cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7701107
title: Database from Ocean acidification affects somatic and otolith growth relationship in fish: evidence from an <i>in situ</i> study.

description: Ocean acidification (OA) may have varied effects on fish eco-physiological responses. Most OA studies have been carried out in laboratory conditions without considering the <i>in situ p</i>CO<sub>2</sub>/pH variability documented for many marine coastal ecosystems. Using a standard otolith ageing technique, we assessed how <i>in situ</i> ocean acidification (ambient, versus end-of-century CO<sub>2</sub> levels) can affect somatic and otolith growth, and their relationship in a coastal fish. Somatic and otolith growth rates of juveniles of the ocellated wrasse <i>Symphodus ocellatus</i> living off a Mediterranean CO<sub>2</sub> seep increased at the high-<i>p</i>CO<sub>2</sub> site. Also, we detected that slower-growing individuals living at ambient <i>p</i>CO<sub>2</sub> levels tend to have larger otoliths at the same somatic length (i.e. higher relative size of otoliths to fish body length) than faster-growing conspecifics living under high <i>p</i>CO<sub>2 </sub>conditions, with this being attributable to the so-called ‘growth effect’. Our findings suggest the possibility of contrasting OA effects on fish fitness, with higher somatic growth rate and possibly higher survival associated with smaller relative size of otoliths that could impair fish auditory and vestibular sensitivity.
DOI: 10.6084/m9.figshare.7680404.v1
title: R code from Speed-mediated properties of schooling

description: Code used for statistical analysis
DOI: 10.6084/m9.figshare.7701107.v2
title: Database from Ocean acidification affects somatic and otolith growth relationship in fish: evidence from an <i>in situ</i> study.

description: Ocean acidification (OA) may have varied effects on fish eco-physiological responses. Most OA studies have been carried out in laboratory conditions without considering the <i>in situ p</i>CO<sub>2</sub>/pH variability documented for many marine coastal ecosystems. Using a standard otolith ageing technique, we assessed how <i>in situ</i> ocean acidification (ambient, versus end-of-century CO<sub>2</sub> levels) can affect somatic and otolith growth, and their relationship in a coastal fish. Somatic and otolith growth rates of juveniles of the ocellated wrasse <i>Symphodus ocellatus</i> living off a Mediterranean CO<sub>2</sub> seep increased at the high-<i>p</i>CO<sub>2</sub> site. Also, we detected that slower-growing individuals living at ambient <i>p</i>CO<sub>2</sub> levels tend to have larger otoliths at the same somatic length (i.e. higher relative size of otoliths to fish body length) than faster-growing conspecifics living under high <i>p</i>CO<sub>2 </sub>conditions, with this being attributable to the so-called ‘growth effect’. Our findings suggest the possibility of contrasting OA effects on fish fitness, with higher somatic growth rate and possibly higher survival associated with smaller relative size of otoliths that could impair fish auditory and vestibular sensitivity.
DOI: 10.6084/m9.figshare.7701107.v1
title: Database from Ocean acidification affects somatic and otolith growth relationship in fish: evidence from an <i>in situ</i> study

description: Ocean acidification (OA) may have varied effects on fish eco-physiological responses. Most OA studies were carried out in laboratory conditions without considering the <i>in situ p</i>CO<sub>2</sub>/pH variability documented for many marine coastal ecosystems. Using a standard otolith ageing technique, we assessed how <i>in situ</i> ocean acidification (ambient, versus end-of-century CO<sub>2</sub> levels) can affect can affect somatic and otolith growth, and their relationship in a coastal fish. Somatic and otolith growth rates of juveniles from a population of the ocellated wrasse <i>Symphodus ocellatus</i> living off a Mediterranean CO<sub>2</sub> seep, increased at the high-<i>p</i>CO<sub>2</sub> site. Also, we detected that slower growing individuals living at ambient pCO<sub>2</sub> levels tend to have larger otoliths at the same somatic length (i.e. higher relative size of otoliths to fish body length) than faster growing conspecifics living under high pCO<sub>2 </sub>conditions, with this being attributable to the so-called ‘growth effect’. Our findings suggest the possibility of contrasting OA effects on fish fitness, with higher somatic growth rate and possibly higher survival associated to smaller relative size of otoliths that could impair fish auditory and vestibular sensitivity.
DOI: 10.6084/m9.figshare.7701668
title: Raw Data from Variability in the durability of CRISPR-Cas immunity.

description: The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria <i>Streptococcus thermophilus</i> against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology.This article is part of the themed issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7701668.v2
title: Raw Data from Variability in the durability of CRISPR-Cas immunity.

description: The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria <i>Streptococcus thermophilus</i> against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology.This article is part of the themed issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7701668.v1
title: Raw Data from Variability in the durability of clustered regularly interspaced short palindromic repeats-Cas immunity

description: The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various CRISPR (clustered regularly interspaced short palindromic repeats)-Cas alleles of the bacteria <i>Streptococcus thermophilus</i> against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be due to variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology.This article is part of the themed issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7710377
title: Citizen Science Data 2 from Citizen science in Lebanon—a case study for groundwater quality monitoring.

description: Physical, chemical and biological test result data
DOI: 10.6084/m9.figshare.7710377.v2
title: Citizen Science Data 2 from Citizen science in Lebanon—a case study for groundwater quality monitoring.

description: Physical, chemical and biological test result data
DOI: 10.6084/m9.figshare.7710377.v1
title: Citizen Science Data 2 from Citizen science in Lebanon—a case study for ground water quality monitoring

description: Physical, chemical and biological test result data
DOI: 10.6084/m9.figshare.7717961
title: Stata (14) scripts from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers.

description: Stata do files to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7717967
title: Data table from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers.

description: Raw data table to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7717961.v2
title: Stata (14) scripts from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers.

description: Stata do files to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7717961.v1
title: Stata (14) scripts from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers

description: Stata do files to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7717967.v2
title: Data table from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers.

description: Raw data table to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7717967.v1
title: Data table from Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers

description: Raw data table to reproduce all results presented in the paper and in the electronic supplementary material
DOI: 10.6084/m9.figshare.7718321
title: S6 CRISPR_target_results from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718303
title: S7 ARG_ACR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718321.v2
title: S6 CRISPR_target_results from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718321.v1
title: S2 ARG_CRISPR_Cas from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718303.v2
title: S7 ARG_ACR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718303.v1
title: S3 PA_AB_Mutation from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.