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Pandemics are a recurring theme in human history, with evidence from the beginning of civilization up to the current Corona virus disease 2019 (COVID-19) pandemic. The genotype of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that has paralyzed the entire world since early 2020 is most closely related to a coronavirus from bats, eventually passed via Pangolins, although is not identical (Zhu et al., 2020). One of the most accredited hypotheses is that the virus first infected a human at or near a wet market in Wuhan, in the Hubei region of China; this city was the epicenter of the outbreak. In spite of some dis-information which circulates in the social media, it is clear that the virus originates in the over-exploitation of a wildlife at risk of transmission of diseases to humans and, moreover, in danger of extinction. In spite of the very numerous alerts which have been given in the past about the risk of a major outbreak coming from bats which host a high number of SARS viruses, the uncontrolled use of wildlife as a source of meat, bones, scales, blood, horns, hair and many other tissues has never ceased. These products, coming from poaching of endangered and not farmed species, feed both un-official and official markets of food or/and pharmacopeia. We should clearly affirm here that these processes should stop in a near future as they are not only destroying biodiversity but also producing pandemics which have major socio-economical consequences.

The prevalence of low virulence classical swine fever virus (CSFV) strains makes viral eradication difficult in endemic countries. However, the determinants for natural CSFV attenuation and persistence in the field remain unidentified. The aim of the present study was to assess the role of the RNase activity of CSFV Erns in pathogenesis, immune response, persistent infection, and viral transmission in pigs. To this end, a functional cDNA clone pPdR-H30K-36U with an Erns lacking RNase activity was constructed based on the low virulence CSFV field isolate Pinar de Rio (PdR). Eighteen 5-day-old piglets were infected with vPdR-H30K-36U. Nine piglets were introduced as contacts. The vPdR-H30K-36U virus was attenuated in piglets compared to the parental vPdR-36U. Only RNA traces were detected in sera and body secretions and no virus was isolated from tonsils, showing that RNase inactivation may reduce CSFV persistence and transmissibility. The vPdR-H30K-36U mutant strongly activated the interferon-α (IFN-α) production in plasmacytoid dendritic cells, while in vivo, the IFN-α response was variable, from moderate to undetectable depending on the animal. This suggests a role of the CSFV Erns RNase activity in the regulation of innate immune responses. Infection with vPdR-H30K-36U resulted in higher antibody levels against the E2 and Erns glycoproteins and in enhanced neutralizing antibody responses when compared with vPdR-36U. These results pave the way toward a better understanding of viral attenuation mechanisms of CSFV in pigs. In addition, they provide novel insights relevant for the development of DIVA vaccines in combination with diagnostic assays for efficient CSF control. info:eu-repo/semantics/publishedVersion

Summary Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific‐ and unspecific‐parent TRD) and genotypic (additive‐ and dominance‐TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent‐specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.

In a globalized world, parasites are often brought in contact with new potential hosts. When parasites successfully shift host, severe diseases can emerge at a large cost to society. However, the evolutionary processes leading to successful shifts are rarely understood, hindering risk assessment, prevention, or mitigation of their effects. Here, we screened populations of Varroa destructor, an ectoparasitic mite of the honeybee genus Apis, to investigate their genetic structure and reproductive potential on new and original hosts. From the patterns identified, we deduce the factors that influenced the macro- and microevolutionary processes that led to the structure observed. Among the mite variants identified, we found two genetically similar populations that differed in their reproductive abilities and thus in their host specificity. These lineages could interbreed, which represents a threat due to the possible increased virulence of the parasite on its original host. However, interbreeding was unidirectional from the host-shifted to the nonshifted native mites and could thus lead to speciation of the former. The results improve our understanding of the processes affecting the population structure and evolution of this economically important mite genus and suggest that introgression between shifted and nonshifted lineages may endanger the original host. Supplementary Information The online version contains supplementary material available at 10.1007/s10340-020-01322-7.

Summary Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine‐scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing.We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally.These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

Darwinian evolution preferentially follows mutational pathways whose individual steps increase fitness. Alternative pathways with mutational steps that do not increase fitness are less accessible. Here, we show that mistranslation, the erroneous incorporation of amino acids into nascent proteins, can increase the accessibility of such alternative pathways and, ultimately, of high fitness genotypes. We subject populations of the beta‐lactamase TEM‐1 to directed evolution in Escherichia coli under both low‐ and high‐mistranslation rates, selecting for high activity on the antibiotic cefotaxime. Under low mistranslation rates, different evolving TEM‐1 populations ascend the same high cefotaxime‐resistance peak, which requires three canonical DNA mutations. In contrast, under high mistranslation rates they ascend three different high cefotaxime‐resistance genotypes, which leads to higher genotypic diversity among populations. We experimentally reconstruct the adaptive DNA mutations and the potential evolutionary paths to these high cefotaxime‐resistance genotypes. This reconstruction shows that some of the DNA mutations do not change fitness under low mistranslation, but cause a significant increase in fitness under high‐mistranslation, which helps increase the accessibility of different high cefotaxime‐resistance genotypes. In addition, these mutations form a network of pairwise epistatic interactions that leads to mutually exclusive evolutionary trajectories towards different high cefotaxime‐resistance genotypes. Our observations demonstrate that protein mistranslation and the phenotypic mutations it causes can alter the evolutionary exploration of fitness landscapes and reduce the predictability of evolution., High mistranslation can increase the fitness benefits of adaptive DNA mutations, and thus help open evolutionary paths to alternative high‐fitness genotypes (left panel) that would be inaccessible under low mistranslation (right panel).

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137

The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding. We study the influence of mutation rates and population sizes on final mean population fitness, on the substitution rates of mutations, and on population diversity. We show that evolutionary dynamics cannot be understood as a function of mutation rate µ, population size N, or population mutation rate Nµ alone. For example, at a given mutation rate, clonal interference prevents the fixation of beneficial mutations as population size increases, but larger populations still arrive at a higher mean fitness. In addition, at the highest population mutation rates we study, mean final fitness increases with population size, because small populations are driven to low fitness by the relatively higher incidence of mutations they experience. Our observations show that mutation rate and population size can interact in complex ways to influence the adaptive dynamics of a population on a biophysically motivated fitness landscape.

Allopolyploids possess complete sets of genomes derived from different parental species and exhibit a range of variation in various traits. Reproductive traits may play a key role in the reproductive isolation between allopolyploids and their parental species, thus affecting the thriving of allopolyploids. However, empirical data, especially in natural habitats, comparing reproductive trait variation between allopolyploids and their parental species remain rare. Here, we documented the flowering phenology and floral morphology of the allopolyploid wild plantCardamine flexuosaand its diploid parentsC. amaraandC. hirsutain their native range in Switzerland. The flowering ofC. flexuosastarted at an intermediate time compared with those of the parents and the flowering period ofC. flexuosaoverlapped with those of the parents.Cardamine flexuosaresembledC. hirsutain the size of flowers and petals and the length/width ratio of petals, while it resembledC. amarain the length/width ratio of flowers. These results provide empirical evidence of the trait-dependent variation of allopolyploid phenotypes in natural habitats at the local scale. They also suggest that the variation in some reproductive traits inC. flexuosais associated with self-fertilization. Therefore, it is helpful to consider the mating system in furthering the understanding of the processes that may have shaped trait variation in polyploids in nature.

