cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12471461.v6
title: Knight et al, unpublished.

description: <b>1. </b>Global MLST phylogeny (nwk file for manuscript figure 2)<b><br></b><b><br></b><b>2. </b>Supplementary Data<b><br></b>
DOI: 10.6084/m9.figshare.12470720
title: Additional file 1 of Patient feedback to improve quality of patient-centred care in public hospitals: a systematic review of the evidence

description: Additional file 1. Risk of bias assessment.
DOI: 10.6084/m9.figshare.12470720.v1
title: Additional file 1 of Patient feedback to improve quality of patient-centred care in public hospitals: a systematic review of the evidence

description: Additional file 1. Risk of bias assessment.
DOI: 10.6084/m9.figshare.12470654
title: Additional file 9 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 9 V1V3_hADT_CL.fa. V1-V3 trimmed 16S rRNA gene human aerodigestive tract clone library dataset (V1V3_hADT_CL dataset).
DOI: 10.6084/m9.figshare.12470651
title: Additional file 8 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 8. V1V3_sinonasal_SMRT_ASV.fa. Sequences of the resulting 204 ASVs in the FL_sinonasal_SMRT_ASV dataset trimmed to the V1-V3 region (V1V3_sinonasal_SMRT_ASV dataset).
DOI: 10.6084/m9.figshare.12470642
title: Additional file 5 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 5 eHOMDv15.1_V1V3_Supraspecies_TS.fa. The 16S rRNA gene V1-V3 eHOMD training set (V1V3_Supraspecies_TS).
DOI: 10.6084/m9.figshare.12470645
title: Additional file 6 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 6. FL_sinonasal_SMRT_ASV.fa. Sequences of the resulting 204 ASVs in the Earl-Mell sinonasal 16S rRNA gene dataset (FL_sinonasal_SMRT_ASV dataset).
DOI: 10.6084/m9.figshare.12470648
title: Additional file 7 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 7. Earl-Mell_sinonasal_analysis.xlsx with legend and tabs A-D. Species-level taxonomic assignment of the Earl-Mell sinonasal 16S rRNA gene dataset.
DOI: 10.6084/m9.figshare.12470654.v1
title: Additional file 9 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 9 V1V3_hADT_CL.fa. V1-V3 trimmed 16S rRNA gene human aerodigestive tract clone library dataset (V1V3_hADT_CL dataset).
DOI: 10.6084/m9.figshare.12470645.v1
title: Additional file 6 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 6. FL_sinonasal_SMRT_ASV.fa. Sequences of the resulting 204 ASVs in the Earl-Mell sinonasal 16S rRNA gene dataset (FL_sinonasal_SMRT_ASV dataset).
DOI: 10.6084/m9.figshare.12470648.v1
title: Additional file 7 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 7. Earl-Mell_sinonasal_analysis.xlsx with legend and tabs A-D. Species-level taxonomic assignment of the Earl-Mell sinonasal 16S rRNA gene dataset.
DOI: 10.6084/m9.figshare.12470651.v1
title: Additional file 8 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 8. V1V3_sinonasal_SMRT_ASV.fa. Sequences of the resulting 204 ASVs in the FL_sinonasal_SMRT_ASV dataset trimmed to the V1-V3 region (V1V3_sinonasal_SMRT_ASV dataset).
DOI: 10.6084/m9.figshare.12470633
title: Additional file 2 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 2 eHOMDv15.1_FL_Compilation_TS.fa. The 16S rRNA gene full-length eHOMD training set (FL_Compilation_TS).
DOI: 10.6084/m9.figshare.12470636
title: Additional file 3 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 3. V1V3_eHOMDSim_250N100.fa. The simulated eHOMD-derived V1V3_eHOMDSim_250N100 dataset.
DOI: 10.6084/m9.figshare.12470642.v1
title: Additional file 5 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 5 eHOMDv15.1_V1V3_Supraspecies_TS.fa. The 16S rRNA gene V1-V3 eHOMD training set (V1V3_Supraspecies_TS).
DOI: 10.6084/m9.figshare.12470633.v1
title: Additional file 2 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 2 eHOMDv15.1_FL_Compilation_TS.fa. The 16S rRNA gene full-length eHOMD training set (FL_Compilation_TS).
DOI: 10.6084/m9.figshare.12470627
title: Additional file 19 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 19. eight2seven.R. Custom-written R function that converts the dada2::assignTaxonomy() output from eight to seven taxonomic levels for compatibility with downstream applications.
DOI: 10.6084/m9.figshare.12470636.v1
title: Additional file 3 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 3. V1V3_eHOMDSim_250N100.fa. The simulated eHOMD-derived V1V3_eHOMDSim_250N100 dataset.
DOI: 10.6084/m9.figshare.12470618
title: Additional file 16 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 16. Simulated_R2_350_R1_20-200.7z. Simulated eHOMD-derived dataset versions with R2 fixed at 350 bp and R1 fragments from the V3 primer ranging from 20 to 200 bp.
DOI: 10.6084/m9.figshare.12470621
title: Additional file 17 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 17. Simulated_R2_140-350_R1_200.7z. Simulated eHOMD-derived dataset versions with R1 fixed at 200 bp and R2 fragments from the V1 primer ranging from 140 to 350 bp.
DOI: 10.6084/m9.figshare.12470624
title: Additional file 18 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 18. FL_hADT_CL.fa. Full-length 16S rRNA gene human aerodigestive tract clone library dataset (FL_hADT_CL dataset).
DOI: 10.6084/m9.figshare.12470624.v1
title: Additional file 18 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 18. FL_hADT_CL.fa. Full-length 16S rRNA gene human aerodigestive tract clone library dataset (FL_hADT_CL dataset).
DOI: 10.6084/m9.figshare.12470627.v1
title: Additional file 19 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 19. eight2seven.R. Custom-written R function that converts the dada2::assignTaxonomy() output from eight to seven taxonomic levels for compatibility with downstream applications.
DOI: 10.6084/m9.figshare.12470609
title: Additional file 15 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 15. Original GenBank accession numbers for all the sequences compiled in the V1V3_Supraspecies_TS training set linked to their unique IDs in Additional file 14.
DOI: 10.6084/m9.figshare.12470618.v1
title: Additional file 16 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 16. Simulated_R2_350_R1_20-200.7z. Simulated eHOMD-derived dataset versions with R2 fixed at 350 bp and R1 fragments from the V3 primer ranging from 20 to 200 bp.
DOI: 10.6084/m9.figshare.12470621.v1
title: Additional file 17 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 17. Simulated_R2_140-350_R1_200.7z. Simulated eHOMD-derived dataset versions with R1 fixed at 200 bp and R2 fragments from the V1 primer ranging from 140 to 350 bp.
DOI: 10.6084/m9.figshare.12470600
title: Additional file 1 of Using health facility deaths to estimate population causes of neonatal and child mortality in four African countries

