cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12763447.v1
title: Raw data from Natural barriers: waterfall transit by small flying animals

description: Data sets and raw digitization data. (sheet 1) Hummingbirds’ kinematics. (Sheet 2) insects’ kinematics. (sheet 3) balls’ kinematics. (sheet 4-11) 3D digitized points in Cartesian system XYZ in cm of four male hummingbirds flying in still air (control) and crossing through a waterfall. Point 1 (beak), point 2 (eye), point3 (tail base), point 4 (tail tip at the middle), point5 (right wingtip), point 6 (right shoulder), point 7 (left shoulder), point8 (left wingtip), point 9 (right tailtip). (sheet 12-44) 3D digitized points in Cartesian system XYZ in cm of 33 insects (7 bottleflies 24 house flies, one cranefly and one fruit fly crossing through a waterfall. Point 1 (head) and point 2 (abdomen).(sheet 45-46) 2D trajectories in Cartesian system XY in cm of 59 plastic balls shot against a waterfall. Digitalization software is described in: Hedrick, T. L. (2008). Software techniques for two- and three-dimensional kinematic measurements of biological and biomimetic systems. Bioinspir. Biomim. 3, 034001
DOI: 10.6084/m9.figshare.12763437
title: Matlab code from The dynamics of trait variance in multi-species communities

description: Solves population-level and species-level models, and generates figures in manuscript
DOI: 10.6084/m9.figshare.12763437.v1
title: Matlab code from The dynamics of trait variance in multi-species communities

description: Solves population-level and species-level models, and generates figures in manuscript
DOI: 10.6084/m9.figshare.12763419
title: JDoonan_table S1_ESM.xlsx from Host–microbiota–insect interactions drive emergent virulence in a complex tree disease

description: Forest declines caused by climate disturbance, insect pests and microbial pathogens threaten the global landscape, and tree diseases are increasingly attributed to the emergent properties of complex ecological interactions between the host, microbiota and insects. To address this hypothesis, we combined reductionist approaches (single and polyspecies bacterial cultures) with emergentist approaches (bacterial incoluations in an oak infection model with the addition of insect larvae) to unravel the gene expression landscape and symptom severity of host–microbiota–insect interactions in the Acute Oak Decline (AOD) pathosystem. AOD is a complex decline disease characterized by predisposing abiotic factors, inner bark lesions driven by a bacterial pathobiome, and larval galleries of the bark-boring beetle <i>Agrilus biguttatus</i>. We identified expression of key pathogenicity genes in <i>Brenneria goodwinii</i>, the dominant member of the AOD pathobiome, tissue-specific gene expression profiles, cooperation with other bacterial pathobiome members in sugar catabolism, and demonstrated amplification of pathogenic gene expression in the presence of <i>Agrilus</i> larvae. This study highlights the emergent properties of complex host–pathobiota–insect interactions that underlie the pathology of diseases that threaten global forest biomes.
DOI: 10.6084/m9.figshare.12763419.v1
title: JDoonan_table S1_ESM.xlsx from Host–microbiota–insect interactions drive emergent virulence in a complex tree disease

description: Forest declines caused by climate disturbance, insect pests and microbial pathogens threaten the global landscape, and tree diseases are increasingly attributed to the emergent properties of complex ecological interactions between the host, microbiota and insects. To address this hypothesis, we combined reductionist approaches (single and polyspecies bacterial cultures) with emergentist approaches (bacterial incoluations in an oak infection model with the addition of insect larvae) to unravel the gene expression landscape and symptom severity of host–microbiota–insect interactions in the Acute Oak Decline (AOD) pathosystem. AOD is a complex decline disease characterized by predisposing abiotic factors, inner bark lesions driven by a bacterial pathobiome, and larval galleries of the bark-boring beetle <i>Agrilus biguttatus</i>. We identified expression of key pathogenicity genes in <i>Brenneria goodwinii</i>, the dominant member of the AOD pathobiome, tissue-specific gene expression profiles, cooperation with other bacterial pathobiome members in sugar catabolism, and demonstrated amplification of pathogenic gene expression in the presence of <i>Agrilus</i> larvae. This study highlights the emergent properties of complex host–pathobiota–insect interactions that underlie the pathology of diseases that threaten global forest biomes.
DOI: 10.6084/m9.figshare.12763401
title: Martins_table S3_ESM from Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Status of genera as survivors or victims of the K/Pg extinction, or as newly originating taxa in the Paleocene.
DOI: 10.6084/m9.figshare.12763404
title: Martins_table S2_ESM from Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Sexual dimorphism data for Paleocene ostracod populations
DOI: 10.6084/m9.figshare.12763398
title: Martins_table S1_ESM from Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Sexual dimorphism data for Cretaceous ostracod populations
DOI: 10.6084/m9.figshare.12763404.v1
title: Martins_table S2_ESM from Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Sexual dimorphism data for Paleocene ostracod populations
DOI: 10.6084/m9.figshare.12763401.v1
title: Martins_table S3_ESM from Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Status of genera as survivors or victims of the K/Pg extinction, or as newly originating taxa in the Paleocene.
DOI: 10.6084/m9.figshare.12763397
title: Younng-onset T2D progression (Supporting)_ Aug 2020.pdf

