Mass Mortality of Adult Male Subantarctic Fur Seals: Are Alien Mice the Culprits?

Background: Mass mortalities of marine mammals due to infectious agents are increasingly reported. However, in contrast to previous die-offs, which were indiscriminate with respect to sex and age, here we report a land-based mass mortality of Subantarctic fur seals with apparent exclusivity to adult males. An infectious agent with a male-predilection is the most plausible explanation for this die-off. Although pathogens with gender-biased transmission and pathologies are unusual, rodents are known sources of male-biased infectious agents and the invasive Mus musculus house mouse, occurs in seal rookeries. Methodology / Principal Findings: Molecular screening for male-biased pathogens in this potential rodent reservoir host revealed the absence of Cardiovirus and Leptospirosis genomes in heart and kidney samples, respectively, but identified a novel Streptococcus species with 30 % prevalence in mouse kidneys. Conclusions / Significance: Inter-species transmission through environmental contamination with this novel bacterium, whose congenerics display male-bias and have links to infirmity in seals and terrestrial mammals (including humans)

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

To date, the contribution of disrupted potentially cis-regulatory conserved non-coding sequences (CNCs) to human disease is most likely underestimated, as no systematic screens for putative deleterious variations in CNCs have been conducted. As a model for monogenic disease we studied the involvement of genetic changes of CNCs in the cis-regulatory domain of FOXL2 in blepharophimosis syndrome (BPES). Fifty-seven molecularly unsolved BPES patients underwent high-resolution copy number screening and targeted sequencing of CNCs. Apart from three larger distant deletions, a de novo deletion as small as 7.4 kb was found at 283 kb 5′ to FOXL2. The deletion appeared to be triggered by an H-DNA-induced double-stranded break (DSB). In addition, it disrupts a novel long non-coding RNA (ncRNA) PISRT1 and 8 CNCs. The regulatory potential of the deleted CNCs was substantiated by in vitro luciferase assays. Interestingly, Chromosome Conformation Capture (3C) of a 625 kb region surrounding FOXL2 in expressing cellular systems revealed physical interactions of three upstream fragments and the FOXL2 core promoter. Importantly, one of these contains the 7.4 kb deleted fragment. Overall, this study revealed the smallest distant deletion causing monogenic disease and impacts upon the concept of mutation screening in human disease and developmental disorders in particular

Carrion Availability in Space and Time

Introduction Availability of carrion to scavengers is a central issue in carrion ecology and management, and is crucial for understanding the evolution of scavenging behaviour. Compared to live animals, their carcasses are relatively unpredictable in space and time in natural conditions, with a few exceptions (see below, especially Sect. “Carrion Exchange at the Terrestrial-Aquatic Interface”). Carrion is also an ephemeral food resource due to the action of a plethora of consumers, from microorganisms to large vertebrates, as well as to desiccation (i.e., loss of water content; DeVault et al. 2003; Beasley et al. 2012; Barton et al. 2013; Moleón et al. 2014). With a focus on vertebrate carcasses, here we give an overview of (a) the causes that produce carrion, (b) the rate of carrion production, (c) the factors affecting carrion quality, and (d) the distribution of carrion in space and time, both in terrestrial and aquatic environments (including their interface). In this chapter, we will focus on naturally produced carrion, whereas non-natural causes of animal mortality are described in chapter “Human-Mediated Carrion: Effects on Ecological Processes”. However, throughout this chapter we also refer to extensive livestock carrion, because in the absence of strong restrictions such as those imposed in the European Community after the bovine spongiform encephalopathy crisis (Donázar et al. 2009; Margalida et al. 2010), the spatiotemporal availability of carrion of extensive livestock and wild ungulates is similar

The next generation of rodent eradications: Innovative technologies and tools to improve species specificity and increase their feasibility on islands

Rodents remain one of the most widespread and damaging invasive alien species on islands globally. The current toolbox for insular rodent eradications is reliant on the application of sufficient anticoagulant toxicant into every potential rodent territory across an island. Despite significant advances in the use of these toxicants over recent decades, numerous situations remain where eradication is challenging or not yet feasible. These include islands with significant human populations, unreceptive stakeholder communities, co-occurrence of livestock and domestic animals, or vulnerability of native species. Developments in diverse branches of science, particularly the medical, pharmaceutical, invertebrate pest control, social science, technology and defense fields offer potential insights into the next generation of tools to eradicate rodents from islands. Horizon scanning is a structured process whereby current problems are assessed against potential future solutions. We undertook such an exercise to identify the most promising technologies, techniques and approaches that might be applied to rodent eradications from islands. We highlight a Rattus-specific toxicant, RNA interference as species-specific toxicants, rodenticide research, crab deterrent in baits, prophylactic treatment for protection of non-target species, transgenic rodents, virus vectored immunocontraception, drones, self-resetting traps and toxicant applicators, detection probability models and improved stakeholder community engagement methods. We present a brief description of each method, and discuss its application to rodent eradication on islands, knowledge gaps, challenges, whether it is incremental or transformative in nature and provide a potential timeline for availability. We outline how a combination of new tools may render previously intractable rodent eradication problems feasible

Geographic Tools for Eradication Programs of Insular Non-Native Mammals

Non-native mammals are major drivers of ecosystem change and biodiversity loss; this is especially apparent on islands. However, techniques exist to remove non-native mammals, providing a powerful conservation tool. Conservation practitioners are now targeting larger islands for restoration. Leveraging existing and developing new techniques and technologies will prove critical to successful eradications on large islands. Using the removal of introduced goats (Capra hircus) from Santiago Island, Galápagos as a case study, we present a suite of Geographic Information System (GIS) tools that aid island conservation actions. GIS tools were incorporated into the three phases of the eradication campaign: planning, hunting, and monitoring. Further, these tools were adopted for three eradication techniques: ground-based hunting, aerial hunting by helicopter, and Judas goats. These geographic approaches provide a foundation for statistical, spatial, and economic analyses that should increase the capability and efficiency of removal campaigns. Given limited conservation funds and the dire status of many insular species, efficiently removing non-native mammals from islands is of paramount global conservation importance

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Background: A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are available to this end. McCarthy et al recently demonstrated the large differences in prediction of loss-of-function (LoF) variation when RefSeq and Ensembl transcripts are used for annotation, highlighting the importance of the reference transcripts on which variant functional annotation is based. Results: We describe a detailed analysis of the similarities and differences between the gene and transcript annotation in the GENCODE and RefSeq genesets. We demonstrate that the GENCODE Comprehensive set is richer in alternative splicing, novel CDSs, novel exons and has higher genomic coverage than RefSeq, while the GENCODE Basic set is very similar to RefSeq. Using RNAseq data we show that exons and introns unique to one geneset are expressed at a similar level to those common to both. We present evidence that the differences in gene annotation lead to large differences in variant annotation where GENCODE and RefSeq are used as reference transcripts, although this is predominantly confined to non-coding transcripts and UTR sequence, with at most 30% of LoF variants annotated discordantly. We also describe an investigation of dominant transcript expression, showing that it both supports the utility of the GENCODE Basic set in providing a smaller set of more highly expressed transcripts and provides a useful, biologically-relevant filter for further reducing the complexity of the transcriptome. Conclusions: The reference transcripts selected for variant functional annotation do have a large effect on the outcome. The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features. We propose that the GENCODE Comprehensive set has great utility for the discovery of new variants with functional potential, while the GENCODE Basic set is more suitable for applications demanding less complex interpretation of functional variants