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AimAssessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide.LocationBotswana.MethodsBetween 2010 and 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence and colonization, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide.ResultsWildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyaena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species.Main ConclusionsWe highlight the necessity of data sharing and propose a generalizable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally. published

The Mexican cavefish, Astyanax mexicanus (Characidae), has become an important model in evolutionary physiology and developmental biology, providing insights into the evolution of sensory systems, pigmentation, and metabolism. In contrast, comparatively little is known about the natural history and trophic ecology of this elusive cave inhabitant. We investigated cavefish from three independently colonized cave systems (Pachon, Tinaja, and Sabinos), which are located in the Sierra de El Abra of northeastern Mexico. Samples were collected multiple times throughout the year to investigate variation in body size, sex ratios, proportions of individuals with empty guts, and diet composition. We found consistent differences in body size among caves, and sex ratios were generally female biased, although to varying degrees. Gut content analyses indicated that cavefish consume food throughout the year, and diets are dominated by detritus, plant materials, and aquatic invertebrates. Especially in the Pachon cave, where we had the densest sampling, there was evidence for seasonal changes in diet composition that coincided with the rainy and dry seasons. Our findings potentially suggest that the cave environments in this system are characterized by continual nutrient limitation, rather than intermittent periods of starvation.

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate. Ancient human genomes uncover historical hard sweeps Hard sweeps were common in ancient West Eurasian populations A historical hard sweep in the MHC-III region Admixture can obscure historical hard sweeps Evolutionary scenarios underlying sweep signal dilution The mutational basis of the Eurasian hard sweeps Discussion Methods

The protection of wetlands is a cornerstone in the conservation of pond-breeding amphibians. Because protected wetlands are rarely natural areas, but are often man-made, at least in Europe, it is important that they are well managed to fulfill their intended function. Appropriate management requires knowledge of the ecology of the species, particularly habitat requirements. Here, we combine species monitoring data and habitat mapping data in an analysis where our goal was to describe the factors that determine the occupancy of amphibian species in federally protected amphibian breeding sites. As expected, every species had its own habitat requirements, often a combination of both a terrestrial and aquatic habitat (i.e., landscape complementation). In most species, occupancy was strongly positively affected with the amount of aquatic habitat, but predicted occupancy probabilities were low because the amount of aquatic habitat was low in most sites. The area or proportion of ruderal vegetation also had positive effects on multiple species, while other types of terrestrial habitat (e.g., meadows) led to low occupancy probabilities. The total area of the protected breeding sites was never included in a final model and connectivity was important only for one species (Triturus cristatus). The latter finding implies that the quality of the landscape between breeding sizes is more important than distance per se, while the former implies that the area of some specific habitats within breeding sites is crucial for high occupancies. Thus, increasing the amount of aquatic habitats and likewise terrestrial habitats within protected areas would make them more likely to achieve their conservation objectives. Our study is an example of how the joint analysis of monitoring data and habitat data (based on mapping in the field) can lead to evidence-based suggestions on how to improve conservation practice.

Determining the density trends of a guild of species can help illuminate their interactions, and the impacts that humans might have on them. We estimated the density trends from 2013 to 2017 of the clouded leopard Neofelis nebulosa, leopard cat Prionailurus bengalensis and marbled cat Pardofelis marmorata in Nam Et—Phou Louey National Park (NEPL), Laos, using camera trap data and spatial capture-recapture models. Mean (± SD) density estimates (individuals/100 km2) for all years were 1.77 ± 0.30 for clouded leopard, 1.50 ± 0.30 for leopard cat, and 3.80 ± 0.70 for marbled cat. There was a declining trend in density across the study years for all three species, with a ≥ 90% probability of decline for clouded leopard and leopard cat and an 83% probability of decline for marbled cat. There was no evidence that mesopredator release occurred as a result of tiger (Panthera tigris) and leopard (P. pardus) extirpations. We believe that snaring, the factor that led to the extirpation of tiger and leopard in NEPL, is now contributing to the decline of smaller felids, to an extent that over-rides any potential effects of mesopredator release on their densities and interactions. We recommend that the NEPL managers implement a more systematic and intensified snare removal program, in concert with extensive community outreach and engagement of local people to prevent the setting of snares. These actions might be the only hope for saving the remaining members of the felid community in NEPL.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

Fundamental concepts in biology are often challenging to understand. More strikingly, studies also report incorrect or incomplete understanding of such concepts for undergraduate natural science students even after instruction. Recent research suggests that embedding conceptual information in a narrative could support students’ learning process and facilitate conceptual change. Therefore, we designed learning materials covering complex concepts in biology either in the form of a narrative presenting the to-be-learned concepts in a historical context or as an expository text as control. We then assessed conceptual understanding and potential learning mechanisms. Results indicate that students learned from narrative texts and expository texts to a similar extent. However, if the prior knowledge was higher, the effect on learning was bigger in the narrative group than in the expository group. Moreover, the narrative led to better enjoyment and a higher germane cognitive load than the expository text material., Proceedings Annual Meeting of the Cognitive Science Society, 44, ISSN:1069-7977, Proceedings of the 44th Annual Conference of the Cognitive Science Society

The aim of this study was to analyze inpatient antibiotic consumption during the first 16 months of the COVID-19 pandemic in Switzerland. The entire period (January 2018–June 2021) was divided into the prepandemic period, the first and second waves, and the intermediate period. In the first year of the pandemic, total overall inpatient antibiotic consumption measured in defined daily doses (DDD) per 100 bed-days remained stable (+1.7%), with a slight increase in ICUs of +4.2%. The increase in consumption of broad-spectrum antibiotics was +12.3% overall and 17.3% in ICUs. The segmented regression model of monthly data revealed an increase in overall antibiotic consumption during the first wave but not during the second wave. In the correlation analysis performed in a subset of the data, a significant positive association was found between broad-spectrum antibiotic consumption and an increasing number of hospitalized COVID-19 patients (p = 0.018). Restricting this dataset to ICUs, we found significant positive correlations between the number of hospitalized COVID-19 patients and total antibiotic consumption (p = 0.007) and broad-spectrum antibiotic consumption (p < 0.001). In conclusion, inpatient antibiotic use during the different periods of the COVID-19 pandemic varied greatly and was predominantly notable for broad-spectrum antibiotics.

