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4,694 results for “data analysis”
Data from: Newspaper coverage of maternal health in Bangladesh, Rwanda, and South Africa: a quantitative and qualitative content analysis
Objective: To examine newspaper coverage of maternal health in three countries that have made varying progress towards Millennium Development Goal 5 (MDG 5): Bangladesh (on track), Rwanda (making progress, but not on track) and South Africa (no progress). Design: We analysed each country's leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We quantified the number of maternal health articles published from 1 January 2008 to 31 March 2013. We conducted a content analysis of subset of 190 articles published from 1 October 2010 to 31 March 2013. Results: Bangladesh's The Daily Star published 579 articles related to maternal health from 1 January 2008 to 31 March 2013, compared to 342 in Rwanda's The New Times/The Sunday Times and 253 in South Africa's Sunday Times/The Times over the same time period. The Daily Star had the highest proportion of stories advocating for or raising awareness of maternal health. Most maternal health articles in The Daily Star (83%) and The New Times/The Sunday Times (69%) used a 'human-rights' or 'policy-based' frame compared to 41% of articles from Sunday Times/The Times. Conclusions: In the three countries included in this study, which are on different trajectories towards MDG 5, there were differences in the frequency, tone and content of their newspaper coverage of maternal health. However, no causal conclusions can be drawn about this association between progress on MDG 5 and the amount and type of media coverage of maternal health.
Data from: A meta-analysis of nestedness and turnover components of beta diversity across organisms and ecosystems
The number of studies investigating the nestedness and turnover components of beta diversity has increased substantially, but our general understanding of the drivers of turnover and nestedness remains elusive. Here, we examined the effects of species traits, spatial extent, latitude and ecosystem type on the nestedness and turnover components of beta diversity. From the 99 studies that partition total beta diversity into its turnover and nestedness components, we assembled 269 and 259 data points for the pairwise and multiple site beta-diversity metrics, respectively. Our data covered a broad variation in species dispersal type, body size and trophic position. The data were from freshwater, marine and terrestrial realms, and encompassed geographical areas from the tropics to near polar regions. We used linear modelling as a meta-regression tool to analyse the data.Pairwise turnover, multiple site turnover and total beta diversity all decreased significantly with latitude. In contrast, multiple site nestedness showed a positive relationship with latitude. Beta-diversity components did not generally differ among the realms. The turnover component and total beta diversity increased with spatial extent, whereas nestedness was scale invariant for pairwise metrics. Multiple site beta-diversity components did not vary with spatial extent. Surprisingly, passively dispersed organisms had lower turnover and total beta diversity than flying organisms. Body size showed a relatively weak relationship with beta diversity but had important interactions with trophic position, thus also affecting beta diversity via interactive effects. Producers had significantly higher average pairwise turnover and total beta diversity than carnivores. The present results provide evidence that species turnover, being consistently the larger component of total beta diversity, and nestedness are related to the latitude of the study area and intrinsic organismal features. We showed that two beta-diversity components had generally opposing patterns with regard to latitude. We highlight that beta-diversity partition may give additional insights into the underlying causes of spatial variability in biotic communities compared with total beta diversity alone.
Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica
The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here we address the question whether two highly different methods - Fst outlier analysis and admixture analysis - detect largely the same set of non-neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves Macoma balthica rubra and M. b. balthica descend from two independent trans-Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca 8000 years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak, M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non-neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism (AFLP) markers as significant Fst outliers. Genomic clines analysis detects 31 out of 84 markers as non-neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non-neutral effects.
Data from: Australian native mammals recognise and respond to alien predators: a meta-analysis
Prey naiveté is a failure to recognise novel predators and thought to cause exaggerated impacts of alien predators on native wildlife. Yet there is equivocal evidence in the literature for native prey naiveté towards aliens. To address this, we conducted a meta-analysis of Australian mammal responses to native and alien predators. Australia has the world's worst record of extinction and declines of native mammals, largely due to two alien predators introduced some 150 years ago: the feral cat, Felis catus, and European red fox, Vulpes vulpes. Analysis of 94 responses to predator cues show that Australian mammals consistently recognise alien foxes as a predation threat, possibly because of thousands of years experience with another canid predator, the dingo, Canis lupus dingo. We also found consistent recogntion responses towards feral cats, however in 4 of the 7 studies available, these responses were of risk-taking behaviour rather than antipredator behaviour. Our results suggest that a simple failure to recognise alien predators is not behind the ongoing exaggerated impacts of alien predators in Australia. Instead, our results highlight an urgent need to better understand the appropriateness of antipredator responses in prey towards alien predators in order to understand native prey vulnerability.
