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opencc-zeroDec 2019View details →

Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status

Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (Crotalus oreganus) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.

opencc-zeroAug 2020View details →

Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers

Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.

opencc-by-4.0Aug 2020View details →

Extended Data: Population structure of Salmonella serotype Mbandaka

This project contains supplementary figures associated with the project.

opencc-by-4.0Sep 2020View details →

Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations: data related to publication

Data related to the following publication: "Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations"

opencc-zeroSep 2020View details →

Data from: Genetic structure in Orkney island mice: isolation promotes morphological diversification

Following human occupation, the house mouse has colonized numerous islands, exposing the species to a wide variety of environments. Such a colonization process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess. Here, we jointly analyse genetic and morphometric variation in the house mice (Mus musculus domesticus) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bio-proxy of human structure and practices even at a very local scale.

opencc-zeroSep 2020View details →

Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems

Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.

Data from: Sensing the structural characteristics of surfaces: Texture encoding by a bottom-dwelling fish

The texture of contacted surfaces influences our perception of the physical environment and modulates behavior. Texture perception and its neural encoding mechanisms have traditionally been studied in the primate hand, yet animals of all types live in richly textured environments and regularly interact with textured surfaces. Here we explore texture sensation in a different type of vertebrate limb by investigating touch and potential texture encoding mechanisms in the pectoral fins of fishes, the forelimb homologs. We investigated the pectoral fins of the round goby (Neogobius melanostomus), a bottom-dwelling species that lives on substrate types of varying roughness and whose fins frequently contact the bottom. Analysis shows that the receptive field sizes of fin ray afferents are small and afferents exhibit response properties to tactile motion that are consistent with those of primates and other animals studied previously. In response to a periodic stimulus (coarse gratings), afferents phase lock to the stimulus temporal frequency and thus can provide information about surface texture. These data demonstrate that fish can have the capability to sense the tactile features of their near range physical environment with fins.

Data from: Spatial structure maintains diversity of pyocin inhibition in household Pseudomonas aeruginosa

Nearly all bacteria produce narrow-spectrum antibiotics called bacteriocins. Studies have shown that bacteriocins can mediate microbial interactions, but the mechanisms underlying patterns of inhibition are less well understood. We assembled a spatially structured collection of isolates of Pseudomonas aeruginosa from bathroom and kitchen sink drains in nine households. Growth inhibition of these P. aeruginosa by bacteriocins, known as pyocins in this species, was measured using pairwise inhibition assays. Carbon source usage of these isolates was measured and genetic distance was estimated using multilocus sequencing. We found that as the distance between sites of isolation increased, there was a significantly higher probability of inhibition, and that pyocin inhibition and susceptibility vary greatly among isolates collected from different houses. We also detected support for other mechanisms influencing diversity: inhibition outcomes were influenced by the type of drain from which isolates were collected, and while we found no indication that carbon source utilization influences inhibition, inhibition was favored at an intermediate genetic distance. Overall, these results suggest that the combined effects of dispersal limitation among sites and competitive exclusion within them maintain diversity in pyocin inhibition and susceptibility phenotypes, and that additional processes such as local adaptation and effects of phylogenetic distance could further contribute to spatial variability.

Data from: Allometric scaling of eDNA production in stream-dwelling brook trout (Salvelinus fontinalis) inferred from population size structure

Environmental DNA (eDNA) concentration exhibits a positive correlation with organism abundance in nature, but modelling this relationship could be substantially improved by incorporating the biology of eDNA production. A recent model (Yates et al. 2020) extended models of physiological allometric scaling to eDNA production, hypothesizing that brook trout eDNA production scales non-linearly with mass as a power-function with scaling coefficients < 1 in lakes. To validate this hypothesis, we re-analysed data from Wilcox et al. (2016) that examined the correlation between eDNA concentration and brook trout abundance in streams. We found that allometrically scaled mass (ASM) (e.g. ∑(individual mass0.36) best described patterns of eDNA concentration across streams (r2 = 0.43). ASM exhibited substantially improved model fit relative to biomass (r2 = 0.31, ∆AIC = 5.19), indicating that eDNA production did not scale linearly with biomass. However, the explanatory power of ASM was comparable to density (r2 = 0.40, ∆AIC = 1.25). Additionally, the optimal scaling coefficient estimated from the data (0.36) was substantially lower than that found in Yates et al. (2020) (0.72). Discrepancies between datasets could be attributable to ecological differences between study habitats (streams vs lakes) or due to the exclusion of juveniles (i.e. individuals < 75 mm) that can be abundant in stream environments. Nevertheless, this study adds to the growing body of literature demonstrating that individual eDNA production does not scale linearly with biomass.

opencc-zeroSep 2020View details →

Data from: Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively manage this insect pest, we analyzed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour-joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contribute to developing effective management strategies for this pest.

Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1053 P. americana and other Periplaneta species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the USA.

Data from: Butterfly and moth communities differ in their response to habitat structure in rainforests of Mount Cameroon

Mechanisms structuring tropical communities are still under-studied, especially in Afrotropical rainforests. Although insect herbivores are considered to depend on plant diversity, we hypothesized that vegetation structure, together with other microhabitat characteristics, can be more important for some insects. Here, we compared habitat associations of fruit-feeding butterflies and moths, two ecologically different groups of Lepidoptera, in three rainforest localities in foothills of Mount Cameroon, West/Central Africa. Based on a comprehensive dataset of 16,040 specimens of 398 species systematically collected by 240 traps at 48 plots (altogether 9.68 ha), we analyzed how plant community composition, habitat openness, and forest structure affect communities of butterflies and moths. We expected different habitat descriptors to predict communities of the two insect groups. Habitats of tropical fruit-feeding moth communities have never been studied before. In both analyses of species richness and community structure, butterfly communities depended mostly on forest openness. Moth species richness depended on plant diversity and forest openness, whilst the latter substantially influenced their community composition. Additionally, we revealed differences in habitat associations between understory and canopy communities of both groups. Whilst species richness of understory communities was not influenced by any habitat characteristics, it generally followed the general patterns in canopies. By contrast, composition of understory communities followed the general patterns, whilst effects of habitat characteristics on canopy communities were minor for butterflies and none for moths. The differences between such closely related groups of herbivorous insects warn against generalization based on single-taxon studies and highlight the need of community-wide research of tropical rainforests.

Frog tongue segmentation data for a realistic vascular structure in modelling

In the last decade, numerical models have been an increasingly important tool in biological and medical science both for the fundamental understanding of physiology as well as the potential for novel diagnostics and treatments tools in clinical application. In this paper, a nonlinear multi-scale model framework is developed for blood flow distribution in the full vascular system of an organ. We couple a quasi 1D vascular graph model to represent blood flow in larger vessels and a porous media model to describe flow in smaller vessels and capillary bed. The vascular model is based on Poiseuille's law, with pressure correction by elasticity and pressure drop estimation at vessels junctions. The porous capillary bed is modelled as a two-compartment domain (artery and venous) using Darcy's law. The fluid exchange between the artery and venous capillary bed compartments are defined as blood perfusion. The numerical experiments show that the proposed model for blood circulation: 1) is closely dependent on the structure and parameters of both the vascular vessels and of the capillary bed, and 2) it provides a realistic blood circulation in the organ. The advantage of the proposed model is that it is complex enough to reliably capture the main underlying physiological function, yet highly flexible as it offers the possibility of incorporating various local effects. Furthermore, the numerical implementation of the model is straightforward and allows for simulations on a regular desktop computer.

Data from: Brachial supporting structure of Spiriferida (Brachiopoda)

The filter-feeding organ of some extinct brachiopods is supported by a skeletal apparatus called the brachidium. Although relatively well-studied in Atrypida and Athyridida, the brachidial morphology is usually neglected in Spiriferida. To investigate the variations of brachidial morphology in Spiriferida, 65 species belonging to eight superfamilies were analyzed. Based on the presence/absence of the jugal processes and normal/modified primary lamellae of the spiralia, four types of brachidium are recognized. Type-I (with jugal processes) and Type-II (without jugal processes), both having normal primary lamellae, could give rise to each other by losing/re-evolving the jugal processes. Type-III, without jugal processes, originated from Type-II through the evolution of the modified lateral-convex primary lamellae, and it gave rise to Type-IV subsequently by evolving the modified medial-convex primary lamellae. Besides, the evolution of brachidia within individual evolutionary lineages must be clarified, as two or more types can be present within a single family. Type-III and Type-IV are closely associated with the prolongation of the crura, representing innovative modifications of the feeding apparatus in response to the probably shift in the position of the mouth towards the anterior, allowing for more efficient feeding on particles entering the mantle cavity from the anterior gape. Meanwhile, the modified primary lamellae adjusted/regulated the feeding currents. The absence of spires in some taxa with Type-IV brachidium might suggest that they developed a similar lophophore to that in some extant brachiopods, which can extend out of the shell.The filter-feeding organ of some extinct brachiopods is supported by a skeletal apparatus called the brachidium. Although relatively well-studied in Atrypida and Athyridida, the brachidial morphology is usually neglected in Spiriferida. To investigate the variations of brachidial morphology in Spiriferida, 65 species belonging to eight superfamilies were analyzed. Based on the presence/absence of the jugal processes and normal/modified primary lamellae of the spiralia, four types of brachidium are recognized. Type-I (with jugal processes) and Type-II (without jugal processes), both having normal primary lamellae, could give rise to each other by losing/re-evolving the jugal processes. Type-III, without jugal processes, originated from Type-II through the evolution of the modified lateral-convex primary lamellae, and it gave rise to Type-IV subsequently by evolving the modified medial-convex primary lamellae. Besides, the evolution of brachidia within individual evolutionary lineages must be clarified, as two or more types can be present within a single family. Type-III and Type-IV are closely associated with the prolongation of the crura, representing innovative modifications of the feeding apparatus in response to the probably shift in the position of the mouth towards the anterior, allowing for more efficient feeding on particles entering the mantle cavity from the anterior gape. Meanwhile, the modified primary lamellae adjusted/regulated the feeding currents. The absence of spires in some taxa with Type-IV brachidium might suggest that they developed a similar lophophore to that in some extant brachiopods, which can extend out of the shell.

