A review of potential techniques for identifying individual stoats (Mustela erminea) visiting control or monitoring stations

Abstract

We review ways of individually identifying stoats (Mustela erminea) and similar small mammals from visits to bait stations or to monitoring devices in the field. Tracking devices are the cheapest and most practical method currently available of measuring the presence of a particular species, but there has been little research on the recognition of individuals. Elongation of tracking tunnels, or using sooty plates rather than ink to record prints, may improve detectability of individual markings. Recording visits to bait stations or tracking tunnels from DNA sequencing of hair or skin samples is likely to be prohibitively expensive for many monitoring programmes. Identification of stoats visiting bait stations or tracking tunnels using electronic devices has great potential, but these techniques are impracticably expensive because stoats move over such large areas that individual receivers and data loggers would be needed for each bait station. Chemical bait markers such as rhodamine B may be the most suitable method for identifying which animals have used a particular bait station.     

OpenAWSEM with Open3SPN2: A fast,flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.     

The influence of allyl trenbolone (Regumate) on the timing,duration and endocrinology of parturition in sows

A study was undertaken to evaluate the effects of using an oral progestagen for synchronisation of parturition in the sow. Multiparous Landrace X Large White sows were fed 20 mg allyl trenbolone daily from day 110 to 115 of gestation then 15 mg on day 116 (Group R; N = 12); untreated sows of similar background served as controls (Group C; N = 9). Blood samples, taken at 8-h intervals from day 110 of gestation to onset of parturition, then every 4 h until parturition was complete, were assayed for plasma levels of progesterone, unconjugated oestrone, cortisol and prolactin. Duration of farrowing, incidence of stillbirths and individual piglet birth weights were recorded. Five Group R sows farrowed during the period of progestagen administration, while for the remaining 7, the mean interval from last progestagen treatment to emergence of first piglet was 31.6 ±5.5 h. Gestation length, duration of parturition, and mean interval between successive births all were longer in Group R than in Group C (116.5 ± 0.34 compared with 115.0 ± 0.52 days, P < 0.01; 9.73 ± 1.98 compared with 3.08 ± 0.70 h, P < 0.01; and 53.4 ± 10.2 compared with 16.2 ± 2.4 min., P < 0.01, respectively). No significant treatment differences were apparent for litter size at birth, proportion stillborn or piglet birth weights. Profile analysis showed that plasma progesterone levels in Group R were lower (P < 0.05) during the 30 h prefarrowing, suggesting a longer mean interval between functional luteolysis and parturition in these animals. In both Groups plasma levels of unconjugated oestrone rose in the prefarrowing period, the levels being higher (P < 0.05) in Group R Peak oestrone levels occurred at the commencement of, and had declined to low levels by the completion of, farrowing. Cortisol levels exhibited a pattern similar to that of oestrone, although peak levels at parturition were lower in Group R (P < 0.01). Plasma prolactin levels in the 24 h prepartum rose faster and reached higher levels (P < 0.05) in Group C than Group R, but the difference was no longer apparent subsequent to first piglet emergence. It is concluded that the use of this progestagen to delay parturition upset the synchronisation of endocrine events at farrowing, resulting in an increased duration of parturition.     

A comparative study of the function of heterospecific vocal mimicry in European passerines

Although heterospecific vocal imitation is well documented inpasserines, the evolutionary correlates of this phenomenon arepoorly known. Here, we studied interspecific variation in vocalmimicry in a comparative study of 241 European songbirds. Wetested whether vocal mimicry is a mode of repertoire acquisitionor whether it resulted from imperfect song learning. We alsoinvestigated the effect of the degree of contact with the vocalenvironment (with species having larger ranges, abundance, orbeing long lived having a higher degree of mimicry) and a possiblelink with cognitive capacity (an overall larger brain in specieswith mimicry). Finally, we determined the potential evolutionaryrole of vocal mimicry in different interspecific contexts, predictingthat mimicry may affect the intensity of brood parasitism, predation,or degree of hybridization. While controlling for research effortand phylogenetic relationships among taxa, we found that effectsizes for intersong interval, brain size, breeding dispersal,abundance, age-dependent expression of repertoires, and predationrisk reached a level that may indicate evolutionary importance.Vocal mimicry seems to be a consequence of song continuity ratherthan song complexity, may partially have some cognitive componentbut may also be dependent on the vocal environment, and mayattract the attention of predators. However, estimates of sexualselection and interspecific contacts due to brood parasitismand hybridization varied independently of vocal mimicry. Therefore,mimicry may have no function in female choice for complex songsand may be weakly selected via interspecific associations. Thesefindings provide little evidence for vocal mimicry having evolvedto serve important functions in most birds.     

