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MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics
<p><strong>MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics</strong></p> <p>Rémi Allio<sup>1</sup>, Alex Schomaker-Bastos<sup>2,†</sup>, Jonathan Romiguier<sup>1</sup>, Francisco Prosdocimi<sup>2</sup>, Benoit Nabholz<sup>1</sup>, and Frédéric Delsuc<sup>1</sup></p> <p><sup>1</sup><em>Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France.</em></p> <p><sup>2</sup><em>Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.</em></p> <p><sup>†</sup><em> In Memoriam (08/01/2015) </em></p> <p> </p> <p><em><strong>Correspondence</strong></em></p> <p>Rémi Allio</p> <p>Email: <a href="mailto:remi.allio@umontpelier.fr">remi.allio@umontpellier.fr</a></p> <p>Frédéric Delsuc</p> <p>Email: <a href="mailto:frederic.delsuc@umontpellier.fr">frederic.delsuc@umontpellier.fr</a></p> <p> </p> <p><strong><em>Running head</em></strong></p> <p>Mitochondrial signal from UCE capture data</p> <p> </p> <p><strong>Abstract</strong><strong> </strong></p> <p>Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routinely inferring phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries allowing confirming species identification using COI barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By leveraging the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mito-nuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing in diverse taxa.</p> <p> </p> <p><strong><em>Figures & Tables</em></strong></p> <p><strong>Figure 1.</strong> Conceptualization of the pipeline used to assemble and extract UCE and mitochondrial signal from ultraconserved element sequencing data.</p> <p><strong>Figure 2</strong>. Comparison of the efficiency of the assemblers in terms of: A) computational time, B) number of potentially mitochondrial contigs identified, and C) number of mitochondrial genes annotated. Violin plots reflect the data distribution with a horizontal line indicating the median. Note that for the three metagenomic assemblers, 5 CPUs were used compared to 35 CPUs for Trinity. Plots were obtained using PlotsOfData (Postma & Goedhart 2019).</p> <p><strong>Figure 3.</strong> Phylogenomic relationships of ants (Formicidae). AA) Mito-nuclear phylogenetic differences among subfamily relationships based on the UCE and mtDNA supermatrices obtained with the assembler MetaSPAdes assembler. Clades corresponding to subfamilies were collapsed. Inter-subfamily relationships with UFBS < 95% were collapsed. Non-maximal node support values are reported. B) The topology obtained reflects the results of phylogenetic analyses based on the amino acid mitochondrial supermatrix (using MetaSPAdes as assembler). Histograms reflect the percent of UCEs (light grey) and mitochondrial genes (dark grey) recovered for each species. Illustrative pictures (*): <em>Diacamma sp</em>. (Ponerinae; top left), <em>Formica sp</em>. (Formicinae; top right), and <em>Messor barbarus </em>(Myrmicinae; bottom right).</p> <p><strong>Table 1. </strong>Summary statistics on assembly results according to the assembler used. The values are averages over the 501 assemblies, except for the assembly time, which is a median value. The two tables report specific statistics for A) ultraconserved elements data, and B) mitochondrial data. Note that 35 CPUs were used for Trinity whereas 5 CPUs were used for other assemblers.</p> <p><strong>Table 2.</strong> Statistical comparison between the performances of the different assemblers. Statistical significance was estimated with a paired non parametric test (paired wilcoxon test). *** = <em>p</em><0.001; ** = <em>p</em><0.01; * = <em>p</em><0.05; NS = <em>p</em>>0.05; and (+)/(-) is the result of the comparison between the row and the column.</p> <p> </p> <p><strong><em>Appendices</em></strong></p> <p><strong>Appendix S1.</strong> List of the 501 UCE libraries (SRA accessions) and associated metadata.</p> <p><strong>Appendix S2.</strong> Summary statistics on mitochondrial signal recovered per species and depending on the assembler used. The table provides the number of contigs and genes recovered with MitoFinder and the size of each annotated gene.</p> <p><strong>Appendix S3.