Data for: Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils

Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils (Sarcophilus harrisii) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark-recapture data sets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. DFTD negatively influences devils' likelihood of interaction within their network, an effect which increases with increasing tumour load. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.

opencc-by-4.0Nov 2020View details →

Data associated to the manuscript "Structural and dynamic properties of soda-lime-silica in the liquid phase"

Contains input files and data used to generate the figures of the article: Structural and dynamic properties of soda-lime-silica in the liquid phase Alessandra Serva, Allan Guerault, Yoshiki Ishii, Emmanuelle Gouillart, Ekaterina Burov, and Mathieu Salanne, arXiv, 2009.07198, 2020 https://arxiv.org/abs/2009.07198 The folder *DATA_ASCII_FIGURES* contains the processed data used to plot all the figures of the article.

Data from: Elevation and leaf litter interact in determining the structure of ant communities on a tropical mountain

Tropical mountains encompass a wide range of environmental conditions and are useful models for studying drivers of community structure. Invertebrate species richness and abundance show various elevational patterns. However, the drivers of these differences are not well understood, although microhabitat complexity is potentially important. We studied ground-dwelling ants using pitfall trapping and hand collection on Mt. Wilhelm (Papua New Guinea) from 169 to 3,795 m a.s.l. We tested for the effects of elevation and leaf litter depth (as a measure of microhabitat complexity) on ant abundance, species richness and composition. We sampled 118 species, with ants present up to 2,331 m a.s.l. Species richness peaked at mid-elevation (~700 m), but the elevational pattern for abundance varied depending on sampling scale. Leaf litter depth negatively affected abundance once elevation had been accounted for, while elevation and litter depth had an interactive effect on species richness. Species richness was positively related to litter depth at lower elevations, but negatively above ~700 m. Species composition varied with elevation and less strongly with leaf litter depth. We speculate that in the lowlands, litter depth rather than temperature limits ant communities. At high elevations, the deeper litter decreases temperature of the litter layer, and temperature becomes limiting. At mid elevations, temperature is not yet too low, and litter is still relatively deep, hence generating a mid-elevation peak in ant richness. Our results may explain differing richness-elevation patterns of litter arthropods around the world, and provide testable predictions for future studies on this topic.

opencc-by-4.0Dec 2020View details →

CSR++: A Fast, Scalable, Update-Friendly Graph Data Structure (video)

Full video presentation of the paper: CSR++: A Fast, Scalable, Update-Friendly Graph Data Structure. Appears in Session 5 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020 <a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>

opencc-zeroDec 2020View details →

Data from: Infrared antenna-like structures in mammalian fur

Mammalian fur is a highly adaptable structure, with a broad range of well-documented functions. Many small animals, including shrews, most rodents, and some marsupials, have fur composed of at least four types of hair, all with distinctive and complex anatomy. A ubiquitous and unexplained feature is periodic, internal banding with spacing in the 6–12 μm range that hints at an underlying infrared function. One bristle-like form, called guard hair, has the correct shape and internal periodic patterns to function as an infrared antenna. Optical analysis of guard hair from rodents, shrews and antechinus shows precise tuning to the optimum wavelength for thermal imaging. An infrared sensory capability, that provides all-round infrared threat-warning, could explain why common predators of rodents, such as, small cats, snakes and owls have adaptations to conceal their infrared emission. There are many other well-recognised infrared sensors in members of the Reptilia, Insecta, Arachnida, and Mammalia Classes. Such hair structures are not present in bats (aerial predator) and moles (subterranean). Preliminary evidence suggests that wild mice and rats react to infrared sources, but further experimental evidence is required to confirm these results. The tools developed in this work may enable us to understand the other hair-types and their evolution.