Find research datasets worth reusing

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Fig. 3. First parasitic generation emerging Fig. 4. Juveniles migration from a in Development of Steinernema feltiae (Rhabditida: Steinernematidae) in larvae of Chaetonyx robustus (Coleoptera: Orphnidae)

Fig. 3. First parasitic generation emerging Fig. 4. Juveniles migration from a host. from host. Scale bar: 1 mm. Scale bar: 1 mm.

Fig. 4 in Do managed bees drive parasite spread and emergence in wild bees?

Fig. 4. Overview of parasite detection in managed bees in North America and likely instances of parasite transmission between managed and wild bumblebees.

Fig. 3 in Do managed bees drive parasite spread and emergence in wild bees?

Fig. 3. Overview of parasite detection in managed bees in Japan and likely instances of parasite transmission between managed and wild bumblebees.

Fig. 5 in Do managed bees drive parasite spread and emergence in wild bees?

Fig. 5. Overview of parasite detection in managed bees in the British Isles and likely instances of parasite transmission between managed and wild bumblebees.

Fig. 2 in Do managed bees drive parasite spread and emergence in wild bees?

Fig. 2. Highlighting the three main mechanisms that influence parasite infections between managed and wild bee populations. Arrows represent direction of potential parasite spread as a result of the mechanism.

Fig. 1 in Do managed bees drive parasite spread and emergence in wild bees?

Fig. 1. The key factors that may drive disease emergence within and between populations of managed and wild bees. Adapted from Daszak et al. (2000).

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Fig. 3 in Plagiorchis sp. in small mammals of Senegal and the potential emergence of a zoonotic trematodiasis

Fig. 3. Phylogenetic relationships among Plagiorchis spp. inferred by Maximum Likelihood (A) and Bayesian Inference (B) analyses of the cytochrome c oxidase subunit 1 gene data. The taxon Fasciola hepatica (GenBank™ AP017707) was used as outgroup. Nodal support ≥ 80% from likelihood bootstrap replicates and Bayesian posterior probabilities is indicated with an asterisk.

opencc-by-4.0Apr 2019View details →

Fig. 2 in Plagiorchis sp. in small mammals of Senegal and the potential emergence of a zoonotic trematodiasis

Fig. 2. Phylogenetic relationships among Plagiorchis spp. inferred by Maximum Likelihood (ML) and Bayesian Inference (BI) analyses of the internal transcribed spacer sequence data. The black silhouettes represent the hosts from which the molecular data of Plagiorchis spp. were obtained. The taxa Aptorchis aequalis and Aptorchis megacetabulus (GenBank™ EF014729 and EF014730, respectively) were used as outgroups. Nodal support is indicated as ML percentage above and BI posterior probability below each branch.

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Fig. 1 in Plagiorchis sp. in small mammals of Senegal and the potential emergence of a zoonotic trematodiasis

Fig. 1. Histological section of liver from a Hubert's multimammate mouse (Mastomys huberti). A large central bile duct is markedly dilated by the presence of Plagiorchis trematodes (indicated by an asterisk). Marked hyperplasia of the lining biliary epithelium is shown, associated with moderate to marked lymphoplasmacytic cholangitis and mild to moderate lymphoplasmacytic hepatitis of the surrounding portal areas. Scale bar = 500 μm.

opencc-by-4.0Aug 2018View details →

Fig. 1 in Variable changes in nematode infection prevalence and intensity after Rabbit Haemorrhagic Disease Virus emerged in wild rabbits in Scotland and New Zealand

Fig. 1. Differences in mean intensity of nematode parasite infection in rabbits sampled seasonally from New Zealand and Scotland before the spread of RHDV (a), rabbits sampled seasonally from Sotland before and after RHDV (b), and rabbits sampled in autumn season from New Zealand and Scotland before and after RHDV (c). Nematode parasites included T. retortaeformis (i) G. strigosum (ii) and P. ambiguus (iii) found in rabbits sampled in spring (Spr), summer (Sum), autumn (Aut) and winter (Win).

Fig. 11 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 11 Rates of chatter calls in different magpie populations and individuals. a Each mark represents average chattering rate for a single bird from five populations indicated by colours. Figures are numbers for the outliers: 1, 2—jankowskii from the mixed population of Argun'; 3, 4, 5—hybrid birds from the hybridogeneous population of Kerulen. b Each mark represents average chattering rate for a series of chatterings of one selected individual representing jankowskii, leucoptera, and hybrid birds, respectively. Green mark—pair #6 jankowskii from Vladivostok; gray—pair #43 leucoptera from Tsasuchei, Transbaikalia; blue—pair #24 hybrids from Kerulen, eastern Mongolia. X-axis—number of elements per second in a total series of chattering; Y-axis— number of elements per second in a series of 5 elements of chattering

