Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Disentangling host-microbiota complexity through hologenomics.

Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.

Regulation of T(H)2 development by CXCR5+ dendritic cells and lymphotoxin-expressing B cells.

Although cognate encounters between antigen-bearing dendritic cells (DCs) that express the chemokine receptor CCR7 and CCR7(+) naive T cells take place in the T cell zone of lymph nodes, it is unknown whether the colocalization of DCs and T cells in the T cell area is required for the generation of effector cells. Here we found that after infection with an intestinal nematode, antigen-bearing DCs and CD4(+) T cells upregulated the chemokine receptor CXCR5 and localized together outside the T cell zone by a mechanism dependent on the chemokine CXCL13, B cells and lymphotoxin. Notably, lymphotoxin-expressing B cells, CXCR5-expressing DCs and T cells, and CXCL13 were also necessary for development of interleukin 4 (IL-4)-producing type 2 helper T cells (T(H)2 cells), which suggests that T(H)2 differentiation can initiate outside the T cell zone.

Multi-level tuberculosis of the spine identified by 18 F-FDG-PET/CT and concomitant urogenital tuberculosis: a case report from the spinal TB X cohort.

BACKGROUND: Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb) and typically infects the lungs. However, extrapulmonary forms of TB can be found in approximately 20% of cases. It is suggested, that up to 10% of extrapulmonary TB affects the musculoskeletal system, in which spinal elements (spinal tuberculosis, STB) are involved in approximately 50% of the cases. STB is a debilitating disease with nonspecific symptoms and diagnosis is often delayed for months to years. In our Spinal TB X Cohort, we aim to describe the clinical phenotype of STB using whole-body 18 F-fluorodeoxyglucose positron emission tomography computed tomography (PET/CT) and to identify a specific gene expression profile for the different stages of dissemination on PET/CT. Here we report on the first patient recruited into our cohort who underwent PET/CT before treatment initiation, at 6-months and at 12-months - time of TB treatment completion. CASE PRESENTATION: A 27-year-old immunocompetent male presented with severe thoracolumbar back pain for 9 months with severe antalgic gait and night sweats. Magnetic resonance imaging (MRI) of the whole spine revealed multilevel spinal disease (T5/6, T11/12, L3/4) in keeping with STB. After informed consent and recruitment into the Spinal TB X Cohort, the patient underwent PET/CT as per protocol, which revealed isolated multilevel STB (T4-7, T11/12, L3/4) with no concomitant lung or urogenital lesion. However, sputum and urine were Xpert MTB/RIF Ultra positive and Mtb was cultured from the urine sample. CT-guided biopsy of the T11/12 lesion confirmed drug-sensitive Mtb on Xpert MTB/RIF Ultra and the patient was started on TB treatment according to local guidelines for 12 months. The 6-month follow-up PET/CT revealed new and existing spinal lesions with increased FDG-uptake despite significant improvement of clinical features and laboratory markers. After 9 months of treatment, the patient developed an acute urethral stricture, most likely due to urogenital TB, and a suprapubic catheter was inserted. The 12-month PET/CT showed significantly decreased PET/CT values of all lesions, however, significant persistent spinal inflammation was present at the end of TB treatment. Clinically, the patient was considered cured by the TB control program and currently awaits urethroplasty. CONCLUSIONS: In our case, PET/CT emerged as a valuable imaging modality for the initial assessment, surpassing MRI by revealing more comprehensive extensive disease. Subsequent PET/CT scans at 6-month uncovered new lesions and increased inflammation in existing ones, while by the end of TB treatment, all lesions exhibited improvement. However, the interpretation of FDG avidity remains ambiguous, whether it correlates with active infection and viable Mtb. or fibro- and osteoblast activity indicative of the healing process. Additionally, the absence of extraspinal TB lesions on PET/CT despite positive microbiology from sputum and urine maybe explained by paucibacillary, subclinical infection of extraspinal organs. The Spinal TB X Cohort endeavours to shed light on whole-body imaging patterns at diagnosis, their evolution midway through TB treatment, and upon treatment completion. Ultimately, this study aims to advance our understanding of the biology of this complex disease.

Sample plug induced peak splitting in capillary electrophoresis studied using dual backscattered interferometry and fluorescence detection.

