Metastability of non-reversible mean-field Potts model with three spins

We examine a non-reversible, mean-field Potts model with three spins on a set with $N\uparrow\infty$ points. Without an external field, there are three critical temperatures and five different metastable regimes. The analysis can be extended by a perturbative argument to the case of small external fields. We illustrate the case of large external fields with some phenomena which are not present in the absence of external field.Comment: 34 pages, 12 figure

Structural and electronic properties of Pb1-xCdxTe and Pb1-xMnxTe ternary alloys

A systematic theoretical study of two PbTe-based ternary alloys, Pb1-xCdxTe and Pb1-xMnxTe, is reported. First, using ab initio methods we study the stability of the crystal structure of CdTe - PbTe solid solutions, to predict the composition for which rock-salt structure of PbTe changes into zinc-blende structure of CdTe. The dependence of the lattice parameter on Cd (Mn) content x in the mixed crystals is studied by the same methods. The obtained decrease of the lattice constant with x agrees with what is observed in both alloys. The band structures of PbTe-based ternary compounds are calculated within a tight-binding approach. To describe correctly the constituent materials new tight-binding parameterizations for PbTe and MnTe bulk crystals as well as a tight-binding description of rock-salt CdTe are proposed. For both studied ternary alloys, the calculated band gap in the L point increases with x, in qualitative agreement with photoluminescence measurements in the infrared. The results show also that in p-type Pb1-xCdxTe and Pb1-xMnxTe mixed crystals an enhancement of thermoelectrical power can be expected.Comment: 10 pages, 13 figures, submitted to Physical Review

Density-independent prey choice, taxonomy, life history, and web characteristics determine the diet and biocontrol potential of spiders (Linyphiidae and Lycosidae) in cereal crops

Spiders are among the dominant invertebrate predators in agricultural systems and are significant regulators of insect pests. The precise dynamics of biocontrol of pests in the field are, however, poorly understood. This study investigates how density-independent prey choice, taxonomy, life stage, sex, and web characteristics affect spider diet and biocontrol. We collected spiders in four genera of Linyphiidae (i.e., Bathyphantes, Erigone, Tenuiphantes, and Microlinyphia), and individuals from the Lycosidae genus Pardosa, and their proximate prey communities from barley fields in Wales, UK between April and September 2018. We analyzed the gut contents of 300 individual spiders using DNA metabarcoding. From the 300 spiders screened, 89 prey taxa were identified from 45 families, including a wide range of pests and predators. Thrips were the dominant prey, present in over a third of the spiders sampled, but a type IV functional response appears to reduce their predation at peak abundances. Spider diets significantly differed based on web characteristics, but this depended on the genus and sex of the spider and it was not the principal separating factor in the trophic niches of linyphiids and lycosids. Diets significantly differed between spider genera and life stages, reflected in different propensities for intraguild predation and pest predation. Adult spiders predated a greater diversity of other predators, and juveniles predated a greater diversity of pests. Overall, Tenuiphantes spp. and Bathyphantes spp. exhibited the greatest individual potential for biocontrol of the greatest diversity of pest genera. The greater trophic niche complementarity of Pardosa spp. and Erigone spp., however, suggests that their complementary predation of different pests might be of greater overall benefit to biocontrol. Sustainable agriculture should aim to optimize conditions throughout the cropping cycle for effective biocontrol, prioritizing provision for a diversity of spiders which predate a complementary diversity of pest species

Money spider dietary choice in pre‐ and post‐harvest cereal crops using metabarcoding

Money spiders (Linyphiidae) are an important component of conservation biological control in cereal crops, but they rely on alternative prey when pests are not abundant, such as between cropping cycles. To optimally benefit from these generalist predators, prey choice dynamics must first be understood. Money spiders and their locally available prey were collected from cereal crops 2 weeks pre‐ and post‐harvest. Spider gut DNA was amplified with two novel metabarcoding primer pairs designed for spider dietary analysis, and sequenced. The combined general and spider‐exclusion primers successfully identified prey from 15 families in the guts of the 46 linyphiid spiders screened, whilst avoiding amplification of Erigone spp. The primers show promise for application to the diets of other spider families such as Agelenidae and Pholcidae. Distinct invertebrate communities were identified pre‐ and post‐harvest, and changes in spider diet and, to a lesser extent, prey choice reflected this. Spiders were found to consume one another more than expected, indicating their propensity towards intraguild predation, but also consumed common pest families. Changes in spider prey choice may redress prey community changes to maintain a consistent dietary intake. Consistent provision of alternative prey via permanent refugia should be considered to sustain effective conservation biocontrol

