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Mineralogy and origin of aerosol from an arc basaltic eruption: case study of Tolbachik volcano, Kamchatka
<p>Intense emission of volcanic aerosol accompanied the 2012-13 basaltic effusive eruption of Tolbachik volcano, Kamchatka. The aerosols sampled contain sulfuric acid droplets, glassy particles and 70 mineral phases. All aerosol particles may be classified by their origin. The fragmentation aerosol includes magma fragments: silicate glass clasts, silicate microspheres and small phenocrysts (olivine, pyroxene and magnetite). The alteration aerosol comprises particles of quenched silicate melt covered with secondary minerals (fluorides, sulfates and oxides/hydroxides of rock-forming elements) and fragments of altered rocks composed solely of secondary minerals. The condensation aerosol dominated the mass during the later stages of the eruption when the explosive activity had ceased, and was characterized by the greatest variety of particle compositions. Na-K sulfate and Fe(III) oxide made more than 95% of the solid fraction of the condensation aerosol. The remaining 5% were represented by native elements (Au, Ag-Pt alloy, Pt); sulfides of Fe, Cu, Ag and Re; oxides and hydroxides of Al, Fe, Cu, Zn, Mo, W, Te, Ta and Zr; halides of Al, Mg, Na, K, Ca, Cd, Pb, Ag and Tl; sulfates of Na, K, Pb, Ca and Ba; the only silicate was As-bearing orthoclase. Droplets of H<sub>2</sub>SO<sub>4</sub> formed the liquid phase of the condensation aerosol. Some of the aerosols, such as magnetite spherules or phosphate-carbonate-fluorite association, likely had a nonvolcanic origin (country rocks, wood fly ash). Physical and chemical properties of minerals from the volcanic aerosols have an effect on the geochemical and environmental behavior of the trace elements emitted by volcanoes.</p>
Data from: The role of hybridisation in the origin and evolutionary persistence of vertebrate parthenogens: a case study of Darevskia lizards
Obligate parthenogenesis is found in only 0.1% of vertebrate species, is thought to be relatively short lived and is typically of hybrid origin. However, neither the evolutionary persistence of asexuality in vertebrates, nor the conditions that allow the generation of new parthenogenetic lineages are currently well understood. It has been proposed that vertebrate parthenogenetic lineages arise from hybridisation between two divergent taxa within a specific range of phylogenetic distances (the "Balance Hypothesis"). Moreover, parthenogenetic species often maintain a certain level of hybridisation with their closest sexual relatives, potentially generating new polyploid hybrid lineages. Here we address the role of hybridisation in the origin and evolutionary lifespan of vertebrate parthenogens. We use a set of microsatellite markers to characterize the origins of parthenogens in the lizard genus Darevskia to study the distinctiveness of sexual and asexual taxa currently in sympatry, and to analyse the evolutionary consequences of interspecific hybridisation between asexual females and sexual males. We find that parthenogens result from multiple past hybridisation events between species from specific lineages over a range of phylogenetic distances. This suggests that the Balance Hypothesis needs to make allowance for lineage-specific effects, as envisaged in the "Phylogenetic Constraint Hypothesis". Our results show recurrent backcrossing between sexual and parthenogenetic Darevskia but neither gene flow nor formation of new asexual lineages is found. We suggest that, along with their demographic advantage, parthenogens gain additional leverage to outcompete sexuals in nature when the retention of sexual reproductive machinery allows backcrossing with their sexual ancestors.
Data from: Relationship type affects the reliability of dispersal distance estimated using pedigree inferences in partially sampled populations: a case study involving invasive American mink in Scotland
Estimating dispersal—a key parameter for population ecology and management—is notoriously difficult. The use of pedigree assignments, aided by likelihood-based software, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software-derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals. Additionally, we simulated scenarios to investigate the accuracy of pairwise inferences. Estimates of dispersal distance varied greatly when derived from different inferred pairwise relationships, with mother–offspring relationship being the shortest (average = 21 km) and the most accurate. Pairs assigned as maternal half-siblings were inaccurate, with 64%–97% falsely assigned, implying that estimates for these relationships in the wild population were unreliable. The false assignment rate was unrelated to the software-derived assignment probabilities at high dispersal rates. Assignments were more accurate when the inferred parents were older and immigrants and when dispersal rates between subpopulations were low (1% and 2%). Using 30 instead of 15 loci increased pairwise reliability, but half-sibling assignments were still inaccurate (>59% falsely assigned). The most reliable approach when using inferred pairwise relationships in polygamous species would be not to use half-sibling relationship types. Our simulation approach provides guidance for the application of pedigree inferences under partial sampling and is applicable to other systems where pedigree assignments are used for ecological inference.