The appearance of unexpected peaks in capillary electrophoresis (CE) is common and can lengthen the time of method development as assay conditions and experimental parameters are varied to understand and mitigate the effects of the additional peaks. Additional peaks can arise when a single-analyte zone is split into multiple zones. Understanding the underlying mechanism of these phenomena, recognizing conditions that favor its presence, and knowing how to confirm and eliminate the effect are important for efficient method optimization. In this study, we examine how the overlap of analyte zones with the sample plug can lead to peak splitting. This is explored experimentally using dual detection CE, which enables both the sample plug and analyte zones to be independently and simultaneously measured from the same detection volume. Simulations performed via COMSOL Multiphysics confirm the origin of the splitting and help guide experiments to reduce and eliminate the effect. Our findings show that this peak splitting mechanism can arise in separations of both small and large molecules but is, especially, prevalent in separations of slowly migrating macromolecules. This effect is also more prevalent when using a short length-to-detector, as is commonly found in microfluidic applications. A simple diffusion-less model is introduced to develop strategies for reducing peak splitting that avoids modifying the apparatus, such as by lengthening the separation length, which can be difficult. Decreasing the sample plug length and slowing the electroosmotic flow can both reduce this effect, which is confirmed experimentally.

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population.

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

Tissue-Specific Toxicokinetics of Aqueous Radium-226 in an Estuarine Mussel, Geukensia demissa.

Radiological contamination of coastal habitats poses potential risk for native fauna, but the bioavailability of aqueous radium (Ra) and other dissolved metals to marine bivalves remains unclear. This study was the first to examine the tissue-specific disposition of aqueous 226Ra in a coastal mussel, specifically the Atlantic ribbed mussel Geukensia demissa. Most organ groups reached steady-state concentrations within 7 days during experimental exposure, with an average uptake rate constant of 0.0013 mL g-1 d-1. When moved to Ra-free synthetic seawater, mussels rapidly eliminated aqueous 226Ra (average elimination rate constant 1.56 d-1). The biological half-life for aqueous 226Ra ranged from 8.9 h for the gills and labial palps to 15.4 h for the muscle. Although previous field studies have demonstrated notable 226Ra accumulation in the soft tissues of marine mussels and that, for freshwater mussels, tissue-incorporated 226Ra derives primarily from the aqueous phase, our tissue-specific bioconcentration factors (BCFs) were on the order of (8.3 ± 1.5) × 10-4 indicating low accumulation potential of aqueous 226Ra in estuarine mussels. This suggests marine and estuarine mussels obtain 226Ra from an alternate route, such as particulate-sorbed Ra ingested during filter-feeding or from a contaminated food source.

Warm and arid regions of the world are hotspots of superorganism complexity.

Biologists have long been fascinated by the processes that give rise to phenotypic complexity of organisms, yet whether there exist geographical hotspots of phenotypic complexity remains poorly explored. Phenotypic complexity can be readily observed in ant colonies, which are superorganisms with morphologically differentiated queen and worker castes analogous to the germline and soma of multicellular organisms. Several ant species have evolved 'worker polymorphism', where workers in a single colony show quantifiable differences in size and head-to-body scaling. Here, we use 256 754 occurrence points from 8990 ant species to investigate the geography of worker polymorphism. We show that arid regions of the world are the hotspots of superorganism complexity. Tropical savannahs and deserts, which are typically species-poor relative to tropical or even temperate forests, harbour the highest densities of polymorphic ants. We discuss the possible adaptive advantages that worker polymorphism provides in arid environments. Our work may provide a window into the environmental conditions that promote the emergence of highly complex phenotypes.

The evolution of sour taste.

The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.

Sugar-seeking insects as a source of diverse bread-making yeasts with enhanced attributes.