Undergraduate students frequently struggle to understand biological concepts. Embedding conceptual information in a historical narrative holds the potential to support their learning. We developed learning materials comparing narrative or expository texts and assessed students’ conceptual understanding via post-tests. Results showed that students, who read the narrative text, understood the concept of randomness better. No difference was found for the enzyme energetics concept. Furthermore, students in the narrative group reported higher situational interest after the intervention.

Background Obesity is caused by an imbalance between energy intake, i.e. eating and energy expenditure (EE). Severe obesity is more prevalent in women than men worldwide, and obesity pathophysiology and the resultant obesity-related disease risks differ in women and men. The underlying mechanisms are largely unknown. Pre-clinical and clinical research indicate that ovarian hormones may play a major role. Objective and rationale We systematically reviewed the clinical and pre-clinical literature on the effects of ovarian hormones on the physiology of adipose tissue (AT) and the regulation of AT mass by energy intake and EE. Search methods Articles in English indexed in PubMed through January 2016 were searched using keywords related to: (i) reproductive hormones, (ii) weight regulation and (iii) central nervous system. We sought to identify emerging research foci with clinical translational potential rather than to provide a comprehensive review. Outcomes We find that estrogens play a leading role in the causes and consequences of female obesity. With respect to adiposity, estrogens synergize with AT genes to increase gluteofemoral subcutaneous AT mass and decrease central AT mass in reproductive-age women, which leads to protective cardiometabolic effects. Loss of estrogens after menopause, independent of aging, increases total AT mass and decreases lean body mass, so that there is little net effect on body weight. Menopause also partially reverses women's protective AT distribution. These effects can be counteracted by estrogen treatment. With respect to eating, increasing estrogen levels progressively decrease eating during the follicular and peri-ovulatory phases of the menstrual cycle. Progestin levels are associated with eating during the luteal phase, but there does not appear to be a causal relationship. Progestins may increase binge eating and eating stimulated by negative emotional states during the luteal phase. Pre-clinical research indicates that one mechanism for the pre-ovulatory decrease in eating is a central action of estrogens to increase the satiating potency of the gastrointestinal hormone cholecystokinin. Another mechanism involves a decrease in the preference for sweet foods during the follicular phase. Genetic defects in brain α-melanocycte-stimulating hormone-melanocortin receptor (melanocortin 4 receptor, MC4R) signaling lead to a syndrome of overeating and obesity that is particularly pronounced in women and in female animals. The syndrome appears around puberty in mice with genetic deletions of MC4R, suggesting a role of ovarian hormones. Emerging functional brain-imaging data indicates that fluctuations in ovarian hormones affect eating by influencing striatal dopaminergic processing of flavor hedonics and lateral prefrontal cortex processing of cognitive inhibitory controls of eating. There is a dearth of research on the neuroendocrine control of eating after menopause. There is also comparatively little research on the effects of ovarian hormones on EE, although changes in ovarian hormone levels during the menstrual cycle do affect resting EE. Wider implications The markedly greater obesity burden in women makes understanding the diverse effects of ovarian hormones on eating, EE and body adiposity urgent research challenges. A variety of research modalities can be used to investigate these effects in women, and most of the mechanisms reviewed are accessible in animal models. Therefore, human and translational research on the roles of ovarian hormones in women's obesity and its causes should be intensified to gain further mechanistic insights that may ultimately be translated into novel anti-obesity therapies and thereby improve women's health.

Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological diversification and (pre)historical colonizations, migrations and extinctions. In the current era of high- throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges.We present the r package smartsnp for fast and user- friendly computation of PCA on single-nucleotide polymorphism (SNP) data. Inspired by the current field- standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient samples onto a modern genetic space while also providing permutation- based multivariate tests for population differences in genetic diversity (both location and dispersion).Our extensive benchmarks show that smartsnp's PCA is 2– 4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of sample and SNP sizes. All four smartsnp functions (smart_pca, smart_permanova, smart_permdisp and smart_mva) process datasets with up to 100 samples and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient- human and wolf genotypes.The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low- coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies.

Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (Poecilia mexicana) that inhabit distinct habitat types (hydrogen-sulphide-rich springs and adjacent nonsulphidic streams). For each individual, we quantified different metrics of burst swimming during simulated predator attacks, steady swimming and gill ventilation. Coinciding with predictions, we documented significant population differences in all aspects of performance, with fish from sulphidic habitats exhibiting higher steady swimming performance and higher ventilation capacity, but slower burst swimming. There was a significant functional trade-off between steady and burst swimming, but not between different aspects of locomotion and ventilation. Although our findings about population differences in locomotion performance largely parallel the results from previous studies, we provide novel insights about how morphological variation might impact ventilation and ultimately oxygen acquisition. Overall, our analyses provided insights into the functional consequences of previously documented phenotypic variation, which will help to disentangle the effects of different sources of selection that may coincide along complex environmental gradients.

Animals contribute significantly to nutrient cycling through excretion, but most studies consider their effects under relatively benign abiotic conditions. Disturbances such as drought may alter animals’ nutrient contributions through shifts in species composition and biomass. Headwater streams are particularly vulnerable to extreme climate events and thus might show rapid changes in stream biota and their ecosystem effects. We tested how biomass and subsequent ecosystem effects (nutrient cycling) of an intermittent prairie stream community changed during a drought. We quantified the biomass and contributions to nutrient cycling for assemblages comprising fishes, crayfish, and tadpoles in 12 isolated pools over 3 months encompassing the harshest drought on record for Kings Creek, KS, U.S.A. We predicted that macroconsumer biomass would decline with pool surface area and that differences in macroconsumer biomass and taxonomic composition would lead to different contributions of pool assemblages to nutrient cycling. The biomass of pool assemblages declined with decreasing pool size, a pattern apparently driven by mortality, emigration, or metamorphosis. We also observed a change in assemblage structure of drying pools during drought relative to pool size, shifting dominance toward species with more drought‐resistant traits. Accordingly, assemblage nitrogen (N) excretion rates declined as pool biomass was reduced, leading to a 58% reduction in N available to epilithic biofilms. Phosphorus (P) excretion rates declined from June to July, but increased in August, as species with high P excretion rates maintained similar proportional biomass and biomass of a non‐native fish increased. Molar N:P of pool assemblage excretion declined significantly throughout the drought and coincided with loss of southern redbelly dace (Chrosomus erythrogaster: Cyprinidae). Animal‐mediated nutrient cycling was altered by the loss of biomass and stoichiometric traits of taxa that differed in their occurrences and ability to tolerate abiotic conditions during drought. Elevated availability of dissolved N in isolated pools may increase N uptake rates by biofilms during drought conditions, indicating the importance of N excreted by aggregated macroconsumers, especially those with unique stoichiometric traits. While the significance of shifts in the composition of freshwater communities to ecosystems is not entirely known, additional losses in ecosystem function and changes in community structure may follow episodes of severe drought.