description: Additional file 1. a. Community and health facility causes of neonatal deaths in four sub-Saharan Africa countries. b. Community and health facility causes of 1–59-month deaths in four sub-Saharan Africa countries.
DOI: 10.6084/m9.figshare.12470606
title: Additional file 2 of Using health facility deaths to estimate population causes of neonatal and child mortality in four African countries

description: Additional file 2. All projections of CSMF accuracy comparing population cause distributions estimated with verbal autopsies of facility deaths to observed population cause distributions from verbal autopsies of community and facility deaths, in four sub-Saharan Africa countries.
DOI: 10.6084/m9.figshare.12470603
title: Additional file 14 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 14. V1V3_Supraspecies_TS training set with sequences labelled as unique IDs.
DOI: 10.6084/m9.figshare.12470609.v1
title: Additional file 15 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 15. Original GenBank accession numbers for all the sequences compiled in the V1V3_Supraspecies_TS training set linked to their unique IDs in Additional file 14.
DOI: 10.6084/m9.figshare.12470594
title: Additional file 12 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 12. Original GenBank accession numbers for all the sequences compiled in the FL_Compilation_TS training set linked to their unique IDs in Additional file 11.
DOI: 10.6084/m9.figshare.12470600.v1
title: Additional file 1 of Using health facility deaths to estimate population causes of neonatal and child mortality in four African countries

