cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7844687.v1
title: Data matrix from Species richness and disparity of parareptiles across the end-Permian mass extinction

description: The amniote clade Parareptilia is notable in that members of the clade exhibited a wide array of morphologies, were successful in a variety of ecological niches and survived the end-Permian mass extinction. In order to better understand how mass extinction events can affect clades that survive them, we investigate both the species richness and morphological diversity (disparity) of parareptiles over the course of their history. Furthermore, we examine our observations in the context of other metazoan clades, in order to identify post-extinction survivorship patterns that are present in the clade. The results of our study indicate that there was an early increase in parareptilian disparity, which then fluctuated over the course of the Permian, before it eventually declined sharply towards the end of the Permian and into the Triassic, corresponding with the end-Permian mass extinction event. Interestingly, this is a different trend to what is observed regarding parareptile richness, that shows an almost continuous increase until its overall peak at the end of the Late Permian. Moreover, richness did not experience the same sharp drop at the end of the Permian, reaching a plateau until the Anisian, before dropping sharply and remaining low, with the clade going extinct at the end of the Triassic. This observed pattern is likely due to the fact that, despite the extinction of several morphologically distinct parareptile clades, the procolophonoids, one of the largest parareptilian clades, were diversifying across the Permian–Triassic boundary. With the clade's low levels of disparity and eventually declining species richness, this pattern most resembles a ‘dead clade walking’ pattern.
DOI: 10.6084/m9.figshare.7844672.v2
title: Para supertree R2 from Species richness and disparity of parareptiles across the end-Permian mass extinction.

description: The amniote clade Parareptilia is notable in that members of the clade exhibited a wide array of morphologies, were successful in a variety of ecological niches and survived the end-Permian mass extinction. In order to better understand how mass extinction events can affect clades that survive them, we investigate both the species richness and morphological diversity (disparity) of parareptiles over the course of their history. Furthermore, we examine our observations in the context of other metazoan clades, in order to identify post-extinction survivorship patterns that are present in the clade. The results of our study indicate that there was an early increase in parareptilian disparity, which then fluctuated over the course of the Permian, before it eventually declined sharply towards the end of the Permian and into the Triassic, corresponding with the end-Permian mass extinction event. Interestingly, this is a different trend to what is observed regarding parareptile richness, that shows an almost continuous increase until its overall peak at the end of the Late Permian. Moreover, richness did not experience the same sharp drop at the end of the Permian, reaching a plateau until the Anisian, before dropping sharply and remaining low, with the clade going extinct at the end of the Triassic. This observed pattern is likely to be due to the fact that, despite the extinction of several morphologically distinct parareptile clades, the procolophonoids, one of the largest parareptilian clades, were diversifying across the Permian–Triassic boundary. With the clade's low levels of disparity and eventually declining species richness, this pattern most resembles a ‘dead clade walking’ pattern.
DOI: 10.6084/m9.figshare.7844672.v1
title: Para supertree R2 from Species richness and disparity of parareptiles across the end-Permian mass extinction

