cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9974348.v1
title: Table S6 from Expression analyses of cave mollies (<i>Poecilia mexicana</i>) reveal key genes involved in the early evolution of eye regression

description: Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish <i>Poecilia mexicana</i> (cave molly) exhibit reduced—albeit functional—eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of <i>P. mexicana</i> to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 29 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-seven of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in <i>P. mexicana</i>, shedding further light on regressive evolution in cavefish.
DOI: 10.6084/m9.figshare.9974342.v1
title: Table S7 from Expression analyses of cave mollies (<i>Poecilia mexicana</i>) reveal key genes involved in the early evolution of eye regression

description: Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish <i>Poecilia mexicana</i> (cave molly) exhibit reduced—albeit functional—eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of <i>P. mexicana</i> to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 29 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-seven of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in <i>P. mexicana</i>, shedding further light on regressive evolution in cavefish.
DOI: 10.6084/m9.figshare.9989246
title: Table S3 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table of protein-coding human intelligence-related SNPs detected in juvenile Area X modules. Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9989240
title: Table S1 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table displays behaviorally relevant genes that show transcriptional convergence between songbird Area X (Burkett et al, 2018) and human putamen (Pfenning et al, 2014).
DOI: 10.6084/m9.figshare.9989246.v2
title: Table S3 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table of protein-coding human intelligence-related SNPs detected in juvenile Area X modules. Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9989243
title: Table S2 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table of non-coding human intelligence-related SNP genes detected in juvenile Area X modules. Variants associated with changes in gene expression are shown under 'eQTL Direction.' Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9989246.v1
title: Table S3 from Birdsong as a window into language origins and evolutionary neuroscience

description: Table of protein-coding human intelligence-related SNPs detected in juvenile Area X modules. Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9989240.v2
title: Table S1 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table displays behaviorally relevant genes that show transcriptional convergence between songbird Area X (Burkett et al, 2018) and human putamen (Pfenning et al, 2014).
DOI: 10.6084/m9.figshare.9989243.v2
title: Table S2 from Birdsong as a window into language origins and evolutionary neuroscience.

description: Table of non-coding human intelligence-related SNP genes detected in juvenile Area X modules. Variants associated with changes in gene expression are shown under 'eQTL Direction.' Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9989240.v1
title: Table S1 from Birdsong as a window into language origins and evolutionary neuroscience

description: Table displays behaviorally relevant genes that show transcriptional convergence between songbird Area X (Burkett et al, 2018) and human putamen (Pfenning et al, 2014).
DOI: 10.6084/m9.figshare.9989243.v1
title: Table S2 from Birdsong as a window into language origins and evolutionary neuroscience

description: Table of non-coding human intelligence-related SNP genes detected in juvenile Area X modules. Variants associated with changes in gene expression are shown under 'eQTL Direction.' Primary juvenile Area X module assignment is listed under "module.x". Gene significance score for the variability induction paradigm is listed under "gs.ns.ud.entropy.effect" (column heading preserved from original publication in Burkett et al. 2018). FDR corrected p value q is listed under "q.gs.ns.ud.entropy.effect".
DOI: 10.6084/m9.figshare.9999947
title: Data for BdvsSm Assay (color corrected) from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Data used in analysis of Bd vs Sm assay as per Bell et al.
DOI: 10.6084/m9.figshare.9999947.v2
title: Data for BdvsSm Assay (color corrected) from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Data used in analysis of Bd vs Sm assay as per Bell et al.
DOI: 10.6084/m9.figshare.9999956
title: In vivo Acris Experiment Data from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Data collected from the in vivo Acris experiment including date, treatment, Bd detection, mortality, mass, and alpha diversity data.
DOI: 10.6084/m9.figshare.9999947.v1
title: Data for BdvsSm Assay (color corrected) from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host

description: Data used in analysis of Bd vs Sm assay as per Bell et al.
DOI: 10.6084/m9.figshare.9999953
title: Sm Growth Curves from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Growth curves at 21C comparing WT and mutant-pigM Sm
DOI: 10.6084/m9.figshare.9999956.v2
title: In vivo Acris Experiment Data from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Data collected from the in vivo Acris experiment including date, treatment, Bd detection, mortality, mass, and alpha diversity data.
DOI: 10.6084/m9.figshare.9999953.v2
title: Sm Growth Curves from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host.

description: Growth curves at 21C comparing WT and mutant-pigM Sm
DOI: 10.6084/m9.figshare.10029239
title: Full model and model dredging txt files from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.9999956.v1
title: In vivo Acris Experiment Data from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host

description: Data collected from the in vivo Acris experiment including date, treatment, Bd detection, mortality, mass, and alpha diversity data.
DOI: 10.6084/m9.figshare.9999953.v1
title: Sm Growth Curves from <i>Serratia marcescens</i> shapes cutaneous bacterial communities and influences survival of an amphibian host

description: Growth curves at 21C comparing WT and mutant-pigM Sm
DOI: 10.6084/m9.figshare.10029239.v2
title: Full model and model dredging txt files from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029245
title: Datasets of hippocampal subsection and brain area dimorphism plus the phylogenetic tree used from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029239.v1
title: Full model and model dredging txt files from Primate hippocampus size and organization are predicted by sociality but not diet

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029242
title: R code for all the analysis included from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029245.v2
title: Datasets of hippocampal subsection and brain area dimorphism plus the phylogenetic tree used from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029236
title: Results from all the PGSL analysis in separate txt files with ANOVA tables from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029242.v2
title: R code for all the analysis included from Primate hippocampus size and organization are predicted by sociality but not diet.

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.