description: JCEM submission Aug 2020
DOI: 10.6084/m9.figshare.12763394
title: Traits sources

description: Traits sources of the 277 macrobenthic taxa contained in SAMT database
DOI: 10.6084/m9.figshare.12763397.v1
title: Younng-onset T2D progression (Supporting)_ Aug 2020.pdf

description: JCEM submission Aug 2020
DOI: 10.6084/m9.figshare.12762772
title: Additional file 4 of Do sequential lineups impair underlying discriminability?

description: Additional file 4: Supplement 1. Fitting SDT-MAX to Simultaneous Lineup Data.
DOI: 10.6084/m9.figshare.12763394.v1
title: Traits sources

description: Traits sources of the 277 macrobenthic taxa contained in SAMT database
DOI: 10.6084/m9.figshare.12762772.v1
title: Additional file 4 of Do sequential lineups impair underlying discriminability?

description: Additional file 4: Supplement 1. Fitting SDT-MAX to Simultaneous Lineup Data.
DOI: 10.6084/m9.figshare.12762758
title: Additional file 9 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 9: Table S3. Description of linkage disequilibrium (LD) blocks per linkage group in the association mapping collection. A LD block consists in a series of at least 2 markers which are in significant LD (r2 &gt; 0.8) with at least one trait-associated marker (underlined marker). LD blocks are named in consecutive numerical order following their linkage group (LG) name. cM*: genetic position, in centiMorgan of each marker along the genetic map of the corresponding linkage group; LD (r2) **: r2 value of each marker with the other markers of the same LD block.
DOI: 10.6084/m9.figshare.12762749
title: Additional file 6 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 6: Table S2. Description of the association mapping collection. This table presents the list of the pea accessions composing the association mapping collection with their end-use, cultivation status, geographical origin and sowing type. The ‘DAPC_Cluster (k)’ column shows assignation of the 363 pea accessions to a cluster based on the discriminant analysis of principal components (DAPC). The ‘Dendrogram_Cluster (k)’ column shows the allocation of individuals to clusters based on the dendrogram using Nei genetic distances between accessions. The description of the pea accessions is extracted from Burstin et al. [55]. CRB Code: Code used for the association mapping, also named collection of biological resources (CRB). *: sowing type modified for this accession, according to Yenne et al. [79].
DOI: 10.6084/m9.figshare.12762758.v1
title: Additional file 9 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 9: Table S3. Description of linkage disequilibrium (LD) blocks per linkage group in the association mapping collection. A LD block consists in a series of at least 2 markers which are in significant LD (r2 &gt; 0.8) with at least one trait-associated marker (underlined marker). LD blocks are named in consecutive numerical order following their linkage group (LG) name. cM*: genetic position, in centiMorgan of each marker along the genetic map of the corresponding linkage group; LD (r2) **: r2 value of each marker with the other markers of the same LD block.
DOI: 10.6084/m9.figshare.12762749.v1
title: Additional file 6 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 6: Table S2. Description of the association mapping collection. This table presents the list of the pea accessions composing the association mapping collection with their end-use, cultivation status, geographical origin and sowing type. The ‘DAPC_Cluster (k)’ column shows assignation of the 363 pea accessions to a cluster based on the discriminant analysis of principal components (DAPC). The ‘Dendrogram_Cluster (k)’ column shows the allocation of individuals to clusters based on the dendrogram using Nei genetic distances between accessions. The description of the pea accessions is extracted from Burstin et al. [55]. CRB Code: Code used for the association mapping, also named collection of biological resources (CRB). *: sowing type modified for this accession, according to Yenne et al. [79].
DOI: 10.6084/m9.figshare.12762740
title: Additional file 3 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 3: Table S1. Description of the Pisum sativum linkage groups (LGs) used in the present study. The number of SNP markers, the genetic length (in cM, from Tayeh et al. [36]) and the average minor allele frequency (MAF) are shown for each LG.
DOI: 10.6084/m9.figshare.12762731
title: Additional file 14 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 14: Table S8. Daily air and soil temperatures during the field experiment in Clermont-Ferrand Theix.
DOI: 10.6084/m9.figshare.12762740.v1
title: Additional file 3 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 3: Table S1. Description of the Pisum sativum linkage groups (LGs) used in the present study. The number of SNP markers, the genetic length (in cM, from Tayeh et al. [36]) and the average minor allele frequency (MAF) are shown for each LG.
DOI: 10.6084/m9.figshare.12762725
title: Additional file 12 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 12: Table S6. Description of the pea association mapping collection as described in Additional file 6 and the correspondence of the genotyping results of accessions at the Hr locus.
DOI: 10.6084/m9.figshare.12762728
title: Additional file 13 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 13: Table S7. Description of accessions of the pea reference collection for their haplotype at the frost damage (FD)-associated loci of the GWA study and at the Hr locus. At the linkage groups (LGs) I, II, III, V, VI and VII, the favorable haplotypes are shown by a red background, the unfavorable haplotypes by a blue background, as described in the legend of Additional file 10. Accessions with undefined haplotypes or intermediate haplotypes were not presented. The same colour code has been used to describe the favorable (red background: Hr) and unfavorable (blue background: hr) allele for the Hr gene, as determined in Lejeune-Hénaut et al. [21]. The mean frost damage score observed in the field experiment as well as its standard error (SE) are given. Frost scores are ranging from 0 (no damage) to 5 (dead plant). The passport data of accessions are extracted from the Additional file 6.
DOI: 10.6084/m9.figshare.12762728.v1
