Impact of climate on the population dynamics of an alpine ungulate: a long-term study of the Tatra chamois Rupicapra rupicapra tatrica

Global warming is considered as a phenomenon having a negative effect on animals living in cold climate. However, herbivorous species inhabiting cold zones may potentially benefit from increase of temperature as this influence duration of vegetation period and increase food resources. In this study, we analyze the impact of climate factors on the long-term dynamics of an isolated and unhunted population of the Tatra chamois Rupicapra rupicapra tatrica. The population growth rate, based on autumnal chamois counting carried out from 1957 to 2016, were correlated with a set of climatic variables. We tested the hypothesis that high temperatures in summer could have a positive impact on the population, since they influence vegetation growth, which ensure food resources. On the other hand, heavy falls of snow and long-lasting and deep snow cover could adversely affect the population by reducing population survival during the winter. The results of this study indicate that climatic variables best explaining the autoregressed population growth rate (from the autumn of year t-1 to the autumn of year t) were the mean summer temperature of year t-1: the population increase was greater following a warmer summer in year t-1 and, in lower extent, the total precipitation during winter: the population decrease was greater following a winter with heavy snowfall. Duration and thickness of snow cover have no negative effect on population growth rate. The results indicate that the population dynamic of the Tatra chamois is determined in the long term by weather conditions, mainly by temperature, when kids are birthing and growing. The results of this work highlight that climatic changes may be responsible for the population dynamic of high-mountain species. Climate warming may lead to increase in duration of vegetation period in cold climatic zones, what may in turn have positive effect on herbivorous species, which relay upon food resources limited by low temperatures within vegetation period.

Ameliorating the adverse cardiorespiratory effects of chemical immobilization by inducing general anaesthesia in sheep and goats: implications for physiological studies of large wild mammals

Chemical immobilization is necessary for the physiological study of large wild animals. However, the immobilizing drugs can adversely affect the cardiovascular and respiratory systems, yielding data that do not accurately represent the normal, resting state. We hypothesize that these adverse effects can be ameliorated by reversing the immobilizing agent while holding the animal under general anaesthesia. We used habituated sheep Ovis aries (N = 5, 46.9 ± 5.3 kg body mass, mean ± SEM) and goats Capra hircus (N = 4, 27.7 ± 2.8 kg) as ungulate models for large wild animals, and measured their cardiorespiratory function under three conditions: (1) mild sedation (midazolam), as a proxy for the normal resting state, (2) immobilization (etorphine and azaperone), and (3) general anaesthesia (propofol) followed by etorphine antagonism (naltrexone). Cardiac output for both sheep and goats remained unchanged across the three conditions (overall means of 6.2 ± 0.9 and 3.3 ± 0.3 L min^-1, respectively). For both sheep and goats, systemic and pulmonary mean arterial pressures were significantly altered from initial midazolam levels when administered etorphine + azaperone, but those arterial pressures were restored upon transition to propofol anaesthesia and antagonism of the etorphine. Under etorphine + azaperone, minute ventilation decreased in the sheep, though this decrease was corrected under propofol, while the minute ventilation in the goats remained unchanged throughout. Under etorphine + azaperone, both sheep and goats displayed arterial blood hypoxia and hypercapnia (relative to midazolam levels), which failed to completely recover under propofol, indicating that more time might be needed for the blood gases to be adequately restored. Nonetheless, many of the confounding cardiorespiratory effects of etorphine were ameliorated when it was antagonized with naltrexone while the animal was held under propofol, indicating that this procedure can largely restore the cardiovascular and respiratory systems closer to a normal, resting state.

Vocal tract modelling in fallow deer: are male groans nasalized?

Males of several species of deer have a descended and mobile larynx, resulting in an unusually long vocal tract, which can be further extended by lowering the larynx during call production. Formant frequencies are lowered as the vocal tract is extended, as predicted when approximating the vocal tract as a uniform quarter wavelength resonator. However, formant frequencies in polygynous deer follow uneven distribution patterns, indicating that the vocal tract configuration may in fact be rather complex. We CT-scanned the head and neck region of two adult male fallow deer specimens with artificially extended vocal tracts and measured the cross-sectional areas of the supra-laryngeal vocal tract along the oral and nasal tracts. The CT data were then used to predict the resonances produced by three possible configurations, including the oral vocal tract only, the nasal vocal tract only, or combining the two. We found that the area functions from the combined oral and nasal vocal tracts produced resonances more closely matching the formant pattern and scaling observed in fallow deer groans than those predicted by the area functions of the oral vocal tract only or of the nasal vocal tract only. This indicates that the nasal and oral vocal tracts are both simultaneously involved in the production of a non-human mammal vocalization, and suggests that the potential for nasalization in putative oral loud calls should be carefully considered.

Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

BACKGROUND

Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events.

RESULTS

Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.

CONCLUSIONS

We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.

Comparative in vitro and in vivo effects of chlorpyrifos oxon in the outbred CD-1 mouse (Mus musculus) and great plains toad (Anaxyrus cognatus)

We compared biochemical, functional, and behavioral responses to the organophosphorus anticholinesterase chlorpyrifos oxon (CPO) in mice (Mus musculus, CD-1) and toads (Anaxyrus cognatus, Great Plains toad). Toads were substantially less sensitive to acute lethality of CPO based on the maximum tolerated (nonlethal) dose (toads, 77 mg/kg; mice, 5.9 mg/kg). Sublethal exposures led to classical signs of toxicity (increased involuntary movements, autonomic secretions) in mice but hypoactivity in toads. Motor performance in an inclined plane test was not affected by CPO in mice but was altered at the highest dosage in toads. Acetylcholinesterase (AChE), butyrylcholinesterase, monoacylglycerol lipase, and fatty acid amide hydrolase activities in brain were inhibited in mice but not in toads, and fatty acid amide hydrolase activity in the liver was inhibited in both species. Toad brain AChE was less sensitive to in vitro inhibition by CPO (50% inhibitory concentration [IC50; 20 min, 37 °C], 101 vs 7.8 nM; IC50 [20 min, 26 °C], 149 vs 6.2 nM), and studies of inhibitor kinetics indicated substantially lower anticholinesterase potency of CPO against the toad brain enzyme. Using an in vitro indirect inhibition assay, preincubation of CPO with toad brain homogenate was more effective than an equivalent mouse brain homogenate at reducing CPO potency. These data suggest that the relatively low sensitivity of toads to cholinergic toxicity is based on the low sensitivity of brain AChE, which in turn may be attributable to more effective target-site detoxification. Environ Toxicol Chem 2018;37:1898-1906. © 2018 SETAC.

In vivo fractionation of mercury isotopes in tissues of a mammalian carnivore (Neovison vison)

The use of isotope ratios to trace Hg contamination sources in environmental compartments is now generally accepted. However, for biota and especially for mammals, it is still unknown if and/or how Hg isotopes fractionate in vivo and which tissue is most representative of the source(s) of contamination. We measured fractionation of Hg in mink (Neovison vison) tissues (fur, brain, blood, liver, kidney) collected during a controlled feeding experiment where captive mink were fed differing amounts of methylmercury. There was no significant effect of dietary MeHg concentrations on Hg fractionation in most tissues. Net fractionation of Hg, i.e., fractionation corrected for diet (δ²⁰²Hg_tissue-δ²⁰²Hg_diet) was observed in all tissues with the greatest net fractionation occurring in the mink liver (-1.39‰) and kidney (-0.95‰). Less net fractionation, occurred in the brain (-0.12‰), blood (0.38‰) and fur (0.30‰). In the absence of brain tissue, fur is a suitable proxy which is readily obtainable and can be non-lethally collected. In these mink, it appears that biochemical processes such as demethylation, contribute to significant fractionation of Hg in the liver and kidney, but not as much in the brain and fur, where transport of Hg via thiol-containing complexes may be more important.