</strong> Summary statistics of barcoding analyses. Detailed results for both BOLDsystem and Megablast analyses are provided for each CO1 recovered with MitoFinder using MetaSPAdes.</p> <p><strong>Appendix S4.</strong> Detailed results of tree distance analyses realized with Dquad (Ranwez, Criscuolo, & Douzery 2010). Trees obtained with each assembler with mitochondrial amino acid supermatrix, mitochondrial nucleotide supermatrix, and UCE nucleotide supermatrix were compared with each others.</p> <p><strong>Appendix S5</strong>. List of Genbank accession numbers for newly generated mitchondrial contigs.</p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>Assembly_results.tar.gz</strong> Contains all contigs obtained for each species with the different assemblers implemented in MitoFinder.</p> <p><strong>MitoFinder_annotations.tar.gz</strong> Contains MitoFinder annotations for each species. (based on the contigs obtained with MetaSPAdes)</p> <p><strong>UCE_results.tar.gz</strong> Contains all annotated UCE obtained for each species after UCE identification with PHYLUCE. (MetaSPAdes)</p> <p><strong>Final_mtDNA_alignments.tar.gz</strong> Contains the final mitochondrial gene alignments. (MetaSPAdes)</p> <p><strong>Final_UCE_alignments.tar.gz</strong> Contains the final UCE alignments. (MetaSPAdes)</p> <p><strong>Final_mtDNA_matrices.tar.gz</strong> Contains the final mi tochondrial supermatrices (AA and NT) used for the phylogenetic analyses. (MetaSPAdes)</p> <p><strong>Metaspades_final_UCE_matrix.phy</strong> The final UCE supermatrix used for the phylogenetic analyses. (MetaSPAdes)</p>
Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS
<p>Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS data for the Applied Medical Science MSci Research Project. </p>
MarTREC Data Set for Report: Large Scale Evaluation of Erosion Resistance of Biocementation against Bridge Scour and Roadway Shoulder Erosion
<p>Data set used for the report, "Large Scale Evaluation of Erosion Resistance of Biocementation against Bridge Scour and Roadway Shoulder Erosion". The purpose of the report was to develop an alternative approach for armoring the riverbed with biocementation through MICP to mitigate soil erosion. Long-term erosion exposed to outdoor environment, rainfall induced erosion, and accelerated erosion were conducted on MICP-treated samples to prove the feasibility of the MICP technique for potential applications in prevention of bridge scour and road shoulder erosion. The experimental work and discussion about the testing results indicated that exposing to outdoor environment could result in sharp decrease on UCS for MICP-treated samples. But the MICP-treated samples had better resistance to rainfall induced erosion. The bio-surface treatment gave significant help for cement-treated samples to resist accelerated erosion and water absorption, especially the multiple bio-surface treatments method, no erosion could be measured and 5% lower water absorption was achieved after the cement-treated sample was triple treated by bio-surface treatments. The pure MICP-treated samples were also good at resisting accelerated erosion and water absorption. Furthermore, fiber addition and multiple MICP treatments could improve their resistance. The maximum erosion rate of single MICP-treated samples reduced from 0.16 mm/min to 0 mm/min after triple MICP treatment cycles applied on the samples. Extra MICP treatments on soil samples improved the resistance to water absorption significantly. The triple MICP-treated samples achieved a 6% lower absorption than single-treated samples. All these results indicated that the bio-mediated particulate material based on MICP can provide an effective solution for problematic cases of sandy soil in prevention of bridge scour and road shoulder erosion.</p>
A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub
<p>The data set schema, fields description, and analysis scripts are in the GitHub artifact repository.</p> <p>https://github.com/linncy/icsme2020-docker-study</p> <p> </p> <p>@inproceedings{LinICSME20,<br>author={Changyuan Lin and Sarah Nadi and Hamzeh Khazaei},<br>title={A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub},<br>booktitle={Proceedings of the 36th IEEE International Conference on Software Maintenance and Evolution (ICSME)},<br>year={2020},<br>url_Paper={https://www.dropbox.com/s/3bktcmdr7rlw1ic/LinICSME20.pdf}<br>}</p>
