Drawing mitochondrial genomes with circularMT.

SUMMARY: Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high throughput 'next generation' DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and noncoding feature complement, their order and strand orientation. However, there are few dedicated applications that generate high quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication quality images, of linear and circular mitochondrial genome maps, either individually, or integrated into an analysis pipeline. AVAILABILITY AND IMPLEMENTATION: Both applications are implemented in C#, with binaries, source code and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319). SUPPLEMENTARY INFORMATION: This paper has no supplementary data.

Phylogenetic analyses reveal bat communities in Northwestern Mexico harbor a high diversity of novel cryptic ectoparasite species.

Parasites are integral parts of ecosystem function and important drivers of evolutionary processes. Characterizing ectoparasite diversity is fundamental to studies of host-parasite interactions, evolution, and conservation, and also for understanding emerging disease threats for some vector borne pathogens. With more than 1400 species, bats represent the second most speciose mammalian clade, but their ectoparasite fauna are poorly known for most species. We sequenced mitochondrial Cytochrome Oxidase C subunit I and nuclear 18S ribosomal gene fragments, and used Bayesian phylogenetic analyses to characterize ectoparasite taxon identity and diversity for 17 species of parasitized bats sampled along the Baja California peninsula and in Northwestern Mexico. The sequence data revealed multiple novel lineages of bat bugs (Cimicidae), flies (Nycteribiidae and Streblidae), and ticks (Argasidae). Within families, the new linages showed more than 10% sequence divergence, which is consistent with separation at least at the species level. Both families of bat flies showed host specificity, particularly on Myotis species. We also identified new records for the Baja peninsula of one tick (Carios kelleyi), and of five Streblid bat fly species. One Nycteribiid bat fly haplotype from Pallid bat (Antrozous pallidus) hosts was found throughout the peninsula, suggesting potential long distance co-dispersal with hosts. Different bat bug and tick communities were found in the north and south of the peninsula. This study is the first systematic survey of bat ectoparasites in the Baja California peninsula, revealing novel lineages that are highly genetically differentiated from other parts of North America. For some ectoparasite species, haplotype distributions may reflect patterns of bat migration. This work is a first step in characterizing ectoparasite diversity over the Baja California peninsula, and understanding how ecological and evolutionary interactions shape bat ectoparasite communities among host species in different parts of their ranges.

Sampling from commercial vessel routes can capture marine biodiversity distributions effectively.

Collecting fine-scale occurrence data for marine species across large spatial scales is logistically challenging but is important to determine species distributions and for conservation planning. Inaccurate descriptions of species ranges could result in designating protected areas with inappropriate locations or boundaries. Optimizing sampling strategies therefore is a priority for scaling up survey approaches using tools such as environmental DNA (eDNA) to capture species distributions. In a marine context, commercial vessels, such as ferries, could provide sampling platforms allowing access to undersampled areas and repeatable sampling over time to track community changes. However, sample collection from commercial vessels could be biased and may not represent biological and environmental variability. Here, we evaluate whether sampling along Mediterranean ferry routes can yield unbiased biodiversity survey outcomes, based on perfect knowledge from a stacked species distribution model (SSDM) of marine megafauna derived from online data repositories. Simulations to allocate sampling point locations were carried out representing different sampling strategies (random vs regular), frames (ferry routes vs unconstrained), and number of sampling points. SSDMs were remade from different sampling simulations and compared with the "perfect knowledge" SSDM to quantify the bias associated with different sampling strategies. Ferry routes detected more species and were able to recover known patterns in species richness at smaller sample sizes better than unconstrained sampling points. However, to minimize potential bias, ferry routes should be chosen to cover the variability in species composition and its environmental predictors in the SSDMs. The workflow presented here can be used to design effective sampling strategies using commercial vessel routes globally for eDNA and other biodiversity survey techniques. This approach has potential to provide a cost-effective method to access remote oceanic areas on a regular basis and can recover meaningful data on spatiotemporal biodiversity patterns.

