. pictilis from Austria. Trophic interactions of the genus are discussed.

Unlabelled: •, Premise of the Study: Recent molecular studies provide a phylogenetic framework and some dated nodes for the monocot genus Smilax. The Caribbean Havanensis group of Smilax is part of a well-supported "New World clade" with a few disjunct taxa in the Old World. Although the fossil record of the genus is rich, it has been difficult to assign fossil taxa to extant groups based on their preserved morphological characters.•, Methods: Leaf fossils from Europe and Asia Minor were studied comparatively and put into a phylogenetic and biogeographic context using a molecular phylogeny of the genus.•, Key Results: Fossils from the early Miocene of Anatolia represent a new species of Smilax with systematic affinities with the Havanensis group. The leaf type encountered in the fossil species is exclusively found in species of the Havanensis group among all modern Smilax. Scattered fossils of this type from the Miocene of Greece and Austria, previously referred to Quercus (Fagaceae), Ilex (Aquifoliaceae), and Mahonia (Berberidaceae) also belong to the new species.•, Conclusions: The new Smilax provides first fossil evidence of the Havanensis group and proves that this group had a western Eurasian distribution during the Miocene. The age of the fossils is in good agreement with the (molecular-based) purported split between the Havanensis and Hispida groups within Smilax. The Miocene Smilax provides evidence that all four subclades within the "New World clade" had a disjunct intercontinental distribution during parts of the Neogene involving trans-Atlantic crossings (via floating islands or the North Atlantic land bridge) and the Beringia land bridge., (© 2015 Botanical Society of America, Inc.)

Applying early names, with or without original material, to genealogical species is challenging. For morels this task is especially difficult because of high morphological stasis and high plasticity of apothecium color and shape. Here we propose a nomenclatural revision of true morels (Morchella, Pezizales) from Europe and North America, based on molecular phylogenetic analyses of portions of the genes for RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2), translation elongation factor-1α (TEF1), the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS), and partial nuc 28S rDNA D1-D2 domains (28S). The 107 newly sequenced collections were from both continents, including 48 types, together with previously published sequences. Names are applied to 30 of the 65 currently recognized genealogical species. Results of the present study revealed that the number of Morchella species in Europe (n = 21) is nearly identical to that in North America (n = 22). Only seven species were found on both continents, consistent with previous reports of high continental endemism within the genus. Presently it is not possible to tell whether the transoceanic disjunctions were due to human activities, migration across a Bering land bridge or long-distance dispersal. In an effort to stabilize the taxonomy, due in part to the recent publication of synonyms for 11 of the species, accepted names are presented together with their corresponding later synonyms. A new subclade that includes holotypes of M. castanea and M. brunneorosea is identified in sect. Morchella (Esculenta Clade). Lectotypes for Morchella deliciosa, M. eximia and M. tridentina are designated here, as well as epitypes for M. dunalii, M. eximia, M. purpurascens and M. vulgaris. Morchella conica was determined to be illegitimate, and further research is required to determine the identity of M. elata and M. inamoena., (© 2015 by The Mycological Society of America.)

Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.

Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives-smaller geographical scales deliver higher accuracy.

Analyses of the dynamics of diseases in wild populations typically assume all individuals to be identical. However, profound effects on the long-term impact on the host population can be expected if the disease has age and sex dependent dynamics. The Phocine Distemper Virus (PDV) caused two mass mortalities in European harbour seals in 1988 and in 2002. We show the mortality patterns were highly age specific on both occasions, where young of the year and adult (>4 yrs) animals suffered extremely high mortality, and sub-adult seals (1-3 yrs) of both sexes experienced low mortality. Consequently, genetic differences cannot have played a main role explaining why some seals survived and some did not in the study region, since parents had higher mortality levels than their progeny. Furthermore, there was a conspicuous absence of animals older than 14 years among the victims in 2002, which strongly indicates that the survivors from the previous disease outbreak in 1988 had acquired and maintained immunity to PDV. These specific mortality patterns imply that contact rates and susceptibility to the disease are strongly age and sex dependent variables, underlining the need for structured epidemic models for wildlife diseases. Detailed data can thus provide crucial information about a number of vital parameters such as functional herd immunity. One of many future challenges in understanding the epidemiology of the PDV and other wildlife diseases is to reveal how immune system responses differ among animals in different stages during their life cycle. The influence of such underlying mechanisms may also explain the limited evidence for abrupt disease thresholds in wild populations.