‘Communication’ in weakly electric fish, Gnathonemus petersii (Mormyridae) II. Interaction of electric organ discharge activities of two fish

The electric organ discharges (EODs) of pairs of weakly electric fish, Gnathonemus petersii, were simultaneously recorded to study the significance of the EODs as communication signals. In a 400-litre tank a larger fish (12 to 15 cm) was passively moved within a shelter tube toward a smaller specimen (6 to 9 cm), either in steps or a continuous move. The movement was stopped at that distance when at least one fish significantly lowered or ceased its EOD activity. From this ‘threshold interfish distance’ the spatial range of a ‘communication field’ was found to extend about 30 cm from the fish. At threshold distances an EOD frequency increase caused a temporary EOD activity cessation in the second fish. The spontaneous irregular EOD pattern of the fish displaying the increased EOD rate changed into a regular one with almost equal time intervals between fish pulses.     

Digit ratios, secondary sexual characters and condition in barn swallows Hirundo rustica

The second and fourth digit length ratio (2D:4D) is sexuallydimorphic in many vertebrates. This ratio has been suggestedto provide an estimate of steroid levels encountered duringprenatal development, which may have organizational consequencesfor physiology and behavior of adults. However, recent studiesshowed that the relation between digit ratio and steroids seemsinconsistent and may vary among species and populations. Wetested the hypothesis that digit ratios would be correlatedwith the expression of secondary sexual characters, using thebarn swallow (Hirundo rustica) as a model system. This was doneby testing whether variation in 2D:4D ratio was correlated withtail length and features of song, which are important secondarysexual characters positively correlated with circulating steroidconcentration in adult birds. Furthermore, we examined the predictionthat male and female digit ratios would correlate with bodymass in an antagonistic way. There was no significant sexualdimorphism in digit ratio, which may be due to low levels ofsexual selection in this population. Adult right 2D:4D ratiowas negatively linked to tail length but not to male song output.Moreover, right 2D:4D ratio was negatively correlated with bodymass in male and positively in females. These results are consistentwith high digit ratios reflecting low levels of testosteronein this bird species.     

Gape coloration reliably reflects immunocompetence of barn swallow (Hirundo rustica) nestlings

In some passerines, parents allocate more food to offspringwith the brightest red gapes, but the function of parental decisionsbased on offspring gape coloration is unknown. We hypothesizethat gape coloration is part of a communication system wherenestlings reveal their condition to attending parents, whichmay thus base their decisions on reliable signals of offspringreproductive value. We analyze the effects of brood size manipulation,injection with an immunogen and food deprivation, on gape coloration,morphology, and T-cell–mediated immunocompetence of nestlingbarn swallows (Hirundo rustica). For each gape we measured threecomponents of coloration (hue, saturation, and brightness) andobtained an overall color score by principal component analysis.Enlargement of brood size and injection with an antigen resultedin less red and less saturated and brighter gape color. Nestlingsin enlarged broods had smaller body mass and T-cell–mediatedimmunocompetence compared to those in reduced broods. A positivecovariation existed between redness and saturation of gape colorand T-cell–mediated immunocompetence. Gape color siblingsraised in different nests did not depend on parentage. Thus,condition-dependent gape coloration can reveal different componentsof nestling state on which parents may base their adaptive decisionsabout allocation of care to the offspring.