Data from: Missed opportunities for HIV testing among patients newly presenting for HIV care at a Swiss university hospital: a retrospective analysis
Objectives: To determine the frequency of missed opportunities (MOs) among patients newly-diagnosed with HIV, risk factors for presenting MOs, and the association between MOs and late presentation to care. Design: Retrospective analysis Setting: HIV outpatient clinic at a Swiss tertiary hospital Participants: Patients aged ≥18 years old newly presenting for HIV care between 2010 and 2015 Measures: Number of medical visits, up to five years preceding HIV diagnosis, at which HIV testing had been indicated, according to Swiss HIV testing recommendations. A visit at which testing was indicated but not performed was considered a MO for HIV testing. Results: Complete records were available for all 201 new patients of whom 51% were male and 33% from sub-Saharan Africa. Thirty patients (15%) presented with acute HIV infection while 119 patients (59%) were late presenters (LPs) (CD4 counts <350 cells/mm3 at diagnosis). Ninety-four patients (47%) had presented at least one MO, of whom 44 (47%) had multiple MOs. MOs were more frequent among individuals from sub-Saharan Africa, men who have sex with men, and patients under follow-up for chronic disease. MOs were less frequent in LPs than non-LPs (42.5% versus 57.5%, P = 0.03). Conclusions: At our centre, 47% of patients presented at least one MO. Whilst our late presentation rate is higher than the national figure of 49.8%, LPs were less likely to experience MOs, suggesting that these patients were diagnosed late through presenting late, rather than through being failed by our hospital. We conclude that, in addition to optimising physician-initiated testing, access to testing must be improved among patients unaware they are at HIV risk and who do not seek health care.
Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis transcriptome datasets, we identified 13,230 intergenic transcripts of which 6,480 can be classified as lincRNAs. Expression of 2,708 lincRNAs was detected by RNA-seq experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and pri-miRNAs. A subset of lincRNA genes show organ-specific expression whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CBP20, and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these 3 proteins are also needed for splicing of a small group of intron-containing lincRNAs.
Data from: Occurrence and phylogenetic analysis of bovine respiratory syncytial virus in outbreaks of respiratory disease in Norway
Background: Bovine respiratory syncytial virus (BRSV) is one of the major pathogens involved in the bovine respiratory disease (BRD) complex. The seroprevalence to BRSV in Norwegian cattle herds is high, but its role in epidemics of respiratory disease is unclear. The aims of the study were to investigate the etiological role of BRSV and other respiratory viruses in epidemics of BRD and to perform phylogenetic analysis of Norwegian BRSV strains. Results: BRSV infection was detected either serologically and/or virologically in 18 (86%) of 21 outbreaks and in most cases as a single viral agent. When serology indicated that bovine coronavirus and/or bovine parainfluenza virus 3 were present, the number of BRSV positive animals in the herd was always higher, supporting the view of BRSV as the main pathogen. Sequencing of the G gene of BRSV positive samples showed that the current circulating Norwegian BRSVs belong to genetic subgroup II, along with other North European isolates. One isolate from an outbreak in Norway in 1976 was also investigated. This strain formed a separate branch in subgroup II, clearly different from the current Scandinavian sequences. The currently circulating BRSV could be divided into two different strains that were present in the same geographical area at the same time. The sequence variations between the two strains were in an antigenic important part of the G protein. Conclusion: The results demonstrated that BRSV is the most important etiological agent of epidemics of BRD in Norway and that it often acts as the only viral agent. The phylogenetic analysis of the Norwegian strains of BRSV and several previously published isolates supported the theory of geographical and temporal clustering of BRSV.