Background There is growing evidence that equine papillomavirus type 2 (EcPV2) infection is causally associated with the development of equine genital squamous cell carcinomas (SCCs). Early stages of disease present clinically as plaques or wart-like lesions which can gradually progress to tumoural lesions. Histologically these lesions are inconsistently described as benign hyperplasia, papilloma, penile intraepithelial neoplasia (PIN), carcinoma in situ (CIS) or SCC. Guidelines for histological classification of early SCC precursor lesions are not precisely defined, leading to potential misdiagnosis. The aim of this study was to identify histologic criteria and diagnostic markers allowing for a more accurate diagnosis of EcPV2-associated equine penile lesions. Results A total of 61 archived equine penile lesions were histologically re-assessed and classified as benign hyperplasia, papilloma, CIS or SCC. From these, 19 representative lesions and adjacent normal skin were comparatively analysed for the presence of EcPV2 DNA and transcripts using PCR and RNA in situ hybridisation (RISH). All lesional samples were positive by EcPV2 PCR and RISH, while adjacent normal skin was negative. RISH analysis yielded signal distribution patterns that allowed distinction of early (hyperplasia, papilloma) from late stage lesions (CIS, SCC). Subsequently, the 19 lesions were further assessed for expression of p53, Ki67, MCM7 and MMP1 by immunohistochemistry (IHC). All four proteins were expressed in both normal and lesional tissue. However, p53 expression was up-regulated in basal keratinocyte layers of papillomas, CIS and SCCs, as well as in upper keratinocyte layers of CIS and SCCs. MCM7 expression was only up-regulated in upper proliferating keratinocyte layers of papillomas, CIS and SCCs. Conclusion This study proposes combining a refined histological protocol for analysis of equine penile lesions with PCR- and/or RISH based EcPV2-screening and p53/MCM7 IHC to more accurately determine the type of lesion. This may help to guide the choice of optimum treatment strategy, especially at early stages of disease.

The UVR8 photoreceptor in Arabidopsis thaliana is specific for ultraviolet-B (UV-B; 280-315 nm) radiation and its activation leads to a number of UV-B acclimation responses, including the accumulation of flavonoids. UVR8 participates in a signaling cascade involving COP1 and HY5 so that the absence of any of these components results in a reduction in the ability of a plant to accumulate flavonoids in response to UV; Cop1 mutants show high dropouts and hy5-ks50 hyh double mutants show very low levels of flavonoids. The predominant phenolics in Arabidopsis thaliana are sinapic acid derivatives as well as non-aclyated quercetin and kaempferol di- and triglycosides containing glucose and rhamnose as glycosylated sugar moieties. How this flavonoid profile in Arabidopsis thaliana is affected by UV radiation, how rapidly these changes occur in changing UV conditions, and which components of the UV-B signalling pathway are involved in rapid UV acclimatization reactions is poorly understood. In the present study, we examined these questions by characterizing the flavonoid profiles of Arabidopsis thaliana signalling mutants and wild types grown under different UV levels of constant UV-B+PAR ratios and then transferring a subset of plants to alternate UV conditions. Results indicate that flavonoid accumulation in Arabidopsis thaliana is triggered by UV and this response is amplified by higher levels of UV but not by all compounds to the same extent. The catechol structure in quercetin seems to be less important than the glycosylation pattern, e.g. having 2 rhamnose moieties in determining responsivity. At low UV+PAR intensities the introduction of UV leads to an initial tendency of increase of flavonoids in the wild types that was detected after 3 days. It took 7 days for these changes to be detected in plants grown under high UV+PAR intensities suggesting a priming of PAR. Thus, the flavonoid profile in Arabidopsis thaliana is altered over time following exposure to UV and PAR, but the functional significance of these changes is currently unclear.

Umbilical preservation can be challenging, particularly in complex cases involving simultaneous ventral hernia repair and abdominoplasty. Although the umbilicus serves no functional purpose, removal of the umbilicus can draw unwanted attention to the abdominal area and can cause emotional distress to patients. There are several well documented options for umbilical reconstruction. We present a new umbilical reconstruction technique relevant for such cases. This neoumbilicoplasty allows for preservation of the original umbilicus with relocation and reconstruction using local flaps. The technique is relatively simple and the time needed is minimal. The result is a natural, well positioned umbilicus using the principles of spare part surgery.

The evolutionarily recent dispersal of Anatomically Modern Humans (AMH) out of Africa and across Eurasia provides an opportunity to study rapid genetic adaptation to multiple new environments. Genomic analyses of modern human populations have detected limited signals of strong selection such as hard sweeps, but genetic admixture between populations is capable of obscuring these patterns and is well known in recent human history, such as during the Bronze Age4. Here we show that ancient human genomic datasets contain multiple genetic signatures of strong selection including 57 hard sweeps, many with strong associations with cold adaptation. Similar genetic signatures of adaptation are also observed in adaptively-introgressed archaic hominin loci, as well as modern Arctic human groups. Consistent targets include the regulation of fat storage, skin physiology, cilia function and neural development; with multiple associations to modern western diseases. The spatiotemporal patterns of the hard sweeps allow reconstruction of early AMH population dispersals, and reveal a prolonged period of genetic adaptation (~80-50,000 years) following their initial out of Africa movement, before a rapid spread across Eurasia reaching as far as Australia.

