cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9830843
title: Child data from Echoes from the past: synaesthetic colour associations reflect childhood gender stereotypes.

description: De-identified, preprocessed child data
DOI: 10.6084/m9.figshare.9830846
title: Analysis Routine from Echoes from the past: synaesthetic colour associations reflect childhood gender stereotypes.

description: R code to produce numbers/graphs from this paper
DOI: 10.6084/m9.figshare.9830837.v1
title: Adult data from Echoes from the past: synesthetic colour associations reflect childhood gender stereotypes

description: De-identified, preprocessed adult data
DOI: 10.6084/m9.figshare.9830843.v2
title: Child data from Echoes from the past: synaesthetic colour associations reflect childhood gender stereotypes.

description: De-identified, preprocessed child data
DOI: 10.6084/m9.figshare.9830843.v1
title: Child data from Echoes from the past: synesthetic colour associations reflect childhood gender stereotypes

description: De-identified, preprocessed child data
DOI: 10.6084/m9.figshare.9830846.v2
title: Analysis Routine from Echoes from the past: synaesthetic colour associations reflect childhood gender stereotypes.

description: R code to produce numbers/graphs from this paper
DOI: 10.6084/m9.figshare.9830846.v1
title: Analysis Routine from Echoes from the past: synesthetic colour associations reflect childhood gender stereotypes

description: R code to produce numbers/graphs from this paper
DOI: 10.6084/m9.figshare.9853208
title: Supplementary File 2 from Inferring Atlantic salmon post-smolt migration patterns using genetic assignment.

description: The datasets supporting the manuscript
DOI: 10.6084/m9.figshare.9853208.v2
title: Supplementary File 2 from Inferring Atlantic salmon post-smolt migration patterns using genetic assignment.

description: The datasets supporting the manuscript
DOI: 10.6084/m9.figshare.9853208.v1
title: Supplementary File 2 from Inferring Atlantic salmon post-smolt migration patterns using genetic assignment

description: The datasets supporting the manuscript
DOI: 10.6084/m9.figshare.9905681
title: Supplementary Tables S1 - S4 from Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction.

description: Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland–Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised timescale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
DOI: 10.6084/m9.figshare.9905681.v2
title: Supplementary Tables S1 - S4 from Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction.

description: Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland–Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised timescale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
DOI: 10.6084/m9.figshare.9905681.v1
title: Supplementary Tables S1 - S4 from Recalibration of insect evolutionary timescale using Mount San Giorgio fossils suggests survival of key lineages through the end-Permian Extinction

description: Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland–Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised timescale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
DOI: 10.6084/m9.figshare.9918698
title: Appendix A1 and Supplementary Tables from How well do revegetation plantings capture genetic diversity?.

description: Analysis results by study for comparisons of genetic diversity in revegetation plantings to natural stands (Appendix A1), supplementary tables of count data for chi-squared tests (Table S1) and genetic comparisons where multiple cohorts were sampled within a study (Table S2)
DOI: 10.6084/m9.figshare.9918698.v2
title: Appendix A1 and Supplementary Tables from How well do revegetation plantings capture genetic diversity?.

description: Analysis results by study for comparisons of genetic diversity in revegetation plantings to natural stands (Appendix A1), supplementary tables of count data for chi-squared tests (Table S1) and genetic comparisons where multiple cohorts were sampled within a study (Table S2)
DOI: 10.6084/m9.figshare.9918707
title: Appendix A from Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: <i>Theodoxus</i>).

description: Table S1, Table S2, Figure S1
DOI: 10.6084/m9.figshare.9918698.v1
title: Appendix A1 and Supplementary Tables from How well do revegetation plantings capture genetic diversity?

description: Analysis results by study for comparisons of genetic diversity in revegetation plantings to natural stands (Appendix A1), supplementary tables of count data for chi-squared tests (Table S1) and genetic comparisons where multiple cohorts were sampled within a study (Table S2)
DOI: 10.6084/m9.figshare.9918707.v2
title: Appendix A from Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: <i>Theodoxus</i>).

description: Table S1, Table S2, Figure S1
DOI: 10.6084/m9.figshare.9918707.v1
title: Appendix A from Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: Theodoxus)

description: Table S1, Table S2, Figure S1
DOI: 10.6084/m9.figshare.9942794
title: Trichechus manatus from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles.

description: Kappa-casein sequence from the manatee (Trichechus manatus)
DOI: 10.6084/m9.figshare.9942788
title: kappa case in alignment from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles.

description: Alignment of kappa-casein sequences used in the study
DOI: 10.6084/m9.figshare.9942794.v2
title: Trichechus manatus from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles.

description: Kappa-casein sequence from the manatee (Trichechus manatus)
DOI: 10.6084/m9.figshare.9942788.v2
title: kappa case in alignment from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles.

description: Alignment of kappa-casein sequences used in the study
DOI: 10.6084/m9.figshare.9942794.v1
title: Trichechus manatus from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles

description: Kappa-casein sequence from the manatee (Trichechus manatus)
DOI: 10.6084/m9.figshare.9942788.v1
title: kappa case in alignment from Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles

description: Alignment of kappa-casein sequences used in the study
DOI: 10.6084/m9.figshare.9963872
title: Supplementary Code from Cross-scale cooperation enables sustainable use of a common-pool resource.

description: Mathematica notebook (.nb) used to generate our results.
DOI: 10.6084/m9.figshare.9963872.v2
title: Supplementary Code from Cross-scale cooperation enables sustainable use of a common-pool resource.

description: Mathematica notebook (.nb) used to generate our results.
DOI: 10.6084/m9.figshare.9963872.v1
title: Supplementary Code from Cross-scale cooperation enables sustainable use of a common-pool resource

description: Mathematica notebook (.nb) used to generate our results.
DOI: 10.6084/m9.figshare.9971627
title: Table S1 from Functional identification of a <i>Streptomyces lividans</i> FKBP-like protein involved in the folding of overproduced secreted proteins.

description: Proteins analysed by the Selected Reaction Monitoring experiment (SRM/MRM)
DOI: 10.6084/m9.figshare.9971627.v2
title: Table S1 from Functional identification of a <i>Streptomyces lividans</i> FKBP-like protein involved in the folding of overproduced secreted proteins.

description: Proteins analysed by the Selected Reaction Monitoring experiment (SRM/MRM)
DOI: 10.6084/m9.figshare.9971627.v1
title: Table S1 from Functional identification of a <i>Streptomyces lividans</i> FKBP-like protein involved in the folding of overproduced secreted proteins

description: Proteins analysed by the Selected Reaction Monitoring experiment (SRM/MRM)
DOI: 10.6084/m9.figshare.9974351
title: Table S5 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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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.9974348
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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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
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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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.9974351.v2
title: Table S5 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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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.9974348.v2
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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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.v2
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 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signalling. Twenty-six 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.9974351.v1
title: Table S5 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.