During the identification of Moroccan samples a plant belonging to Isothecium with characteristics of I. alopecuroides (Dubois) Isov. and, to a smaller degree, I. algarvicum W.E. Nicholson and Dixon was found. Problems with attributing the plant to any of the European Isothecium species and the known large morphological variation in I. alopecuroides suggested that molecular studies were needed to evaluate patterns of relationships in this complex. We investigated one nuclear and one chloroplast marker from 66 samples (gametophytes) of Isothecium alopecuroides and from 18 samples of other Isothecium species. Parsimony and likelihood (via Bayesian analysis) were used as optimality criteria to compute phylogenetic trees. Bootstrapping and posterior probabilities were used, not only to quantify support, but also to evaluate competing phylogenetic alternatives in consensus networks. Finally, split decomposition and neighbour net analysis were used to compute distance based split networks, in order to avoid systematic error. The observed discrepancy among morphological and molecular data suggests that none of the European species Isothecium alopecuroides, I. holtii and I. myosuroides are monophyletic as defined by traditional morphological characters. Convergent morphological evolution cannot explain the discrepancy in this particular case; instead exchange of genetic material among Isothecium species is considered a potential explanation for the molecular diversity within morphospecies.

Fossil pollen records indicate that Hippophaë rhamnoides (Sea Buckthorn) was widespread on late- and early postglacial raw soils throughout much of central and northern Europe, but that Early Holocene reforestation restricted populations to northern coastal habitats, or along mountain streams in the Alps, Pyrenees, and Carpathians. We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA-restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic structure, and expansion demographic history of this dioecious and wind-pollinated shrub at its range-wide scale in Europe and Asia Minor. Four major Chsi phylogroups of unresolved relationships were identified with estimated divergences approximately 172,000 years ago. Large-scale phylogeographic structures of nuclear and cytoplasmic markers were congruent in identifying (i) southeastern Europe as the most likely source of colonization into central Europe and Scandinavia, and (ii) the area just north of the Alps as a contact zone between populations from the Alps and the east/central European-Scandinavian lineage. Coalescence-based analyses (i.e. nested clade analysis and mismatch distributions) of Chsi variation were able to detect at least four major episodes of population growth, all within about the last 40,000 years. In particular, these analyses identified a nearly synchronized timing of population expansions in various parts of the species' range in central-eastern Europe/Asia Minor, most likely correlating with the Younger Dryas Stadial ( approximately 13,000-11,600 years ago). It remains to be established whether the phylogeographic history of H. rhamnoides, and particularly its rapid response to the rapid environmental changes of the Younger Dryas cold snap, is unique to the species, or whether it is shared with other cold-tolerant shrub (or grassland) species known from late-glacial raw soils in Europe.

We present new and revised data for the phocine distemper virus (PDV) epidemics that resulted in the deaths of more than 23 000 harbour seals Phoca vitulina in 1988 and 30,000 in 2002. On both occasions the epidemics started at the Danish island of Anholt in central Kattegat, and subsequently spread to adjacent colonies in a stepwise fashion. However, this pattern was not maintained throughout the epidemics and new centres of infection appeared far from infected populations on some occasions: in 1988 early positive cases were observed in the Irish Sea, and in 2002 the epidemic appeared in the Dutch Wadden Sea, 6 wk after the initiation of the outbreak at Anholt Island. Since the harbour seal is a rather sedentary species, such 'jumps' in the spread among colonies suggest that another vector species could have been involved. We discussed the role of sympatric species as disease vectors, and suggested that grey seal populations could act as reservoirs for PDV if infection rates in sympatric species are lower than in harbour seals. Alternatively, grey seals could act as subclinical infected carriers of the virus between Arctic and North Sea seal populations. Mixed colonies of grey and harbour seal colonies are found at all locations where the jumps occurred. It seems likely that grey seals, which show long-distance movements, contributed to the spread among regions. The harbour seal populations along the Norwegian coast and in the Baltic escaped both epidemics, which could be due either to genetic differences among harbour seal populations or to immunity. Catastrophic events such as repeated epidemics should be accounted for in future models and management strategies of wildlife populations.