Companion for "Measuring Phenology Uncertainty with Large Scale Image Processing"
<p>This is the software and dataset companion for the paper entitled "Measuring Phenology Uncertainty with Large Scale Image Processing". Further instructions can be found in the README.org file.</p>
RadioGx: Analysis of Large-Scale Radio-Genomic Data
<p>This dataset contains an index of RadioSet objects available for download using the RadioGx R package. Each of the RSet objects are hosted in their own separate Zenodo uploads. The RadioGx R package is available for download from Bioconductor.</p>
Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes
<p>The widespread legalization of <i>Cannabis</i> has opened the industry to using contemporary analytical techniques for chemotype analysis. Chemotypic data has been collected on a large variety of oil profiles inherent to the cultivars that are commercially available. The unknown gene regulation and pharmacokinetics of dozens of cannabinoids offer opportunities of high interest in pharmacology research. Retailers in many medical and recreational jurisdictions are typically required to report chemical concentrations of at least some cannabinoids. Commercial cannabis laboratories have collected large chemotype datasets of diverse <i>Cannabis</i> cultivars. In this work a data set of 17,600 cultivars tested by Steep Hill Inc., is examined using machine learning techniques to interpolate missing chemotype observations and cluster cultivars into groups based on chemotype similarity. The results indicate cultivars cluster based on their chemotypes, and that some imputation methods work better than others at grouping these cultivars based on chemotypic identity. Due to the missing data and to the low signal to noise ratio for some less common cannabinoids, their behavior could not be accurately predicted. These findings have implications for characterizing complex interactions in cannabinoid biosynthesis and improving phenotypical classification of <i>Cannabis</i> cultivars.</p>
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
<p>This page links to the data associated with the publication "ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets ". The data have been curated and analyzed using our open-source R package, ToxicoGx (https://github.com/bhklab/ToxicoGx) and are available publicly in the ToxicoDB web application (www.toxicodb.ca). Please see the included DOIs below, or download the .csv file which contains the names, dates and DOIs of all datasets listed here.</p> <p>The TGGATES data was generated by Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023.<br> <br> Data:</p> <ul> <li>TGGATEs humanldh (<a href="https://doi.org/10.5281/zenodo.3762812">https://doi.org/10.5281/zenodo.3762812</a>)</li> <li>TGGATEs humandna (<a href="https://doi.org/10.5281/zenodo.4024859">https://doi.org/10.5281/zenodo.4024859</a>)</li> <li>TGGATEs ratldh (<a href="https://doi.org/10.5281/zenodo.3762817">https://doi.org/10.5281/zenodo.3762817</a>)</li> <li>TGGATEs ratdna (<a href="https://doi.org/10.5281/zenodo.4024918">https://doi.org/10.5281/zenodo.4024918</a>)</li> </ul> <p>This Drug Matrix data was generated by Ganter B, Snyder RD, Halbert DN, Lee MD. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics [Internet]. 2006 Oct;7(7):1025–1044. Available from: http://dx.doi.org/10.2217/14622416.7.7.1025 PMID: 17054413.</p> <p>Data:</p> <ul> <li>Drug Matrix (<a href="https://doi.org/10.5281/zenodo.3766569">https://doi.org/10.5281/zenodo.3766569</a>)</li> </ul>
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs rat dataset)
<p>This data was generated by Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023. The data have been curated and analyzed using our open-source R package, <em>ToxicoGx</em> (<a href="https://github.com/bhklab/ToxicoGx">https://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html</a>), and are available publicly in the <em>ToxicoDB </em>web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).</p>
Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems
Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.