Comparison of polymeric immunoglobulin receptor between fish and mammals

Polymeric immunoglobulin receptor (pIgR) functions in transporting polymeric immunoglobulin across epithelial cells into external secretion in animals. During animal evolution, fish was situated at a transition point on the phylogenetic spectrum between species possessing only innate immunity (i.e., invertebrates) and species depending heavily on adaptive immunity (i.e., mammals). Previous studies reported that fish and mammals significantly differ in pIgR. This review summarized the differences in pIgR structure, function, and transcriptional regulation between fish and mammals. A model of the transcriptional regulation of the pIgR gene was suggested. In this model, microbes could activate Toll-like receptor, trigger the cascade reactions in the signaling pathway, and then activate transcription factors that regulate pIgR expression through combining with the pIgR promoter. This review provides some suggestions for further studies on the function and regulatory mechanism of pIgR in fish and other animals.

Genome-scale DNA sequence data and the evolutionary history of placental mammals

We present a genomic data set comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals. The loci were aligned with their protein sequences. The aligned protein sequences were then back translated into their original DNA sequences. The alignments were further filtered to remove individual sequences from each alignment exhibiting long branches or other unusual features. The data is deposited in figshare (http://figshare.com/articles/cds_5162.zip/6031190) and will be useful as a test data set for large-scale phylogenomic analysis.

Seminal plasma proteomes and sperm fertility

During ejaculation, the spermatozoa are transported by the seminal plasma, a fluid resulting from secretions originating mainly from the prostate and the seminal vesicles in mammals. The interaction of the seminal plasma with spermatozoa induces binding of seminal proteins onto the sperm surface and membrane remodeling potentially impacting the sperm transport, survival and fertilizing ability in the female genital tract. The seminal plasma also contains peptides and proteins involved in the inflammatory and immune response of the female tract. Therefore the seminal plasma proteome has been investigated in a large range of taxa, including mammals, birds, fishes and insect species. The association of the seminal plasma with semen preservation or fertility identified proteic markers of seminal plasma function in domestic species. This review summarizes the current knowledge in seminal plasma proteomes and proteic markers of sperm preservation in animal species.

Draft genome sequence of Japanese wood mouse, Apodemus speciosus

The wood mouse (genus Apodemus) is one of the most common rodents in broad-leaf forests in the temperate zone of the Palaearctic region. Molecular studies of wood mice have critically enhanced the understanding of their evolution and ancestral biogeographic events. However, their molecular data are currently only limited to partial mitochondrial sequences and a few genes. Therefore, we sequenced the wood mouse genome to facilitate the acquisition of useful resources for inferring their molecular evolution. We sampled a wild wood mouse at Tsukuba, Japan, and sequenced its whole-genome using the Illumina Hiseq. 2000. To reduce the risk of non-randomness, three paired-end libraries (insert sizes: 150, 300, and 500 bp) and, two mate-pair reads (insert sizes: 8 and 20 kbp) were constructed. In total, we generated approximately 210 Gbp data. From these sequences, we reconstructed 336,124 scaffolds. These data will enhance our understanding of the evolution and ecological factors that affect their genetic constitution. The genome scaffolds generated are available in the National Center Biotechnology Information (NCBI) BioProject with accession number PRJDB5914.

Hiss and snort call types of wild-living giraffes Giraffa camelopardalis: acoustic structure and context

OBJECTIVES

Vocalization as part of vigilance behaviour is widespread across animal taxa, including ruminants. Calls of wild-living giraffes have never been recorded and spectrographically investigated. This study reports the acoustic structure of vigilance-related hiss and snort calls of wild-living giraffes Giraffa camelopardalis.

RESULTS

The hiss and snort calls were emitted during five recording sessions produced by nine individual giraffes (8 adults and 1 subadult) in their natural environment in Namibia (3 individuals) and Kenya (6 individuals). These calls attended vigilance behaviour toward humans in hides or in vehicles and cheetahs as natural predators of giraffe young. This study provides spectrographic analyses of 22 hiss and 20 snort calls. The giraffe hisses were broadband vocalizations of an average duration of 0.72 s (from 0.24 to 1.04 s) and a peak frequency of 0.69 kHz. The giraffe snorts were broadband pulsed calls of an average duration of 0.28 s (from 0.13 to 0.55 s), a peak frequency at 0.20 kHz and comprised a prominent low-frequency pulsation of 23.7 pulses/s. The acoustic structure of giraffe hisses is reminiscent of vigilance-related hisses of musk deer Moschus moschiferus. Giraffe snorts differ from snorts of other ruminants by their prominent pulsed pattern.

Annual and spatial variation in composition and activity of terrestrial mammals on two replicate plots in lowland forest of eastern Ecuador

Terrestrial mammals are important components of lowland forests in Amazonia (as seed dispersal agents, herbivores, predators) but there are relatively few detailed studies from areas that have not been affected by human activities (e.g., hunting, logging). Yet, such information is needed to evaluate effects of humans elsewhere. We used camera traps to sample medium to large-sized terrestrial mammals at a site in lowland forests of eastern Ecuador, one of the most biologically rich areas in the world. We deployed cameras on two study plots in terra firme forest at Tiputini Biodiversity Station. Sixteen cameras were arranged 200 m apart in a 4 × 4 grid on each plot. Cameras were operated for  60 days in January–March, 2014–2017, for a total of 3,707 and 3,482 trap-days on the two plots (Harpia, Puma). A total of 28 species were recorded; 26 on Harpia and 25 on Puma. Number of species recorded each year was slightly greater on Harpia whereas overall capture rates (images/100 trap-days) were higher on Puma. Although most species were recorded on each plot, differences in capture rates meant that yearly samples on a given plot were more similar to each other than to samples on the other plot. Images of most species showed a clumped distribution pattern on each plot; Panthera onca was the only species that did not show a clumped distribution on either plot. Images at a given camera location showed no evidence of autocorrelation with numbers of images at nearby camera locations, suggesting that species were responding to small-scale differences in habitat conditions. A redundancy analysis showed that environmental features within 50 or 100 m of camera locations (e.g., elevation, variation in elevation, slope, distance to streams) accounted for significant amounts of variation in distribution patterns of species. Composition and relative importance based on capture rates were very similar to results from cameras located along trails at the same site; similarities decreased at increasing spatial scales based on comparisons with results from other sites in Ecuador and Peru.