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes., DNA Research, 25 (1), ISSN:1340-2838, ISSN:1756-1663

The t haplotype in house mice is a well-known selfish genetic element with detrimental, nonadditive fitness consequences to its carriers: recessive lethal mutations cause t/t homozygotes to perish in utero. Given the severe genetic incompatibility imposed by the t haplotype, we predict females to avoid fertilization by t haplotype incompatible males. Indeed, some of the strongest evidence for compatibility mate choice is related to the t haplotype in house mice. However, all previous evidence for compatibility mate choice in this system is based on olfactory preference. It is so far unknown how general these preferences are and whether they are relevant in an actual mating context. Here, we assess female compatibility mate choice related to t haplotypes in a setting that – for the first time – allowed females to directly interact and mate with males. This approach enabled us to analyse female behaviour during the testing period, and the resulting paternity success and fitness consequences of a given choice. We show that genetic incompatibilities arising from the t haplotype had severe indirect fitness consequences and t females avoided fertilization by t incompatible males. The results are inconclusive whether this avoidance of t fertilization by t females was caused by pre- or post-copulatory processes.

Males from different populations of the same species often differ in their sexually selected traits. Variation in sexually selected traits can be attributed to sexual selection if phenotypic divergence matches the direction of sexual selection gradients among populations. However, phenotypic divergence of sexually selected traits may also be influenced by other factors, such as natural selection and genetic constraints. Here, we document differences in male sexual traits among six introduced Australian populations of guppies and untangle the forces driving divergence in these sexually selected traits.\ud Using an experimental approach, we found that male size, area of orange coloration, number of sperm per ejaculate and linear sexual selection gradients for male traits differed among populations. Within populations, a large mismatch between the direction of selection and male traits suggests that constraints may be important in preventing male traits from evolving in the direction of selection. Among populations, however, variation in sexual selection explained more than half of the differences in trait variation, suggesting that, despite within-population constraints, sexual selection has contributed to population divergence of male traits. Differences in sexual traits\ud were also associated with predation risk and neutral genetic distance. Our study highlights the importance of sexual selection in trait divergence in introduced populations, despite the presence of constraining factors such as predation risk and evolutionary history.

Specimens of the enigmatic, monotypic European genus Zuskamira Pont, 1987 (Sepsidae) were initially collected only from the lower central Swedish provinces of Darlana, Uppland and Västmanland. However, the same species was subsequently found much more south in Lower-Saxony and Schleswig-Holstein although Germany is overall well sampled for sepsid flies. Here we report a further (longitudinal) range expansion based on new localities in Southern Finland. New localities for Finland and Sweden are here added and we discuss briefly the habitat requirements of the species.

Pollination is an early and critical step in plant reproduction, leading to successful fertilization. It consists of many sequential processes, including adhesion of pollen grains onto the surface of stigmatic papilla cells, foot formation to strengthen pollen-stigma interaction, pollen hydration and germination, and pollen tube elongation and penetration. We have focused on an examination of the expressed genes in papilla cells, to increase understanding of the molecular systems of pollination. From three representative species of Brassicaceae (Arabidopsis thaliana, A. halleri and Brassica rapa), stigmatic papilla cells were isolated precisely by laser microdissection, and cell type-specific gene expression in papilla cells was determined by RNA sequencing. As a result, 17,240, 19,260 and 21,026 unigenes were defined in papilla cells of A. thaliana, A. halleri and B. rapa, respectively, and, among these, 12,311 genes were common to all three species. Among the17,240 genes predicted in A. thaliana, one-third were papilla specific while approximately half of the genes were detected in all tissues examined. Bioinformatics analysis revealed that genes related to a wide range of reproduction and development functions are expressed in papilla cells, particularly metabolism, transcription and membrane-mediated information exchange. These results reflect the conserved features of general cellular function and also the specific reproductive role of papilla cells, highlighting a complex cellular system regulated by a diverse range of molecules in these cells. This study provides fundamental biological knowledge to dissect the molecular mechanisms of pollination in papilla cells and will shed light on our understanding of plant reproduction mechanisms.

Male seahorses (genus Hippocampus) provide all post-fertilization parental care, yet despite high levels of paternal investment, these species have long been thought to have conventional sex roles, with female mate choice and male–male competition. Recent studies of the pot-bellied seahorse (Hippocampus abdominalis) have shown that sex-role reversal occurs in high-density female-biased populations, indicating that male mating preferences may lead to sexual selection on females in this species. Egg size, egg number, and offspring size all correlate positively with female body size in Hippocampus, and by choosing large mating partners, male seahorses may increase their reproductive success. While male brood size is also positively correlated with body size, small H. abdominalis males can carry exceptionally large broods, suggesting that the fecundity benefits of female preference for large partners may be limited. We investigated the importance of body size in reproductive decisions of H. abdominalis, presenting focal individuals of both sexes with potential mating partners of different sizes. Mating preferences were quantified in terms of time spent courting each potential partner. Male seahorses were highly active throughout the mate-choice trials and showed a clear behavioral preference for large partners, while females showed significantly lower levels of activity and equivocal mating preferences. The strong male preferences for large females demonstrated here suggest that sexual selection may act strongly on female body size in wild populations of H. abdominalis, consistent with predictions on the importance of female body size for reproductive output in this species.

In 1995, Benjamini and Hochberg published an influential paper propagating the false discovery rate (FDR) as a means to correct for alpha error inflation due to multiple hypothesis testing (Benjamini & Hochberg 1995). The FDR was quickly taken up by the scientific research community, foremost within molecular biology. The popularity of this method is illustrated by the fact that by the time of writing of this commentary their paper has already been cited over 50 000 times. Over the last few years, the FDR has also gained popularity in behavioural biology, where, unfortunately, it is frequently applied incorrectly. This seems to be due to the misconception that the FDR is a less stringent alternative to the Bonferroni correction for alpha error inflation. This assumption is erroneous because FDR and Bonferroni corrections address different problems and are not interchangeable. The Bonferroni correction adjusts the rejection threshold, so that the overall likelihood of making at least one incorrect type 1 inference (i.e. reporting an effect when there is none and committing an alpha error) remains at the chosen significance threshold (usually 5%), even when multiple hypotheses are tested within one study. The FDR, on the other hand, resets the threshold level in such a way that only 5% of the positive inferences are false positive findings (type 1, or alpha errors). This is, clearly, a different and usually less ambitious criterion. But, what should we aim for? In the following sections, I first elaborate on both concepts and, then, summarize which one to use for which question and which kind of data within behavioural biology.