There is growing evidence that equine papillomavirus type 2 (EcPV2) infection is etiologically associated with the development of genital squamous cell carcinoma (SCC) and precursor lesions in equids. However, the precise mechanisms underlying neoplastic progression remain unknown. To allow the study of EcPV2-induced carcinogenesis, we aimed to establish a primary equine cell culture model of EcPV2 infection. Three-dimensional (3D) raft cultures were generated from equine penile perilesional skin, plaques and SCCs. Using histological, molecular biological and immunohistochemical methods, rafts versus corresponding natural tissue sections were compared with regard to morphology, presence of EcPV2 DNA, presence and location of EcPV2 gene transcripts and expression of epithelial, mesenchymal and tumor/proliferation markers. Raft cultures from perilesional skin harboring only a few EcPV2-positive (EcPV2+) cells accurately recapitulated the differentiation process of normal skin, whilst rafts from EcPV2+ penile plaques were structurally organized but showed early hyperplasia. Rafts from EcPV2+ SCCs exhibited pronounced hyperplasia and marked dysplasia. Raft levels of EcPV2 oncogene transcription (E6/E7) and expression of tumor/proliferation markers p53, Ki67 and MCM7 expression positively correlated with neoplastic progression, again reflecting the natural situation. Three-dimensional raft cultures accurately reflected major features of corresponding ex vivo material, thus constituting a valuable new research model to study EcPV2-induced carcinogenesis.

The efficacy of translocation as a method for conserving species in peril has not been fully evaluated. Post‐release monitoring rarely involves long‐term assessments and initial success metrics may not translate to population viability. In particular, genetic factors may play a critical role in fitness following release as founder effect, genetic drift, inbreeding depression and outbreeding depression can influence extinction risk. As part of a multi‐year recovery effort, we translocated populations of the endangered Stephens' kangaroo rat (Dipodomys stephensi; SKR), in order to restore population connectivity. Here we evaluate the success of the translocation efforts through long‐term population estimation and genetic analyses. We conducted post‐release assessments for 9 years, and used Bayesian clustering analysis and principal components analysis (PCA) of 24 microsatellite markers developed for this species to assess genetic admixture between source and translocated populations. Demographic results indicate long‐term translocation success, as evidenced by founder survival and establishment, and population growth and regulation. Genetic results show admixture at the release site between genetically discrete source populations, provide definitive evidence that translocated individuals, not immigrants, produced offspring at the release site, that these offspring successfully reproduced and that even with moderate to great genetic differentiation of source populations, outbreeding depression was not detected. Despite the historical failure of heteromyid translocation efforts, our long‐term study illustrates how the development of species‐specific best practices led to an effective strategy for SKR recovery. More broadly, our results suggest efforts that use a systematic hypothesis‐testing framework alongside long‐term monitoring offer great promise in improving translocation outcomes.

Divergent selection along ecological gradients can lead to speciation, and replicated speciation events occur when populations of multiple lineages undergo divergence following colonization of similar environments. In such instances, it remains unclear to what extent reproductive isolation evolves via convergent mechanisms at the genomic level due to biases associated with shared ancestry and variation in selection associated with geographic replicates typically studied in this context. We used a unique system in which three species of poeciliid fishes occur in sympatry in a toxic, hydrogen sulfide (H2S)-rich spring and an adjacent nonsulfidic stream to examine shared patterns of adaptive divergence across multiple levels of biological organization. Despite small spatial scales, we found strong genetic differentiation between populations in sulfidic and nonsulfidic habitats mediated by strong selection against migrants between habitat types. High levels of reproductive isolation were accompanied by convergent patterns of adaptation in morphological and physiological traits, as well as genome-wide patterns of gene expression across all three species. Furthermore, the mitochondrial genomes of each species exhibit shared signatures of selection on key genes involved in H2S toxicity. However, contrary to predictions of speciation theory, analyses of divergence across the nuclear genomes neither revealed evidence for clear genomic islands of speciation nor substantial congruence of outlier regions across population pairs. Instead, heterogenous regions of divergence spread across the genome suggest that selection for polygenic physiological adaptations likely facilitated the rapid evolution of high levels of reproductive isolation. Overall, we demonstrate that substantial convergence across multiple levels of biological organization can be mediated by non-convergent modifications at the genomic level. By disentangling variation in natural selection from lineage-specific evolution in this system of highly divergent, yet sympatric lineages, our results emphasize the outsized role of the genomic substrate upon which selection acts in driving convergent evolution at the phenotypic level.Significance StatementDivergent lineages that coexist in sympatry and are exposed to the same sources of natural selection provide a unique opportunity to study convergent evolution across levels of organization because confounding factors associated with geographic replications are eliminated. Using three sympatric lineages of livebearing fishes inhabiting toxic and adjacent nontoxic habitats, we show that the convergent evolution of phenotypic adaptation and reproductive isolation can evolve in the absence of substantial convergence at the genomic level. Our results suggest that the nature of selection is less important in producing genomic convergence than the initial genomic substrates that are available for selection to act on.

Visual sensitivity and body pigmentation are often shaped by both natural selection from the environment and sexual selection from mate choice. One way of quantifying the impact of the environment is by measuring how traits have changed after colonization of a novel habitat. To do this, we studied Poecilia mexicana populations that have repeatedly adapted to extreme sulphidic (H2S containing) environments. We measured visual sensitivity using opsin gene expression, as well as body pigmentation and water transmission for populations in four independent drainages. Both visual sensitivity and body pigmentation showed significant parallel shifts towards greater medium wavelength sensitivity and reflectance in sulphidic populations. The light spectrum was only subtly different between environments and overall, we found no significant correlations between the light environment and visual sensitivity or body pigmentation. Altogether we found that sulphidic habitats select for differences in visual sensitivity and pigmentation; our data suggest that this effect is unlikely to be driven purely by the water’s spectral properties and may instead be from other correlated ecological changes.