Tributyltin: Advancing the Science on Assessing Endocrine Disruption with an Unconventional Endocrine-Disrupting Compound

Tributyltin (TBT) has been recognized as an endocrine disrupting chemical (EDC) for several decades. However, only in the last decade, was its primary endocrine mechanism of action (MeOA) elucidated-interactions with the nuclear retinoid-X receptor (RXR), peroxisome proliferator-activated receptor γ (PPARγ), and their heterodimers. This molecular initiating event (MIE) alters a range of reproductive, developmental, and metabolic pathways at the organism level. It is noteworthy that a variety of MeOAs have been proposed over the years for the observed endocrine-type effects of TBT; however, convincing data for the MIE was provided only recently and now several researchers have confirmed and refined the information on this MeOA. One of the most important lessons learned from years of research on TBT concerns apparent species sensitivity. Several aspects such as the rates of uptake and elimination, chemical potency, and metabolic capacity are all important for identifying the most sensitive species for a given chemical, including EDCs. For TBT, much of this was discovered by trial and error, hence important relationships and important sensitive taxa were not identified until several decades after its introduction to the environment. As recognized for many years, TBT-induced responses are known to occur at very low concentrations for molluscs, a fact that has more recently also been observed in fish species. This review explores the MeOA and effects of TBT in different species (aquatic molluscs and other invertebrates, fish, amphibians, birds, and mammals) according to the OECD Conceptual Framework for Endocrine Disruptor Testing and Assessment (CFEDTA). The information gathered on biological effects that are relevant for populations of aquatic animals was used to construct Species Sensitivity Distributions (SSDs) based on No Observed Effect Concentrations (NOECs) and Lowest Observed Effect Concentrations (LOECs). Fish appear at the lower end of these distributions, showing that they are as sensitive as molluscs, and for some species, even more sensitive. Concentrations in the range of 1 ng/L for water exposure (10 ng/g for whole-body burden) have been shown to elicit endocrine-type responses, whereas mortality occurs at water concentrations ten times higher. Current screening and assessment methodologies as compiled in the OECD CFEDTA are able to identify TBT as a potent endocrine disruptor with a high environmental risk for the original use pattern. If those approaches had been available when TBT was introduced to the market, it is likely that its use would have been regulated sooner, thus avoiding the detrimental effects on marine gastropod populations and communities as documented over several decades.

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

Background

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals.

Results

After a search for publications containing keywords: “whole genome”, “transcriptome or exome sequencing data”, and “genome-wide genotyping array data” authors looked for information related to genetic signatures ascribable to positive selection in Arctic or Antarctic mammalian species. Publications related to Human, Arctic fox, Yakut horse, Mammoth, Polar bear, and Minke whale were chosen. The compendium of genes that potentially underwent positive selection in >1 of these six species consisted of 416 genes. Twelve of them showed traces of positive selection in three species. Gene ontology term enrichment analysis of 416 genes from the compendium has revealed 13 terms relevant to the scope of this study. We found that enriched terms were relevant to three major groups: terms associated with collagen proteins and the extracellular matrix; terms associated with the anatomy and physiology of cilium; terms associated with docking. We further revealed that genes from compendium were over-represented in the lists of genes expressed in the lung and liver.

Conclusions

A compendium combining mammalian genes involved in adaptation to cold environment was designed, based on the intersection of positively selected genes from six Arctic and Antarctic species. The compendium contained 416 genes that have been positively selected in at least two species. However, we did not reveal any positively selected genes that would be related to cold adaptation in all species from our list. But, our work points to several strong candidate genes involved in mechanisms and biochemical pathways related to cold adaptation response in different species.

Electronic supplementary material

The online version of this article (10.1186/s12863-017-0580-9) contains supplementary material, which is available to authorized users.

The head turn paradigm to assess auditory laterality in cats: influence of ear position and repeated sound presentation

In most humans, speech is predominantly processed by the left hemisphere. This auditory laterality was formerly thought to be an exclusive human characteristic, but is now suggested to have pre-human origins. In studies on auditory laterality in nonhuman animals, the head turn paradigm has become very popular due to its non-invasive character. Although there are implications that the head turn direction indicates functional dominance of the contralateral hemisphere in processing a given sound, the validity of the paradigm is under debate. To validate the paradigm via comparison with imaging or electrophysiological methods, it is first necessary to establish turning biases at the individual level. Recently, the domestic cat, a common model in hearing research, has been found to show turning biases at the group level. To assess individual turning asymmetries in cats, we repeatedly presented kitten isolation calls and assessed whether differences in conveyed arousal changed the previously described left-wards lateralisation of conspecific vocalizations. Based on responses to 50 playback presentations (25 of high and 25 of low arousal), we calculated individual head turn indices. Based on the total data set, we found no consistent individual turning bias, irrespective of call category or sex of the receiver. Although the playback paradigm was chosen carefully to reduce any effects of lateralized loudness perception or changes in motivation due to habituation, individual head turn biases changed significantly in concordance with habituation to repeated playback-presentations and was predictable by small deflections in ear position prior to listening. When splitting the data set according to a decline in responsiveness after seven playback presentations, we revealed an initial left turning bias for most of our subjects (i.e., significant at the group level). We propose that this left turning bias is related to right hemisphere dominance in processes like vigilance behaviour or general arousal rather than on auditory processing, as such. Our findings suggest that both the experimental sequence and sound level differences, induced by asymmetric ear positions, strongly influence the outcome of the head turn paradigm and should be taken into account when evaluating auditory laterality at the behavioural level.

Update on forebrain evolution: From neurogenesis to thermogenesis

Comparative developmental studies provide growing understanding of vertebrate forebrain evolution. This short review directs the spotlight to some newly emerging aspects, including the evolutionary origin of the proliferative region known as the subventricular zone (SVZ) and of intermediate progenitor cells (IPCs) that populate the SVZ, neural circuits that originated within homologous regions across all amniotes, and the role of thermogenesis in the acquisition of an increased brain size. These data were presented at the 8th European Conference on Comparative Neurobiology.

Preputial diverticulum dilation in a Goettingen minipig

Preputial dilation is an infrequently reported condition in pigs. The pathophysiology and etiology is unclear. Causes for diverticulum dilation are proposed to be chronic preputial diverticulitis with subsequent fibrosis of the preputial cavity, phimosis of the preputial orifice or the preputial diverticulum, but the large majority of cases are reportedly idiopathic in nature. Surgical interventions include ablative procedures, but many cases are not treated because of an assumed lack of clinical relevance in pigs not used for breeding. We report a case of progressive preputial dilation that recurred after surgical intervention. Histopathological examination revealed no primary inflammatory condition, contrary to literature suggesting a role for inflammatory mediators in pathogenesis. Phimosis of the preputial orifice was noted post mortem and might be a contributing factor. These findings partially contradict the current assumptions in regards to pathophysiology and treatment choices in the literature and warrant further investigation into alternative therapeutic interventions for this condition.

Macrophages are required to coordinate mouse digit tip regeneration

In mammals, macrophages are known to play a major role in tissue regeneration. They contribute to inflammation, histolysis, re-epithelialization, revascularization and cell proliferation. Macrophages have been shown to be essential for regeneration in salamanders and fish, but their role has not been elucidated in mammalian epimorphic regeneration. Here, using the regenerating mouse digit tip as a mammalian model, we demonstrate that macrophages are essential for the regeneration process. Using cell-depletion strategies, we show that regeneration is completely inhibited; bone histolysis does not occur, wound re-epithelialization is inhibited and the blastema does not form. Although rescue of epidermal wound closure in the absence of macrophages promotes blastema accumulation, it does not rescue cell differentiation, indicating that macrophages play a key role in the redifferentiation of the blastema. We provide additional evidence that although bone degradation is a component, it is not essential to the overall regenerative process. These findings show that macrophages play an essential role in coordinating the epimorphic regenerative response in mammals.