Data from: Robust inference on large-scale species habitat use with interview data: the status of jaguars outside protected areas in Central America
Evaluating range-wide habitat use by a target species requires information on species occurrence over broad geographic regions, a process made difficult by species rarity, large spatiotemporal sampling domains, and imperfect detection. We address these challenges in an assessment of habitat use for jaguars (Panthera onca) outside protected areas in Central America. Occurrence records were acquired within 12 putative corridors using interviews with knowledgeable corridor residents. We developed a Bayesian hierarchical occupancy model to gain robust inference, allowing for heterogeneity introduced in the sampling process over space and time, using records of jaguar occurrence prone to false positives and false negatives. Probability of false detection of jaguars increased with the number of interviews conducted per unit (from 5.42% to 7.74% given <4 and ≥4 observers per unit). True probability of detection (mean=0.58) increased with the number of days interviewees spent in a survey unit per year. Failing to account for false positives biased predicted habitat use high (˜1.8x), especially where occurrence records were sparse. Probability of site use by jaguars increased with greater forest cover, prey richness, and distance from human settlements, and decreased with greater agricultural cover, elevation, and distance from protected areas. Site use probabilities averaged 0.15-0.97 by corridor, providing relatively fine-scale resolution of predicted jaguar occurrence consistent with known patterns of jaguar gene flow across Central America. Model validation, accounting for both false positives and negatives in the observation process, indicated moderate correspondence between model-predicted observations and actual observations for withheld data (0.65, 95% CRI 0.59–0.71), with sensitivity and specificity rates of 0.69 (0.61 – 0.77) and 0.59 (0.50 – 0.68), respectively. These results demonstrate that reliable predictions can be achieved despite the complexity of large-scale, interview-based analyses of species occurrence. Synthesis and applications. Our Bayesian hierarchical occupancy model accommodated heterogeneity caused by typical sampling inequities and idiosyncrasies associated with interview data, yielding robust estimates of jaguar habitat use. Our approach is applicable to any wide-ranging and readily identifiable species and has particular utility for rare species in human-dominated landscapes where traditional survey techniques (e.g., camera traps) may be impractical.
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs human dataset)
<p>This data was generated by Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023. The data have been curated and analyzed using our open-source R package, <em>ToxicoGx</em> (<a href="http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html">http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html</a>), and are available publicly in the <em>ToxicoDB </em>web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).</p>
Comparability of Raman Spectroscopic Configurations: A Large Scale Cross-Laboratory Study
<p><strong>Slightly processed raw data for the paper 'Comparability of Raman Spectroscopic Configurations: A Large Scale Cross-Laboratory Study'</strong></p> <ul> <li>The processing include a spike removal to allow an interpolation to a common wavenumber axis.</li> <li>Always three files belong to each other: wavenumber axis file (wx_XYZ), spectral intensity file (spec_XYZ) and metadata file (meta_XYZ). The ‘XYZ’ refers to the samples measured (see the publication and its SI for details).</li> </ul>
Drivers of large-scale geographical variation in sexual systems of woody plants
<p><b>Aim: </b>Sexual systems strongly influence angiosperm evolution, and play important roles in community assembly and species responses to climate change. However, geographical variation in proportions of different sexual systems (dioecy, monoecy, and hermaphroditism) in response to changes in climate, life-history traits and evolutionary age remains poorly understood. Here, we map the geographical variation in proportions of different sexual systems and hypothesize that the prevalence of hermaphrodites increases with aridity due to their advantages in colonizing harsh environment, whereas dioecy is most successful in humid regions with tall-canopy vegetation and old floras.</p> <p><b>Location: </b>China</p> <p><b>Time period: </b>Current</p> <p><b>Major taxa studied:</b> Woody angiosperms</p> <p><b>Methods: </b>Using data on sexual systems and distributions of 10,449 woody species in China, we estimated the proportions of different sexual systems in local floras (50 × 50 km grid cells). Spatial linear models, phylogenetic general linear models and structural equation models were used to compare the relative influences of climate, plant height and evolutionary age on geographical variation in proportions of different sexual systems.</p> <p><b>Results: </b>We found contrasting geographical patterns in the proportions of different sexual systems. The proportions of dioecy and monoecy increased with plant height and were highest in humid regions with older floras, while that of hermaphroditism decreased with plant height and was highest in arid regions with younger floras. Plant height was the strongest correlate of sexual system frequency. Climate influenced sexual system frequency both directly and indirectly via its effects on plant height.</p> <p><b>Main conclusions: </b>Our study provides the first continuous map of sexual system composition in woody floras over a large spatial scale. Our findings suggest that mature plant height, reflecting plant longevity, dominates geographical variation in sexual systems and that the proportions of different sexual systems in local floras may reflect their correlated evolution with traits in response to climate changes.</p>
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
Raw data for predicting sample success for large-scale ancient DNA studies on marine mammals
<p>In recent years, non-human ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, the skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.</p>
Data from: Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats (Eidolon helvum)
Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) provide rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.