Significance Environmental factors can promote phenotypic variation through alterations in the epigenome and mediate adaptation of an organism to the environment. Observations suggest the adaptation of Poecilia mexicana fish to toxic, hydrogen sulfide–rich environments in southern Mexico may, in part, be promoted through epigenetic DNA methylation alterations that became generationally stable and are inherited to subsequent generations independent of the environment. Environmental epigenetics may provide an important mechanism mediating adaptation in this species. This is an observation that the epigenome is stably inherited generationally through the germline after the removal of an environmental stressor (i.e., hydrogen sulfide) from a wild population., Environmental factors can promote phenotypic variation through alterations in the epigenome and facilitate adaptation of an organism to the environment. Although hydrogen sulfide is toxic to most organisms, the fish Poecilia mexicana has adapted to survive in environments with high levels that exceed toxicity thresholds by orders of magnitude. Epigenetic changes in response to this environmental stressor were examined by assessing DNA methylation alterations in red blood cells, which are nucleated in fish. Males and females were sampled from sulfidic and nonsulfidic natural environments; individuals were also propagated for two generations in a nonsulfidic laboratory environment. We compared epimutations between the sexes as well as field and laboratory populations. For both the wild-caught (F0) and the laboratory-reared (F2) fish, comparing the sulfidic and nonsulfidic populations revealed evidence for significant differential DNA methylation regions (DMRs). More importantly, there was over 80% overlap in DMRs across generations, suggesting that the DMRs have stable generational inheritance in the absence of the sulfidic environment. This is an example of epigenetic generational stability after the removal of an environmental stressor. The DMR-associated genes were related to sulfur toxicity and metabolic processes. These findings suggest that adaptation of P. mexicana to sulfidic environments in southern Mexico may, in part, be promoted through epigenetic DNA methylation alterations that become stable and are inherited by subsequent generations independent of the environment.

Wild-type adeno-associated virus (AAV) can only replicate in the presence of helper factors, which can be provided by coinfecting helper viruses such as adenoviruses and herpesviruses. The AAV genome consists of a linear, single-stranded DNA (ssDNA), which is converted into different molecular structures within the host cell. Using high-throughput sequencing, we found that herpes simplex virus 1 (HSV-1) coinfection leads to a shift in the type of AAV genome end recombination. In particular, open-end inverted terminal repeat (ITR) recombination was enhanced, whereas open-closed ITR recombination was reduced in the presence of HSV-1. We demonstrate that the HSV-1 protein ICP8 plays an essential role in HSV-1-mediated interference with AAV genome end recombination, indicating that the previously described ICP8-driven mechanism of HSV-1 genome recombination may be underlying the observed changes. We also provide evidence that additional factors, such as products of true late genes, are involved. Although HSV-1 coinfection significantly changed the type of AAV genome end recombination, no significant change in the amount of circular AAV genomes was identified. IMPORTANCE Adeno-associated virus (AAV)-mediated gene therapy represents one of the most promising approaches for the treatment of genetic diseases. Currently, various GMP-compatible production methods can be applied to manufacture clinical-grade vector, including methods that employ helper factors derived from herpes simplex virus 1 (HSV-1). Yet, to date, we do not fully understand how HSV-1 interacts with AAV. We observed that HSV-1 modulates AAV genome ends similarly to the genome recombination events observed during HSV-1 replication and postulate that further improvements of the HSV-1 production platform may enhance packaging of the recombinant AAV particles. ispartof: JOURNAL OF VIROLOGY vol:95 issue:13 ispartof: location:United States status: published

Herpes Simplex Virus Type-1 (HSV-1) forms progeny in the nucleus within distinct membrane-less inclusions, the viral replication compartments (VRCs), where viral gene expression, DNA replication, and packaging occur. The way in which the VRCs maintain spatial integrity remains unresolved. Here, we demonstrate that the essential viral transcription factor ICP4 is an intrinsically disordered protein (IDP) capable of driving protein condensation and liquid–liquid phase separation (LLPS) in transfected cells. Particularly, ICP4 forms nuclear liquid-like condensates in a dose- and time-dependent manner. Fluorescence recovery after photobleaching (FRAP) assays revealed rapid exchange rates of EYFP-ICP4 between phase-separated condensates and the surroundings, akin to other viral IDPs that drive LLPS. Likewise, HSV-1 VRCs revealed by EYFP-tagged ICP4 retained their liquid-like nature, suggesting that they are phase-separated condensates. Individual VRCs homotypically fused when reaching close proximity and grew over the course of infection. Together, the results of this study demonstrate that the HSV-1 transcription factor ICP4 has characteristics of a viral IDP, forms condensates in the cell nucleus by LLPS, and can be used as a proxy for HSV-1 VRCs with characteristics of liquid–liquid phase-separated condensates.

Equine sarcoids (ES) were diagnosed in 12 Somali wild asses (SWA) (Equus africanus somaliensis) from 10 different institutions of the SWA European Endangered Species Programme from 1976 to 2019. Samples of surgically excised masses, biopsies, or necropsy samples were submitted for histologic and virologic analysis. In addition, tissue samples from one onager (Equus hemionus onager), one kulan (Equus hemionus kulan), and two Hartmann's mountain zebras (HMZ) (Equus zebra hartmannae) were examined. Histology confirmed the diagnosis of ES exhibiting the typical microscopic features. Polymerase chain reaction detected bovine papillomavirus type 1 (BPV1) DNA in eight SWA samples and bovine papillomavirus type 2 (BPV2) DNA in one SWA sample. The onager, kulan, and one HMZ sample tested positive for BPV1. The other HMZ tested positive for BPV1 and BPV2. This is the first report of ES in an onager. Surgical excision was the treatment elected by most veterinarians. A follow-up survey of the cases over several years after clinical diagnosis and therapy revealed variable individual outcome with ES recurrence in four cases. Three SWA and the kulan were euthanized due to the severity of the lesions. Nine affected SWA were males with seven having a sarcoid located at the prepuce. Because a genetic disposition is a risk factor for the development of ES in horses, this may also be true for endangered wild equids with few founder animals in their studbook history. Innovative approaches regarding therapy and prevention of ES in wild equids are therefore highly encouraged.

