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Data from: Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set
The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A 13-gene anchored hybrid enrichment probe set ('BUTTERFLY2.0'), that includes standard markers used in butterfly phylogenetics, captured sequences from decades-old museum specimens, and appears to be a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life. Our dataset comprises up to 10,898 aligned base pairs from each of the 22 species of Hedylidae and 19 outgroups. Eleven of the thirteen loci were captured from 100% of the taxa, and the remaining loci were captured from ≥94% of taxa. The inferred phylogeny had robust support at 80% of nodes. Our results are consistent with morphological work, with Macrosoma tipulata sister to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved only once from diurnality in Hedylidae, and showed that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family.
Data from: Small volume plasma exchange for Guillain-Barré syndrome in resource-limited settings: a phase II safety and feasibility study
OBJECTIVE: To assess the safety and feasibility of small volume plasma exchange (SVPE) as an alternative to standard plasma exchange (PE) or intravenous immunoglobulin (IVIg) for Guillain-Barré syndrome (GBS) patients. DESIGN: Non-randomized, single arm, interventional trial. SETTING: National Institute of Neurosciences and Hospital, Dhaka, Bangladesh. PARTICIPANTS: Twenty adult (>18 years) patients with GBS presented within 2 weeks of onset of weakness who were unable to walk unaided for more than 10 meters. INTERVENTIONS: SVPE involves blood cell sedimentation in a blood bag and removal of supernatant plasma after blood cells are re-transfused. This procedure was repeated three to six times a day, for eight consecutive days. OUTCOME MEASURES: Serious adverse events (SAE) were defined as severe sepsis and deep venous thrombosis related to the central vein catheter (CVC) used during SVPE. SVPE was considered safe if less than 5/20 patients experienced a SAE, and feasible if 8 L plasma could be removed within 8 days in at least 15/20 patients. RESULTS Median patient age 33 years (IQR 23-46; range 18-55); 13 (65%) were male. Median MRC sum score was 20 (IQR 0-29; range 0-36); three (15%) patients required mechanical ventilation. One patient developed SAE (severe sepsis, possibly related to CVC). Minor adverse effects were transient hypotension in 10 (50%) patients; CVC-associated bleeding in 10 (50%); transfusion reaction to fresh frozen plasma in 4 (20%); and hypo-albuminemia, anaemia or electrolyte imbalance in 4 (20%). Removal of 8 L plasma was possible in 15 (75%) patients. GBS disability score improved by at least one grade in 14 (70%) patients four weeks after SVPE started. No patients died. CONCLUSION: SVPE seems a safe and feasible alternative treatment to standard PE or IVIg for GBS; further studies of clinical efficacy in low-resource developing countries are warranted. TRIAL REGISTRATION: Clinicaltrials.gov NCT02780570 on May 23, 2016. Strength and limitations of the study: 1. The strength of this study underlies the novel and simple technique of SVPE, which is much less expensive than conventional immunotherapies (plasma exchange and intravenous immunoglobulin). 2. SVPE is corroborated as safe and feasible for the first time in a prospective and standardized cohort of patients with Guillain-Barré syndrome (GBS). 3. The intrinsic limitations of this study are its non-randomized, single arm nature, which is conducted in a single center with a limited sample size of GBS patients. 4. Clinical efficacy of SVPE on patients with GBS was a secondary end-point assessment and therefore deserves a randomized controlled trial in future to assess the clinical efficacy of SVPE for the patients with GBS.
Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.
Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.
Data from: Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings
Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions. A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies. The impact of P. falciparum sexual stage immunity on the infectious reservoir for malaria has never been studied in natural settings. Repeated measurements were carried out at start-wet, peak-wet and dry season, and provided data on antibody responses against gametocyte/gamete antigens Pfs48/45 and Pfs230 as anti-gametocyte immunity. Data on high and low-density infections and their infectiousness to anopheline mosquitoes were obtained using quantitative molecular methods and mosquito feeding assays, respectively. An event-driven model for P. falciparum sexual stage immunity was developed and fit to data using an agent based malaria model infrastructure. We found that Pfs48/45 and Pfs230 antibody densities increased with increasing concurrent gametocyte densities; associated with 55–70% reduction in oocyst intensity and achieved up to 44% reduction in proportions of infected mosquitoes. We showed that P. falciparum sexual stage immunity significantly reduces transmission of microscopic (p < 0.001) but not submicroscopic (p = 0.937) gametocyte infections to mosquitoes and that incorporating sexual stage immunity into mathematical models had a considerable impact on the contribution of different age groups to the infectious reservoir of malaria. Human antibody responses to gametocyte antigens are likely to be dependent on recent and concurrent high-density gametocyte exposure and have a pronounced impact on the likelihood of onward transmission of microscopic gametocyte densities compared to low density infections. Our mathematical simulations indicate that anti-gametocyte immunity is an important factor for predicting and understanding the composition and dynamics of the human infectious reservoir for malaria.
Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets
The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic spacer for 619 individuals representing ca. 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84 selected species and combined in a more limited analysis with the other data sets to provide greater resolution. In a well-resolved, supported consensus, most clades were present in more than one individual analysis. All the currently recognized minor genera of "core" Maxillariinae (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium) are embedded within a polyphyletic Maxillaria s.l. Our results support the recognition of a more restricted Maxillaria, of some previously published segregate genera (Brasiliorchis, Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of several novel clades at the generic level. These revised monophyletic generic concepts should minimize further nomenclatural changes, encourage monographic studies, and facilitate more focused analyses of character evolution within Maxillariinae.
Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
How does timing of flowering affect competition for pollinators, flower visitation and seed set in an early spring grassland plant?
<p><span>Knowledge on how the timing of flowering is related to plant fitness and species interactions is crucial </span><span>to understand consequences of phenological shifts as they occur under climate change. Early flowering </span><span>plants may face advantages of low competition for pollinators and disadvantages of low pollinator </span><span>abundances and unfavourable weather conditions. However, it is unknown how this trade-off changes </span><span>over the season and how the timing affects reproductive success. On eight grasslands we recorded </span><span>intra-seasonal changes in pollinators, co-flowering plants, weather conditions, flower visitation </span><span>rates, floral longevity and seed set of </span><span>Pulsatilla vulgaris</span><span>. Although bee abundances and the number of </span><span>pollinator-suitable hours were low at the beginning of the season, early flowers of </span><span>P. vulgaris</span><span> received </span><span>higher flower visitation rates and estimated total number of bee visits than later flowers, which was </span><span>positively related to seed set. Flower visitation rates decreased over time and with increasing number of </span><span>co-flowering plants, which competed with </span><span>P. vulgaris</span><span> for pollinators. Low interspecific competition for </span><span>pollinators seems to be a major driver for early flowering dates. Thus, non-synchronous temporal shifts </span><span>of co-flowering plants as they may occur under climate warming can be expected to strongly affect </span><span>plant-pollinator interactions and the fitness of the involved plants.</span></p>
Data from: Estimating polymorphic growth curve sets with non-chronological data
<p>1. When we collect the growth curves of many individuals, orderly variation in the curves is often observed rather than a completely random mixture of various curves. Small individuals may exhibit similar growth curves, but the curves differ from those of large individuals, whereby the curves gradually vary from small to large individuals. It has been recognized that after standardization with the asymptotes, if all the growth curves are the same (anamorphic growth curve set), the growth curve sets can be estimated using non-chronological data; otherwise, i.e., if the growth curves are not identical after standardization with the asymptotes (polymorphic growth curve set), this estimation is not feasible. However, because a given set of growth curves determines the variation in the observed data, it may be possible to estimate polymorphic growth curve sets using non-chronological data.</p> <p>2. In this study, we developed an estimation method by deriving the likelihood function for polymorphic growth curve sets. The method involves simple maximum likelihood estimation. The weighted nonlinear regression and least squares method after the log-transform of the anamorphic growth curve sets were included as special cases.</p> <p>3. The growth curve sets of the height of cypress (<i>Chamaecyparis obtusa</i>) and larch (<i>Larix kaempferi</i>) trees were estimated. With the model selection process using the AIC and likelihood ratio test, the growth curve set for cypress was found to be polymorphic, whereas that for larch was found to be anamorphic. Improved fitting using the polymorphic model for cypress is due to resolving underdispersion (less dispersion in real data than model prediction).</p> <p>4. The likelihood function for model estimation depends not only on the distribution type of asymptotes, but the definition of the growth curve set as well. Consideration of these factors may be necessary, even if environmental explanatory variables and random effects are introduced.</p>
Data from: Species limits and phylogenomic relationships of Darwin's finches remain unresolved: potential consequences of a volatile ecological setting
Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.