Simple Summary In recent years, the interest in the use of data from routine herd records in the monitoring of dairy welfare at farm level has increased. This review compiles 13 papers to outline the current potential of data-based variables for animal welfare monitoring. All the identified studies showed associations between data-based variables and farm-level dairy cow welfare and therefore provide a first indication of the possible use and suitability of data-based variables for welfare monitoring. However, we found that the definitions of animal welfare, its assessment on the farm, and the data-based variables varied considerably. Consequently, the current state of research does not allow a conclusive assessment of the potential of data-based variables for animal welfare monitoring. Therefore, future research is needed to clarify the potential of data-based variables. Harmonisation of the data-based variables and the use of valid measurements that reflect the multidimensionality of welfare could contribute to increased comparability between the studies. Abstract During the last years, the interest in data-based variables (DBVs) as easy-to-obtain, cost-effective animal welfare indicators has continued to grow. This interest has led to publications focusing on the relationship between DBVs and animal welfare. This review compiles 13 papers identified through a systematic literature search to provide an overview of the current state of research on the relationship between DBVs and dairy cow welfare at farm level. The selected papers were examined regarding their definition of animal welfare and classified according to this definition into three categories: (a) papers evaluating DBVs as predictors of animal welfare violations, (b) papers investigating the relationship between DBVs and animal-based measurements, and (c) papers investigating the relationship of DBVs to scores of welfare assessments like the Welfare Quality protocol or to overall welfare scores at farm level. In addition, associations between DBVs and indicators of animal welfare were extracted, grouped by the type of DBV, and examined for replications that may confirm the associations. All the identified studies demonstrated associations between DBVs and animal welfare. Overall, the first indications of a possible suitability of DBVs for predicting herds with animal welfare violations as well as good or poor animal welfare status were given. The evaluation of relationships between DBVs and animal-based measurements (ABMs) found mortality-based DBVs to be frequently associated with ABMs. However, owing to varying definitions of animal welfare, the use of different variants of DBVs, and different methods used to assess DBVs, the studies could only be compared to a limited extent. Future research would benefit from a harmonisation of DBVs and the use of valid measurements that reflect the multidimensionality of welfare. Data sources rarely investigated so far may have the potential to provide additional DBVs that can contribute to the monitoring of cow welfare at farm level.

While environmental science, and ecology in particular, is working to provide better understanding to base sustainable decisions on, the way scientific understanding is developed can at times be detrimental to this cause. Locked-in debates are often unnecessarily polarized and can compromise any common goals of the opposing camps. The present paper is inspired by a resolved debate from an unrelated field of psychology where Nobel laureate David Kahneman and Garry Klein turned what seemed to be a locked-in debate into a constructive process for their fields. The present paper is also motivated by previous discourses regarding the role of thresholds in natural systems for management and governance, but its scope of analysis targets the scientific process within complex social-ecological systems in general. We identified five features of environmental science that appear to predispose for locked-in debates: 1) The strongly context dependent behaviour of ecological systems. 2) The dominant role of single hypothesis testing. 3) The high prominence given to theory demonstration compared investigation. 4) The effect of urgent demands to inform and steer policy. This fertile ground is further cultivated by human psychological aspects as well as the structure of funding and publication systems.

International audience; The Paleolithic site of Mutzig, discovered by chance in 1992 (Sainty, 1992), has been the focus of several excavations since 2009. Located in Alsace (Bas-Rhin, France), it is presently one of only a handful of sites reliably attributed to the Middle Paleolithic in this area; it thus provides rare evidence for a zone still relatively unknown for Early Prehistoric remains. The excellent preservation of the remains and the long stratigraphic sequence, with 6 to 8 in situ archaeological levels, make Mutzig a potential reference site for environmental and behavioral analyses for the Middle Paleolithic of the region. At least four archaeological levels contain burnt elements, and one level features a hearth structure. Taken together, the archaeological material, which is abundant in each of the different layers, forms an assemblage of more than 3000 faunal remains and more than 1500 lithic artifacts. Analyses of this site provides valuable insights into the environment and Neandertal ways of life in Alsace. In this paper, we present only the general results, more detailed presentations of the lithic and faunal remains will be presented in other papers (Diemer, this volume; Sévêque, this volume). The faunal remains recovered from the human occupations in levels 5 and 7 reflect the same relatively cold steppe-like environmental context and include reindeer, woolly mammoth, steppe horse, steppe bison and woolly rhinoceros. Small vertebrates also indicate a cold climate, but not related to the Pleniglacial. Confirmed isotopic data (oxygen and carbon isotope measurements of horse and mammoth teeth) indicate temperatures lower than those of today and an open environment. Levels 9 and 10, however, tend to reveal a more temperate climate. The available OSL and ESR/U-series dates place the Mutzig occupations within the Early Weichselian Glacial (MIS 5, ca. 90,000 BP), an attribution which biometric analyses and large and small fauna record tend to corroborate (Koehler et al., 2016a).; Le site paléolithique moyen de Mutzig constitue un gisement exceptionnel pour la région du Rhin supérieur. Localisé en Alsace (Bas-Rhin) et découvert fortuitement en 1992 (Sainty, 1992), il fait l’objet de recherches systématiques depuis 2009 dans le cadre d’une fouille programmée. Ce gisement offre une très bonne conservation des vestiges archéologiques, puisque éléments lithiques, faune, microfaune, charbons et structures de combustion y sont bien préservés et présents en grande quantité. Localisés sous un abri sous-roche en grès rose aujourd’hui effondré, six à huit niveaux archéologiques en place ont été pour le moment mis en évidence, le substrat n’ayant pas été encore atteint. Ils sont tous rattachables au Paléolithique moyen, plus précisément au Début Glaciaire Weichselien, datés par OSL et ESR/U-Th autour de 90 000 ans. Mais si les niveaux 5 et 7 présentent un signal paléoenvironnemental de steppe froide et sèche, les niveaux 9 et 10 tendraient à montrer un climat plus tempéré et des zones boisées mieux représentées. Bien qu’ils exposent une même ambiance technique pour l’industrie lithique, des différences sont perceptibles. Le développement de la fouille planimétrique couplé aux approches pluridisciplinaires (anthracologie ; palynologie ; micromorphologie ; sédimentologie ; pétrographie ; archéozoologie ; microfaune ; analyses isotopiques ; études lithiques ; études des foyers) permet des premières reconstitutions des occupations néandertaliennes (Koehler et al., 2016a). Le présent article traite des données générales, les présentations détaillées des restes lithiques et faunistiques font l’objet d’articles spécifiques (Diemer, ce volume ; Sévêque, ce volume).

Over the last two decades, awareness of the negative repercussions of flaws in the planning, conduct and reporting of preclinical research involving experimental animals has been growing. Several initiatives have set out to increase transparency and internal validity of preclinical studies, mostly publishing expert consensus and experience. While many of the points raised in these various guidelines are identical or similar, they differ in detail and rigour. Most of them focus on reporting, only few of them cover the planning and conduct of studies. The aim of this systematic review is to identify existing experimental design, conduct, analysis and reporting guidelines relating to preclinical animal research. A systematic search in PubMed, Embase and Web of Science retrieved 13 863 unique results. After screening these on title and abstract, 613 papers entered the full-text assessment stage, from which 60 papers were retained. From these, we extracted unique 58 recommendations on the planning, conduct and reporting of preclinical animal studies. Sample size calculations, adequate statistical methods, concealed and randomised allocation of animals to treatment, blinded outcome assessment and recording of animal flow through the experiment were recommended in more than half of the publications. While we consider these recommendations to be valuable, there is a striking lack of experimental evidence on their importance and relative effect on experiments and effect sizes

Groundwater belongs to the spatially most extensive, but least explored freshwater systems. On a global scale, the species richness of several subterranean invertebrate taxa parallels species richness found in surface waters, while on a local scale species richness hardly exceeds 20 species. This results in a high contribution of groundwater ecosystems to regional β- and γ-diversity, and to a smaller degree to α-diversity, and deserves focused attention. In general, more species are to be found in large cave systems. The second largest cave system in Europe is Holloch in Switzerland. In this paper we revised the taxonomic, phylogenetic and ecological diversity of the amphipod community in the Holloch cave system. While previous records listed five geographically widespread species of the genus Niphargus for this cave system, we could not confirm the presence of any of those species, but rather found three highly distinct species new to science. In this paper we describe Niphargus styx sp. nov., Niphargus ...

