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Fig. 4. A in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Fig. 4. A. Live coloration of Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838) (photo: E. Vigneux). B. Live coloration of M. ustulatum (Nobili, 1899) (photo: P. Keith).
Genetic data and underlying taxa and GenBank sources of diatoms used in phylogenetic analysis for the diatom genus Nupela
<p>Supplementary material for the manuscript: Kulikovskiy M., Maltsev Y., Glushchenko A., Gusev E., Kapustin D., Kuznetsova I., Kociolek J.P. Preliminary molecular phylogeny of the diatom genus <em>Nupela</em> with the description of a new species and consideration of the interrelationships of taxa in the suborder Neidiineae D.G. Mann sensu E.J. Cox. Fottea</p> <p>Molecular investigation of diatom genera <em>Nupela</em> and <em>Brachysira</em> is conducted using strains from Indonesia and Vietnam. New species from the genus <em>Nupela indonesica</em> sp. nov. is described using combined approach. <em>Nupela lesothensis</em> (Schoeman) Lange-Bertalot is investigated using molecular data too. Phylogenetic analysis shows that <em>Nupela</em> and <em>Brachysira</em> are not closest genera. Morphology of <em>Nupela</em> and it differences from <em>Brachysira</em> is discussed. The genus <em>Nupela</em> is differs from all other diatom taxa by having coalescent hymenes ouside of areolae but not inside. Facultative development of raphe between different <em>Nupela</em> species is discussed.<br> SUPPLEMENT S1. Taxa and DNA sequence data used in phylogenetic analysis.<br> SUPPLEMENT S2. Final alignment of 2-gene DNA sequence data used for phylogenetic analysis in FASTA format.<br> SUPPLEMENT S3. Maximum Likelihood tree of <em>Nupela</em> species (indicated in bold) constructed from a concatenated alignment of 163 partial rbcL and partial 18S rDNA sequences of 1806 characters. Values near the horizontal lines (slash) are bootstrap support from RAxML analyses (<50 are not shown). Species from the centric diatoms were used as an outgroup. Families indicated according COX (2015).</p>
Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)
<p>Early life phenotypic data from three <em>Betula pendula</em> common garden experiments spread across the species latitudinal range in Europe.</p>
Summary statistics data for "Genetic Analyses Support the Contribution of mRNA N6-methyladenosine (m6A) Modification to Human Diseases Heritability"
<p>We included the summary statistics data associated with our manuscript "<strong>Genetic Analyses Support the Contribution of mRNA <em>N</em><sup>6</sup>-methyladenosine (m<sup>6</sup>A) Modification to Human Diseases Heritability". </strong></p> <p>We also included the newly imputed genotype data for the 60 YRI individuals involved in our study, the joint m<sup>6</sup>A peaks tested (locations of the molecular phetnotype in BED12 format) and normalized log odds ratio (enrichment) of these joint peaks (molecular phenotype data). </p>
GECCO Industrial Challenge 2017 Dataset: A water quality dataset for the 'Monitoring of drinking-water quality' competition at the Genetic and Evolutionary Computation Conference 2017, Berlin, Germany.
<p>Dataset of the 'Industrial Challenge: Monitoring of drinking-water quality' competition hosted at The Genetic and Evolutionary Computation Conference (GECCO) July 15th-19th 2017, Berlin, Germany</p> <p> </p> <p>The task of the competition was to develop an anomaly detection algorithm for a water- and environmental data set.</p> <p> </p> <p>Included in zenodo: </p> <p>- dataset of water quality data</p> <p>- additional material and descriptions provided for the competition</p> <p> </p> <p>The competition was organized by:</p> <p>M. Friese, J. Stork, A. Fischbach, M. Rebolledo, T. Bartz-Beielstein (TH Köln)</p> <p> </p> <p>The dataset was provided and prepared by:</p> <p>Thüringer Fernwasserversorgung,</p> <p>IMProvT research project (S. Moritz)</p> <p><br> </p> <p>Industrial Challenge: Monitoring of drinking-water quality</p> <p> </p> <p>Description:</p> <p>Water covers 71% of the Earth's surface and is vital to all known forms of life. The provision of safe and clean drinking water to protect public health is a natural aim. Performing regular monitoring of the water-quality is essential to achieve this aim.</p> <p>Goal of the GECCO 2017 Industrial Challenge is to analyze drinking-water data and to develop a highly efficient algorithm that most accurately recognizes diverse kinds of changes in the quality of our drinking-water.</p> <p> </p> <p>Submission deadline:</p> <p>June 30, 2017</p> <p>Official webpage:</p> <p><a href="http://www.spotseven.de/gecco-challenge/gecco-challenge-2017/">http://www.spotseven.de/gecco-challenge/gecco-challenge-2017/</a></p>
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs
<p>The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated the inner workings of RNAP, and mutations in genes encoding RNAP drive adaptation of <i>Escherichia coli</i> to many health- and industry-relevant environments, yet a paucity of systematic analyses has hampered our understanding of the fitness benefits and trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and confer insensitivity to killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships <i>in vivo</i> and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.</p>
Data from: Genetic and environmental canalization are not correlated among altitudinally varying populations of Drosophila melanogaster