The identification of Oligo-Miocene mammalian palaeocommunities from the Riversleigh World Heritage Area, Australia and an appraisal of palaeoecological techniques

Fourteen of the best sampled Oligo-Miocene local faunas from the Riversleigh World Heritage Area, north-western Queensland, Australia are analysed using classification and ordination techniques to identify potential mammalian palaeocommunities and palaeocommunity types. Abundance data for these faunas are used, for the first time, in conjunction with presence/absence data. An early Miocene Faunal Zone B and two middle Miocene Faunal Zone C palaeocommunities are recognised, as well as one palaeocommunity type. Change in palaeocommunity structure, between the early Miocene and middle Miocene, may be the result of significant climate change during the Miocene Carbon Isotope Excursion. The complexes of local faunas identified will allow researchers to use novel palaeocommunities in future analyses of Riversleigh’s fossil faunas. The utility of some palaeoecological multivariate indices and techniques is examined. The Dice index is found to outperform other binary similarity/distance coefficients, while the UPGMA algorithm is more useful than neighbour joining. Evidence is equivocal for the usefulness of presence/absence data compared to abundance.

Environmental DNA enables detection of terrestrial mammals from forest pond water

Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.

The core transcriptome of mammalian placentas and the divergence of expression with placental shape

INTRODUCTION

The placenta is arguably the most anatomically variable organ in mammals even though its primary function is conserved.

METHOD

Using RNA-Seq, we measured the expression profiles of 55 term placentas of 14 species of mammals representing all major eutherian superordinal clades and marsupials, and compared the evolution of expression across clades.

RESULTS

We identified a set of 115 core genes which is expressed (FPKM ≥10) in all eutherian placentas, including genes with immune-modulating properties (ANXA2, ANXA1, S100A11, S100A10, and LGALS1), cell-cell interactions (LAMC1, LUM, and LGALS1), invasion (GRB2 and RALB) and syncytialization (ANXA5 and ANXA1). We also identified multiple pre-eclampsia associated genes which are differentially expressed in Homo sapiens when compared to the other 13 species. Multiple genes are significantly associated with placenta morphology, including EREG and WNT5A which are both associated with placental shape.

DISCUSSION

115 genes are important for the core functions of the placenta in all eutherian species analyzed. The molecular functions and pathways enriched in the core placenta align with the evolutionarily conserved functionality of the placenta.

A conflict of interest: the evolutionary arms race between mammalian APOBEC3 and lentiviral Vif

Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins are mammalian-specific cellular deaminases and have a robust ability to restrain lentivirus replication. To antagonize APOBEC3-mediated antiviral action, lentiviruses have acquired viral infectivity factor (Vif) as an accessory gene. Mammalian APOBEC3 proteins inhibit lentiviral replication by enzymatically inserting G-to-A hypermutations in the viral genome, whereas lentiviral Vif proteins degrade host APOBEC3 via the ubiquitin/proteasome-dependent pathway. Recent investigations provide evidence that lentiviral vif genes evolved to combat mammalian APOBEC3 proteins. In corollary, mammalian APOBEC3 genes are under Darwinian selective pressure to escape from antagonism by Vif. Based on these observations, it is widely accepted that lentiviral Vif and mammalian APOBEC3 have co-evolved and this concept is called an "evolutionary arms race." This review provides a comprehensive summary of current knowledge with respect to the evolutionary dynamics occurring at this pivotal host-virus interface.

Data on the fungal species consumed by mammal species in Australia

The data reported here support the manuscript Nuske et al. (2017) [1]. Searches were made for quantitative data on the occurrence of fungi within dietary studies of Australian mammal species. The original location reported in each study was used as the lowest grouping variable within the dataset. To standardise the data and compare dispersal events from populations of different mammal species that might overlap, data from locations were further pooled and averaged across sites if they occurred within 100 km of a random central point. Three locations in Australia contained data on several (>7) mycophagous mammals, all other locations had data on 1–3 mammal species. Within these three locations, the identity of the fungi species was compared between mammal species’ diets. A list of all fungi species found in Australian mammalian diets is also provide along with the original reference and fungal synonym names.

Endocrinology of osmoregulation and thermoregulation of Australian desert tetrapods: A historical perspective

Many Australian tetrapods inhabit desert environments characterised by low productivity, unpredictable rainfall, high temperatures and high incident solar radiation. Maintaining a homeostatic milieu intérieur by osmoregulation and thermoregulation are two physiological challenges faced by tetrapods in deserts, and the endocrine system plays an important role in regulating these processes. There is a considerable body of work examining the osmoregulatory role of antidiuretic hormones for Australian amphibians, reptiles and mammals, with particular contributions concerning their role and function for wild, free-living animals in arid environments. The osmoregulatory role of the natriuretic peptide system has received some attention, while the role of adrenal corticosteroids has been more thoroughly investigated for reptiles and marsupials. The endocrinology of thermoregulation has not received similar attention. Reptiles are best-studied, with research examining the influence of arginine vasotocin and melatonin on body temperature, the role of prostaglandins in heart rate hysteresis and the effect of melanocyte-stimulating hormone on skin reflectivity. Australian mammals have been under-utilised in studies examining the regulation, development and evolution of endothermy, and there is little information concerning the endocrinology of thermoregulation for desert species. There is a paucity of data concerning the endocrinology of osmoregulation and thermoregulation for Australian desert birds. Studies of Australian desert fauna have made substantial contributions to endocrinology, but there is considerable scope for further research. A co-ordinated approach to examine arid-habitat adaptations of the endocrine system in an environmental and evolutionary context would be of particular value.

Water-fat MRI in a hibernator reveals seasonal growth of white and brown adipose tissue without cold exposure

Obligate hibernators, such as ground squirrels, display circannual patterns which persist even under constant laboratory conditions, suggesting that they are regulated by endogenous rhythms. Brown adipose tissue (BAT) is important for thermogenesis during periodic arousals from hibernation when core body temperature rises spontaneously from 5 to 37 °C. In most small eutherians BAT growth requires several weeks of cold exposure. We hypothesized that in the thirteen-lined ground squirrel (Ictidomys tridecemlineatus), a hibernator, BAT growth is regulated, in part, by an endogenous rhythm and we predicted that this growth would precede the hibernation season without cold exposure. We tested this prediction using repeated water-fat magnetic resonance imaging over a year, including the hibernation season. Thoracic BAT depots increased in volume from spring through autumn even though animals were housed at ~22 °C. Subsequent cold exposure (5 °C) enlarged the thoracic BAT further. The fat fraction of this tissue fell significantly during the period of peak growth, indicating relative increases in non-triglyceride components, perhaps mitochondria or vasculature. We also found that the proportion of the body consisting of white adipose tissue (WAT) increased steadily from spring through autumn, and fell throughout hibernation, mirroring changes in body mass. Unlike BAT, WAT fat fractions remained constant (near 90%) throughout the year. Future studies will evaluate the significance of photoperiod and cold exposure on the growth of these tissues. We also found tissue with a fat fraction characteristic of BAT in the head near the eyes, a potentially novel discovery that requires further confirmation.