In this paper, a laboratory goniometer system for performing multi-angular measurements under controlled illumination conditions is described. A commercially available robotic arm enables the acquisition of a large number of measurements over the full hemisphere within a short time span making it much faster than other goniometers. In addition, the presented set-up enables assessment of anisotropic reflectance and emittance behaviour of soils, leaves and small canopies. Mounting a spectrometer enables acquisition of either hemispherical measurements or measurements in the horizontal plane. Mounting a thermal camera allows directional observations of the thermal emittance. This paper also presents three showcases of these different measurement set-ups in order to illustrate its possibilities. Finally, suggestions for applying this instrument and for future research directions are given, including linking the measured reflectance anisotropy with physically-based anisotropy models on the one hand and combining them with field goniometry measurements for joint analysis with remote sensing data on the other hand. The speed and flexibility of the system offer a large added value to the existing pool of laboratory goniometers.

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts., Author Summary Malaria leads to the loss of over 440,000 lives annually; accelerating research to discover new candidate drugs is a priority. Medicines for Malaria Venture (MMV) has distilled over 25,000 compounds that kill malaria parasites in vitro into a group of 400 representative compounds, called the "Malaria Box". These Malaria Box sets were distributed free-of-charge to research laboratories in 30 different countries that work on a wide variety of pathogens. Fifty-five groups compiled >290 assay results for this paper describing the many activities of the Malaria Box compounds. The collective results suggest a potential mechanism of action for over 130 compounds against malaria and illuminate the most promising compounds for further malaria drug development research. Excitingly some of these compounds also showed outstanding activity against other disease agents including fungi, bacteria, other single-cellular parasites, worms, and even human cancer cells. The results have ignited over 30 drug development programs for a variety of diseases. This open access effort was so successful that MMV has begun to distribute another set of compounds with initial activity against a wider range of infectious agents that are of public health concern, called the Pathogen Box, available now to scientific labs all over the world (www.PathogenBox.org).

Land surface radiation and energy budgets are critical to address a variety of scientific and application issues related to climate trends, weather predictions, hydrologic and biogeophysical modeling, and the monitoring of ecosystem health and agricultural crops. This is an introductory paper to the special issue of land surface radiation and energy budgets from an international conference on this subject. The temporal trends of these components are first discussed in the context of climate change and human induced land use changes. After a brief introduction to the conference, results from each paper of this special issue are summarized.

Condition-dependence of male ornaments is thought to provide honest signals on which females can base their sexual choice for genetic quality. Recent studies show that condition-dependence patterns can vary within populations. Although long-term association is thought to promote honest signalling, no study has explored the influence of pairing context on the condition-dependence of male ornaments. In this study, we assessed the influence of natural variation in body condition on song rate in zebra finches ( Taeniopygia guttata ) in three different situations: during short and long encounters with an unfamiliar female, and within heterosexual mated pairs. We found consistent individual differences in male directed and undirected song rate. Moreover, body condition had a positive effect on song rate in paired males. However, male song rate was not influenced by body condition during short or long encounters with unfamiliar females. Song rate appears to be an unreliable signal of condition to prospective females as even poor-condition birds can cheat and sing at a high rate. By contrast, paired females can reliably use song rate to assess their mate's body condition, and possibly the genetic quality. We propose that species' characteristics, such as mating system, should be systematically taken into account to generate relevant hypotheses about the evolution of condition-dependent male ornaments.

In many animal societies, individuals differ consistently in their ability to win agonistic interactions, resulting in dominance hierarchies. These differences arise due to a range of factors that can influence individuals’ abilities to win agonistic interactions, spanning from genetically driven traits through to individuals’ recent interaction history. Yet, despite a century of study since Schjelderup-Ebbe's seminal paper on social dominance, we still lack a general understanding of how these different factors work together to determine individuals’ positions in hierarchies. Here, we first outline five widely studied factors that can influence interaction outcomes: intrinsic attributes, resource value asymmetry, winner–loser effects, dyadic interaction-outcome history and third-party support. A review of the evidence shows that a variety of factors are likely important to interaction outcomes, and thereby individuals’ positions in dominance hierarchies, in diverse species. We propose that such factors are unlikely to determine dominance outcomes independently, but rather form part of feedback loops whereby the outcomes of previous agonistic interactions (e.g. access to food) impact factors that might be important in subsequent interactions (e.g. body condition). We provide a conceptual framework that illustrates the multitude potential routes through which such feedbacks can occur, and how the factors that determine the outcomes of dominance interactions are highly intertwined and thus rarely act independently of one another. Further, we generalise our framework to include multi-generational feed-forward mechanisms: how interaction outcomes in one generation can influence the factors determining interaction outcomes in the next generation via a range of parental effects. This general framework describes how interaction outcomes and the factors determining them are linked within generations via feedback loops, and between generations via feed-forward mechanisms. We then highlight methodological approaches that will facilitate the study of feedback loops and dominance dynamics. Lastly, we discuss how our framework could shape future research, including: how feedbacks generate variation in the factors discussed, and how this might be studied experimentally; how the relative importance of different feedback mechanisms varies across timescales; the role of social structure in modulating the effect of feedbacks on hierarchy structure and stability; and the routes of parental influence on the dominance status of offspring. Ultimately, by considering dominance interactions as part of a dynamic feedback system that also feeds forward into subsequent generations, we will understand better the factors that structure dominance hierarchies in animal groups. published

Fertilization is a key event for sexually reproducing plants. Pollen–stigma adhesion, which is the first step in male–female interaction during fertilization, requires proper pollen wall patterning. Callose, which is a β-1.3-glucan, is an essential polysaccharide that is required for pollen development and pollen wall formation. Mutations in CALLOSE SYNTHASE 5 (CalS5) disrupt male meiotic callose accumulation; however, how CalS5 activity and callose synthesis are regulated is not fully understood. In this paper, we report the isolation of a kompeito-1 (kom-1) mutant defective in pollen wall patterning and pollen–stigma adhesion in Arabidopsis thaliana. Callose was not accumulated in kom-1 meiocytes or microspores, which was very similar to the cals5 mutant. The KOM gene encoded a member of a subclass of Rhomboid serine protease proteins that lacked active site residues. KOM was localized to the Golgi apparatus, and both KOM and CalS5 genes were highly expressed in meiocytes. A 220 kDa CalS5 protein was detected in wild-type (Col-0) floral buds but was dramatically reduced in kom-1. These results suggested that KOM was required for CalS5 protein accumulation, leading to the regulation of meiocyte-specific callose accumulation and pollen wall formation.