description: Additional file 1. a. Community and health facility causes of neonatal deaths in four sub-Saharan Africa countries. b. Community and health facility causes of 1–59-month deaths in four sub-Saharan Africa countries.
DOI: 10.6084/m9.figshare.12470606.v1
title: Additional file 2 of Using health facility deaths to estimate population causes of neonatal and child mortality in four African countries

description: Additional file 2. All projections of CSMF accuracy comparing population cause distributions estimated with verbal autopsies of facility deaths to observed population cause distributions from verbal autopsies of community and facility deaths, in four sub-Saharan Africa countries.
DOI: 10.6084/m9.figshare.12470594.v1
title: Additional file 12 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 12. Original GenBank accession numbers for all the sequences compiled in the FL_Compilation_TS training set linked to their unique IDs in Additional file 11.
DOI: 10.6084/m9.figshare.12470603.v1
title: Additional file 14 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 14. V1V3_Supraspecies_TS training set with sequences labelled as unique IDs.
DOI: 10.6084/m9.figshare.12470576
title: Additional file 11 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 11. FL_Compilation_TS training set with sequences labeled as unique IDs.
DOI: 10.6084/m9.figshare.12470573
title: Additional file 10 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 10. V1V3_HMPnares_ASV.fa. ASVs derived from the HMP nares 16S rRNA gene V1-V3 dataset (V1V3_HMPnares_ASV dataset).
DOI: 10.6084/m9.figshare.12470573.v1
title: Additional file 10 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 10. V1V3_HMPnares_ASV.fa. ASVs derived from the HMP nares 16S rRNA gene V1-V3 dataset (V1V3_HMPnares_ASV dataset).
DOI: 10.6084/m9.figshare.12470576.v1
title: Additional file 11 of Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

description: Additional file 11. FL_Compilation_TS training set with sequences labeled as unique IDs.
DOI: 10.6084/m9.figshare.12470507
title: Additional file 5 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 5: Table S4. ChIP-qPCR primers.
DOI: 10.6084/m9.figshare.12470507.v1
title: Additional file 5 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 5: Table S4. ChIP-qPCR primers.
DOI: 10.6084/m9.figshare.12470489
title: Additional file 3 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 3: Table S2. ID4 RNA-seq differentially expressed genes.
DOI: 10.6084/m9.figshare.12470498
title: Additional file 4 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 4: Table S3. Putative ID4 interaction proteins identified by RIME.
DOI: 10.6084/m9.figshare.12470489.v1
title: Additional file 3 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 3: Table S2. ID4 RNA-seq differentially expressed genes.
DOI: 10.6084/m9.figshare.12470498.v1
title: Additional file 4 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 4: Table S3. Putative ID4 interaction proteins identified by RIME.
DOI: 10.6084/m9.figshare.12470483
title: Additional file 2 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 2: Table S1. ChIP-seq and ChIP-exo MACS peaks.
DOI: 10.6084/m9.figshare.12470483.v1
title: Additional file 2 of Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

description: Additional file 2: Table S1. ChIP-seq and ChIP-exo MACS peaks.
DOI: 10.6084/m9.figshare.12470435
title: Additional file 1 of Predictors of the use and approval of CAM: results from the German General Social Survey (ALLBUS)

description: Additional file 1. The unabridged results of the CCA including all 24 unrotated variates, all variables and the canonical correlations.
DOI: 10.6084/m9.figshare.12470435.v1
title: Additional file 1 of Predictors of the use and approval of CAM: results from the German General Social Survey (ALLBUS)