Data from: How traffic facilitates population expansion of invasive species along roads: the case of common ragweed in Germany
1. Because common ragweed (Ambrosia artemisiifolia L., henceforth Ambrosia) has negative effects on human health, it is a common focus for management, which would benefit from a better understanding of the underlying mechanisms by which the species spreads. Road systems are known to be invasion corridors, but the conduit function of vehicles for the rapid spread of Ambrosia along roads and for population extension along roadside verges has not yet been demonstrated convincingly. 2. To quantify the effect of different traffic volumes on the dispersal and population extension of Ambrosia we used two approaches: First, by combining field experiments along roads with records of the seed rain around single plants, we simulated a combined dispersal kernel that revealed the interactions between primary dispersal and traffic-mediated secondary dispersal. Second, we recorded seedling recruitment around isolated roadside populations over two years to determine how traffic-related parameters affect population extension. 3. The longest traffic-mediated dispersal distances exceeded those of primary dispersal by about one order of magnitude. Traffic volume had a significant positive effect on dispersal distances and on the lateral deposition of seeds on the road verge. 4. Seedling recruitment around isolated roadside populations was significantly higher in the driving direction than against, but only at the distance where the major seed rain of traffic-mediated dispersal is to be expected according to the combined dispersal kernel (3-15 m). 5. Synthesis and applications: This study isolates effects of road traffic from confounding mechanisms (e.g. mowing machinery, propagule pressure from infested fields) on common ragweed (Ambrosia artemsiifolia L.) invasions. Results demonstrate traffic-mediated dispersal in Ambrosia invasions as a routine and predictable process that facilitates population extension in the direction of traffic along roadsides, depending on traffic volume. This highlights the importance of prioritizing mowing along high use roads and mowing of isolated populations to prevent seed abscission and further spread of common ragweed Ambrosia.
Data from: Skin autofluorescence and subclinical atherosclerosis in mild to moderate chronic kidney disease: a case-control study
Advanced glycation end-products (AGEs) are increased and predict mortality in patients with chronic kidney disease (CKD) who are undergoing hemodialysis, irrespective of the presence of type 2 diabetes. However, little information exits about the relationship between AGEs and subclinical atherosclerosis at the early stages of CKD. A case-control study was performed including 87 patients with mild-to-moderate stages of CKD (glomerular filtration rate from 89 to 30 ml/min/per 1.73m2) and 87 non-diabetic non-CKD subjects matched by age, gender, body mass index, and waist circumference. Skin autofluorescence (AF), a non-invasive assessment of AGEs, was measured. The presence of atheromatous disease in carotid and femoral arteries was evaluated using vascular ultrasound, and vascular age and SCORE risk were estimated. Patients with mild-to-moderate stages of CKD showed an increase in skin AF compared with control subjects (2.5±0.6 vs. 2.2±0.4 AU, p<0.001). A skin AF value >2.0 AU was accompanied by a 3-fold increased risk of detecting the presence of an atheromathous plaque (OR 3.0, 95% CI 1.4–6.5, p = 0.006). When vascular age was assessed through skin AF, subjects with CKD were almost 12 years older than control subjects (70.3±25.5 vs. 58.5±20.2 years, p = 0.001). Skin AF was negatively correlated with glomerular filtration rate (r = -0.354, p<0.001) and LDL-cholesterol (r = -0.269, p = 0.001), and positively correlated with age (r = 0.472, p<0.001), pulse pressure (r = 0.238, p = 0.002), and SCORE risk (r = 0.451, p<0.001). A stepwise multivariate regression analysis showed that age and glomerular filtration rate independently predicted skin AF (R2 = 0.289, p<0.001). Skin AF is elevated in patients with mild-to-moderate CKD compared with control subjects. This finding may be independently associated with the glomerular filtration rate and the presence of subclinical atheromatous disease. Therefore, the use of skin AF may help to accurately evaluate the real cardiovascular risk at the early stages of CKD.