Data from: Systematic review on barriers and enablers for access to diabetic retinopathy screening services in different income settings
Background: Diabetic retinopathy (DR) can lead to visual impairment and blindness if not detected and treated in time. Knowing the barriers/enablers in advance in contrasting different country income settings may accelerate development of a successful DR screening (DRS) program. This would be especially applicable in the low-income settings with the rising prevalence of DR. Objectives: The aim of this systematic review is to identify and contrast the barriers/enablers to DRS for different contexts using both consumers i.e., people with diabetes (PwDM) and provider perspectives and system level factors in different country income settings. Methods: We searched MEDLINE, Embase, CENTRAL in the Cochrane Library from the databases start date to December 2018. We included the studies reported on barriers and enablers to access DRS services based at health care facilities. We categorised and synthesized themes related to the consumers (individuals), providers and the health systems (environment) as main dimensions according to the constructs of social cognitive theory, supported by the quantitative measures i.e., odds ratios as reported by each of the study authors. Main Results: We included 77 studies primarily describing the barriers and enablers. Most of the studies were from high income settings (72.7%, 56/77) and cross sectional in design (76.6%, 59/77). From the perspectives of consumers, lack of knowledge, attitude, awareness and motivation were identified as major barriers. The enablers were fear of blindness, proximity of screening facility, experiences of vision loss and being concerned of eye complications. In providers' perspectives, lack of skilled human resources, training programs, infrastructure of retinal imaging and cost of services were the main barriers. Higher odds of uptake of DRS services was observed when PwDM were provided health education (odds ratio (OR) 4.3) and having knowledge on DR (OR range 1.3-19.7). Conclusion: Knowing the barriers to access DRS is a pre-requisite in development of a successful screening program. The awareness, knowledge and attitude of the consumers, availability of skilled human resources and infrastructure emerged as the major barriers to access to DRS in any income setting.
Data from: Stable isotope-based location in a shelf sea setting: accuracy and precision are comparable to light-based location methods
Retrospective determination of location for marine animals would facilitate investigations of migration, connectivity and food provenance. Predictable spatial variations in carbon and nitrogen isotopes in primary production across shelf seas provide a basis for stable isotope-based location. Here, we assess the accuracy and precision that can be obtained through dietary-isotope-based location methods. We build isoscapes from jellyfish tissues and use these to assign scallops of fixed and known individual location, and herring with well-understood population-level distributions in the North Sea. Accuracy and precision for retrospective isotope-based location in the North Sea were of a similar order to light-based location devices, with 75% of individual scallops assigned correctly to areas representing c. 30% of the North Sea, with a mean linear error on the order of 102 km. Applying assignment methods to an alternative migratory species (herring) resulted in ecologically realistic assignments consistent with fisheries survey data. Location methods based on dietary isotopes such as carbon and nitrogen recover the spatial origin of nutrients assimilated into tissues, and this may not correspond directly to the physical location if either the test animal or its prey is highly migratory. Stable isotope-based location can be applied to any marine-feeding organism or derived food product, but the ecological meaning of any assigned area will be more difficult to interpret for large, high trophic level, migratory animals with relatively slow isotopic assimilation rates.
Data from: Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets
The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl 16 intron, sequences of the internal transcribed spacer ITS region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.
Data from: Development of a simple, practice-based tool to assess quality of paediatric emergency care delivery in resource-limited settings: identifying critical actions via a Delphi study
Objective: Provision of timely, high-quality care for the initial management of critically ill children in African hospitals remains a challenge. Monitoring the completion of critical actions during resuscitations can inform efforts to reduce variability and improve outcomes. We sought to develop a practice-based tool based on contextually relevant actions identified via a Delphi process. Our goal was to develop a tool that could identify gaps in care, facilitate identification of training and standardized assessment to support quality improvement efforts. Design: Six sentinel conditions were selected based on disease epidemiology and mortality at rural and urban African emergency departments. Potential critical actions were identified through focused literature review. These actions were evaluated within a three-round modified Delphi process. A set of logistical filters was applied to the candidate list to derive a practice-based tool. Setting and participants: Attendees at an international emergency medicine conference comprised an expert panel of 25 participants, with 84% working primarily in African settings. Consensus rounds allowing novel responses were conducted via online and in-person surveys. Results: The expert panel generated 199 actions that apply to six conditions in emergently ill children. Application of appropriateness criteria refined this to 92 candidate actions across seven categories: core skills, active seizure, altered mental status, diarrheal illness, febrile illness, respiratory distress, polytrauma. From these, we identified 28 actions for inclusion in a practice-based tool contextually relevant to the initial management of critically ill children in Africa. Conclusions: A group consensus process identified critical actions for severely ill children with select sentinel conditions in emergency paediatric care in an African setting. Absence of these actions during resuscitation might reflect modifiable gaps in quality of care. The resulting practice-based tool is context-relevant and can serve as a foundation for training and quality improvement efforts in African hospitals and emergency departments.