Insects represent a particularly interesting habitat in which to search for novel yeasts of value to industry. Insect-associated yeasts have the potential to have traits relevant to modern food and beverage production due to insect-yeast interactions, with such traits including diverse carbohydrate metabolisms, high sugar tolerance, and general stress tolerance. Here, we consider the potential value of insect-associated yeasts in the specific context of baking. We isolated 63 yeast strains from 13 species of hymenoptera from the United States, representing 37 yeast species from 14 genera. Screening for the ability to ferment maltose, a sugar important for bread production, resulted in the identification of 13 strains of Candida, Lachancea, and Pichia species. We assessed their ability to leaven dough. All strains produced baked loaves comparable to a commercial baking strain of Saccharomyces cerevisiae. The same 13 strains were also grown under various sugar and salt conditions relevant to osmotic challenges experienced in the manufacturing processes and the production of sweet dough. We show that many of these yeast strains, most notably strains of Lachancea species, grow at a similar or higher rate and population size as commercial baker's yeast. We additionally assessed the comparative phenotypes and genetics of insect-associated S. cerevisiae strains unable to ferment maltose and identified baking-relevant traits, including variations in the HOG1 signaling pathway and diverse carbohydrate metabolisms. Our results suggest that non-conventional yeasts have high potential for baking and, more generally, showcase the success of bioprospecting in insects for identifying yeasts relevant for industrial uses.

Phylogeography and population genetics of a widespread cold-adapted ant, Prenolepis imparis.

As species arise, evolve and diverge, they are shaped by forces that unfold across short and long timescales and at both local and vast geographical scales. It is rare, however, to be able document this history across broad sweeps of time and space in a single species. Here, we report the results of a continental-scale phylogenomic analysis across the entire range of a widespread species. We analysed sequences of 1402 orthologous ultraconserved element (UCE) loci from 75 individuals to identify population genetic structure and historical demographic patterns across the continent-wide range of a cold-adapted ant, the winter ant, Prenolepis imparis. We recovered five well-supported, genetically isolated clades representing lineages that diverged from 8.2-2.2 million years ago. These include: (i) an early diverging lineage located in Florida, (ii) a lineage that spans the southern United States, (iii) populations that extend across the midwestern and northeastern United States, (iv) populations from the western United States and (v) populations in southwestern Arizona and Mexico. Population genetic analyses revealed little or no gene flow among these lineages, but patterns consistent with more recent gene flow among populations within lineages, and localized structure with migration in the western United States. High support for five major geographical lineages and lack of evidence of contemporary gene flow indicate in situ diversification across the species' range, producing relatively ancient lineages that persisted through subsequent climate change and glaciation during the Quaternary.

Citizen Science as an Ecosystem of Engagement: Implications for Learning and Broadening Participation.

The bulk of research on citizen science participants is project centric, based on an assumption that volunteers experience a single project. Contrary to this assumption, survey responses (n = 3894) and digital trace data (n = 3649) from volunteers, who collectively engaged in 1126 unique projects, revealed that multiproject participation was the norm. Only 23% of volunteers were singletons (who participated in only one project). The remaining multiproject participants were split evenly between discipline specialists (39%) and discipline spanners (38% joined projects with different disciplinary topics) and unevenly between mode specialists (52%) and mode spanners (25% participated in online and offline projects). Public engagement was narrow: The multiproject participants were eight times more likely to be White and five times more likely to hold advanced degrees than the general population. We propose a volunteer-centric framework that explores how the dynamic accumulation of experiences in a project ecosystem can support broad learning objectives and inclusive citizen science.

Conspecific cues, not starvation, mediate barren urchin response to predation risk.

Prey state and prey density mediate antipredator responses that can shift community structure and alter ecosystem processes. For example, well-nourished prey at low densities (i.e., prey with higher per capita predation risk) should respond strongly to predators. Although prey state and density often co-vary across habitats, it is unclear if prey responses to predator cues are habitat-specific. We used mesocosms to compare the habitat-specific responses of purple sea urchins (Strongylocentrotus purpuratus) to waterborne cues from predatory lobsters (Panulirus interruptus). We predicted that urchins from kelp forests (i.e., in well-nourished condition) tested at low densities typically observed in this habitat would respond more strongly to predation risk than barren urchins (i.e., in less nourished condition) tested at high densities typically observed in this habitat. Indeed, when tested at densities associated with respective habitats, urchins from forests, but not barrens, reduced kelp grazing by 69% when exposed to lobster risk cues. Barren urchins that were unresponsive to predator cues at natural, high densities suddenly responded strongly to lobster cues when conspecific densities were reduced. Strong responses of low densities of barren urchins persisted across feeding history (i.e. 0-64 days of starvation). This suggests that barren urchins can respond to predators but typically do not because of high conspecific densities. Because high densities of urchins in barrens should weaken the non-consumptive effects of lobsters, urchins in these habitats may continue to graze in the presence of predators thereby providing a feedback that maintains urchin barrens.