Reflections on bird and mammal risk assessment for plant protection products in the European Union: Past, present, and future

The use of plant protection products on agricultural crops can result in exposure of birds and mammals to toxic chemicals. In the European Union, the risks from such exposures are assessed under the current (2009) guidance document from the European Food Safety Authority (EFSA), designed to increase the realism of the theoretical risk assessments in comparison to its predecessor (SANCO/4145/2000). Since its adoption over 7 yr ago, many plant protection products have been evaluated successfully using the 2009 EFSA guidance document. However, there are still significant areas of improvement recommended for future revisions of this guidance. The present Focus article discusses experiences to date with the current scheme, including levels of conservatism in input parameters and interpretation by regulatory authorities together with proposals for how the guidance document could be improved when it is revised in the not too distant future. Several areas for which further guidance is recommended have been identified, such as the derivation of ecologically relevant bird and mammal reproductive endpoints and the use of modeling approaches to contextualize risk assessments. Areas where existing databases could be improved were also highlighted, including the collation of relevant focal species across Europe and expansion of the residue database for food items. To produce a realistic and useable guidance document in the future, it is strongly recommended that there is open and constructive communication between industry, regulatory authorities, and the EFSA. Such collaboration would also encourage harmonization between member states, thus reducing workloads for both industry and regulatory authorities. Environ Toxicol Chem 2017;36:565-575. © 2017 SETAC.

Grizzly bear (Ursus arctos horribilis) locomotion: forelimb joint mechanics across speed in the sagittal and frontal planes

The majority of terrestrial locomotion studies have focused on parasagittal motion and paid less attention to forces or movement in the frontal plane. Our previous research has shown that grizzly bears produce higher medial ground reaction forces (lateral pushing from the animal) than would be expected for an upright mammal, suggesting frontal plane movement may be an important aspect of their locomotion. To examine this, we conducted an inverse dynamics analysis in the sagittal and frontal planes, using ground reaction forces and position data from three high-speed cameras of four adult female grizzly bears. Over the speed range collected, the bears used walks, running walks and canters. The scapulohumeral joint, wrist and the limb overall absorb energy (average total net work of the forelimb joints, -0.97 W kg^-1). The scapulohumeral joint, elbow and total net work of the forelimb joints have negative relationships with speed, resulting in more energy absorbed by the forelimb at higher speeds (running walks and canters). The net joint moment and power curves maintain similar patterns across speed as in previously studied species, suggesting grizzly bears maintain similar joint dynamics to other mammalian quadrupeds. There is no significant relationship with net work and speed at any joint in the frontal plane. The total net work of the forelimb joints in the frontal plane was not significantly different from zero, suggesting that, despite the high medial ground reaction forces, the forelimb acts as a strut in that plane.

Moderate evidence for a Lombard effect in a phylogenetically basal primate

When exposed to enhanced background noise, humans avoid signal masking by increasing the amplitude of the voice, a phenomenon termed the Lombard effect. This auditory feedback-mediated voice control has also been found in monkeys, bats, cetaceans, fish and some frogs and birds. We studied the Lombard effect for the first time in a phylogenetically basal primate, the grey mouse lemur, Microcebus murinus. When background noise was increased, mouse lemurs were able to raise the amplitude of the voice, comparable to monkeys, but they did not show this effect consistently across context/individuals. The Lombard effect, even if representing a generic vocal communication system property of mammals, may thus be affected by more complex mechanisms. The present findings emphasize an effect of context, and individual, and the need for further standardized approaches to disentangle the multiple system properties of mammalian vocal communication, important for understanding the evolution of the unique human faculty of speech and language.

Aging effects on the binaural interaction component of the auditory brainstem response in the Mongolian gerbil: Effects of interaural time and level differences

The effect of interaural time difference (ITD) and interaural level difference (ILD) on wave 4 of the binaural and summed monaural auditory brainstem responses (ABRs) as well as on the DN1 component of the binaural interaction component (BIC) of the ABR in young and old Mongolian gerbils (Meriones unguiculatus) was investigated. Measurements were made at a fixed sound pressure level (SPL) and a fixed level above visually detected ABR threshold to compensate for individual hearing threshold differences. In both stimulation modes (fixed SPL and fixed level above visually detected ABR threshold) an effect of ITD on the latency and the amplitude of wave 4 as well as of the BIC was observed. With increasing absolute ITD values BIC latencies were increased and amplitudes were decreased. ILD had a much smaller effect on these measures. Old animals showed a reduced amplitude of the DN1 component. This difference was due to a smaller wave 4 in the summed monaural ABRs of old animals compared to young animals whereas wave 4 in the binaural-evoked ABR showed no age-related difference. In old animals the small amplitude of the DN1 component was correlated with small binaural-evoked wave 1 and wave 3 amplitudes. This suggests that the reduced peripheral input affects central binaural processing which is reflected in the BIC.

Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

Background

Bitter taste perception is essential for species with selective food intake, enabling them to avoid unpalatable or toxic items. Previous studies noted a marked variation in the number of TAS2R genes among various vertebrate species, but the underlying causes are not well understood. Laurasiatherian mammals have highly diversified dietary niche, showing repeated evolution of specialized feeding preferences in multiple lineages and offering a unique chance to investigate how various feeding niches are associated with copy number variation for bitter taste receptor genes.

Results

Here we investigated the evolutionary trajectories of TAS2Rs and their implications on bitter taste perception in whole-genome assemblies of 41 Laurasiatherian species. The number of intact TAS2Rs copies varied considerably, ranging from 0 to 52. As an extreme example of a narrow dietary niche, the Chinese pangolin possessed the lowest number of intact TAS2Rs (n = 2) among studied terrestrial vertebrates. Marine mammals (cetacea and pinnipedia), which swallow prey whole, presented a reduced copy number of TAS2Rs (n = 0-5). In contrast, independent insectivorous lineages, such as the shrew and insectivorous bats possessed a higher TAS2R diversity (n = 52 and n = 20-32, respectively), exceeding that in herbivores (n = 9-22) and omnivores (n = 18-22).

Conclusions

Besides herbivores, insectivores in Laurasiatheria tend to have more functional TAS2Rs in comparison to carnivores and omnivores. Furthermore, animals swallowing food whole (cetacean, pinnipedia and pangolin) have lost most functional TAS2Rs. These findings provide the most comprehensive view of the bitter taste gene repertoire in Laurasiatherian mammals to date, casting new light on the relationship between losses and gains of TAS2Rs and dietary specialization in mammals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-016-0161-1) contains supplementary material, which is available to authorized users.

Newcastle disease virus-vectored West Nile fever vaccine is immunogenic in mammals and poultry

Background

West Nile virus (WNV) is an emerging zoonotic pathogen which is harmful to human and animal health. Effective vaccination in susceptible hosts should protect against WNV infection and significantly reduce viral transmission between animals and from animals to humans. A versatile vaccine suitable for different species that can be delivered via flexible routes remains an essential unmet medical need. In this study, we developed a recombinant avirulent Newcastle disease virus (NDV) LaSota strain expressing WNV premembrane/envelope (PrM/E) proteins (designated rLa-WNV-PrM/E) and evaluated its immunogenicity in mice, horses, chickens, ducks and geese.