No borders on a fragile planet: Introducing four lay models of social psychological precarity to support global human identification and citizenship.

Measures such as Identification with all humanity (IWAH) and global identification and citizenship (GHIC) are positivity correlated with measures of humanitarianism, cosmopolitanism and environmental concern. Research using these measures suggests that most citizens have low-global identification scores. This article sheds light on this finding by investigating how global identification relates to precarity and migration (neither of which are measured in the IWAH/GHIC). The study conducted in England, Scotland and Sweden introduces a qualitative dialogical approach to GHIC. This involves measuring migration-mobility in dialogical interviews and controlling and removing borders on world maps-using an interactive world mapping task (N = 23). Participants articulate four social representations relating to a fragile earth, enduring colonial settler/native conflict, ingroup/outgroup conflict or, in contrast, a cooperative plentiful planet where borders are unnecessary. Such social representations demonstrate the importance of planetary consciousness and relate to four lay models of social psychological precarity related to intergroup competition, global conflict, economic rationality and human-made borders. In conclusion, all participants employ lay models of social psychological precarity when discussing sovereignty, migration and belonging. We recommend psychologists investigating GHIC include measures of social psychological precarity and migration-mobility.

Evidence for strain-specific virulence of Trichomonas gallinae in African columbiformes.

Infection by parasites or pathogens can have marked physiological impacts on individuals. In birds, infection may affect moult and feather growth, which is an energetically demanding time in the annual cycle. Previous work has suggested a potential link between clinically visible Trichomonas gallinae infection and wing length in turtle doves Streptopelia turtur arriving on breeding grounds. First, T. gallinae infection was characterized in 149 columbids from 5 species, sampled on turtle dove wintering grounds in Senegal during the moulting period, testing whether infection by T. gallinae is linked to moult. Trichomonas gallinae prevalence was 100%, so rather than testing for differences between infected and uninfected birds, we tested for differences in moult progression between birds infected by different T. gallinae strains. Twelve strains of T. gallinae were characterized at the internal transcribed spacer 1 (ITS1)/5.8S/ITS2 region, of which 6 were newly identified within this study. In turtle doves only, evidence for differences in wing length by strain was found, with birds infected by strain Tcl-1 having wings nearly 6 mm longer than those infected with strain GEO. No evidence was found for an effect of strain identity within species on moult progression, but comparisons between infected and uninfected birds should be further investigated in species where prevalence is lower.

Assessing rates of parasite coinfection and spatiotemporal strain variation via metabarcoding: Insights for the conservation of European turtle doves Streptopelia turtur.

Understanding the frequency, spatiotemporal dynamics and impacts of parasite coinfections is fundamental to developing control measures and predicting disease impacts. The European turtle dove (Streptopelia turtur) is one of Europe's most threatened bird species. High prevalence of infection by the protozoan parasite Trichomonas gallinae has previously been identified, but the role of this and other coinfecting parasites in turtle dove declines remains unclear. Using a high-throughput sequencing approach, we identified seven strains of T. gallinae, including two novel strains, from ITS1/5.8S/ITS2 ribosomal sequences in turtle doves on breeding and wintering grounds, with further intrastrain variation and four novel subtypes revealed by the iron-hydrogenase gene. High spatiotemporal turnover was observed in T. gallinae strain composition, and infection was prevalent in all populations (89%-100%). Coinfection by multiple Trichomonas strains was rarer than expected (1% observed compared to 38.6% expected), suggesting either within-host competition, or high mortality of coinfected individuals. In contrast, coinfection by multiple haemosporidians was common (43%), as was coinfection by haemosporidians and T. gallinae (90%), with positive associations between strains of T. gallinae and Leucocytozoon suggesting a mechanism such as parasite-induced immune modulation. We found no evidence for negative associations between coinfections and host body condition. We suggest that longitudinal studies involving the recapture and investigation of infection status of individuals over their lifespan are crucial to understand the epidemiology of coinfections in natural populations.