Data from: Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae)
Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well-differentiated nuclear marker frequencies should be treated separately. However a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here we re-explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long-term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re-introduction efforts for G. pusilla which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.
Data from: Conservation under uncertainty: optimal network protection strategies for worst-case disturbance events
1. Conservation goals are ideally set after a thorough understanding of potential threats; however, predicting future spatial patterns of threats, such as disturbance, remains challenging. Here, we develop a novel extension of network fortification-interdiction models (NFIM) that deals with uncertainty in future spatial patterns of disturbance by optimally selecting sites that will best mitigate a worst-case scenario for a given magnitude of disturbance. 2. This approach uses information on between-patch movement probabilities and patch-specific survival, which can be estimated from mark-recapture data, to optimize life expectancy. Optimization occurs in three interrelated stages: protection, followed by disturbance, and then assessment. 3. We applied the modeling approach to two mark-recapture data sets: Roseate terns Sterna dougallii in the northeastern United States and the Everglade snail kite Rostrhamus sociabilis plumbeus in Florida. We contrasted the results to a more conventional approach of protecting sites that maximize connectivity (by minimizing the distances among protected sites) and a bi-objective model that maximizes connectivity and the number of individuals under protection. 4. Protecting sites that best mitigate future worst-case disturbance scenarios consistently resulted in higher predicted life expectancies than protecting patches that minimize dispersal distance. Predicted life expectancy was similar between NFIM and the biobjective model for the small roseate tern network, yet, the NFIM predicted higher life expectancy than any of the scenarios in the bi-objective model in the snail kite network. 5. Synthesis and applications. This application of interdiction models prescribed a combination of patches for protection that results in the least possible decrease in life expectancy. Our analyses of the snail kite and roseate tern networks suggest that managing to protect these prescribed patches by the network fortification interdiction model (i.e. protecting against the worst-case disturbance scenario) is more beneficial than managing patches that minimize dispersal distance or maximize the number of individuals under protection if the conservation goal is to ensure the long term persistence of a species.
Data from: Accuracy of identifications of mammal species from camera trap images: a northern Australian case study
Camera traps are a powerful and increasingly popular tool for mammal research, but like all survey methods, they have limitations. Identifying animal species from images is a critical component of camera trap studies, yet while researchers recognize constraints with experimental design or camera technology, image misidentification is still not well understood. We evaluated the effects of a species' attributes (body mass and distinctiveness) and individual observer variables (experience and confidence) on the accuracy of mammal identifications from camera trap images. We conducted an Internet‐based survey containing 20 questions about observer experience and 60 camera trap images to identify. Images were sourced from surveys in northern Australia and included 25 species, ranging in body mass from the delicate mouse (Pseudomys delicatulus, 10 g) to the agile wallaby (Macropus agilis, >10 kg). There was a weak relationship between the accuracy of mammal identifications and observer experience. However, accuracy was highest (100%) for distinctive species (e.g. Short‐beaked echidna [Tachyglossus aculeatus]) and lowest (36%) for superficially non‐distinctive mammals (e.g. rodents like the Pale field‐rat [Rattus tunneyi]). There was a positive relationship between the accuracy of identifications and body mass. Participant confidence was highest for large and distinctive mammals, but was not related to participant experience level. Identifications made with greater confidence were more likely to be accurate. Unreliability in identifications of mammal species is a significant limitation to camera trap studies, particularly where small mammals are the focus, or where similar‐looking species co‐occur. Integration of camera traps with conventional survey techniques (e.g. live‐trapping), use of a reference library or computer‐automated programs are likely to aid positive identifications, while employing a confidence rating system and/or multiple observers may lead to a collection of more robust data. Although our study focussed on Australian species, our findings apply to camera trap studies globally.