title: Additional file 13 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 13: Table S7. Description of accessions of the pea reference collection for their haplotype at the frost damage (FD)-associated loci of the GWA study and at the Hr locus. At the linkage groups (LGs) I, II, III, V, VI and VII, the favorable haplotypes are shown by a red background, the unfavorable haplotypes by a blue background, as described in the legend of Additional file 10. Accessions with undefined haplotypes or intermediate haplotypes were not presented. The same colour code has been used to describe the favorable (red background: Hr) and unfavorable (blue background: hr) allele for the Hr gene, as determined in Lejeune-Hénaut et al. [21]. The mean frost damage score observed in the field experiment as well as its standard error (SE) are given. Frost scores are ranging from 0 (no damage) to 5 (dead plant). The passport data of accessions are extracted from the Additional file 6.
DOI: 10.6084/m9.figshare.12762722
title: Additional file 11 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 11: Table S5. List of annotated genes underlying genome-wide association loci of frost tolerance in pea. Genes that were located in an interval of ±1 Mb on both sides of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 &gt; 0.8) with the former ones, are listed. For each identified gene, the nearest marker significantly detected by GWAS (underlined font) or marker in LD with associated marker(s) (non-underlined font) is shown. The annotation of genes was extracted from Pisum sativum v.1a genome JBrowse available at https://urgi.versailles.inra.fr/Species/Pisum [39]. Genes positions in the pea genome assembly v.1a are presented by their assigned chromosomes and physical positions indicated in bp. Genes which are not assigned to one of the seven chromosomes, are represented by their physical positions on unanchored scaffolds. a: Annotation refined with the homologous gene from Medicago truncatula available on the Pisum sativum v.1a genome JBrowse, and whose corresponding gene function was identified from the Medicago truncatula v4.0 genome JBrowse available on www.medicagogenome.org . b: Annotation refined with the homologous gene from Glycine max available on the Pisum sativum v.1a genome JBrowse and whose corresponding gene function was identified from the genome v9.0 assembly V1.1 available on http://soykb.org/gene_card.php . c: Annotation refined with the predicted protein function of transcript sequences corresponding to mapped SNPs, extracted from Table S10 in Tayeh et al. [36].
DOI: 10.6084/m9.figshare.12762731.v1
title: Additional file 14 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 14: Table S8. Daily air and soil temperatures during the field experiment in Clermont-Ferrand Theix.
DOI: 10.6084/m9.figshare.12762722.v1
title: Additional file 11 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 11: Table S5. List of annotated genes underlying genome-wide association loci of frost tolerance in pea. Genes that were located in an interval of ±1 Mb on both sides of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 &gt; 0.8) with the former ones, are listed. For each identified gene, the nearest marker significantly detected by GWAS (underlined font) or marker in LD with associated marker(s) (non-underlined font) is shown. The annotation of genes was extracted from Pisum sativum v.1a genome JBrowse available at https://urgi.versailles.inra.fr/Species/Pisum [39]. Genes positions in the pea genome assembly v.1a are presented by their assigned chromosomes and physical positions indicated in bp. Genes which are not assigned to one of the seven chromosomes, are represented by their physical positions on unanchored scaffolds. a: Annotation refined with the homologous gene from Medicago truncatula available on the Pisum sativum v.1a genome JBrowse, and whose corresponding gene function was identified from the Medicago truncatula v4.0 genome JBrowse available on www.medicagogenome.org . b: Annotation refined with the homologous gene from Glycine max available on the Pisum sativum v.1a genome JBrowse and whose corresponding gene function was identified from the genome v9.0 assembly V1.1 available on http://soykb.org/gene_card.php . c: Annotation refined with the predicted protein function of transcript sequences corresponding to mapped SNPs, extracted from Table S10 in Tayeh et al. [36].
DOI: 10.6084/m9.figshare.12762725.v1
title: Additional file 12 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 12: Table S6. Description of the pea association mapping collection as described in Additional file 6 and the correspondence of the genotyping results of accessions at the Hr locus.
DOI: 10.6084/m9.figshare.12762719
title: Additional file 10 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 10: Table S4. Marker haplotype analysis of the association mapping collection. For each linkage group (LG), the list of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 &gt; 0.8) with the former ones is shown. The third line shows genetic positions from the consensus map of Tayeh et al. [36]. The fourth line indicates the LD blocks composed and named as mentioned in the legend of Additional file 9. The following lines show the allelic composition of haplotypes defined by LD blocks and individual associated markers at each of the 6 frost tolerance loci on linkage groups (LGs) I, II, III, V, VI and VII. For each frost damage (FD)-associated marker, the favorable allele is in red font and the unfavorable allele in blue font. Haplotypes are named in consecutive numerical order following their linkage group name; only haplotypes without missing values or heterozygous markers and carried by more than 3% of the lines from the association mapping collection are listed. For each haplotype, accessions and their mean phenotypic values ± standard error of the variables significantly associated with marker(s) in the linkage group are shown. Significant differences between haplotypes were assayed by a SNK means comparison test; favorable haplotypes are shown by a red background and unfavorable haplotypes by a blue background, regarding the SNK test. Haplotypes with a white background are classified in intermediate groups.
DOI: 10.6084/m9.figshare.12762709
title: Additional file 4 of scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