Fig. 12 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 12 Violin plot diagram of the chatter call speed (elements per second) of Eurasian magpie populations across regions. X-axis presents a set of populations; Y-axis—elements per second. Box outlines the interquantile range (25%, 75%), whiskers represent range without outliers, central bar is the median, red dot is the mean, and figure shape is the probability density. The brackets on the top denote statistically significant pairwise differences (GamesHowell test, p<0.05)

Fig. 9 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 9 Population genetic structure based on unlinked SNP markers. Scatter plots of principal component analysis (PCA) show individual variation in components one and two (a) and three and four (b). The amount of variance explained by each PC is shown in parentheses. I—leucoptera,

Fig. 7 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 7 Bayesian skyline plots (BSPs) for effective female population sizes for haplogroups, subspecies, and populations of Pica pica. a Comparison of 6 haplogroups, depicted in the network Fig. 4. b Comparison of 6 subspecies. c Comparison of 4 populations of P. p. jankowskii. d Comparison of 3 populations of P. p. leucoptera.

Fig. 6 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 6 Mismatch distribution of nucleotide differences in populations representing different haplogroups as at Figs. 4 and 5. X-axis— number of nucleotide differences; Y-axis—proportion (frequency). Solid lines—expected distributions (under expectation of population growth); dashed lines—observed distributions. a Haplogroup 1:

Fig. 5 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 5 Time-calibrated Bayesian tree based on mitochondrial control region sequences of Pica pica. Numbers at the branches indicate Bayesian posterior probability values (left) and bootstrap values of the ML analysis (right, in percent). Triangle widths are proportional to specimen numbers. Blue bars next to nodes indicate 95% credibility intervals for their age estimates. The figures in bold and the time scale below are in million years (Ma) before present

Fig. 4 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 4 Phylogenetic medianjoining network based on 256 mitochondrial control region sequences. Sizes of circles correspond to the number of birds sharing this haplotype; branch lengths are proportional to the number of substitutions and those over 2 are shown at the branches. Haplogroups 1–6 are indicated by numbers

Fig. 2 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 2 Map of sampling localities for mitochondrial DNA analysis in the zone of contact between Pica pica leucoptera and Pica pica jankowskii. Distribution of haplotypes is indicated by colours: Pica

opencc-by-4.0Jul 2019View details →

The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

Supporting data for  "The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe" =========================================================================================== Abstract: -------- The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly S. lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of  ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1,966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb  and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the S. lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate respectively Actinopterygii single-copy orthologs. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.   Files: ------ <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.cds.renamed.fa">sanlu.cds.renamed.fa </a> - Coding sequences of predicted  protein-coding genes  <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genes.filt.gff3">sanlu.genes.filt.gff3 </a> - gff3 file of predicted protein coding genes <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genes.pep.fa">sanlu.genes.pep.fa </a> - predicted peptide sequences  <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genome.ctg.fasta">sanlu.genome.ctg.fasta </a> - Sander lucioperca genome assembly at contig-level <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genome.scf.fa">sanlu.genome.scf.fa </a> - Sander lucioperca genome assembly at scaffold-level <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Sanlu.genome.masked.fasta">Sanlu.genome.masked.fasta </a>- Repeats-masked Sander lucioperca genome assembly at scaffold-level <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Sanlu.genome.repeats.gff">Sanlu.genome.repeats.gff </a>  - Gff3 file of predicted repeats in Sander lucioperca genome <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Additional_File_2.xlsx">Additional_File_2.xlsx </a> - Functional annotations of Sander lucioperca genes by SwissProt, NR RefSeq, TrEMBL and InterPro databases <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.repeats.lib.fasta">sanlu.repeats.lib.fasta </a> - Predicted repeats library in Sander lucioperca in FASTA format <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.csv">sanlu_miRNA.csv </a>  Predicted micro RNA families in CSV tab file  <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.bed">sanlu_miRNA.bed </a> - Predicted micro RNA families in BED file format <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.html">sanlu_miRNA.html </a><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.bed"> </a> - Predicted micro RNA families in HTML <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_rRNA.fasta">sanlu_rRNA.fasta </a> - Predicted ribosomal  RNA (rRNA)  sequences in FASTA file format <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_rRNA.gff">sanlu_rRNA.gff </a> - Predicted ribosomal  RNA (rRNA)  sequences in GFF file format <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/trna.genes.csv">trna.genes.csv </a> - Predicted transfer  RNA (tRNA)  genes in CSV tab file <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/SpeciesTree_rooted_node_labels.txt">SpeciesTree_rooted_node_labels.txt </a> - Predicted phylogenetic tree in NEWICK format <a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/SpeciesTreeAlignment.fa">SpeciesTreeAlignment.fa </a> - Species tree alignment in FASTA, based on 1.1 single copy orthologs