Data from: Small- to large-scale patterns of ground-dwelling spider (Araneae) diversity across northern Canada
We examined how Arctic spider (Araneae) biodiversity is distributed at multiple spatial scales in Northern Canada using a standardized hierarchical sampling design. We investigated which drivers, environmental or spatial, influence the patterns observed. Spatial patterns of species richness and composition of Arctic spiders were assessed in 12 sites located in Arctic, Subarctic, and North-Boreal regions, across 30 degrees of latitude and 80 degrees of longitude. Variation of diversity was partitioned in relation to multiple environmental and spatial drivers of diversity patterns. Over 23, 000 adult spiders, representing 306 species in 14 families, were collected in Northern Canada, with 107 species (35% of the total species collected) representing new Territorial or Provincial records. Spider diversity was structured at the regional scale across ecoclimatic regions but not with latitude. Longitudinal patterns of spider diversity across Canada may be explained by post-glacial dispersal. At local scales, diversity was non-randomly distributed, and possibly limited by biotic interactions. We recommend the use of ecoclimatic regions as a framework for conservation of biodiversity in Northern Canada and spiders as useful bioindicators which can help us understand the effects of climate change across ecoclimatic regions of northern Canada.
Data from: Camera-based occupancy monitoring at large scales: power to detect trends in grizzly bears across the Canadian Rockies
Monitoring carnivores is critical for conservation, yet challenging because they are rare and elusive. Few methods exist for monitoring wide-ranging species over large spatial and sufficiently long temporal scales to detect trends. Remote cameras are an emerging technology for monitoring large carnivores around the world because of their low cost, non-invasive methodology, and their ability to capture pictures of species of concern that are difficult to monitor. For species without uniquely identifiable spots, stripes, or other markings, cameras collect detection/non-detection data that are well suited for monitoring trends in occupancy as its own independent useful metric of species distribution, as well as an index for abundance. As with any new monitoring method, prospective power analysis is essential to ensure meaningful trends can be detected. Here we test camera-based occupancy models as a method to monitor changes in occupancy of a threatened species, grizzly bears (Ursus arctos), at large landscape scales, across 5 Canadian national parks (~21,000 km2). With n = 183 cameras, the top occupancy model estimated regional occupancy to be 0.79 across all 5 parks. We evaluate the statistical power to detect simulated 5–40% declines in occupancy between two sampling years and test applied questions of how power is affected by the spatial scale of interest (park level vs. regional level), the number of cameras deployed, and duration of camera deployment. We also explore several ecological mechanisms (i.e., spatial patterns) of decline in occupancy, and examine how power changes when focusing only on grizzly bears family groups. As hypothesized, statistical power increased with the number of cameras and with the number of days deployed. Power was unaffected, however, by the ecological mechanisms of decline, indicating that our systematic sampling design can detect a decline regardless of whether occupancy declined due to range edge attrition, ecological trap or other mechanisms. Despite their lower occupancy, power was similarly high for grizzly bear family groups compared to grizzly bears in general. We highlight which study design attributes contributed to high power and we provide advice for establishing cost-effective camera-based programs for monitoring large carnivore occupancy at large spatial scales.
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.