Data from: Fencing solves human‐wildlife conflict locally but shifts problems elsewhere: a case study using functional connectivity modelling of the African elephant
1. Fencing is one of the commonest methods for mitigating human-wildlife conflicts. At the same time, fencing is considered to be of one of the most pressing emerging threats to conservation globally. Although fences act as barriers and eventually can cause population isolation and fragmentation, it is challenging to quantitatively predict the possible consequences fences have for wildlife. 2. Here, we model how fencing designed to mitigate human-elephant conflict (HEC) on the Borderlands between Kenya and Tanzania will affect functional connectivity and movement corridors for African elephants. Specifically, we (1) model functional landscape connectivity integrating natural and anthropogenic factors; (2) predict seasonal movement corridors used by elephants in non-protected areas; and (3) evaluate whether fencing in one area can potentially intensify human-wildlife conflicts elsewhere. 3. We used GPS movement and remote sensing data to develop monthly step-selection functions to model functional connectivity. For future scenarios, we used a currently ongoing fencing project designed for human-elephant conflict mitigation within the study area. We modelled movement corridors using least-cost path and circuit theory methods, evaluated their predictive power and quantified connectivity changes resulting from the planned fencing. 4. Our results suggest that fencing will not cause landscape fragmentation and will not change functional landscape connectivity dramatically. However, fencing will lead to a loss of connectivity locally and will increase the potential for HEC in new areas. We estimated that wetlands important for movement corridors will be more intensively used by the elephants, which may also cause problems of overgrazing. Seasonal analysis highlighted an increasing usage of non-protected lands in the dry season and equal importance of the pinch point wetlands for preserving overall function connectivity. 5. Synthesis and applications. Fencing is a solution to small-scale HEC problems, but will not solve the issue at a broader scale. Moreover, our results highlight that it may intensify the conflicts and overuse of habitat patches in other areas, thereby negating any conservation benefits. If fencing is employed on a broader scale, then it is imperative that corridors are integrated within the protected area network to ensure local connectivity of affected species.
Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea
Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages RepARK and RepeatMasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Ephydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabeled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labeled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.
Data from: DNA metabarcoding diet analysis for species with parapatric versus sympatric distribution: a case study on subterranean rodents
Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.
Data from: Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study
Logical connections exist between evolutionary modularity and heterochrony, two unifying and structuring themes in the expanding field of evolutionary developmental biology. The former sees complex phenotypes as being made up of semi-independent units of evolutionary transformation; the latter requires such a modular organization of phenotypes to occur in a localized or mosaic fashion. This conceptual relationship is illustrated here by analyzing the evolutionary changes in the cranidial ontogeny of two related species of Cambrian trilobites. With arguments from comparative developmental genetics and functional morphology, we delineate putative evolutionary modules within the cranidium and examine patterns of evolutionary changes in ontogeny at both global and local scales. Results support a case of mosaic heterochrony, i.e. a combination of local heterochronies affecting the different parts individuated in the cranidium, leading to the complex pattern of allometric repatterning observed at the global scale. Through this example, we show that recasting morphological analyses of complex phenotypes with a priori knowledge or hypotheses about their organizational and variational properties can significantly improve our interpretation and understanding of evolutionary changes among related taxa, fossil and extant. Such considerations open avenues to investigate the large-scale dynamics of modularity and its role in phenotypic evolution.