An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data

1. Metabarcoding provides a powerful tool for investigating biodiversity and trophic interactions, but the high sensitivity of this methodology makes it vulnerable to errors, resulting in artefacts in the final data. Metabarcoding studies thus often utilise minimum sequence copy thresholds (MSCTs) to remove artefacts that remain in datasets; however, there is no consensus on best practice for the use of MSCTs. 2. To mitigate erroneous reporting of results and inconsistencies, this study discusses and provides guidance for best-practice filtering of metabarcoding data for the ascertainment of conservative and accurate data. Several of the most commonly used MSCTs were applied to example datasets of Eurasian otter Lutra lutra and cereal crop spider (Araneae: Linyphiidae and Lycosidae) diets. 3. Changes in both the method and threshold value considerably affected the resultant data. Of the MSCTs tested, it was concluded that the optimal method for the examples given combined a sample-based threshold with removal of maximum taxon contamination, providing stringent filtering of artefacts while retaining target data. 4. Choice of threshold value differed between datasets due to variation in artefact abundance and sequencing depth, thus studies should employ controls (mock communities, negative controls with no DNA and unused MID tag combinations) to select threshold values appropriate for each individual study

DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink (Leiolopisma telfairii)

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration

Relating neuromuscular control to functional anatomy of limb muscles in extant archosaurs

Electromyography (EMG) is used to understand muscle activity patterns in animals. Understanding how much variation exists in muscle activity patterns in homologous muscles across animal clades during similar behaviours is important for evaluating the evolution of muscle functions and neuromuscular control. We compared muscle activity across a range of archosaurian species and appendicular muscles, including how these EMG patterns varied across ontogeny and phylogeny, to reconstruct the evolutionary history of archosaurian muscle activation during locomotion. EMG electrodes were implanted into the muscles of turkeys, pheasants, quail, guineafowl, emus (three age classes), tinamous and juvenile Nile crocodiles across 13 different appendicular muscles. Subjects walked and ran at a range of speeds both overground and on treadmills during EMG recordings. Anatomically similar muscles such as the lateral gastrocnemius exhibited similar EMG patterns at similar relative speeds across all birds. In the crocodiles, the EMG signals closely matched previously published data for alligators. The timing of lateral gastrocnemius activation was relatively later within a stride cycle for crocodiles compared to birds. This difference may relate to the coordinated knee extension and ankle plantarflexion timing across the swing‐stance transition in Crocodylia, unlike in birds where there is knee flexion and ankle dorsiflexion across swing‐stance. No significant effects were found across the species for ontogeny, or between treadmill and overground locomotion. Our findings strengthen the inference that some muscle EMG patterns remained conservative throughout Archosauria: for example, digital flexors retained similar stance phase activity and M. pectoralis remained an ‘anti‐gravity’ muscle. However, some avian hindlimb muscles evolved divergent activations in tandem with functional changes such as bipedalism and more crouched postures, especially M. iliotrochantericus caudalis switching from swing to stance phase activity and M. iliofibularis adding a novel stance phase burst of activity

GeoWaVe: Geometric median clustering with weighted voting for ensemble clustering of cytometry data

Motivation Clustering is an unsupervised method for identifying structure in unlabelled data. In the context of cytometry, it is typically used to categorise cells into subpopulations of similar phenotypes. However, clustering is greatly dependent on hyperparameters and the data to which it is applied as each algorithm makes different assumptions and generates a different ‘view’ of the dataset. As such, the choice of clustering algorithm can significantly influence results, and there is often not one preferred method but different insights to be obtained from different methods. To overcome these limitations, consensus approaches are needed that directly address the effect of competing algorithms. To the best of our knowledge, consensus clustering algorithms designed specifically for the analysis of cytometry data are lacking. Results We present a novel ensemble clustering methodology based on geometric median clustering with weighted voting (GeoWaVe). Compared to graph ensemble clustering methods that have gained popularity in scRNA-seq analysis, GeoWaVe performed favourably on different sets of high-dimensional mass and flow cytometry data. Our findings provide proof of concept for the power of consensus methods to make the analysis, visualisation and interpretation of cytometry data more robust and reproducible. The wide availability of ensemble clustering methods is likely to have a profound impact on our understanding of cellular responses, clinical conditions, and therapeutic and diagnostic options

Overcoming the pitfalls of merging dietary metabarcoding into ecological networks

The construction of increasingly detailed species interaction networks is extending the potential applications of network ecology, providing an opportunity to understand complex eco-evolutionary interactions, ecosystem service provision and the impacts of environmental change on ecosystem functioning. Dietary metabarcoding is a rapidly growing tool increasingly used to construct ecological networks of trophic interactions, enabling the determination of individual animal diets including difficult-to-distinguish prey taxa and even for species where traditional dietary analyses are unsuitable (e.g. fluid feeders and small invertebrates). Several challenges, however, surround the use of dietary metabarcoding, especially when metabarcoding-based interactions are merged with observation-based species interaction data. We describe the difficulties surrounding the quantification of species interactions, sampling perspective discrepancy (i.e. zoocentric vs. phytocentric sampling), experimental biases, reference database omissions and assumptions regarding direct and indirect consumption events. These problems are not, however, insurmountable. Effective experimental design and data curation with appropriate attention paid to these problems renders the incorporation of dietary metabarcoding into ecological network analysis a powerful tool for the construction of highly resolved networks. Throughout, we discuss how these problems should be addressed when merging data to construct ecological networks