<p>Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves is limited, despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as a correlated response to environmental canalization (congruence model). Yet, empirical evidence has not consistently supported predictions of a correlation between genetic and environmental canalization. In a recent study, a population of <em>Drosophila </em>adapted to high altitude showed evidence of genetic decanalization relative to those from low altitudes. Using strains derived from these populations, we tested if they varied for multiple aspects of environmental canalization We observed the expected differences in wing size, shape, cell (trichome) density and mutational defects between high- and low-altitude populations. However, we observed little evidence for a relationship between measures of environmental canalization with population or with defect frequency. Our results do not support the predicted association between genetic and environmental canalization.</p>
Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes
Prior to 1900, coyotes (Canis latrans) were restricted to the western and central regions of North America, but by the early 2000s coyotes became ubiquitous throughout the eastern United States. Information regarding morphological and genetic structure of coyote populations in the southeastern United States is limited, and where data exist, they are rarely compared to those from other regions of North America. We assessed geographic patterns in morphology and genetics of coyotes with special consideration of coyotes in the southeastern United States. Mean body mass of coyote populations increased along a west-to-east gradient, with southeastern coyotes being intermediate to western and northeastern coyotes. Similarly, principal component analysis of body mass and linear body measurements suggested that southeastern coyotes were intermediate to western and northeastern coyotes in body size but exhibited shorter tails and ears from other populations. Genetic analyses indicated that southeastern coyotes represented a distinct genetic cluster that differentiated strongly from western and northeastern coyotes. We postulate that southeastern coyotes experienced lower immigration from western populations than did northeastern coyotes, and over time, genetically diverged from both western and northeastern populations. Coyotes colonizing eastern North America experienced different selective pressures than did stable populations in the core range and we offer that the larger body size of eastern coyotes reflect an adaptation that improved dispersal capabilities of individuals in the expanding range.
Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario
<p>Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm <em>Oenocarpus bataua</em> var. <em>bataua </em>which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of <em>O. bataua</em> var. <em>bataua</em> from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in <em>O. bataua</em> within northwestern South America.</p>
Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa
<p>Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. <i>K</i>= 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise <i>F<sub>ST</sub></i>analysis showed genetic differentiation <i>(P < 0.05)</i>between the village, commercial and wild populations. A per marker per population pairwise <i>F<sub>ST</sub></i>analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.</p>
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens
<p>Urban Norway rats (<i>Rattus norvegicus</i>) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens <i>Leptospira interrogans</i>, <i>Bartonella tribocorum</i>, and <i>Clostridium difficile</i>, and found that an individual's pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. <span>Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.</span></p>
Figure 3 in Genetic and morphological heterogeneity within Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopidae)
Figure 3. Eucyclops serrulatus (Fischer) from the Dniester Liman (A, C, E) and Zakarpattia regions (B, D, F) of Ukraine. (A, B) P4, caudal side with feature abbreviations used; (C, D) antenna, caudal side; (E, F) caudal ramus with abbreviations.
Figure 1 in Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region - Greece
Figure 1. The study area in Kastoria region and capture locations (red dots) for the 75 living bears.
Experimental data to the publication "Genetic-optimised aperiodic code for distributed optical fibre sensors"
<p>The source data underlying Figs. 3-5 and Supplementary Figs. 6, 8-14 are provided as a Source Data file.</p>
Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground
<p></p><p>As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.</p><p></p>
The Geometry and Genetics of Hybridization
<p>When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence towards a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the ``composite effects''. Finally, we develop extensions to the model, involving selectively-induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.</p>
Fig. 4 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 4. Amobia burnsi (Malloch, 1930), ♂, NSW, North Head, Sydney Harbour, 14 Feb. 1978, G. Daniels leg. (AM) A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.
Fig. 1 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 1. Maximum likelihood phylogenetic tree indicating the placement of Amobia among the global Miltogramminae, inferred from COI, CYTB, ND4 and EF1α sequence data. With the exception of the three newly sequenced Australian Amobia and Macronychia rubesca, data was acquired from Piwczyński et al. (2017). Node support values are shown for both maximum likelihood analysis (bootstrap support, 1000 iterations; in bold font) and Bayesian analysis (posterior probability, 40 million generations), 'NA' indicates nodes resolved that were not resolved by the Bayesian analysis. Branch length scale = 0.3 nucleotide substitutions per site (calculated by the GTR+G nucleotide substitution model).
Fig. 6 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems
Fig. 6. Amobia serpenta sp. nov., holotype, ♂, NT, Serpentine Gorge, West MacDonnell National Park, 13 Nov. 2017, Johnston, Wallman and Szpila leg. (ANIC). A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.
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.