The objectives of this paper were (i) to perform a systematic review of the literature over the last 21 yr and (ii) to evaluate the efficacy of selective dry cow treatment (SDCT) vs. blanket dry cow treatment (BDCT) in dairy cows regarding the risk of intramammary infection (IMI) after calving, new IMI risk after calving, cure risk during the dry period, and a reduction in antibiotic use at drying-off by meta-analysis. The final number of included studies was n = 3 for IMI risk after calving and n = 5 for new IMI risk after calving, cure risk during the dry period, and antibiotic use. The relative risk (RR) levels for IMI, new IMI, and cure did not differ significantly between SDCT and BDCT. This meta-analysis provides evidence that SDCT seems to be an adequate alternative to BDCT regarding udder health with a simultaneous reduction in antibiotic use. Limitations might arise because of the small number of studies included.:1. Introduction 2. Material and Methods 2.1 Search Strategy 2.2 Study Selection 2.3 Data Extraction 2.4 Assessment of Bias Risk 2.5 Statistical Analysis 3. Results 3.1 Study Selection 3.2 Study Characteristics 3.3 Outcomes 3.4 Risk of Bias 3.5 Pairwise Meta-Analysis 3.6 Subgroup Meta-Analysis 4. Discussion 4.1 Risk of IMI after Calving 4.2 Risk of new IMI after Calving 4.3 Cure Risk during Dry Period 4.4 Antibiotic Use at Drying-Off 4.5 Strengths and Limitations Ziele dieser Studie waren (i) ein systematisches Review über die Literatur der letzten 21 yr zu erstellen sowie (ii) die Effizienz von selektivem Trockenstellen (SDCT) im Vergleich zu konventionellem Trockenstellen (BDCT) bei Milchkühen anhand von Risiko an intramammären Infektionen (IMI) post partum (pp), Neuinfektionenrisiko pp, Heilungsrisiko während dem Trockenstehen und Reduktion des Antibiotikaeinsatzes zum Trockenstellen mittels einer Meta-Analyse zu untersuchen. Die finale Anzahl eingeschlossener Studien war n = 3 für das IMI-Risiko pp sowie n = 5 für Neuinfektionenrisiko pp, Heilungsrisiko während dem Trockenstehen und Antibiotikaeinsatz zum Trockenstellen. Die relativen Risiken für IMI pp, Neuinfektionen pp und Heilung während der Trockenstehperiode unterschieden sich dabei nicht signifikant zwischen SDCT und BDCT. Diese Meta-Analyse erbringt Evidenz, dass SDCT eine adäquate Alternative zu BDCT im Hinblick auf Eutergesundheit und Antibiotikareduktion ist. Limitationen entstehen durch die geringe Anzahl an eingeschlossenen Studien.:1. Introduction 2. Material and Methods 2.1 Search Strategy 2.2 Study Selection 2.3 Data Extraction 2.4 Assessment of Bias Risk 2.5 Statistical Analysis 3. Results 3.1 Study Selection 3.2 Study Characteristics 3.3 Outcomes 3.4 Risk of Bias 3.5 Pairwise Meta-Analysis 3.6 Subgroup Meta-Analysis 4. Discussion 4.1 Risk of IMI after Calving 4.2 Risk of new IMI after Calving 4.3 Cure Risk during Dry Period 4.4 Antibiotic Use at Drying-Off 4.5 Strengths and Limitations

This is the peer reviewed version of the following article: Vitasse, Y., Ursenbacher, S., Klein, G., Bohnenstengel, T., Chittaro, Y., Delestrade, A., ... Lenoir, J. (2021). Phenological and elevational shifts of plants, animals and fungi under climate change in the European Alps. Biological Reviews, 96, 1816-1835, which has been published in final form at https://doi.org/10.1111/brv.12727. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited. Mountain areas are biodiversity hotspots and provide a multitude of ecosystem services of irreplaceable socio-economic value. In the European Alps, air temperature has increased at a rate of about 0.36°C decade−1 since 1970, leading to glacier retreat and significant snowpack reduction. Due to these rapid environmental changes, this mountainous region is undergoing marked changes in spring phenology and elevational distribution of animals, plants and fungi. Long-term monitoring in the European Alps offers an excellent natural laboratory to synthetize climate-related changes in spring phenology and elevational distribution for a large array of taxonomic groups. This review assesses the climatic changes that have occurred across the European Alps during recent decades, spring phenological changes and upslope shifts of plants, animals and fungi from evidence in published papers and previously unpublished data. Our review provides evidence that spring phenology has been shifting earlier during the past four decades and distribution ranges show an upwards trend for most of the taxonomic groups for which there are sufficient data. The first observed activity of reptiles and terrestrial insects (e.g. butterflies) in spring has shifted significantly earlier, at an average rate of −5.7 and −6.0 days decade−1, respectively. By contrast, the first observed spring activity of semi-aquatic insects (e.g. dragonflies and damselflies) and amphibians, as well as the singing activity or laying dates of resident birds, show smaller non-significant trends ranging from −1.0 to +1.3 days decade−1. Leaf-out and flowering of woody and herbaceous plants showed intermediate trends with mean values of −2.4 and −2.8 days decade−1, respectively. Regarding species distribution, plants, animals and fungi (N = 2133 species) shifted the elevation of maximum abundance (optimum elevation) upslope at a similar pace (on average between +18 and +25 m decade−1) but with substantial differences among taxa. For example, the optimum elevation shifted upward by +36.2 m decade−1 for terrestrial insects and +32.7 m decade−1 for woody plants, whereas it was estimated to range between −1.0 and +11 m decade−1 for semi-aquatic insects, ferns, birds and wood-decaying fungi. The upper range limit (leading edge) of most species also shifted upslope with a rate clearly higher for animals (from +47 to +91 m decade−1) than for plants (from +17 to +40 m decade−1), except for semi-aquatic insects (−4.7 m decade−1). Although regional land-use changes could partly explain some trends, the consistent upward shift found in almost all taxa all over the Alps is likely reflecting the strong warming and the receding of snow cover that has taken place across the European Alps over recent decades. However, with the possible exception of terrestrial insects, the upward shift of organisms seems currently too slow to track the pace of isotherm shifts induced by climate warming, estimated at about +62 to +71 m decade−1 since 1970. In the light of these results, species interactions are likely to change over multiple trophic levels through phenological and spatial mismatches. This nascent research field deserves greater attention to allow us to anticipate structural and functional changes better at the ecosystem level.

Animal welfare is an essential component of the future of sustainable agriculture and the United Nations Sustainable Development Goals. There is growing global recognition of the importance of animal welfare, which must always be considered as part of the decision-making around food and nutrition security. Veterinary Services, encompassing public and private veterinarians and para-veterinarians, are custodians of animal welfare and key players in future actions to improve it. The welfare of animals is everyone's responsibility, from the individual farmer and practitioner to policymakers at the national and intergovernmental level. In this paper, after providing background information about current animal welfare issues and identifying animal welfare risks, the authors make a number of recommendations for action at the institutional and individual level. They do so because while the former is essential to generate change at scale and effective resourcing, the latter can create immediate action at a local level and drive change from the ground up. Without coordinated action from Veterinary Services, opportunities to improve animal welfare, alongside human and environmental health and well-being, may very well be lost, and animal welfare may fail to improve or even be at risk of decline.

Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddoni sp. nov. and Leguminaia anatolica sp. nov. Six additional taxa, Unio delicatus stat. rev., Unio eucirrus stat. rev., Unio hueti stat. rev., Unio sesirmensis stat. rev., Unio terminalis stat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensis stat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt and Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities. We thank John Pfeiffer and David Zanatta for their helpful comments and suggestions to improve the quality of the manuscript, Jamie Smith for the help with the shell images and Cindy Bogan for reviewing and formatting several versions of the manuscript and supplementary appendix. We also like to thank the following people for their assistance with the identification and/or access to specimens or images of museumtype lots. Adam Baldinger, Museum of Comparative Zoology, Harvard University, Paul Callomon, Academy of Natural Sciences of Drexel University, Philadelphia, John Pfeiffer Smithsonian Institution, Washington D.C., Karl-Otto Nagel, Senckenberg Museum, Frankfurt, Maxim Vinarski, Saint Petersburg State University, Russia, and Harriot Wood, National Museum of Wales, Cardiff. This work was supported by a Conchological Society of Great Britain & Ireland Grant Award to MLL entitled “Conservation and Phylogeography of the Eastern Mediterranean Naiads (Bivalvia: Unionoida), the European Union’s Horizon 2020 research and innovation programme - BIOPOLIS, grant agreement no. 857251, and the project ConBiomics: the missing approach for the Conservation of Freshwater Bivalves Project No. NORTE-01-0145- FEDER-030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT - Fundação para a Ciência e a Tecnologia, through national funds, the strategic funding UIDB/04423/2020 and UIDP/04423/2020 provided by FCT. FCT also supported MLL (2020.03608.CEECIND), EF (CEECIND/00627/2017), and AGS (SFRH/BD/137935/2018). The Ministry of Science and Higher Education of the Russian Federation supported INB (project 0793-2020- 0005) and AAT (project AAAA-A18-118012390161-9). The Russian Science Foundation funded INB (project No. 21-17-00126), IVV (project 19-14-00066). The Russian Foundation for Basic Research supported AVK (project 18-44-292001). Interactions of authors and writing of the paper were promoted and facilitated by the COST Action CA18239: CONFREMU - Conservation of freshwater mussels: a pan-European approach. info:eu-repo/semantics/publishedVersion

This paper presents 58 new records of the family Dolichopodidae for Bulgaria, Montenegro, North Macedonia and European part of Turkey, collected from 37 localities. Seventeen species are recorded for the first time from Bulgaria, six of which are new to the Balkan Peninsula, 23 species for European Turkey, three of which are new to the entire territory of Turkey, seven species for Montenegro and 11 species for North Macedonia. A checklist of the Dolichopodidae of the Balkan Peninsula is provided. The total number of dolichopodids of the Balkan Peninsula is currently raised to 288 species.

Patterns of actuarial senescence can be highly variable among species. Previous comparative analyses revealed that both age at the onset of senescence and rates of senescence are linked to position of a species along the fast–slow life‐history continuum. As there are few long‐term datasets of wild populations with known‐age individuals, intraspecific (i.e. between‐population) variation in senescence is understudied and limited to comparisons of wild and captive populations of the same species, mostly birds and mammals. In this paper, we examined how population position along the fast–slow life‐history continuum affects intraspecific variation in senescence in an amphibian, Bombina variegata. We used capture–recapture data collected in four populations with contrasting life‐history strategies. Senescence trajectories were analysed using Bayesian capture–recapture models. We show that in populations with fast life histories the onset of actuarial senescence was earlier and individuals aged at a faster rate than individuals in populations with slow life histories. Our study provides one of the few empirical examples of among‐population variation in actuarial senescence patterns in the wild and confirms that the fast–slow life‐history gradient is associated with both macroevolutionary and microevolutionary patterns of actuarial senescence.

The economic importance of genetically improving feed efficiency has been recognized by cattle producers worldwide. It has the potential to considerably reduce costs, minimize environmental impact, optimize land and resource use efficiency, and improve the overall cattle industry’s profitability. Feed efficiency is a genetically complex trait that can be described as units of product output (e.g., milk yield) per unit of feed input. The main objective of this review paper is to present an overview of the main genetic and physiological mechanisms underlying feed utilization in ruminants and the process towards implementation of genomic selection for feed efficiency in dairy cattle. In summary, feed efficiency can be improved via numerous metabolic pathways and biological mechanisms through genetic selection. Various studies have indicated that feed efficiency is heritable, and genomic selection can be successfully implemented in dairy cattle with a large enough training population. In this context, some organizations have worked collaboratively to do research and develop training populations for successful implementation of joint international genomic evaluations. The integration of “-omics” technologies, further investments in high-throughput phenotyping, and identification of novel indicator traits will also be paramount in maximizing the rates of genetic progress for feed efficiency in dairy cattle worldwide.

Cholesterol deficiency (CD) is an autosomal recessive defect in Holstein cattle caused by a mutation in the apolipoprotein B gene (APOB). This paper reports the clinical and pathological phenotype of a case of CD in a 5-months-old Holstein calf. Retarded growth, chronic, intermittent diarrhea, stomatitis, hypocholesterolemia and low blood triglycerides concentrations were the most important clinical and ancillary findings. Histopathologically, inflammation of the digestive organs was the most evident sign. Blood from the patient, the dam, sister1, sister2 and semen of the sire were tested for APOB mutation: the calf resulted homozygous, whereas the dam and the sire resulted heterozygous carriers. Both sisters were APOB mutation free. Cholesterol deficiency should be considered in the differential diagnosis of chronic diarrhea and failure to thrive in Holstein calves.

Background In this paper, we present evidence that biologging is strongly correlated with eye irritation, with sometimes severely impairing effects. A migratory population of the Northern Bald Ibis (Geronticus eremita, NBI) is reintroduced in Europe, in course of a LIFE + project. Since 2014, all individuals have been equipped with GPS-devices. Remote monitoring allows the implementation of focussed measures against major mortality causes. Methods Initially all birds carried battery-powered devices, fixed on the lower back of the birds. Since 2016 an increasing amount of birds has been equipped with solar-powered devices, fixed on the upper back, the more sun-exposed position. In 2016, we observed opacity in the cornea of one eye (unilateral corneal opacity; UCO) during a regular health monitoring for the first time. Results By 2018, a total of 25 birds were affected by UCO, with varying intensity up to blindness. Clinical examination of the birds revealed no clear cause for the symptoms. However, only birds carrying a device on the upper back were affected (2017 up to 70% of this group). In contrast, none of the birds carrying devices on the lower back ever showed UCO symptoms. This unexpected relationship between tagging and UCO was discovered in 2017. After we took countermeasures by removing the device or repositioning it on the lower back, we observed an immediate reduction of the incidence rate without any new cases reported since January 2019. NBI roost with their head on the back, one eye closely placed to the device if it was positioned on the upper back. Thus, we conclude that the most parsimonious explanation for the symptomatology is either a repetitive slight temperature rise in the corneal tissue due to electromagnetic radiation by the GSM module of the device or a repetitive slight mechanical irritation of the corneal surface. Concrete evidence is missing so far. Meanwhile, cases of UCO were found in another NBI population. Conclusion Our observations indicate that further research in the fast-growing field of biologging is urgently needed. The findings question the positioning of devices on the upper back in birds roosting with the head on the back.