Die Anzahl und Variabilität von Viren ist immens. Ihnen allen ist aber gemeinsam, dass sie zur Vermehrung auf eine lebende Zelle angewiesen sind. Viren haben deshalb effiziente Strategien entwickelt, die Zellhüllen zu überwinden und die Makromolekül-Synthese-Mechanismen im Zellinneren für die eigene Replikation zu beanspruchen. Gleichzeitig müssen sie die umfangreichen Abwehrmechanismen des Wirts so beeinflussen, dass der Replikationszyklus mit der Freisetzung von Virusnachkommen abgeschlossen werden kann. Die neusynthetisierten Viren können sich weiter im Wirt verbreiten und auf neue Wirte oder ganze Populationen übergreifen. Die Allgemeine Virologie erläutert die verschiedenen Schritte im Replikationszyklus der Viren und zeigt die vielfältigen Interaktionen zwischen Virus und Wirt auf. Zudem werden Strategien für die Kontrolle von Virusinfektionen sowie für den Einsatz von Viren in der Molekularen Medizin diskutiert. Doppelseitige farbige Darstellungen von wichtigen Viren im Appendix (u. a. Corona-, Herpes-, Pox-, Rhabdo- und Retro-Virus).

Repetitive transcranial magnetic stimulation (rTMS) is now widely used as a means of neuromodulation, but the details of the mechanisms by which rTMS works remain unclarified. As a step forward to unveiling the neural phenomena occurring underneath the TMS coil, we conducted an electrophysiological study using awake and unanesthetized monkeys with subdural electrocorticogram (ECoG) electrodes implanted over the primary motor cortex (MI). We evaluated the effects of low-frequency (1 Hz) and high-frequency (10 Hz) rTMS on the resting-state ECoG signals in the stimulated MI, as well as the motor evoked potentials (MEPs) in the contralateral hand. Following the 1-Hz rTMS application, the ECoG beta band power and the MEP amplitude were significantly decreased. Following the 10-Hz rTMS application, the ECoG high-gamma power and the MEP amplitude significantly increased. Given that beta and high-gamma activities in the ECoG reflect the synchronous firing and the firing frequency of cell assemblies, respectively, in local neural circuits, these results suggest that low-frequency rTMS inhibits neural activity by desynchronizing the firing activity of local circuits, whereas high-frequency rTMS facilitates neural activity by increasing the firing rate of cell assemblies in the local circuits.

Reversing the field Do terrestrial geomagnetic field reversals have an effect on Earth's climate? Cooper et al. created a precisely dated radiocarbon record around the time of the Laschamps geomagnetic reversal about 41,000 years ago from the rings of New Zealand swamp kauri trees. This record reveals a substantial increase in the carbon-14 content of the atmosphere culminating during the period of weakening magnetic field strength preceding the polarity switch. The authors modeled the consequences of this event and concluded that the geomagnetic field minimum caused substantial changes in atmospheric ozone concentration that drove synchronous global climate and environmental shifts. Science , this issue p. 811

SummaryThe current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of COVID-19.

Field photographs of plant species are crucial for research and conservation, but the lack of a centralized database makes them difficult to locate. We surveyed 25 online databases of field photographs and found that they harboured only about 53% of the approximately 125,000 vascular plant species of the Americas. These results reflect the urgent need for a centralized database that can both integrate and complete the photographic record of the world’s flora. Field photographs are essential for research and conservation, but are difficult to access since there is no central database or connection between archives. The 25 leading databases hold only 53% of the plant species of the Americas, illustrating the need for increased work on collecting and standardizing this valuable data.

microRNAs (miRNAs) are post-transcriptional regulators of gene expression and can play an important role in modulating organismal development and physiology in response to environmental stress. However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in Poecilia mexicana, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H2 S). We found that P. mexicana has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to P. mexicana adaptation to sulphidic environments. In silico identification of differentially expressed miRNA-mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H2 S-rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H2 S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H2 S adaptation by promoting functions needed for survival and reducing functions affected by H2 S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H2 S. Overall, this study provides a critical stepping-stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.

As the causative agent of Infectious Bovine Rhinotracheitis (IBR) and Infectious Pustular Vulvovaginitis/Balanoposthitis (IPV/IPB), Bovine alphaherpesvirus 1 (BoHV-1) is responsible for high economic losses in the cattle industry worldwide. This study aimed to establish a fast, colorimetric loop-mediated isothermal amplification (LAMP) assay for the detection of viral DNA. Phenol red is used as pH-sensitive readout, relying on a distinct color change from pink to yellow in case of a positive reaction. LAMP reactions with different primers were compared and a newly designed set targeting the gene encoding the tegument protein V67 provided best results, enabling readout within 8-30 min. LAMP showed less cross-reactions with other ruminant alphaherpesviruses than qPCR but was 10-fold less sensitive. However, LAMP still detected down to 14 copies. The test performance was evaluated using 26 well-characterized nasal swabs from cattle with respiratory disease. All samples were correctly identified when using column-extracted DNA. Using a simple DNA precipitation method, only two weak-positive samples turned indeterminate. Combining this DNA precipitation with a makeshift water bath heated by a gastronomic immersion heater allowed successful application of the colorimetric LAMP assay under resource-limited conditions. This technique can therefore help in managing IBR/IPV outbreaks where sophisticated laboratory equipment is unavailable.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species – Homo luzonensis and H. floresiensis – were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

