Ancestral mitogenome capture of the Southeast Asian banded linsang

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives

Higher masseter muscle mass in grazing than in browsing ruminants

Using cranioskeletal measurements, several studies have generated evidence that grazing ruminants have a more pronounced mastication apparatus, in terms of muscle insertion areas and protuberances, than browsing ruminants, with the resulting hypothesis that grazers should have larger, heavier chewing muscles than browsers. However, the only investigation of this so far [Axmacher and Hofmann (J Zool 215:463–473, 1988)] did not find differences between ruminant feeding types in the masseter muscle mass of 22 species. Here, we expand the dataset to 48 ruminant species. Regardless of phylogenetic control in the statistical treatment, there was a significant positive correlation of body mass and masseter mass, and also a significant association between percent grass in the natural diet and masseter mass. The results support the concept that ruminant species that ingest more grass have relatively larger masseter muscles, possibly indicating an increased requirement to overcome the resistance of grass forage. The comparative chewing resistance of different forage classes may represent a rewarding field of ecophysiological research

Superconception in mammalian pregnancy can be detected and increases reproductive output per breeding season

The concept of superfetation, a second conception during pregnancy, has been controversial for a long time. In this paper we use an experimental approach to demonstrate that female European brown hares (Lepus europaeus) frequently develop a second pregnancy while already pregnant and thereby increase their reproductive success. After a new, successful copulation, we confirmed additional ovulations before parturition in living, late-pregnant females by detecting a second set of fresh corpora lutea using high-resolution ultrasonography. The presence of early embryonic stages in the oviduct, demonstrated by oviduct flushing, next to fully developed fetuses in the uterus is best explained by passage of semen through the late-pregnant uterus; this was confirmed by paternity analysis using microsatellite profiling. Subsequent implantation occurred after parturition. This superfetation, categorized as superconception, significantly increased litter size and permitted females to produce up to 35.4% more offspring per breeding season. It is therefore most likely an evolutionary adaptation

Rumen physiology constrains diet niche: linking digestive physiology and food selection across wild ruminant species

We propose a hypothesis for digestive constraints on the browsing and grazing options available to ruminants: that the diet-niche range (maximum and minimum grass intake) of a species is dependent upon its predisposition to stratified rumen contents, based on observations that this characteristic is a critical step towards enhanced fibre digestion and greater fluid throughput. We compare a physiological (heterogeneity of ingesta fluid content) and an anatomical (the intraruminal papillation pattern) measure with dietary evidence for a range of African and temperate species. Both measures are strongly related to the mean percentage of grass in species’ natural diets, as well as to the maximum and minimum levels of grass intake, respectively. The nature of these effects implies a stratification-level threshold, below which a species will not use a grass-based diet, but above which grass consumption can increase exponentially. However, above this threshold, a minimum percentage of grass in the diet is a prerequisite for optimal performance. We argue that this second constraint is crucial, as it depicts how a greater fluid throughput reduces potential for detoxification of plant secondary compounds, and therefore limits the maximum amount of browse a stratifying species will consume

Whole genome sequencing and methylome analysis of the wild guinea pig

Abstract Background: DNA methylation is a heritable mechanism that acts in response to environmental changes, lifestyle and diseases by influencing gene expression in eukaryotes. Epigenetic studies of wild organisms are mandatory to understand their role in e.g. adaptational processes in the great variety of ecological niches. However, strategies to address those questions on a methylome scale are widely missing. In this study we present such a strategy and describe a whole genome sequence and methylome analysis of the wild guinea pig

Low-cost 3D printed 1 nm resolution smartphone sensor-based spectrometer: instrument design and application in ultraviolet spectroscopy.

We report on the development of a low-cost spectrometer, based on off-the-shelf optical components, a 3D printed housing, and a modified Raspberry Pi camera module. With a bandwidth and spectral resolution of ≈60  nm and 1 nm, respectively, this device was designed for ultraviolet (UV) remote sensing of atmospheric sulphur dioxide (SO2), ≈310  nm. To the best of our knowledge, this is the first report of both a UV spectrometer and a nanometer resolution spectrometer based on smartphone sensor technology. The device performance was assessed and validated by measuring column amounts of SO2 within quartz cells with a differential optical absorption spectroscopy processing routine. This system could easily be reconfigured to cover other UV-visible-near-infrared spectral regions, as well as alternate spectral ranges and/or linewidths. Hence, our intention is also to highlight how this framework could be applied to build bespoke, low-cost, spectrometers for a range of scientific applications

Improving insect conservation management through insect monitoring and stakeholder involvement

In recent years, the decline of insect biodiversity and the imminent loss of provided ecosystem functions and services has received public attention and raised the demand for political action. The complex, multi-causal contributors to insect decline require a broad interdisciplinary and cross-sectoral approach that addresses ecological and social aspects to find sustainable solutions. The project Diversity of Insects in Nature protected Areas (DINA) assesses insect communities in 21 nature reserves in Germany, and considers interactions with plant diversity, pesticide exposure, spatial and climatic factors. The nature reserves border on agricultural land, to investigate impacts on insect diversity. Part of the project is to obtain scientific data from Malaise traps and their surroundings, while another part involves relevant stakeholders to identify opportunities and obstacles to insect diversity conservation. Our results indicate a positive association between insect richness and biomass. Insect richness was negatively related to the number of stationary pesticides (soil and vegetation), pesticides measured in ethanol, the amount of area in agricultural production, and precipitation. Our qualitative survey along with stakeholder interviews show that there is general support for insect conservation, while at the same time the stakeholders expressed the need for more information and data on insect biodiversity, as well as flexible policy options. We conclude that conservation management for insects in protected areas should consider a wider landscape. Local targets of conservation management will have to integrate different stakeholder perspectives. Scientifically informed stakeholder dialogues can mediate conflicts of interests, knowledge, and values to develop mutual conservation scenarios

Complete genome sequences of elephant endotheliotropic herpesviruses 1A and 1B determined directly from fatal cases

A highly lethal hemorrhagic disease associated with infection by elephant endotheliotropic herpesvirus (EEHV) poses a severe threat to Asian elephant husbandry. We have used high-throughput methods to sequence the genomes of the two genotypes that are involved in most fatalities, namely EEHV1A and EEHV1B (species Elephantid herpesvirus 1, genus Proboscivirus, subfamily Betaherpesvirinae, family Herpesviridae). The sequences were determined from postmortem tissue samples, despite the data containing tiny proportions of viral reads among reads from a host for which the genome sequence was not available. The EEHV1A genome is 180,421 bp in size and consists of a unique sequence (174,601 bp) flanked by a terminal direct repeat (2,910 bp). The genome contains 116 predicted protein-coding genes, of which six are fragmented, and seven paralogous gene families are present. The EEHV1B genome is very similar to that of EEHV1A in structure, size, and gene layout. Half of the EEHV1A genes lack orthologs in other members of subfamily Betaherpesvirinae, such as human cytomegalovirus (genus Cytomegalovirus) and human herpesvirus 6A (genus Roseolovirus). Notable among these are 23 genes encoding type 3 membrane proteins containing seven transmembrane domains (the 7TM family) and seven genes encoding related type 2 membrane proteins (the EE50 family). The EE50 family appears to be under intense evolutionary selection, as it is highly diverged between the two genotypes, exhibits evidence of sequence duplications or deletions, and contains several fragmented genes. The availability of the genome sequences will facilitate future research on the epidemiology, pathogenesis, diagnosis, and treatment of EEHV-associated disease