Competition for limiting natural resources generates complex networks of relationships between individuals, both at the intra- and interspecific levels, establishing hierarchical scenarios among different population groups. Within obligate scavengers, and especially in vultures, the coevolutionary mechanisms operating during carrion exploitation are highly specialized and determined in part by agonistic behavior resulting in intra-guild hierarchies. This paper revisits the behavioral and hierarchical organization within the guild of European vultures, on the basis of their agonistic activities during carrion exploitation. We used a dataset distilled from high-quality videorecordings of competitive interactions among the four European vulture species during feeding events. We found a despotic dominance gradient from the larger species to smaller ones, and from the adults to subadults and juveniles, following an age and body size-based linear pattern. The four studied species, and to some extent age classes, show despotic dominance and organization of their guild exerting differential selection to different parts of the carrion. The abundance of these parts could ultimately condition the level of agonistic interactions. We discuss the behavioral organization and the relationship of hierarchies according to the feeding behavior and prey selection, by comparing with other scavenger guilds., A.M. was supported by the Ministry of Science, Innovation and Universities of Spain (project RTI2018-099609-B-C22). Fieldwork was carried out within the framework of the project Technical basis and guidelines for a strategy on feeding of endangered scavengers, commissioned by the Ministry for the Ecological Transition of Spain.

Rhinoleucophenga pallida Hendel, 1917 (type species of the genus) is redescribed based on its female holotype and a male from a nearby locality, and Rhinoleucophenga obesa (Loew, 1872) on its two syntypes, which are designated as the male lectotype and a female paralectotype. Both are valid species. A proposal is made to establish the genus Pseudophortica Sturtevant, 1918 (type species R. obesa), a junior synonym of Rhinoleucophenga, to subgenus rank and include all species of Rhinoleucophenga described or redescribed from males except R. pallida, which is unique in having a remarkable pedunculate surstylus, among other differences. The North American R. obesa is compared to its closest sibling, the South American species Rhinoleucophenga gigantea (Thomson, 1869). The occurrence of R. obesa in Brazil is also questioned, as suggested long ago by Marshall R. Wheeler. The specimens from Brazil previously identified as such most probably belong to the new species described in the present paper as Rhinoleucophenga (Pseudophortica) cantareira sp. nov. (type locality: Parque Estadual da Cantareira, City of São Paulo, State of São Paulo, Brazil). Numerous photomicrographs of their habitus and male terminalia taken with a Smartphone's rear camera and digitally stacked to create images with greater depth of focus are provided. Keywords: Habitus, Illustrations, Lectotype designation, Steganinae, Terminalia

Genotyping non-invasively collected samples is challenging. Nevertheless, genetic monitoring of elusive species like the European wildcat (Felis silvestris silvestris) mainly relies on such samples. Wildcats are likely threatened through introgression with domestic cats (F. silvestris catus). To determine introgression based on single cat hairs, we developed a 96.96 Fluidigm single nucleotide polymorphism (SNP) genotyping array chip. To estimate the accuracy of this method, we compared genotypes of 17 cats called with both Sanger sequencing and Fluidigm. When Sanger sequencing genotypes were considered as a reference, the genotyping error rate with Fluidigm was 0.9 %. We subsequently compared 16 hair samples to tissue samples of the same individual. When the tissue samples were used as a reference, the genotyping error rate in hair samples was 1.6 %. This low error rate allowed reliable recognition of individuals and correct assessment of introgression levels. Thus, the genotyping method presented in this paper is suitable for non-invasively collected samples. It will help conservationists to monitor the introgression rate in wildcat populations based on non-invasive hair sampling and subsequently to conduct effective conservation measures.

Because of technical limitations, an impact of machine milking on the teat tissue cannot be avoided. The continuance of this impact during and after milking depends on a variety of factors related to the physiological regulation of milk ejection, as well as the different production systems and milking machine settings. Milking machine settings aim to achieve a high milking performance, that is, short machine-on time at a maximum of milk harvest. However, a high milking performance level is often related to an impact on the teat tissue caused by vacuum or liner compression that can lead to pathological dimensions of congestion of the tissue or hyperkeratosis as a long-term effect. Toward the end of milking a decrease of milk flow rate causes a raise of mouthpiece and teat end vacuum levels and hence an increase of the impact on the teat tissue and the risk of tissue damage. The mechanical stress by the milking machine activates a cascade of cellular mechanisms that lead to an excessive keratin growth and thickening of the keratin layer. Consequently, a complete closure of the teat canal is disabled and the risk of bacterial invasion and intramammary infection increases. Another consequence of high vacuum impact is fluid accumulation and congestion in the tissue of teat tip and teat basis because of an obstruction in venous return. The present review paper provides an overview of the available scientific information to describe the interaction between different levels and types of system vacuum, mouthpiece chamber vacuum, teat end (claw) vacuum, liner pressure, and the risk of short-term and long-term impacts on the teat tissue.

International audience; Leaf area index (LAI) is a critical vegetation structural variable and is essential in the feedback of vegetation to the climate system. The advancement of the global Earth Observation (EO) has enabled the development of global LAI products and boosted global Earth system modeling studies. This overview provides a comprehensive analysis of LAI field measurements and remote sensing estimation methods, the product validation methods and product uncertainties, and the application of LAI in global studies. First, the paper clarifies some definitions related to LAI and introduces methods to determine LAI from field measurements and remote sensing observations. After introducing some major global LAI products, progress made in temporal compositing and prospects for future LAI estimation are discussed. Subsequently, the overview presents various LAI product validation schemes, uncertainties in global moderate resolution LAI products and high resolution reference data. Finally, applications of LAI in global vegetation change, land surface modeling, and agricultural studies are presented. It is recommended that (1) continued efforts are taken to advance LAI estimation algorithms and provide high temporal and spatial resolution products from current and forthcoming missions; (2) further validation studies be conducted to address the inadequacy of current validation studies, especially for under‐represented regions and seasons; and (3) new research frontiers, such as machine learning algorithms, LiDAR technology, and unmanned aerial vehicles (UAV) be pursued to broaden the production and application of LAI.

Big Data approaches offer potential benefits for improving animal health, but they have not been broadly implemented in livestock production systems. Privacy issues, the large number of stakeholders, and the competitive environment all make data sharing, and integration a challenge in livestock production systems. The Swiss pig production industry illustrates these and other Big Data issues. It is a highly decentralized and fragmented complex network made up of a large number of small independent actors collecting a large amount of heterogeneous data. Transdisciplinary approaches hold promise for overcoming some of the barriers to implementing Big Data approaches in livestock production systems. The purpose of our paper is to describe the use of a transdisciplinary approach in a Big Data research project in the Swiss pig industry. We provide a brief overview of the research project named "Pig Data," describing the structure of the project, the tools developed for collaboration and knowledge transfer, the data received, and some of the challenges. Our experience provides insight and direction for researchers looking to use similar approaches in livestock production system research.