The BioPhorum Development Group Viral Clearance Workstream performed a collaborative retrospective analysis to evaluate packed bed chromatographic resin performance after repeated cycling for two commonly used chromatography steps in biopharmaceutical manufacturing: protein A and anion exchange. Key variables evaluated in the assessment included virus type, resin type, number of reuse cycles, and virus challenge. In this retrospective analysis of viral clearance data on naive versus cycled resin, powered by the availability of a decade’s worth of accumulated industry data, clearance capability was not negatively impacted by resin cycling. This finding is consistent with publications showing that surrogates for viral clearance capabilities could be employed in lieu of testing the viral clearance of cycled resins for protein A and anion exchange chromatography. The rigorous analysis of the retrospective data supports the view that viral clearance studies for cycled resins are not necessary provided that appropriate cleaning methods are applied during repeated use of the chromatography columns. LAY ABSTRACT: The manufacturing processes for biopharmaceutical products often include reusable chromatographic resins that remove process- and product-related impurities as well as potential contaminating viruses. Typically, chromatography resin is “cycled” through repeated steps of resin conditioning, product purification, and resin cleaning. The cycling approach has been evaluated in both small- and full-scale studies that show the performance parameters are maintained. The ability to remove virus is demonstrated separately in a focused small-scale virus-spiking study that is resource-intensive and costly. This paper is a retrospective review of industry data comparing virus removal by naive and repeatedly cycled resins that summarizes the viral clearance impact of re-using protein A and anion exchange chromatography resins. The key variables evaluated in the assessment included virus type, resin type, number of cycles, and virus challenge. In this retrospective analysis, it was found that the viral clearance capability is not negatively impacted by resin cycling. This finding is consistent with other publications and supports the view that viral clearance studies for cycled resins are not necessary if appropriate cleaning methods are applied during the repeated use of the chromatography columns. Abbreviations: AAV-2, Adeno-associated virus; A-MuLV, Amphotropic murine leukemia virus; AEX, Anion-exchange chromatography; B/E, Bind and elute; BVDV, Bovine viral diarrhea virus; C.P.G., Controlled pore glass; DEAE, Diethylaminoethanol; EMCV, Encephalomyocarditis virus; FT, Flow through; HAV, Hepatitis A virus; HSV-1, Herpes simplex virus type 1; LOD, Limit of detection; LOQ, Limit of quantification; LRF, Log10 reduction factor; mAb, Monoclonal antibody; MVM, Minute virus of mice; NaOH, Sodium hydroxide; PA, Protein A; PPV, Porcine parvovirus; QA, Quaternary amine; QP, Quaternized polyethyleneimine; qPCR, Quantitative polymerase chain reaction; Reo3, Reovirus type 3; SuHV-1, Suid herpesvirus; SV40, Simian virus 40; X-MuLV, Xenotropic murine leukemia virus

Ovine herpesvirus 2 (OvHV-2) circulates among sheep without causing disease. However, upon transmission to cattle, the same virus instigates a frequently lethal disease, malignant catarrhal fever (MCF). While the cause of death and pathogenesis of tissue lesions are still poorly understood, MCF is characterized by the accumulation of lymphocytes in various tissues, associated with vasculitis and cell death. As infectious virus is hardly present in these lesions, the cause of cell death cannot be explained simply by viral replication. The significance of our research is in identifying and characterizing a previously overlooked gene of OvHV-2 (Ov8.25), which is highly expressed in animals with MCF. Its encoded protein targets mitochondria, causing apoptosis and necrosis, thus contributing to an understanding of the source and nature of cell death. As the corresponding genetic locus is also active in the context of MCF due to a different macavirus, we may have detected a common denominator of the disease phenotype., Malignant catarrhal fever (MCF) is a rare but frequently lethal disease of certain cloven-hoofed animals. At least 10 different viruses, all members of the Macavirus genus in the subfamily Gammaherpesvirinae, are known as causative agents of MCF. Among these, ovine herpesvirus 2 (OvHV-2) is the most frequent and economically most important MCF agent. Phenotypically, MCF is characterized by severe lymphocytic arteritis-periarteritis, which leads to the accumulation of activated lymphocytes accompanied by apoptosis and necrosis in a broad range of tissues. However, a viral factor that might be responsible for tissue damage has not yet been identified. We have studied a seemingly intergenic locus on the OvHV-2 genome, which was previously shown to be transcriptionally highly active in MCF-affected tissue. We identified by 5′ and 3′ rapid amplification of cDNA ends (RACE) a conserved, double-spliced transcript that encoded a 9.9-kDa hydrophobic protein. The newly detected gene, Ov8.25, and its splicing pattern were conserved among OvHV-2 strains of different origins. Upon transient expression of synthetic variants of this gene in various cell types, including bovine lymphocytes, the protein (pOv8.25) was shown to target mitochondria, followed by caspase-dependent apoptosis and necrosis. Notably, a deletion mutant of the same protein lost these abilities. Finally, we detected pOv8.25 in brain-infiltrating lymphocytes of cattle with MCF. Thus, the cell death-causing properties of pOv8.25 in affected cells may be involved in the emergence of typical MCF-associated apoptosis and necrosis. Thus, we have identified a novel OvHV-2 protein, which might contribute to the phenotype of MCF-related lesions. IMPORTANCE Ovine herpesvirus 2 (OvHV-2) circulates among sheep without causing disease. However, upon transmission to cattle, the same virus instigates a frequently lethal disease, malignant catarrhal fever (MCF). While the cause of death and pathogenesis of tissue lesions are still poorly understood, MCF is characterized by the accumulation of lymphocytes in various tissues, associated with vasculitis and cell death. As infectious virus is hardly present in these lesions, the cause of cell death cannot be explained simply by viral replication. The significance of our research is in identifying and characterizing a previously overlooked gene of OvHV-2 (Ov8.25), which is highly expressed in animals with MCF. Its encoded protein targets mitochondria, causing apoptosis and necrosis, thus contributing to an understanding of the source and nature of cell death. As the corresponding genetic locus is also active in the context of MCF due to a different macavirus, we may have detected a common denominator of the disease phenotype.

One step of the life cycle common to all rotaviruses (RV) studied so far is the formation of viroplasms, membrane-less cytosolic inclusions providing a microenvironment for early morphogenesis and RNA replication. Viroplasm-like structures (VLS) are simplified viroplasm models consisting of complexes of nonstructural protein 5 (NSP5) with the RV core shell VP2 or NSP2. We identified and characterized the domains required for NSP5-VP2 interaction and VLS formation. VP2 mutations L124A, V865A, and I878A impaired both NSP5 hyperphosphorylation and NSP5/VP2 VLS formation. Moreover, NSP5-VP2 interaction does not depend on NSP5 hyperphosphorylation. The NSP5 tail region is required for VP2 interaction. Notably, VP2 L124A expression acts as a dominant-negative element by disrupting the formation of either VLS or viroplasms and blocking RNA synthesis. In silico analyses revealed that VP2 L124, V865, and I878 are conserved among RV species A to H. Detailed knowledge of the protein interaction interface required for viroplasm formation may facilitate the design of broad-spectrum antivirals to block RV replication. IMPORTANCE Alternative treatments to combat rotavirus infection are a requirement for susceptible communities where vaccines cannot be applied. This demand is urgent for newborn infants, immunocompromised patients, adults traveling to high-risk regions, and even for the livestock industry. Aside from structural and physiological divergences among RV species studied before now, all replicate within cytosolic inclusions termed viroplasms. These inclusions are composed of viral and cellular proteins and viral RNA. Viroplasm-like structures (VLS), composed of RV protein NSP5 with either NSP2 or VP2, are models for investigating viroplasms. In this study, we identified a conserved amino acid in the VP2 protein, L124, necessary for its interaction with NSP5 and the formation of both VLSs and viroplasms. As RV vaccines cover a narrow range of viral strains, the identification of VP2 L124 residue lays the foundations for the design of drugs that specifically block NSP5-VP2 interaction as a broad-spectrum RV antiviral.