Origin and expansion of the world's most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina).

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonized its current range. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic single nucleotide polymorphisms from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin of the harbour seal, colonization of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonize and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.

The rhetorical use of the threat of the far-right in the UK Brexit debate.

While attention has been given to understanding support for the far-right, there is a lack of focus on the way in which a threat of the far-right can be used for political ends. This paper addresses this using the UK Brexit debate as an illustration. The question therefore is: What is talk about the far-right used to do in discussions about Brexit? A discursive psychological approach addresses a sample of newspaper reports containing both 'Far-Right' and 'Brexit', from the first quarter of 2019 (n = 45). The analysis identifies a range of uses of talk about the far-right: (1) An opponent of Brexit is called a Nazi by pro-Brexit protesters, who are labelled far-right; (2) A lack of Brexit is presented as fuel for the far-right; (3) Remain supporters reject the idea that a lack of Brexit fuels the far-right; (4) A link with the far-right is rejected by a prominent Brexit supporter; and (5) Support for Brexit is again linked with the far-right. The far-right can be used as a strategic tool by opposing sides of the Brexit debate and - significantly - the supposed threat of the far-right can be used to placate far-right ideas, rather than to genuinely challenge them.

Contaminations contaminate common databases.

The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR-based identifications, not just of parasites and pathogens.

The Antibody Society's antibody validation webinar series.

In the wake of the reproducibility crisis and numerous discussions on how commercially available antibodies as research tool contribute to it, The Antibody Society developed a series of 10 webinars to address the issues involved. The webinars were delivered by speakers with both academic and commercial backgrounds. This report highlights the problems, and offers solutions to help the scientific community appropriately identify the right antibodies and to validate them for their research and development projects. Despite the various solutions proposed here, they must be applied on a case-by-case basis. Each antibody must be verified based on the content of the product sheet, and subsequently through experimentation to confirm integrity, specificity and selectivity. Verification needs to focus on the precise application and tissue/cell type for which the antibody will be used, and all verification data must be reported openly. The various approaches discussed here all have caveats, so a combination of solutions must be considered.

The path to VICTORy - a beginner's guide to success using commercial research antibodies.

Commercial research antibodies are crucial tools in modern cell biology and biochemistry. In the USA some $2 billion a year are spent on them, but many are apparently not fit-for-purpose, and this may contribute to the 'reproducibility crisis' in biological sciences. Inadequate antibody validation and characterization, lack of user awareness, and occasional incompetence amongst suppliers have had immense scientific and personal costs. In this Opinion, I suggest some paths to make the use of these vital tools more successful. I have attempted to summarize and extend expert views from the literature to suggest that sustained routine efforts should made in: (1) the validation of antibodies, (2) their identification, (3) communication and controls, (4) the training of potential users, (5) the transparency of original equipment manufacturer (OEM) marketing agreements, and (5) in a more widespread use of recombinant antibodies (together denoted the 'VICTOR' approach).

The antibody horror show: an introductory guide for the perplexed.

The biological literature reverberates with the inadequacies of commercial research-tool antibodies. The scientific community spends some $2 billion per year on such reagents. Excellent accessible scientific platforms exist for reliably making, validating and using antibodies, yet the laboratory end-user reality is somehow depressing - because they often "don't work". This experience is due to a bizarre and variegated spectrum of causes including: inadequately identified antibodies; inappropriate user and supplier validation; poor user training; and overloaded publishers. Colourful as this may appear, the outcomes for the community are uniformly grim, including badly damaged scientific careers, wasted public funding, and contaminated literature. As antibodies are amongst the most important of everyday reagents in cell biology and biochemistry, I have tried here to gently suggest a few possible solutions, including: a move towards using recombinant antibodies; obligatory unique identification of antibodies, their immunogens, and their producers; centralized international banking of standard antibodies and their ligands; routine, accessible open-source documentation of user experience with antibodies; and antibody-user certification.