Results

Mouse immunization experiments disclosed that rLa-WNV-PrM/E induces significant levels of WNV-neutralizing antibodies and E protein-specific CD4+ and CD8+ T-cell responses. Moreover, recombinant rLa-WNV-PrM/E elicited significant levels of WNV-specific IgG in horses upon delivery via intramuscular immunization, and in chickens, ducks and geese via intramuscular, oral or intranasal immunization.

Conclusions

Our results collectively support the utility of rLa-WNV-PrM/E as a promising WNV veterinary vaccine candidate for mammals and poultry.

Coping with pregnancy after 9months in the dark: Post-hibernation buffering of high maternal stress in arctic ground squirrels

Pregnancy and lactation are key times in the life of female mammals when energetic resources must be brought to bear to produce and nurture offspring. Changes in glucocorticoid (GC) levels are central to this objective, due to their roles in modulating development and physiology and in mediating energetic tradeoffs. We examined GC changes over reproduction in a species living in a harsh seasonal environment: the arctic ground squirrel (Urocitellus parryii). Females become pregnant immediately after emerging from a ∼9month hibernation, and then must begin this pregnancy during an additional month of freezing temperatures and limited food availability. We measured plasma levels of total cortisol, corticosteroid-binding globulin (CBG), and free cortisol in unstressed females at three stages: not-visibly pregnant, visibly pregnant, and lactating. Total cortisol levels were similar in all stages, but CBG levels increased 4-fold from the not-visibly pregnant stage to visibly pregnant and lactating stage. As a result, the free cortisol fraction declined from 51% of total cortisol when females were not-visibly pregnant to only 5% when they were visibly pregnant (remaining low and stable throughout pregnancy) and 10% when they were lactating. This pattern is markedly different from that seen in other mammals, where 10% or less of GCs are free and these tend to increase during gestation. We postulate that the high free cortisol just prior to visible pregnancy is a seasonal adaptation relating either to the pronounced physiological changes the female must undergo after emerging from hibernation and immediately getting pregnant, or to the mobilization of body reserves for energy to permit pregnancy, or both. Thereafter, high CBG levels may shield the developing offspring from the negative effects of cortisol overexposure.

Development and differentiation of the erythroid lineage in mammals

The red blood cell (RBC) is responsible for performing the highly specialized function of oxygen transport, making it essential for survival during gestation and postnatal life. Establishment of sufficient RBC numbers, therefore, has evolved to be a major priority of the postimplantation embryo. The "primitive" erythroid lineage is the first to be specified in the developing embryo proper. Significant resources are dedicated to producing RBCs throughout gestation. Two transient and morphologically distinct waves of hematopoietic progenitor-derived erythropoiesis are observed in development before hematopoietic stem cells (HSCs) take over to produce "definitive" RBCs in the fetal liver. Toward the end of gestation, HSCs migrate to the bone marrow, which becomes the primary site of RBC production in the adult. Erythropoiesis is regulated at various stages of erythroid cell maturation to ensure sufficient production of RBCs in response to physiological demands. Here, we highlight key aspects of mammalian erythroid development and maturation as well as differences among the primitive and definitive erythroid cell lineages.

Species-specific modifications of mandible shape reveal independent mechanisms for growth and initiation of the coronoid

Background

The variation in mandibular morphology of mammals reflects specialisations for different diets. Omnivorous and carnivorous mammals posses large mandibular coronoid processes, while herbivorous mammals have proportionally smaller or absent coronoids. This is correlated with the relative size of the temporalis muscle that forms an attachment to the coronoid process. The role of this muscle attachment in the development of the variation of the coronoid is unclear.

Results

By comparative developmental biology and mouse knockout studies, we demonstrate here that the initiation and growth of the coronoid are two independent processes, with initiation being intrinsic to the ossifying bone and growth dependent upon the extrinsic effect of muscle attachment. A necessary component of the intrinsic patterning is identified as the paired domain transcription factor Pax9. We also demonstrate that Sox9 plays a role independent of chondrogenesis in the growth of the coronoid process in response to muscle interaction.

Conclusions

The mandibular coronoid process is initiated by intrinsic factors, but later growth is dependent on extrinsic signals from the muscle. These extrinsic influences are hypothesised to be the basis of the variation in coronoid length seen across the mammalian lineage.

The quest for mammalian Polycomb response elements: are we there yet?

A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.

The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution

BACKGROUND

Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene.

RESULTS

Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes.

CONCLUSIONS

The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.

Endoscopic Ovariectomy of Exotic Mammals Using a Three-Port Approach

Laparoscopic ovariectomy has been advocated as the preferred sterilization method for dogs for some time. The same arguments and benefits can be extended for many zoologic mammals, including carnivores, suids, primates, lagomorphs, and large rodents. This article summarizes the benefits, equipment options, surgical technique, recovery, and complications associated with this sterilization procedure.

Evaluation of the Blood Film

Evaluation of hemic cell morphology in stained blood film may be the most important part of the hematologic evaluation of exotic animals. The blood film provides important information regarding red blood cell abnormalities, such as changes in cell shape and color, presence of inclusions, and, in the case of lower vertebrates, changes in the position of the cell nucleus. Stained blood film also provides information about changes in leukocyte numbers and morphology, and shows important hemic features of mammalian platelets and the thrombocytes of lower vertebrates. The blood film is needed in the detection and identification of blood parasites.

Grizzly bear (Ursus arctos horribilis) locomotion: gaits and ground reaction forces

Locomotion of plantigrade generalists has been relatively little studied compared with more specialised postures even though plantigrady is ancestral among quadrupeds. Bears (Ursidae) are a representative family for plantigrade carnivorans, they have the majority of the morphological characteristics identified for plantigrade species, and they have the full range of generalist behaviours. This study compared the locomotion of adult grizzly bears (Ursus arctos horribilis Linnaeus 1758), including stride parameters, gaits and analysis of three-dimensional ground reaction forces, with that of previously studied quadrupeds. At slow to moderate speeds, grizzly bears use walks, running walks and canters. Vertical ground reaction forces demonstrated the typical M-shaped curve for walks; however, this was significantly more pronounced in the hindlimb. The rate of force development was also significantly higher for the hindlimbs than for the forelimbs at all speeds. Mediolateral forces were significantly higher than would be expected for a large erect mammal, almost to the extent of a sprawling crocodilian. There may be morphological or energetic explanations for the use of the running walk rather than the trot. The high medial forces (produced from a lateral push by the animal) could be caused by frontal plane movement of the carpus and elbow by bears. Overall, while grizzly bears share some similarities with large cursorial species, their locomotor kinetics have unique characteristics. Additional studies are needed to determine whether these characters are a feature of all bears or plantigrade species.