description: The amniote clade Parareptilia is notable in that members of the clade exhibited a wide array of morphologies, were successful in a variety of ecological niches and survived the end-Permian mass extinction. In order to better understand how mass extinction events can affect clades that survive them, we investigate both the species richness and morphological diversity (disparity) of parareptiles over the course of their history. Furthermore, we examine our observations in the context of other metazoan clades, in order to identify post-extinction survivorship patterns that are present in the clade. The results of our study indicate that there was an early increase in parareptilian disparity, which then fluctuated over the course of the Permian, before it eventually declined sharply towards the end of the Permian and into the Triassic, corresponding with the end-Permian mass extinction event. Interestingly, this is a different trend to what is observed regarding parareptile richness, that shows an almost continuous increase until its overall peak at the end of the Late Permian. Moreover, richness did not experience the same sharp drop at the end of the Permian, reaching a plateau until the Anisian, before dropping sharply and remaining low, with the clade going extinct at the end of the Triassic. This observed pattern is likely due to the fact that, despite the extinction of several morphologically distinct parareptile clades, the procolophonoids, one of the largest parareptilian clades, were diversifying across the Permian–Triassic boundary. With the clade's low levels of disparity and eventually declining species richness, this pattern most resembles a ‘dead clade walking’ pattern.
DOI: 10.6084/m9.figshare.7868735
title: Maximum clade credibility tree for HA segment from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: Maximum clade credibility tree for HA segment
DOI: 10.6084/m9.figshare.7868729
title: Supporting Data from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: Supporting Material containing data used to generate figures and results
DOI: 10.6084/m9.figshare.7868735.v2
title: Maximum clade credibility tree for HA segment from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: Maximum clade credibility tree for HA segment
DOI: 10.6084/m9.figshare.7868741
title: BEAST XML file for HA segment phylogeny from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: BEAST XML file for HA segment phylogeny
DOI: 10.6084/m9.figshare.7868735.v1
title: Maximum clade credibility tree for HA segment from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

description: Maximum clade credibility tree for HA segment
DOI: 10.6084/m9.figshare.7868729.v2
title: Supporting Data from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: Supporting Material containing data used to generate figures and results
DOI: 10.6084/m9.figshare.7868729.v1
title: Supporting Data from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

description: Supporting Material containing data used to generate figures and results
DOI: 10.6084/m9.figshare.7868741.v2
title: BEAST XML file for HA segment phylogeny from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

description: BEAST XML file for HA segment phylogeny
DOI: 10.6084/m9.figshare.7868741.v1
title: BEAST XML file for HA segment phylogeny from Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

description: BEAST XML file for HA segment phylogeny
DOI: 10.6084/m9.figshare.8033990
title: Zip file from Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance.

description: All R scripts for model simulations, figures and analyses presented in this article
DOI: 10.6084/m9.figshare.8033990.v2
title: Zip file from Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance.

description: All R scripts for model simulations, figures and analyses presented in this article
DOI: 10.6084/m9.figshare.7878542
title: Marin.csv from Climate change effects on Black Sigatoka disease of banana.

description: CSV file of latent periods and incubation periods published in Marin et al. (2003)
DOI: 10.6084/m9.figshare.8033990.v1
title: Zip file from Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance

description: All R scripts for model simulations, figures and analyses presented in this article
DOI: 10.6084/m9.figshare.7878536
title: Uchoa.csv from Climate change effects on Black Sigatoka disease of banana.

description: AUDPC, temperature and LWD data abstracted from Uchoa (2010)
DOI: 10.6084/m9.figshare.7878542.v2
title: Marin.csv from Climate change effects on Black Sigatoka disease of banana.

description: CSV file of latent periods and incubation periods published in Marin et al. (2003)
DOI: 10.6084/m9.figshare.7878536.v2
title: Uchoa.csv from Climate change effects on Black Sigatoka disease of banana.

description: AUDPC, temperature and LWD data abstracted from Uchoa (2010)
DOI: 10.6084/m9.figshare.7878536.v1
title: Uchoa.csv from Climate change effects on Black Sigatoka disease of banana

description: AUDPC, temperature and LWD data abstracted from Uchoa (2010)
DOI: 10.6084/m9.figshare.7878542.v1
title: Marin.csv from Climate change effects on Black Sigatoka disease of banana

description: CSV file of latent periods and incubation periods published in Marin et al. (2003)
DOI: 10.6084/m9.figshare.7878548
title: CReg.csv from Climate change effects on Black Sigatoka disease of banana.

description: Example of JRA55 estimates of canopy temperature, canopy surface moisture, and RH for a region of Costa Rica, January 2000.
DOI: 10.6084/m9.figshare.7878533
title: Guapiles.csv from Climate change effects on Black Sigatoka disease of banana.

description: JRA55 estimates of canopy temperature and RH for comparison with Marin et al. (2003) data
DOI: 10.6084/m9.figshare.7878533.v2
title: Guapiles.csv from Climate change effects on Black Sigatoka disease of banana.