International audience; The latitudinal diversity gradient (LDG) is one of the most widely debated patterns in ecology and evolution, associated with hundreds of papers, dozens of hypotheses, and disagreements about its underlying processes. The lack of agreement stems from 1) the verbal nature of existing hypotheses, 2) the failure to mechanistically integrate all relevant ecological and evolutionary processes to the LDG, and 3) the degree to which many empirical patterns are consistent with multiple LDG explanations. We show how mapping LDG hypotheses to a set of key ecological and evolutionary processes leads to a better understanding of the internal logic of those hypotheses. The codification of those processes within a mechanistic eco-evolutionary model is essential for contrasting support for hypotheses and for understanding the relative importance of the processes themselves.

A recent study in PNAS on Tibetan ground tits (1) concludes that inclusive fitness maintains heritable altruism polymorphism if rb = c , which may render equal inclusive fitness in helpful and unhelpful genotypes. We outline flaws in the estimations of rb = c and additive genetic variance, and we propound that current evidence is lacking to justify the conclusions. Sufficient evidence requires that ( i ) helping yields similar benefits to nonhelping, while adequately controlling for potential confounds; and ( ii ) altruism is heritable. First, support for rb = c depends on the validity of the inclusive fitness estimate, which is flawed in the paper by Wang and Lu (1) for the … [↵][1]1To whom correspondence should be addressed. Email: sacha.engelhardt{at}iee.unibe.ch. [1]: #xref-corresp-1-1

Extreme habitats challenge animals with highly adverse conditions, like extreme temperatures or toxic substances. In this paper, we report of a fish (Poecilia mexicana) inhabiting a limestone cave in Mexico. Several springs inside the cave are rich in toxic H2S. We demonstrate that a behavioural adaptation, aquatic surface respiration (ASR), allows for the survival of P. mexicana in this extreme, sulphidic habitat. Without the possibility to perform ASR, the survival rate of P. mexicana was low even at comparatively low H2S concentrations. Furthermore, we show that food limitation affects the survival of P. mexicana pointing to energetically costly physiological adaptations to detoxify H2S

In this paper we present ACEMod, an agent-based modelling framework for studying influenza epidemics in Australia. The simulator is designed to analyse the spatiotemporal spread of contagion and influenza spatial synchrony across the nation. The individual-based epidemiological model accounts for mobility (worker and student commuting) patterns and human interactions derived from the 2006 Australian census and other national data sources. The high-precision simulation comprises 19.8 million stochastically generated software agents and traces the dynamics of influenza viral infection and transmission at several scales. Using this approach, we are able to synthesise epidemics in Australia with varying outbreak locations and severity. For each scenario, we investigate the spatiotemporal profiles of these epidemics, both qualitatively and quantitatively, via incidence curves, prevalence choropleths, and epidemic synchrony. This analysis exemplifies the nature of influenza pandemics within Australia and facilitates future planning of effective intervention, mitigation and crisis management strategies., 24 pages, 11 figures, under review (Simulation Modelling Practice and Theory)

Background Hepatozoon silvestris is an emerging apicomplexan parasite discovered in European wild cats from Bosnia and Herzegovina and blood samples of a domestic cat from Southern Italy in 2017. It has also been identified in Ixodes ricinus collected from a domestic cat in Wales, UK, in 2018. The clinical relevance, pathogenesis and epidemiology of this novel Hepatozoon species are not yet understood. Thus, the objective of this paper was to report and describe the first fatal case of an H. silvestris infection in a domestic cat. Results The cat, which originated from Switzerland, died shortly after presenting clinical signs of lethargy, weakness and anorexia. At necropsy, no specific lesions were observed. Histopathology of the heart revealed a severe lympho-plasmacytic and histiocytic myocarditis. Mature and developing protozoal meronts morphologically compatible with Hepatozoon species were observed associated with the myocardial inflammation. No other lesions were present in any other organ evaluated, and the cat tested negative for retroviral and other immunosuppressive infectious agents. Polymerase chain reaction from the myocardium resulted in a specific amplicon of the Hepatozoon 18S rRNA gene. Sequencing and BLAST analysis revealed 100% sequence identity with H. silvestris. Conclusions The severity of the infection with fatal outcome in an otherwise healthy animal suggests a high virulence of H. silvestris for domestic cats. The presence of this emerging parasite in a domestic cat in Switzerland with no travel history provides further evidence for a geographical distribution throughout Europe.

Intramammary infections induce the initiation of the inflammatory response, resulting in an increase in somatic cell count (SCC) in milk. The SCC includes several different types of cells but does not differentiate between them. On the contrary, the new differential somatic cell count (DSCC) parameter allows for the differentiation between 2 groups of cells: polymorphonuclear neutrophils (PMN) and lymphocytes versus macrophages. Therefore, the aim of this paper was to describe the changes of both DSCC and SCC during mastitis induced by cell wall components from typical mastitis-causing pathogens [lipopolysaccharide (LPS), Escherichia coli; lipoteichoic acid (LTA), Staphylococcus aureus] known to trigger different severities of mastitis. In addition, the effect the glucocorticoid prednisolone (PRED), which is known to attenuate the immune response in the mammary gland, was investigated. Twenty dairy cows were equally divided into 5 groups and treated with LPS, LTA, LPS+PRED, LTA+PRED, or a saline control. Milk samples were taken at the following time points: baseline (d -3, -2, and -1), right before treatment (d 0), 5 h after treatment (d 0.2), early cure phase (d 1 and 2), and late cure phase (d 3, 4, 5, 6, 7, and 14) and analyzed for DSCC and SCC. Mean DSCC values increased significantly from 81% 5 h after treatment and the early cure phase in all groups, except for the groups control and LTA+PRED. This increase clearly reflects a shift in cell populations to predominantly PMN. The SCC increased significantly following the stimulation, too, as expected. Interestingly, we observed cases where SCC increased moderately only whereas DSCC showed an evident increase, meaning that the shift in cell populations occurred even at low SCC levels. The PRED clearly lowered the cell migration in group LTA+PRED. This is the first ever study investigating DSCC during induced mastitis under controlled conditions. The combination of DSCC and SCC could be employed for the earlier detection of mastitis by revealing the shift in cell population independent from the SCC level. Furthermore, combining DSCC and SCC information could help to determine the stage of mastitis because we observed high DSCC and SCC results in the early stage of mastitis but evidently lower DSCC and high SCC in the cure phase. Hence, our results offer the first fundamental insights on how mastitis monitoring could be improved in the frame of dairy herd improvement programs.

Two methodological criticisms of our paper "Synchronizing biological cycles as key to survival under a scenario of global change: The Common quail (Coturnix coturnix) strategy" (Nadal et al., 2018) were proposed in the comment by Rodriguez-Teijeiro et al. (2018) regarding: 1) our estimates of the mean date of arrival, duration of stay and departure stages in the different regions studied; and 2) the analyses carried out to correlate the phenology of the species with changes in the climate variables. The conceptual model that we presented relates the dynamics of this quail population, which moves between short periods of stays, and the spatio-temporal structure of their geographic distribution data, in order to understand the ecology of these birds and to link their movement and residency patterns with geographical area and climate conditions. The probability that quail are resident in a region on any particular date is a result of their overall ecological strategy. We believe that Rodríguez-Teijeiro et al. (2018) have misunderstood our model, leading to their criticism of the statistical tests that we applied., A.M. was supported by a Ramón y Cajal research contract by the Ministry of Economy and Competitiveness (RYC-2012-11867).