description: Additional file 1. The unabridged results of the CCA including all 24 unrotated variates, all variables and the canonical correlations.
DOI: 10.6084/m9.figshare.12470384
title: SRR11853650

description: Raw data of sequencing<br>
DOI: 10.6084/m9.figshare.12470378
title: SRR9681919

description: Raw data of sequencing<br>
DOI: 10.6084/m9.figshare.12470384.v1
title: SRR11853650

description: Raw data of sequencing<br>
DOI: 10.6084/m9.figshare.12470348
title: Table S5 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Gene ontology terms enriched at the putatively introgression sites.
DOI: 10.6084/m9.figshare.12470348.v1
title: Table S5 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Gene ontology terms enriched at the putatively introgression sites.
DOI: 10.6084/m9.figshare.12470327
title: Table S4 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Mapping rate for sympatric <i>P. sinensis</i> and <i>P. pungitius</i>.
DOI: 10.6084/m9.figshare.12470330
title: Sample description from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .xlsx format and contains detailed information about the samples
DOI: 10.6084/m9.figshare.12470324
title: Table S5 : Choosiness-associated CNVs from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .txt format
DOI: 10.6084/m9.figshare.12470318
title: Table S7 : Significantly enriched annotation terms of genes in which Choosiness-associated CNVs occurred from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .xlsx format
DOI: 10.6084/m9.figshare.12470324.v1
title: Table S5 : Choosiness-associated CNVs from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .txt format
DOI: 10.6084/m9.figshare.12470327.v1
title: Table S4 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Mapping rate for sympatric <i>P. sinensis</i> and <i>P. pungitius</i>.
DOI: 10.6084/m9.figshare.12470312
title: Table S6 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Migration rates between sympatric stickleback species.
DOI: 10.6084/m9.figshare.12470315
title: Mathematica notebook from The limits to parapatric speciation 3: Evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation

description: Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky–Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that many incipient species may initially face. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
DOI: 10.6084/m9.figshare.12470330.v1
title: Sample description from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .xlsx format and contains detailed information about the samples
DOI: 10.6084/m9.figshare.12470312.v1
title: Table S6 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Migration rates between sympatric stickleback species.
DOI: 10.6084/m9.figshare.12470318.v1
title: Table S7 : Significantly enriched annotation terms of genes in which Choosiness-associated CNVs occurred from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .xlsx format
DOI: 10.6084/m9.figshare.12470306
title: Table S3 : Consistently divergent CNVs in the Control Test from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .txt format
DOI: 10.6084/m9.figshare.12470309
title: Table S6 : Choosiness-associated CNVs that occur within 1 kb of a gene from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .csv format
DOI: 10.6084/m9.figshare.12470303
title: Table S2. from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: De novo genome assembly of <i>Pungitius sinensis</i>.
DOI: 10.6084/m9.figshare.12470306.v1
title: Table S3 : Consistently divergent CNVs in the Control Test from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .txt format
DOI: 10.6084/m9.figshare.12470303.v1
title: Table S2. from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: De novo genome assembly of <i>Pungitius sinensis</i>.
DOI: 10.6084/m9.figshare.12470309.v1
title: Table S6 : Choosiness-associated CNVs that occur within 1 kb of a gene from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .csv format
DOI: 10.6084/m9.figshare.12470294
title: Table S3 from Genome-wide patterns of divergence and introgression after secondary contact between <i>Pungitius</i> sticklebacks

description: Re-sequenced samples.
DOI: 10.6084/m9.figshare.12470297
title: Table S2 : Consistently divergent CNVs in the Focal Test from The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

description: this file is in .txt format
DOI: 10.6084/m9.figshare.12470315.v1
title: rapid_adaptation.nb from The limits to parapatric speciation 3: Evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation

description: Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky–Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that many incipient species may initially face. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.