description: JRA55 estimates of canopy temperature and RH for comparison with Marin et al. (2003) data
DOI: 10.6084/m9.figshare.7878533.v1
title: Guapiles.csv from Climate change effects on Black Sigatoka disease of banana

description: JRA55 estimates of canopy temperature and RH for comparison with Marin et al. (2003) data
DOI: 10.6084/m9.figshare.7878548.v2
title: CReg.csv from Climate change effects on Black Sigatoka disease of banana.

description: Example of JRA55 estimates of canopy temperature, canopy surface moisture, and RH for a region of Costa Rica, January 2000.
DOI: 10.6084/m9.figshare.7878548.v1
title: CReg.csv from Climate change effects on Black Sigatoka disease of banana

description: Example of JRA55 estimates of canopy temperature, canopy surface moisture, and RH for a region of Costa Rica, January 2000.
DOI: 10.6084/m9.figshare.7892366
title: Supplementary Data from Sexual ornaments but not weapons trade off against testes size in primates.

description: Dataset with references
DOI: 10.6084/m9.figshare.7892366.v2
title: Supplementary Data from Sexual ornaments but not weapons trade off against testes size in primates.

description: Dataset with references
DOI: 10.6084/m9.figshare.7892366.v1
title: Supplementary Data from Sexual ornaments but not weapons trade off against testes size in primates

description: Dataset with references
DOI: 10.6084/m9.figshare.7892777
title: Data S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Character matrix used in phylogenetic analyses in NEXUS file format.
DOI: 10.6084/m9.figshare.7892759
title: Table S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Character matrix used in phylogenetic analyses.
DOI: 10.6084/m9.figshare.7892777.v2
title: Data S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Character matrix used in phylogenetic analyses in NEXUS file format.
DOI: 10.6084/m9.figshare.7892786
title: Data S3 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Strict consensus tree from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7892759.v2
title: Table S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Character matrix used in phylogenetic analyses.
DOI: 10.6084/m9.figshare.7892777.v1
title: Data S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Character matrix used in phylogenetic analyses in NEXUS file format.
DOI: 10.6084/m9.figshare.7892786.v2
title: Data S3 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Strict consensus tree from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7892789
title: Data S2 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Six equally most parsimonious trees from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7892759.v1
title: Table S1 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Character matrix used in phylogenetic analyses.
DOI: 10.6084/m9.figshare.7892780
title: Data S5 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892783
title: Data S4 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892780.v2
title: Data S5 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892786.v1
title: Data S3 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Strict consensus tree from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7892783.v2
title: Data S4 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892789.v2
title: Data S2 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

description: Six equally most parsimonious trees from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7892780.v1
title: Data S5 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892783.v1
title: Data S4 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, <i>Sollasina cthulhu</i>, from the Silurian Herefordshire Lagerstätte, UK. <i>Sollasina cthulhu</i> belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of <i>S. cthulhu</i> in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that <i>Sollasina</i> and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.
DOI: 10.6084/m9.figshare.7892789.v1
title: Data S2 from A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

description: Six equally most parsimonious trees from parsimony analysis in .TRE file format.
DOI: 10.6084/m9.figshare.7906997
title: Table S1 from The history, genome and biology of NCTC 30: a non-pandemic <i>Vibrio cholerae</i> isolate from World War One.

description: Additional genomes used in this study (attached .xls spreadsheet).
DOI: 10.6084/m9.figshare.7906997.v2
title: Table S1 from The history, genome and biology of NCTC 30: a non-pandemic <i>Vibrio cholerae</i> isolate from World War One.

description: Additional genomes used in this study (attached .xls spreadsheet).
DOI: 10.6084/m9.figshare.7907000
title: Table S2 from The history, genome and biology of NCTC 30: a non-pandemic <i>Vibrio cholerae</i> isolate from World War One.

description: Accession numbers for NCTC 30 genome sequencing (attached .xls spreadsheet).