Data from: Are 2D space-use analyses adapted to animals living in 3D environments? A case study on a fish shoal
Methodologies enabling the monitoring of animal movement and behavior in 3-dimensions (3D; x, y, z, the latter accounting for the vertical dimension) are becoming increasingly accessible and can be deployed on entire groups of animals inhabiting 3D habitats. When 2-dimensional (2D; x, y) space-use analyses are used on such groups, their spatial organization is represented as a planar projection of individuals' space-use. Movement on the vertical dimension is ignored and could biased ecological inference made from the spatial structure of the group. We used a digital imaging technique to track movements and feeding behavior of individual animals within a free-range aggregation of juvenile drift-feeding fish (Galaxias anomalus) in 3D and at fine spatiotemporal scales. We estimated spatiotemporal overlap of space-use and feeding territories between group-members using 2D (x, y) and 3D spatial analysis to: (1) describe the spatial structure of the group, (2) identify patterns of resource partitioning, and (3) investigate the relationship between space-use overlap and feeding behavior. We found that overlapping ratios of space-use and feeding territories were over-estimated in 2D, while 3D analysis of space-use provided evidence of spatial partitioning between group-members. We also found that, regardless of the computation used, the overlapping ratios of space-use were positively correlated with overlapping ratios of feeding territories while no effect was found on feeding activity. In conclusion, whilst 3D analysis provided valuable information on the spatial structure of a group, inferences on the ecological function of space-use can also be obtained from 2D analysis.
Data from: Activity and migratory flights of individual free-flying songbirds throughout the annual cycle: method and first case study
We describe a method and device (< 1.2 g) for recording, processing and storing data about activity and location of individuals of free-living songbirds throughout the annual cycle. Activity level was determined every five minutes from five 100 ms samples of accelerometer data with 5 s between the sampling events. Activity levels were stored on an hourly basis throughout the annual cycle, allowing periods of resting/sleep, continuous flight and intermediate activity (foraging, breeding) to be distinguished. Measurements from a light sensor were stored from preprogrammed key stationary periods during the year to provide control information about geographic location. Successful results, including annual actogram, were obtained for a red-backed shrike Lanius collurio carrying out its annual loop migration between northern Europe and southern Africa. The shrike completed its annual migration by performing > 66 (max. 73) nocturnal migratory flights (29 flights in autumn and > 37, max. 44, in spring) adding up to a total of > 434 (max. 495) flight hours. Migratory flights lasted on average 6.6 h with maximum 15.9 h. These flights were aggregated into eight travel episodes (periods of 4–11 nights when flights took place on the majority of nights). Daytime resting levels were much higher during the winter period compared to breeding and final part of spring migration. Daytime resting showed peaks during days between successive nocturnal flights across Sahara, continental Africa and the Arabian Peninsula, indicating that the bird was mostly sleeping between these long migratory flights. Annual activity and flight data for free-living songbirds will open up many new research possibilities. Main topics that can be addressed are e.g. migratory flight performance (total flight investment, numbers and characteristics of flights), timing of stationary periods, activity patterns (resting/sleep, activity level) in different phases of the annual cycle and variability in the annual activity patterns between and within individuals.
Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
Premise of the study: Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target enriched Illumina sequencing libraries. Methods: We perform supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences: a consensus method based on de novo sequence assembly, the use of ambiguity characters, and a novel method for phasing alleles. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves resolution or decreases topological uncertainty. Key Results: We show that it is possible to infer phased alleles from target enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency. Conclusions: We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. In our dataset, the impact of allele phasing on phylogeny is minimal compared to the impact of using phylogenetic reconstruction methods that account for gene tree incongruence.
Data from: Gauging scale effects and biogeographical signals in similarity distance decay analyses: an Early Jurassic ammonite case study
In biogeography, the similarity distance decay (SDD) relationship refers to the decrease in compositional similarity between communities with geographical distance. Although representing one of the most widely used relationships in biogeography, a review of the literature reveals that: (1) SDD is influenced by both spatial extent and sample size; (2) the potential effect of the phylogenetic level has yet to be tested; (3) the effect of a marked biogeographical structuring upon SDD patterns is largely unknown; and (4) the SDD relationship is usually explored with modern, mainly terrestrial organisms, whereas fossil taxa are seldom used in that perspective. Using this relationship, we explore the long-distance dispersal of the Early Jurassic (early Pliensbachian, c. 190.8 Ma to 187.6 Ma) ammonites of the western Tethys and adjacent areas, in a context of marked provincialism. We show that the long-distance dispersal of these ammonites is not related to shell size and shape, but rather to the environmental characteristics of the province to which they belong. This suggests that their long-distance dispersal may have been essentially driven by passive planktonic drift during early juvenile, post-hatching stages. Furthermore, it seems that the SDD relationship is not always an appropriate method to characterize the existence of a biogeographical structuring. We conducted SDD analyses at various spatial, sampling and phylogenetic scales in order to evaluate their sensitivity to scale effects. This multi-scale approach indicates that the sampling scale may influence SDD rates in an unpredictable way and that the phylogenetic level has a major impact on SDD patterns.
Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan
1. To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics. 2. The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real-time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species. 3. In environmental samples, we detected mtDNA of the endemic species at 25 sites and mtDNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey. 4. Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide-ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species.
Data from: The oceanic concordance of phylogeography and biogeography: a case study in Notochthamalus
Dispersal and adaptation are the two primary mechanisms that set the range distributions for a population or species. As such, understanding how these mechanisms interact in marine organisms in particular – with capacity for long-range dispersal and a poor understanding of what selective environments species are responding to – can provide useful insights for the exploration of biogeographic patterns. Previously, the barnacle Notochthamalus scabrosus has revealed two evolutionarily distinct lineages with a joint distribution that suggests an association with one of the two major biogeographic boundaries (~30°S) along the coast of Chile. However, spatial and genomic sampling of this system has been limited until now. We hypothesized that given the strong oceanographic and environmental shifts associated with the other major biogeographic boundary (~42°S) for Chilean coastal invertebrates, the southern mitochondrial lineage would dominate or go to fixation in locations further to the south. We also evaluated nuclear polymorphism data from 130 single nucleotide polymorphisms to evaluate the concordance of the signal from the nuclear genome with that of the mitochondrial sample. Through the application of standard population genetic approaches along with a Lagrangian ocean connectivity model, we describe the codistribution of these lineages through a simultaneous evaluation of coastal lineage frequencies, an approximation of larval behavior, and current-driven dispersal. Our results show that this pattern could not persist without the two lineages having distinct environmental optima. We suggest that a more thorough integration of larval dynamics, explicit dispersal models, and near-shore environmental analysis can explain much of the coastal biogeography of Chile.
Data from: Ecomorphological convergence in Eleutherodactylus frogs: a case of replicate radiations in the Caribbean
Replicate radiations, the repeated multiplication of species associated with ecological divergence, have attracted much attention and generated as much debate. Due to the few well‐studied cases, it remains unclear whether replicate radiations are an exceptional result of evolution or a relatively common example of the power of adaptation by natural selection. We examined the case of Eleutherodactylus frogs, which radiated in the Caribbean islands resulting in more than 160 species that occupy very diverse habitats. A time‐calibrated phylogeny revealed that these frogs independently diversified on all larger islands producing species that occupy a broad range of microhabitats in different islands. Using phylogenetic comparative methods, we found an association between morphological traits and particular microhabitats, and for most microhabitats detected significant morphological convergence. Our results indicate Caribbean Eleutherodactylus are a novel example of replicate radiations, and highlight the predictability of evolutionary processes, as similar ecological opportunities can lead to similar outcomes.
Data from: A case for a joint strategy of diversified bet hedging and plasticity in the pea aphid wing polyphenism
Phenotypic plasticity and diversified bet hedging are strategies for coping with variable environments. Plasticity is favoured when an organism can predict future conditions using environmental cues, while bet hedging is favoured when predictive cues are not available. Theoretical analyses suggest that many organisms should use a mixture of both strategies, because environments often present both scenarios. Here, we examine if the pea aphid wing polyphenism, a well-known case of plasticity, is potentially a mixture of plasticity and bet hedging. In this polyphenism, asexual females produce more winged offspring in crowded conditions, and wingless offspring in uncrowded conditions. We find that pea aphids use plasticity to respond to crowding and we find considerable genetic variation for this response. We further show that individual aphids produce both winged and wingless offspring, consistent with the variability expected in a bet hedging trait. We conclude that the pea aphid wing polyphenism system is probably a mixture of plasticity and bet hedging. Our study adds to a limited list of empirical studies examining mixed strategy usage, and suggests that mixed strategies may be common in dispersal traits.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.