Conspecific recognition and aggression reduction to familiars in newly weaned, socially plastic mammals

Recognising conspecifics and behaving appropriately towards them is a crucial ability for many species. Grey seals (Halichoerus grypus) show varying capabilities in this regard: mother-pup recognition has been demonstrated in some geographical populations but is absent in others, yet there is evidence that individuals aggregate with prior associates. The recognition capabilities of newly weaned grey seal pups were investigated using class recognition trials within the habituation/dishabituation paradigm. Trials took place in pens, using pairs of individuals that either had previously cohabited (familiar) or that had never met before (stranger). Frequencies of olfactory and visual investigative behaviours ('checks') and aggressive interactions were recorded during trials. Familiar individuals recognised each other: paired strangers showed significantly more checks and aggressive interactions than were seen in trials pairing familiars. Oxytocin concentrations in post-trial plasma samples were analysed to investigate the underlying physiology modulating recognition abilities; however, no significant differences were detected between familiar or stranger trials. This study demonstrates that at a young age, grey seals can recognise individuals they have previously encountered. Recognition abilities in this species have adaptive value by allowing the reduction of costly aggressive interactions between familiar conspecifics, which is often cited as the first step towards the evolution of sociality in a species. This study is the first with wild subjects to find conspecific recognition abilities in a pinniped species outside of reproductive contexts. It demonstrates that even largely solitary species can be capable of recognition and pro-social behaviours that benefit them during times when they must aggregate.

A new Cretaceous Metatherian mammal from Henan, China

We report a new deltatheroidan mammal from the Upper Cretaceous of Henna, China. The new taxon, Lotheridium mengi, is based on a nearly complete skull and associated lower jaws with full adult dentition. Deltatheroidans are known mostly from fragmentary specimens from Asia and North America. Previous views on deltatheroidan relationships were diverse, but recent studies favored their metatherian affinity. The new specimen represents the most complete skull known for deltatheroidans and provides additional evidence that deltatheroidans already had the distinctive metatherian dental formula and replacement pattern and several other derived metatherian features, supporting the metatherian status for this clade. The new species also indicates that deltatheroidan mammals were more diverse and had broader geographical distributions than previously thought.

Impact of maternal malnutrition during the periconceptional period on mammalian preimplantation embryo development

During episodes of undernutrition and overnutrition the mammalian preimplantation embryo undergoes molecular and metabolic adaptations to cope with nutrient deficits or excesses. Maternal adaptations also take place to keep a nutritional microenvironment favorable for oocyte development and embryo formation. This maternal-embryo communication takes place via several nutritional mediators. Although adaptive responses to malnutrition by both the mother and the embryo may ensure blastocyst formation, the resultant quality of the embryo can be compromised, leading to early pregnancy failure. Still, studies have shown that, although early embryonic mortality can be induced during malnutrition, the preimplantation embryo possesses an enormous plasticity that allows it to implant and achieve a full-term pregnancy under nutritional stress, even in extreme cases of malnutrition. This developmental strategy, however, may come with a price, as shown by the adverse developmental programming induced by even subtle nutritional challenges exerted exclusively during folliculogenesis and the preimplantation period, resulting in offspring with a higher risk of developing deleterious phenotypes in adulthood. Overall, current evidence indicates that malnutrition during the periconceptional period can induce cellular and molecular alterations in preimplantation embryos with repercussions for fertility and postnatal health.

Rangeland dynamics: investigating vegetation composition and structure of urban and exurban prairie dog habitat

Rapid human population growth and habitat modification in the western United States has led to the formation of urban and exurban rangelands. Many of these rangelands are also home to populations of black-tailed prairie dogs (Cynomys ludovicianus). Our study aimed to compare the vegetation composition of an urban and exurban rangeland, and explore the role that prairie dogs play in these systems. The percent absolute canopy cover of graminoids (grasses and grass-likes), forbs, shrubs, litter, and bare ground were estimated at sampling areas located on and off prairie dog colonies at an urban and an exurban site. Herbaceous forage quality and quantity were determined on plant material collected from exclosure cages located on the colony during the entire growing season, while a relative estimate of prairie dog density was calculated using maximum counts. The exurban site had more litter and plant cover and less bare ground than the urban site. Graminoids were the dominant vegetation at the exurban plots. In contrast, mostly introduced forbs were found on the urban prairie dog colony. However, the forage quality and quantity tests demonstrated no difference between the two colonies. The relative prairie dog density was greater at the urban colony, which has the potential to drive greater vegetation utilization and reduced cover. Exurban rangeland showed lower levels of impact and retained all of the plant functional groups both on- and off-colony. These results suggest that activities of prairie dogs might further exacerbate the impacts of humans in fragmented urban rangeland habitats. Greater understanding of the drivers of these impacts and the spatial scales at which they occur are likely to prove valuable in the management and conservation of rangelands in and around urban areas.

Mechanism-based proteomic screening identifies targets of thioredoxin-like proteins

Thioredoxin (Trx)-fold proteins are protagonists of numerous cellular pathways that are subject to thiol-based redox control. The best characterized regulator of thiols in proteins is Trx1 itself, which together with thioredoxin reductase 1 (TR1) and peroxiredoxins (Prxs) comprises a key redox regulatory system in mammalian cells. However, there are numerous other Trx-like proteins, whose functions and redox interactors are unknown. It is also unclear if the principles of Trx1-based redox control apply to these proteins. Here, we employed a proteomic strategy to four Trx-like proteins containing CXXC motifs, namely Trx1, Rdx12, Trx-like protein 1 (Txnl1) and nucleoredoxin 1 (Nrx1), whose cellular targets were trapped in vivo using mutant Trx-like proteins, under conditions of low endogenous expression of these proteins. Prxs were detected as key redox targets of Trx1, but this approach also supported the detection of TR1, which is the Trx1 reductant, as well as mitochondrial intermembrane proteins AIF and Mia40. In addition, glutathione peroxidase 4 was found to be a Rdx12 redox target. In contrast, no redox targets of Txnl1 and Nrx1 could be detected, suggesting that their CXXC motifs do not engage in mixed disulfides with cellular proteins. For some Trx-like proteins, the method allowed distinguishing redox and non-redox interactions. Parallel, comparative analyses of multiple thiol oxidoreductases revealed differences in the functions of their CXXC motifs, providing important insights into thiol-based redox control of cellular processes.

Evaluation of the blood film

Evaluation of hemic cell morphology in stained blood film may be the most important part of the hematologic evaluation of exotic animals. The blood film provides important information regarding red blood cell abnormalities, such as changes in cell shape and color, presence of inclusions, and, in the case of lower vertebrates, changes in the position of the cell nucleus. Stained blood film also provides information about changes in leukocyte numbers and morphology, and shows important hemic features of mammalian platelets and the thrombocytes of lower vertebrates. The blood film is needed in the detection and identification of blood parasites.

Microsatellite frequencies vary with body mass and body temperature in mammals, suggesting correlated variation in mutation rate

Substitution rate is often found to correlate with life history traits such as body mass, a predictor of population size and longevity, and body temperature. The underlying mechanism is unclear but most models invoke either natural selection or factors such as generation length that change the number of mutation opportunities per unit time. Here we use published genome sequences from 69 mammals to ask whether life history traits impact another form of genetic mutation, the high rates of predominantly neutral slippage in microsatellites. We find that the length-frequency distributions of three common dinucleotide motifs differ greatly between even closely related species. These frequency differences correlate with body mass and body temperature and can be used to predict the phenotype of an unknown species. Importantly, different length microsatellites show complicated patterns of excess and deficit that cannot be explained by a simple model where species with short generation lengths have experienced more mutations. Instead, the patterns probably require changes in mutation rate that impact alleles of different length to different extents. Body temperature plausibly influences mutation rate by modulating the propensity for slippage. Existing hypotheses struggle to account for a link between body mass and mutation rate. However, body mass correlates inversely with population size, which in turn predicts heterozygosity. We suggest that heterozygote instability, HI, the idea that heterozygous sites show increased mutability, could provide a plausible link between body mass and mutation rate.