description: Additional file 4: Supplementary Data. An example report summary document of scTyper.
DOI: 10.6084/m9.figshare.12762712
title: Additional file 1 of Fusion transcript detection using spatial transcriptomics

description: Additional file 1. ST_cis-SAGe ST read counts of the parental genes of the cis-SAGe SLC45A3-ELK4 and C-scores obtained in the clinical tissue samples analysed with Spatial Transcriptomics
DOI: 10.6084/m9.figshare.12762709.v1
title: Additional file 4 of scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

description: Additional file 4: Supplementary Data. An example report summary document of scTyper.
DOI: 10.6084/m9.figshare.12762719.v1
title: Additional file 10 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

description: Additional file 10: Table S4. Marker haplotype analysis of the association mapping collection. For each linkage group (LG), the list of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 &gt; 0.8) with the former ones is shown. The third line shows genetic positions from the consensus map of Tayeh et al. [36]. The fourth line indicates the LD blocks composed and named as mentioned in the legend of Additional file 9. The following lines show the allelic composition of haplotypes defined by LD blocks and individual associated markers at each of the 6 frost tolerance loci on linkage groups (LGs) I, II, III, V, VI and VII. For each frost damage (FD)-associated marker, the favorable allele is in red font and the unfavorable allele in blue font. Haplotypes are named in consecutive numerical order following their linkage group name; only haplotypes without missing values or heterozygous markers and carried by more than 3% of the lines from the association mapping collection are listed. For each haplotype, accessions and their mean phenotypic values ± standard error of the variables significantly associated with marker(s) in the linkage group are shown. Significant differences between haplotypes were assayed by a SNK means comparison test; favorable haplotypes are shown by a red background and unfavorable haplotypes by a blue background, regarding the SNK test. Haplotypes with a white background are classified in intermediate groups.
DOI: 10.6084/m9.figshare.12762703
title: Additional file 2 of scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

description: Additional file 2: Supplementary Table 2–3. This file contains the list of cell markers in each of scTyper.db (Table S2) and CellMarker DB (Table S3) and detailed information such as identifier, study name, species, cell type, gene symbol, and PMID.
DOI: 10.6084/m9.figshare.12762712.v1
title: Additional file 1 of Fusion transcript detection using spatial transcriptomics

description: Additional file 1. ST_cis-SAGe ST read counts of the parental genes of the cis-SAGe SLC45A3-ELK4 and C-scores obtained in the clinical tissue samples analysed with Spatial Transcriptomics
DOI: 10.6084/m9.figshare.12762703.v1
title: Additional file 2 of scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

description: Additional file 2: Supplementary Table 2–3. This file contains the list of cell markers in each of scTyper.db (Table S2) and CellMarker DB (Table S3) and detailed information such as identifier, study name, species, cell type, gene symbol, and PMID.
DOI: 10.6084/m9.figshare.12762680
title: Additional file 3 of Comparative DNA methylome analysis of estrus ewes reveals the complex regulatory pathways of sheep fecundity

description: Additional file 3.
DOI: 10.6084/m9.figshare.12762677
title: Additional file 2 of Comparative DNA methylome analysis of estrus ewes reveals the complex regulatory pathways of sheep fecundity

description: Additional file 2.