Data from: Three-month modified Rankin Scale as a determinant of five-year cumulative costs after ischemic stroke: an analysis of 11,136 patients in Korea
Objective: Stroke is a devastating and costly disease; however, there is a paucity of information on long-term costs and on how they differ according to 3-month modified Rankin scale (mRS), which is a primary outcome variable in acute stroke intervention trials. Methods: We analyzed a prospective multicenter stroke registry (Clinical Research Collaboration for Stroke in Korea) database through linkage with claims data from the National Health Insurance Service with follow up to December 2016. Healthcare expenditures were converted into daily cost individually, and annual and cumulative costs up to 5 years were estimated and compared according to the 3-month mRS. Results: Between January 2011 and November 2013, 11,136 patients were enrolled in the study. The mean age was 68 years, and 58% were men. The median follow-up period was 3.9 years (range 0–5 years). Mean cumulative cost over 5 years was $117,576 US dollar (USD); the cost in the first year after stroke was the highest ($38,152 USD), which increased markedly from the cost a year before stroke ($8,718 USD). The mean 5-year cumulative costs differed significantly according to the 3-month mRS (P<.001); the costs for a 3-month mRS score of 0 or 5 were $53,578 USD and $257,486 USD, respectively. Three-month mRS was an independent determinant of long-term costs after stroke. Conclusions: We shows that 3-month mRS plays an important role in the prediction of long-term costs after stroke. Such estimates relating to 3-month mRS categories may be valuable when undertaking health economic evaluations related to stroke care.
Data from: Anemia and related nutrient deficiencies after Roux-en-Y gastric bypass surgery: a systematic review and meta-analysis
Objective: To obtain a pooled risk estimate on the long-term impact of anaemia and related nutritional deficiencies in patients receiving Roux-en-Y gastric bypass (RYGB) surgery. Design: Systematic review and meta-analysis. Data sources: MEDLINE, EMBASE and Cochrane databases were searched to identify English reports published before 16 May 2014. Eligibility criteria: Articles with case numbers >100, follow-up period >12 months, and complete data from both before and after surgery were selected. Outcomes of interest were changes in baseline measurements of proportion of patients with anaemia, by haemoglobin, haematocrit, ferritin, iron, vitamin B12 and folate levels. Data collection and analysis: Two reviewers independently reviewed data and selected six prospective and nine retrospective studies with a total of 5909 patients. A random effect model with inverse variance weighting was used to calculate summary estimates of outcomes at 6, 12, 24 and 36 months postoperatively. Results: Proportion of patients with anaemia was 12.2% at baseline, which, respectively, increased to 20.9% and 25.9% at 12 and 24 months follow-up, consistent with decreases in haemoglobin and haematocrit levels. Although the serum iron level did not change substantially after surgery, the frequency of patients with ferritin deficiency increased from 7.9% at baseline to 13.4% and 23.0% at 12 and 24 months, respectively, postoperation. Vitamin B12 deficiency increased from 2.3% at baseline to 6.5% at 12 months after surgery in those subjects receiving RYGB. There was no obvious increase in folate deficiency. Conclusions: RYGB surgery is associated with an increased risk of anaemia and deficiencies of iron and vitamin B12, but not folate. Ferritin is more sensitive when serum iron level is within normal range.
Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)
Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within-river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among-drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat-specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.
Data from: Restoration as mitigation: analysis of stream mitigation for coal mining impacts in southern Appalachia
Compensatory mitigation is commonly used to replace aquatic natural resources being lost or degraded but little is known about the success of stream mitigation. This article presents a synthesis of information about 434 stream mitigation projects from 117 permits for surface mining in Appalachia. Data from annual monitoring reports indicate that the ratio of lengths of stream impacted to lengths of stream mitigation projects were < 1 for many projects, and most mitigation was implemented on perennial streams while most impacts were to ephemeral and intermittent streams. Regulatory requirements for assessing project outcome were minimal; visual assessments were the most common and 97% of the projects reported suboptimal or marginal habitat even after 5 years of monitoring. Less than a third of the projects provided biotic or chemical data; most of these were impaired with biotic indices below state standards and stream conductivity exceeding federal water quality criteria. Levels of selenium known to impair aquatic life were reported in 7 of the 11 projects that provided Se data. Overall, the data show that mitigation efforts being implemented in southern Appalachia for coal mining are not meeting the objectives of the Clean Water Act to replace lost or degraded streams ecosystems and their functions.