Transient dynamics during kelp forest recovery from fishing across multiple trophic levels.

Outcomes of management efforts to recover or restore populations of harvested species can be highly dependent on environmental and community context. Predator-prey interactions can alter recovery trajectories, and the timing of management actions within multi-trophic level harvest scenarios may influence the dynamics of recovery and lead to management trade-offs. Recent work using a generalist predator-prey model suggests that management promoting synchronized recovery of predators and prey leads to faster and less variable recovery trajectories than sequential recovery (predator or prey first). However, more complex communities may require different management actions to minimize recovery time and variability. Here, we use a tri-trophic level rocky reef community dynamics model with size-structure and fisheries at multiple trophic levels to investigate the importance of three ecological processes to recovery of fished communities: (1) size-structured predation, (2) non-consumptive effects of predators on prey behavior, and (3) varying levels of recruitment. We also test the effects of initiating recovery from community states associated with varying degrees of fishery-induced degradation and develop a simulation in which the basal resource (kelp) is harvested. In this system, a predator-first closure generally leads to the least volatile and quickest recovery, whether from a kelp forest, urchin barren, or intermediate community state. The benefits gained by selecting this strategy are magnified when recovering from the degraded community, the urchin barren, because initial conditions in the degraded state lead to lengthy recovery times. However, the shape of the size-structured predation relationship can strongly affect recovery volatility, where the differences between alternate management strategies are negated with size-independent predation. External recruitment reduces return times by bolstering the predatory lobster population. These results show that in a tightly linked tri-trophic level food web with top-down control, a predator-first fishery closure can be the most effective strategy to reduce volatility and shorten recovery, particularly when the system is starting from the degraded community state. Given the ubiquity of top predator loss across many ecosystems, we highlight the value of incorporating insights from community ecology into ecosystem management.

A review of clothing microbiology: the history of clothing and the role of microbes in textiles.

Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.

Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets.

We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple insect decline narrative.

Detecting flying insects using car nets and DNA metabarcoding.

Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect richness and occurrence data. Insect and hoverfly richness and diversity were assessed across biogeographic regions and dominant land cover types. We detected 15 out of 19 flying insect orders present in Denmark, with high proportions of especially Diptera compared to Danish estimates, and lower insect richness and diversity in urbanized areas. We detected 319 species not known for Denmark and 174 species assessed in the Danish Red List. Our results indicate that the methodology can assess the flying insect fauna at large spatial scales to a wide extent, but may be, like other methods, biased towards certain insect orders.

Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States.

Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.

Towards advancing scientific knowledge of climate change impacts on short-duration rainfall extremes.

A large number of recent studies have aimed at understanding short-duration rainfall extremes, due to their impacts on flash floods, landslides and debris flows and potential for these to worsen with global warming. This has been led in a concerted international effort by the INTENSE Crosscutting Project of the GEWEX (Global Energy and Water Exchanges) Hydroclimatology Panel. Here, we summarize the main findings so far and suggest future directions for research, including: the benefits of convection-permitting climate modelling; towards understanding mechanisms of change; the usefulness of temperature-scaling relations; towards detecting and attributing extreme rainfall change; and the need for international coordination and collaboration. Evidence suggests that the intensity of long-duration (1 day+) heavy precipitation increases with climate warming close to the Clausius-Clapeyron (CC) rate (6-7% K-1), although large-scale circulation changes affect this response regionally. However, rare events can scale at higher rates, and localized heavy short-duration (hourly and sub-hourly) intensities can respond more strongly (e.g. 2 × CC instead of CC). Day-to-day scaling of short-duration intensities supports a higher scaling, with mechanisms proposed for this related to local-scale dynamics of convective storms, but its relevance to climate change is not clear. Uncertainty in changes to precipitation extremes remains and is influenced by many factors, including large-scale circulation, convective storm dynamics andstratification. Despite this, recent research has increased confidence in both the detectability and understanding of changes in various aspects of intense short-duration rainfall. To make further progress, the international coordination of datasets, model experiments and evaluations will be required, with consistent and standardized comparison methods and metrics, and recommendations are made for these frameworks. This article is part of a discussion meeting issue 'Intensification of short-duration rainfall extremes and implications for flash flood risks'.