The 3rd Antibody Validation meeting: Bath UK 20-21 st September 2018.

The International Antibody Validation meetings offer a welcome British forum for discussing this important topic, which is existentially crucial for the biological sciences community. Now in its 6th year, the biennial meeting is organized by Andrew Chalmers (University of Bath; CiteAb), this year with Carly Dix (Astra Zeneca).  The organizers gathered some 100 members of industry and academia, producers and users, for a day and a half to describe their efforts to ensure that their antibodies have the desired specificity and selectively for well-defined molecular targets. The meeting is largely available as WebCasts ( http://www.antibodyvalidation.co.uk/past-events/2018).

Novel avian paramyxovirus isolated from gulls in Caspian seashore in Kazakhstan.

Three isolates APMV/gull/Kazakhstan/5976/2014, APMV/gull/Kazakhstan/ 5977/2014 and APMV/gull/Kazakhstan/5979/2014, were obtained from independent samples during annual surveillance for avian influenza and paramyxoviruses in wild birds from the Caspian Sea coast in Western Kazakhstan, and were initially identified as putative paramyxoviruses on the basis of electron microscopy. Hemagglutination Inhibition Assays with antisera to nine known APMV serotypes (APMV1-9) indicated no relation to any of them. Next generation sequencing of whole genome sequences indicated the three isolates were genetically identical, and had a nucleotide structure typical for all APMVs, consisting of six genes 3'-NP-P-M-F-HN-L-5'. Phylogenetic analyses, and assessment of amino acid identities, suggested the most closely related lineages to be APMV-2, 8, 10 and 15, but the novel isolate had less than 64% identity to them and all other known avian paramyxoviruses. This value was above levels considered to generally define other APMV serotypes. Estimates of the evolutionary divergence of the nucleotide sequences of the genomes of APMVs have shown that novel Kazakhstan APMV strain was closest to APMV-2, APMV-8, APMV-10 and APMV-15, with calculated distance values of 2.057, 2.058, 2.026 and 2.286 respectively, which is above values considered to differentiate other serotypes (observed minimum was 1.108 between APMV-1 and recently isolated APMV/UPO216/Korea). Together, the data suggest that isolate APMV/gull/Kazakhstan/5976/2014 and other two should be considered as the first representative of a novel APMV-20 group, and is the first time that avian paramyxoviruses have been found infecting members of the gull family, extending the known taxonomic host range.

Integrins as Therapeutic Targets: Successes and Cancers.

Integrins are transmembrane receptors that are central to the biology of many human pathologies. Classically mediating cell-extracellular matrix and cell-cell interaction, and with an emerging role as local activators of TGFß, they influence cancer, fibrosis, thrombosis and inflammation. Their ligand binding and some regulatory sites are extracellular and sensitive to pharmacological intervention, as proven by the clinical success of seven drugs targeting them. The six drugs on the market in 2016 generated revenues of some US$3.5 billion, mainly from inhibitors of α4-series integrins. In this review we examine the current developments in integrin therapeutics, especially in cancer, and comment on the health economic implications of these developments.

High prevalence of Trichomonas gallinae in wild columbids across western and southern Europe.