Data from: Analysis of animal accelerometer data using hidden Markov models
Use of accelerometers is now widespread within animal biologging as they provide a means of measuring an animal's activity in a meaningful and quantitative way where direct observation is not possible. In sequential acceleration data, there is a natural dependence between observations of behaviour, a fact that has been largely ignored in most analyses. Analyses of acceleration data where serial dependence has been explicitly modelled have largely relied on hidden Markov models (HMMs). Depending on the aim of an analysis, an HMM can be used for state prediction or to make inferences about drivers of behaviour. For state prediction, a supervised learning approach can be applied. That is, an HMM is trained to classify unlabelled acceleration data into a finite set of pre-specified categories. An unsupervised learning approach can be used to infer new aspects of animal behaviour when biologically meaningful response variables are used, with the caveat that the states may not map to specific behaviours. We provide the details necessary to implement and assess an HMM in both the supervised and unsupervised learning context and discuss the data requirements of each case. We outline two applications to marine and aerial systems (shark and eagle) taking the unsupervised learning approach, which is more readily applicable to animal activity measured in the field. HMMs were used to infer the effects of temporal, atmospheric and tidal inputs on animal behaviour. Animal accelerometer data allow ecologists to identify important correlates and drivers of animal activity (and hence behaviour). The HMM framework is well suited to deal with the main features commonly observed in accelerometer data and can easily be extended to suit a wide range of types of animal activity data. The ability to combine direct observations of animal activity with statistical models, which account for the features of accelerometer data, offers a new way to quantify animal behaviour and energetic expenditure and to deepen our insights into individual behaviour as a constituent of populations and ecosystems.
Data from: A meta-analysis of non-consumptive predator effects in arthropods: the influence of organismal and environmental characteristics
Non-consumptive effects (NCEs) – changes in prey behavior or physiology in response to predator threat – are common and can be as strong as consumptive effects. However, our knowledge of NCEs in arthropod systems is lacking. Factors related to study organism and environment have the potential to influence the occurrence and magnitude of NCEs in arthropod systems. While factors such as coevolutionary history of natural enemies and their prey, predator cue, predator or prey feeding mode, and refuge availability have been theoretically and empirically examined, no trends have been proposed for arthropods. We compiled 62 studies, yielding 128 predator–prey interactions, which explicitly examined NCEs in experiments where arthropods were identified to species, using a previously published database of papers from 1990 to 2005 and a new database of papers published from 2006 to 2015. Using these data, we conducted a meta-analysis to explore the influence of organismal and environmental characteristics on the magnitude of predator NCEs. Our analysis addressed the following three questions. 1) Does predator–prey coevolution give rise to stronger NCEs than when predator and prey species did not coevolve? 2) What influence does habitat type and refuge availability have on NCEs? 3) How do predator characteristics (cue type, hunting mode and life stage) and prey characteristics (mobility, life stage, specialization, gregariousness and feeding mode) influence NCEs? We found that while NCEs were similar across most measured characteristics, NCEs on prey activity were significantly stronger when predator and prey shared an evolutionary history. Our results support growing evidence that NCEs have a negative effect on prey traits and that behavioral NCEs are stronger than physiological ones. Additional studies are needed to be confident in any emerging patterns, therefore we identify key gaps in the literature on NCEs in arthropod systems and discuss ideas for moving forward.
Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn
Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark–recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1–7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1–10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples >7 days old and estimate that a sampling interval of 4–7 days in summer conditions (i.e. extreme heat and exposure to UV light) will achieve desired sample sizes for mark–recapture analysis while also maximizing efficiency.
Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
Data from: Combining micro-volume isotope analysis and numerical simulation to reproduce fish migration history
1. Tracking the movement of migratory fish is of great importance for efficient conservation, although this has been technically difficult to achieve in small fish to which artificial tags cannot be attached. 2. We show that migration history can be reproduced by combining high-resolution otolith stable oxygen isotope ratio (δ18O) analysis and numerical simulation. 3. High-precision micro-milling and micro-volume carbonate analysing systems had the remarkable capability of extracting the otolith δ18O profiles with 10–30 days resolution. Furthermore, reasonable movements were reproduced by searching the routes consistent with the otolith δ18O profile, using an individual-based model with random swimming behaviour. 4. This method will be a valuable alternative to tagging and electronic loggers for revealing migration routes in early life stages, thereby providing crucial information to understand population structures and the environmental cause of recruitment variabilities, and to validate and improve fish movement models.
Data from: Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10 000 nests
Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high or low predation risk, and whether low-risk areas increased, and high-risk areas decreased in nest density the following year. We created kernel density maps of successful and unsuccessful nests in consecutive years and found no correlation in predation risk and no evidence for adaptive shifts, although nest density was correlated between years. We also examined between-year correlations in nest density and nest success at three smaller spatial scales: individual nesting fields (10–28 ha), 16-ha grid cells and 4-ha grid cells. Here, results were similar across all scales: we found no evidence for year-to-year correlation in nest success but found strong evidence that nest density was correlated between years, and areas of high nest success increased in nest density the following year. Prior research in this system has demonstrated that areas of high nest density have higher nest success, and taken together, our results suggest that ducks may adaptively select nest sites based on the local density of conspecifics, rather than the physical location of last year's nest. In unpredictable environments, current cues, such as the presence of active conspecific nests, may be especially useful in selecting nest sites. The cues birds use to select breeding locations and successfully avoid predators deserve continued attention, especially in systems of conservation concern.
Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinct clusters of loci, each providing an estimate of the species tree that matches previously proposed resolutions of the marsupial phylogeny. We also identify a well supported placement for the enigmatic marsupial moles (Notoryctes) that contradicts previous molecular estimates but is consistent with morphological evidence. The pattern of gene-tree variation across tree-space is characterized by changes in information content, GC content, substitution-model adequacy, and signatures of purifying selection in the data. In a simulation study, we show that incomplete lineage sorting can explain the division of loci into the two tree-topology clusters, as found in our phylogenomic analysis of marsupials. We also demonstrate the potential benefits of minimizing uncertainty from phylogenetic conflict for molecular dating. Our analyses reveal that Australasian marsupials appeared in the early Paleocene, whereas the diversification of present-day families occurred primarily during the late Eocene and early Oligocene. Our methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome-scale data.
Data from: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach
In recent years, the explosion of affordable next generation sequencing technology has provided an unprecedented opportunity to conduct genome-wide studies of adaptive evolution in organisms previously lacking extensive genomic resources. Here, we characterise genome-wide patterns of variability and differentiation using pooled DNA from eight populations of the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and pond environments. We developed a novel genome complexity reduction protocol, defined as paired-end double restriction-site associated DNA (PE dRAD), to maximise read coverage at sequenced locations. This allowed us to identify over 114,000 short consensus sequences and 15,000 SNPs throughout the genome. A total of 6,834 SNPs mapped to a single position on the related three-spined stickleback genome, allowing the detection of genomic regions affected by divergent and balancing selection, both between species and between freshwater and marine populations of the nine-spined stickleback. Gene ontology (GO) analysis revealed 15 genomic regions with elevated diversity, enriched for genes involved in functions including immunity, chemical stimulus response, lipid metabolism and signalling pathways. Comparisons of marine and freshwater populations identified nine regions with elevated differentiation related to kidney development, immunity and MAP kinase pathways. In addition, our analysis revealed that a large proportion of the identified SNPs mapping to LG XII are likely to represent alternative alleles from divergent X and Y chromosomes, rather than true autosomal markers following Mendelian segregation. Our work demonstrates how population-wide sequencing and combining inter- and intra-specific RAD analysis can uncover genome-wide patterns of differentiation and adaptations in a non-model species.
Data from: Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation
BACKGROUND: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. RESULTS: We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern "switch gene" optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. CONCLUSIONS: This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.
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.