Identification of interspecific differences in phase II reactions: determination of metabolites in the urine of 16 mammalian species exposed to environmental pyrene

Interspecific differences in xenobiotic metabolism are a key to determining relative sensitivities of animals to xenobiotics. However, information on domesticated livestock, companion animals, and captive and free-ranging wildlife is incomplete. The present study evaluated interspecific differences in phase II conjugation using pyrene as a nondestructive biomarker of polycyclic aromatic hydrocarbon (PAH) exposure. Polycyclic aromatic hydrocarbons and their metabolites have carcinogenic and endocrine-disrupting effects in humans and wildlife and can have serious consequences. The authors collected urine from 16 mammalian species and analyzed pyrene metabolites. Interspecific differences in urinary pyrene metabolites, especially in the concentration and composition of phase II conjugated metabolites, were apparent. Glucuronide conjugates are dominant metabolites in the urine of many species, including deer, cattle, pigs, horses, and humans. However, they could not be detected in ferret urine even though the gene for ferret Uridine 5'-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) 1A6 is not a pseudogene. Sulfate conjugates were detected mainly in the urine of cats, ferrets, and rabbits. Interestingly, sulfate conjugates were detected in pig urine. Although pigs are known to have limited aryl sulfotransferase activity, the present study demonstrated that pig liver was active in 1-hydroxypyrene sulfation. The findings have some application for biomonitoring environmental pollution.

Recommended survey designs for occupancy modelling using motion-activated cameras: insights from empirical wildlife data

Motion-activated cameras are a versatile tool that wildlife biologists can use for sampling wild animal populations to estimate species occurrence. Occupancy modelling provides a flexible framework for the analysis of these data; explicitly recognizing that given a species occupies an area the probability of detecting it is often less than one. Despite the number of studies using camera data in an occupancy framework, there is only limited guidance from the scientific literature about survey design trade-offs when using motion-activated cameras. A fuller understanding of these trade-offs will allow researchers to maximise available resources and determine whether the objectives of a monitoring program or research study are achievable. We use an empirical dataset collected from 40 cameras deployed across 160 km(2) of the Western Slope of Colorado, USA to explore how survey effort (number of cameras deployed and the length of sampling period) affects the accuracy and precision (i.e., error) of the occupancy estimate for ten mammal and three virtual species. We do this using a simulation approach where species occupancy and detection parameters were informed by empirical data from motion-activated cameras. A total of 54 survey designs were considered by varying combinations of sites (10-120 cameras) and occasions (20-120 survey days). Our findings demonstrate that increasing total sampling effort generally decreases error associated with the occupancy estimate, but changing the number of sites or sampling duration can have very different results, depending on whether a species is spatially common or rare (occupancy = ψ) and easy or hard to detect when available (detection probability = p). For rare species with a low probability of detection (i.e., raccoon and spotted skunk) the required survey effort includes maximizing the number of sites and the number of survey days, often to a level that may be logistically unrealistic for many studies. For common species with low detection (i.e., bobcat and coyote) the most efficient sampling approach was to increase the number of occasions (survey days). However, for common species that are moderately detectable (i.e., cottontail rabbit and mule deer), occupancy could reliably be estimated with comparatively low numbers of cameras over a short sampling period. We provide general guidelines for reliably estimating occupancy across a range of terrestrial species (rare to common: ψ = 0.175-0.970, and low to moderate detectability: p = 0.003-0.200) using motion-activated cameras. Wildlife researchers/managers with limited knowledge of the relative abundance and likelihood of detection of a particular species can apply these guidelines regardless of location. We emphasize the importance of prior biological knowledge, defined objectives and detailed planning (e.g., simulating different study-design scenarios) for designing effective monitoring programs and research studies.

Nuclear organization of cholinergic, catecholaminergic, serotonergic and orexinergic systems in the brain of the Tasmanian devil (Sarcophilus harrisii)

This study investigated the nuclear organization of four immunohistochemically identifiable neural systems (cholinergic, catecholaminergic, serotonergic and orexinergic) within the brains of three male Tasmanian devils (Sarcophilus harrisii), which had a mean brain mass of 11.6g. We found that the nuclei generally observed for these systems in other mammalian brains were present in the brain of the Tasmanian devil. Despite this, specific differences in the nuclear organization of the cholinergic, catecholaminergic and serotonergic systems appear to carry a phylogenetic signal. In the cholinergic system, only the dorsal hypothalamic cholinergic nucleus could be observed, while an extra dorsal subdivision of the laterodorsal tegmental nucleus and cholinergic neurons within the gelatinous layer of the caudal spinal trigeminal nucleus were observed. Within the catecholaminergic system the A4 nucleus of the locus coeruleus complex was absent, as was the caudal ventrolateral serotonergic group of the serotonergic system. The organization of the orexinergic system was similar to that seen in many mammals previously studied. Overall, while showing strong similarities to the organization of these systems in other mammals, the specific differences observed in the Tasmanian devil reveal either order specific, or class specific, features of these systems. Further studies will reveal the extent of change in the nuclear organization of these systems in marsupials and how these potential changes may affect functionality.

Molecular evolution of the tissue-nonspecific alkaline phosphatase allows prediction and validation of missense mutations responsible for hypophosphatasia

ALPL encodes the tissue nonspecific alkaline phosphatase (TNSALP), which removes phosphate groups from various substrates. Its function is essential for bone and tooth mineralization. In humans, ALPL mutations lead to hypophosphatasia, a genetic disorder characterized by defective bone and/or tooth mineralization. To date, 275 ALPL mutations have been reported to cause hypophosphatasia, of which 204 were simple missense mutations. Molecular evolutionary analysis has proved to be an efficient method to highlight residues important for the protein function and to predict or validate sensitive positions for genetic disease. Here we analyzed 58 mammalian TNSALP to identify amino acids unchanged, or only substituted by residues sharing similar properties, through 220 millions years of mammalian evolution. We found 469 sensitive positions of the 524 residues of human TNSALP, which indicates a highly constrained protein. Any substitution occurring at one of these positions is predicted to lead to hypophosphatasia. We tested the 204 missense mutations resulting in hypophosphatasia against our predictive chart, and validated 99% of them. Most sensitive positions were located in functionally important regions of TNSALP (active site, homodimeric interface, crown domain, calcium site, …). However, some important positions are located in regions, the structure and/or biological function of which are still unknown. Our chart of sensitive positions in human TNSALP (i) enables to validate or invalidate at low cost any ALPL mutation, which would be suspected to be responsible for hypophosphatasia, by contrast with time consuming and expensive functional tests, and (ii) displays higher predictive power than in silico models of prediction.