BACKGROUND: Avian trichomonosis is known as a widespread disease in columbids and passerines, and recent findings have highlighted the pathogenic character of some lineages found in wild birds. Trichomonosis can affect wild bird populations including endangered species, as has been shown for Mauritian pink pigeons Nesoenas mayeri in Mauritius and suggested for European turtle doves Streptopelia turtur in the UK. However, the disease trichomonosis is caused only by pathogenic lineages of the parasite Trichomonas gallinae. Therefore, understanding the prevalence and distribution of both potentially pathogenic and non-pathogenic T. gallinae lineages in turtle doves and other columbids across Europe is relevant to estimate the potential impact of the disease on a continental scale. RESULTS: We examined 281 samples from four wild columbid species for Trichomonas infection and determined the genetic lineages. The overall prevalence was 74%. There were significant differences between the species (P = 0.007). The highest prevalence was found in stock doves Columba oenas (86%, n = 79) followed by wood pigeons Columba palumbus (70%, n = 61) and turtle doves (67%, n = 65), while three of five collared doves Streptopelia decaocto (60%) were infected. We found seven different lineages, including four lineages present in columbids in the UK, one lineage already described from Spain and three new lineages, one of those found in a single turtle dove migrating through Italy and another one found in a breeding stock dove. Stock doves from Germany and collared doves from Malta were infected with a potentially pathogenic lineage (lineage A/B), which is known to cause lesions and mortality in columbids, raptors and finches. CONCLUSIONS: Generally, turtle doves showed high prevalence of Trichomonas infection. Furthermore, the potentially pathogenic lineage A/B (or genotype B according to previous literature) was found in a recovering stock dove population. Both findings are worrying for these columbid species due to the occasional epidemic character of trichomonosis, which can have severe negative effects on populations.

Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling.

Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body sizes compared to those of other UK areas. Southwestern UK porpoises showed admixed ancestry between southern and northern ecotypes with a contact zone extending from the northern Bay of Biscay to the Celtic Sea and Channel. Around the UK, ancestry blends from one genetic group to the other along a southwest--northeast axis, correlating with body size variation, consistent with previously reported morphological differences between the two ecotypes. We also detected isolation by distance among juveniles but not in adults, suggesting that stranded juveniles display reduced intergenerational dispersal. The fine-scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.

How Do Intimate Partner Violent Men Talk About Self-Control?

This study investigates discourses that male perpetrators of intimate partner violence (IPV) use regarding self-control when talking about their IPV. Literature addressing the role of self-control in committing and avoiding using violence toward partners is discussed; however, it is shown that self-control has not been investigated from a discursive psychological perspective, in which the function of talk, rather than what this talk says about speakers' cognitions, is analyzed. Discourse analysis of interviews with six male perpetrators, currently attending treatment and selected for their recent and multiple uses of IPV, revealed that talk of lacking self-control was used to account for situations when individuals engaged in violence. Conversely, talk about having self-control was used to account for refraining from IPV. An improvement narrative in which perpetrators of violence talked about moving from lacking to gaining self-control was also evident. Talk about self-control however was not as simple as this suggests because of particular note is the situation where perpetrators offered varying levels of self-control within their accounts of violence where having and lacking self-control was presented simultaneously. This demonstrates that talk about self-control is a discursive device that is used flexibly by perpetrators to manage their accountability for acts of IPV.

High rates of infection by blood parasites during the nestling phase in UK Columbids with notes on ecological associations.

Studies of blood parasite infection in nestling birds rarely find a high prevalence of infection. This is likely due to a combination of short nestling periods (limiting the age at which nestlings can be sampled) and long parasite prepatent periods before gametocytes can be detected in peripheral blood. Here we examine rates of blood parasite infection in nestlings from three Columbid species in the UK. We use this system to address two key hypotheses in the epidemiology of avian haemoparasites: first, that nestlings in open nests have a higher prevalence of infection; and second, that nestlings sampled at 14 days old have a higher apparent infection rate than those sampled at 7 days old. Open-nesting individuals had a 54% infection rate compared with 25% for box-nesters, probably due to an increased exposure of open-nesting species to dipteran vectors. Nestlings sampled at 14 days had a 68% infection rate compared with 32% in nestlings sampled at 7 days, suggesting that rates of infection in the nest are high. Further work should examine nestlings post-fledging to identify rates of successful parasite infection (as opposed to abortive development within a dead-end host) as well as impacts on host post-fledging survival and behaviour.