Data from: Contrasting forms of competition set elevational range limits of species
How abiotic and biotic factors constrain distribution limits at the harsh and benign edges of species ranges is hotly debated, partly because macroecological experiments testing the proximate causes of distribution limits are scarce. It has long been recognized—at least since Darwin's On the Origin of Species—that a harsh climate strengthens competition and thus sets species range limits. Using thorough field manipulations along a large elevation gradient, we show the mechanisms by which temperature determines competition type, resulting in a transition from interference to exploitative competition from the lower to the upper elevation limits in burying beetles (Nicrophorus nepalensis). This transition is an example of Darwin's classic hypothesis that benign climates favor direct competition for highly accessible resources while harsh climates result in competition through resources of high rivalry. We propose that identifying the properties of these key resources will provide a more predictive framework to understand the interplay between biotic and abiotic factors in determining geographic range limits.
Data from: Discrete choice modelling of natal dispersal: "choosing" where to breed from a finite set of available areas
1. Classic natal dispersal studies focus mainly on distance travelled. Although distances capture some of the main selective pressures related to dispersal, this approach cannot easily incorporate the properties of the actual destination vs. the available alternatives. Recently, movement ecology studies have addressed questions on movement decisions in relation to availability of resources and/or availability of suitable habitats through the use of discrete choice models (DCMs), a widely used type of models within econometrics, which explains individual choices as a function of the properties of a finite number of alternatives. 2. In this contribution, we show how the dispersal discrete choice model (DDCM) can be used for analysing natal dispersal data in patchy environments given that the natal and the breeding area of the disperser are observed. We test this method using a case study on Great Tits (Parus major) in an archipelago of small woodlots. 3. Our results show that DDCMs are able to capture the results of classic distance-based approaches and simultaneously allow testing hypotheses on how departure and settlement are affected by variables that characterize the disperser, the natal patch and the breeding area, as well as their interactions. 4. DDCMs can be applied to any other species and system that uses some form of discrete breeding location or a certain degree of discretization can be applied.
Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species
Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that co-evolve with one another, methods for evaluating such patterns in a dual-phylogenetic context remain underdeveloped. Here we extend multivariate permutation-based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may utilize one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.
Data from: Pollen limitation and its influence on natural selection through seed set
Stronger pollen limitation should increase competition among plants, leading to stronger selection on traits important for pollen receipt. The few explicit tests of this hypothesis, however, have provided conflicting support. Using the arithmetic relationship between these two quantities, we show that increased pollen limitation will automatically result in stronger selection (all else equal) although other factors can alter selection independently of pollen limitation. We then test the hypothesis using two approaches. First, we analyze published studies containing information on both pollen limitation and selection. Second, we explore how natural selection measured in one Ontario population of Lobelia cardinalis over three years and two Michigan populations in one year relates to pollen limitation. For the Ontario population we also explore whether pollinator-mediated selection is related to pollen limitation. Consistent with the hypothesis, we find an overall positive relationship between selection strength and pollen limitation both among species and within L. cardinalis. Unexpectedly, this relationship holds even for vegetative traits among species, and was not found in L. cardinalis for pollinator-mediated selection on nearly all trait types.
Data from: Food vibrations: Asian spice sets lips trembling
Szechuan pepper, a widely used ingredient in the cuisine of many Asian countries, is known for the tingling sensation it induces on the tongue and lips. While the molecular mechanism by which Szechuan pepper activates tactile afferent fibres has been clarified, the tingling sensation itself has been less studied, and it remains unclear which fibres are responsible. We investigated the somatosensory perception of tingling in humans to identify the characteristic temporal frequency and compare this to the established selectivity of tactile afferents. Szechuan pepper was applied to the lower lip of participants. Participants judged the frequency of the tingling sensation on the lips by comparing this with the frequencies of mechanical vibrations applied to their right index finger. The perceived frequency of the tingling was consistently at around 50 Hz, corresponding to the range of tactile RA1 afferent fibres. Furthermore, adaptation of the RA1 channel by prolonged mechanical vibration reliably reduced the tingling frequency induced by Szechuan pepper, confirming that the frequency-specific tactile channel is shared between Szechuan pepper and mechanical vibration. Combining information about molecular reactions at peripheral receptors with quantitative psychophysical measurement may provide a unique method for characterizing unusual experiences by decomposing them into identifiable minimal units of sensation.
ScienceDex guides
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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.