Papillomavirus-specific DNA was detected in skin lesions collected from an okapi (Okapia johnstoni) in the Zoo Basel. According to the nucleotide sequence analysis, the virus belongs to the genus Deltapapillomavirus. Based on bioinformatics analysis, we propose to designate the newly identified virus as Okapia johnstoni Papillomavirus type 1 (OjPV1). OjPV1 is genetically most closely related to a recently described giraffe (Giraffa camelopardalis) -specific papillomavirus (GcPV1). Of note, the putative oncogenic E5 proteins from OjPV1 and GcPV1 are more conserved than the L1 proteins. This indicates, that the selection pressure on E5 may be more pronounced than that on the otherwise most conserved major capsid protein L1.

Background Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. Results To investigate the genetic architecture of thermal adaptation — a highly complex trait — we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements reveal extensive metabolic rewiring after only approximately 60 generations in a hot environment. Analysis of genome-wide polymorphisms identifies two interacting selection targets, Sestrin and SNF4Aγ, pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation. Conclusions Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. Because SNF4Aγ also exhibits clinal variation in various Drosophila species, we suggest that this large-effect polymorphism is maintained by temporal and spatial temperature variation in natural environments. Electronic supplementary material The online version of this article (10.1186/s13059-018-1503-4) contains supplementary material, which is available to authorized users.

Ecological speciation, which relies heavily on selection driving the emergence of new species, has become the primary paradigm through which rapid species radiations are understood. In this way, selection, particularly ecological selection, is assumed to be the driver of most species radiations. However, in many radiations, such as the radiation of Lake Malawi’s cichlids, the assumption of selection as the driver of speciation has rarely been explicitly tested, and drift, often, has completely been ignored as potential factor. In order to understand the forces driving the divergence of Lake Malawi cichlids at the microevolutionary level, we studied the genetic and phenotypic divergence of ten allopatric populations of Maylandia zebra. We estimated effective population sizes as proxy for drift. Further, we compared neutral genetic differentiation to divergence in three phenotypic traits: body size, body shape, and melanophore counts. We found small, yet significant, population differentiation in all the studied traits across most populations. Population sizes were small rendering the potential for drift to be high. However, phenotypic differentiation exceeded neutral expectations for all traits suggesting divergent local selection. Our data suggest that natural, and potentially also sexual, selection may be the dominant force driving population differentiation in Lake Malawi’s rock-dwelling cichlids, despite the potential for drift in small populations.

Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.

The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity.

Chironomid head capsules preserved in lake sediments were used to reconstruct 8200 years of summer temperatures in the boreal forest of northeastern Canada. Two training sets were used derived from Canadian and Eastern Canadian transfer functions. Both models reconstructed similar climate patterns, but the Canadian model provided temperatures generally 2-3 ˚C lower than the Eastern Canadian model. Three main thermal changes inferred by chironomids were: (i) the Holocene Thermal Maximum, which occurred between 8 and 5k cal a BP, with temperatures generally higher than today's, maximum temperatures between 8 and 6.5k cal a BP, and an average of þ 0.9 ˚C; (ii) the Medieval Climate Anomaly around 1.1-1.2k cal a BP with an amplitude of þ 0.7 ˚C; and (iii) a colder period reconstructed between the 14th and 19th centuries, corresponding to the Little Ice Age, with summer temperatures on average A0.5 ˚C lower than the climate normal. For each of these three climatic events, the timing and the amplitude of changes were similar with other published regional, North American and Northern Hemisphere records.

Several attempts have been made to categorize equid- and bovid-specific bovine papillomavirus 1 (BPV1) isolates based on sequence tags. This study includes newly determined sequence information from 33 BPV1 isolates of equine, asinine and bovine origin and investigates sequence bias due to host species. Twenty of the viral genomes were sequenced over their entire length and a further thirteen were sequenced, including flanking sequences, at two specific sites, the LCR and the E5 ORF. Alignment and analyses of the sequences did not reveal statistically significant site differences between the sequences of bovine and equid origin. None of the proposed sites of divergence noted by other authors demonstrated significant species-specific characteristics. Our results suggest that BPV1 is shared between equine, asinine and bovine host species, and that viral transfer between bovines and equids is a repeated and ongoing phenomenon.

The value of rewards arises from multiple hedonic and motivational dimensions. Reward-encoding brain regions such as the ventral striatum (VS) are known to process these dimensions. However, the mechanism whereby distinct reward dimensions are selected for neural processing and guiding behavior remains unclear. Here, we used functional imaging to investigate how human individuals make either hedonic (liking) or motivational (wanting) evaluations of everyday items. We found that the two types of evaluations were differently modulated depending on whether participants won or lost these items. Neural activity in the VS encoded both hedonic and motivational dimensions of reward, whereas ventromedial prefrontal activity encoded primarily motivational evaluations and central orbitofrontal activity encoded predominantly hedonic evaluations. These distinct prefrontal representations arose regardless of which judgment was currently relevant for behavior. Critically, the VS preferentially processed the reward dimension currently being evaluated and showed judgment-specific functional connectivity with the dimension-specific prefrontal areas. Thus, our data are in line with a gating mechanism by which prefrontal cortex (PFC)–VS pathways flexibly encode reward dimensions depending on their behavioral relevance. These findings provide a prototype for a generalized information selection mechanism through content-tailored frontostriatal communication., PLoS Biology, 16 (10), ISSN:1544-9173, ISSN:1545-7885