cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4579231
title: Dataset_S4_matrix_4.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579222
title: Dataset_S2_matrix_2.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579216
title: Dataset_S3_matrix_3.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579222.v1
title: Dataset_S2_matrix_2.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579231.v1
title: Dataset_S4_matrix_4.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579213
title: Table_S2_matrix_for_pairwise_correlations.xls from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579210
title: Calycopis_supplemental_table_S1 from When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

description: Two species of hairstreak butterflies from the genus <i>Calycopis</i> are known in the United States: <i>C. cecrops</i> and <i>C. isobeon</i>. Analysis of mitochondrial COI barcodes of <i>Calycopis</i> revealed <i>cecrops</i>-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American <i>Calycopis</i> species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 <i>Calycopis</i> specimens of four species: <i>C. cecrops</i>, <i>C. isobeon</i>, <i>C. quintana</i> and <i>C. bactra</i>. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA <i>Calycopis</i> with atypical barcodes grouped with Central American species <i>C. quintana</i> by mitochondria, nuclear genome trees placed them within typical USA <i>C. cecrops</i> in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between <i>C. cecrops</i> and <i>C. isobeon</i>. About 2.3% of each <i>C. cecrops</i> genome has probably (<i>p</i>-value C. isobeon and about 3.4% of each <i>C. isobeon</i> genome may have come from <i>C. cecrops.</i> The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
DOI: 10.6084/m9.figshare.4579213.v1
title: Table_S2_matrix_for_pairwise_correlations.xls from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579216.v1
title: Dataset_S3_matrix_3.txt from Computational biomechanics changes our view on insect head evolution

description: Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to <i>objectively</i> identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows a highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
DOI: 10.6084/m9.figshare.4579210.v2
title: Calycopis_supplemental_table_S1 from When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

description: Two species of hairstreak butterflies from the genus <i>Calycopis</i> are known in the United States: <i>C. cecrops</i> and <i>C. isobeon</i>. Analysis of mitochondrial COI barcodes of <i>Calycopis</i> revealed <i>cecrops</i>-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American <i>Calycopis</i> species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 <i>Calycopis</i> specimens of four species: <i>C. cecrops</i>, <i>C. isobeon</i>, <i>C. quintana</i> and <i>C. bactra</i>. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA <i>Calycopis</i> with atypical barcodes grouped with Central American species <i>C. quintana</i> by mitochondria, nuclear genome trees placed them within typical USA <i>C. cecrops</i> in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between <i>C. cecrops</i> and <i>C. isobeon</i>. About 2.3% of each <i>C. cecrops</i> genome has probably (<i>p</i>-value C. isobeon and about 3.4% of each <i>C. isobeon</i> genome may have come from <i>C. cecrops.</i> The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
DOI: 10.6084/m9.figshare.4579210.v1
title: Calycopis_supplemental_table_S1 from When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

description: Two species of Hairstreak butterflies from the genus <i>Calycopis</i> are known in the United States: <i>C. cecrops</i> and <i>C. isobeon</i>. Analysis of mitochondrial COI barcodes of <i>Calycopis</i> revealed <i>cecrops</i>-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American <i>Calycopis</i> species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 <i>Calycopis</i> specimens of four species: <i>C. cecrops</i>, <i>C. isobeon</i>, <i>C. quintana</i> and <i>C. bactra</i>. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA <i>Calycopis</i> with atypical barcodes grouped with Central American species <i>C. quintana</i> by mitochondria, nuclear genome trees placed them within typical USA <i>C. cecrops</i> in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between <i>C. cecrops</i> and <i>C. isobeon</i>. About 2.3% of each <i>C. cecrops</i> genome has likely (<i>p</i>-value C. isobeon and about 3.4% of each <i>C. isobeon</i> genome may have come from <i>C. cecrops.</i> The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
DOI: 10.6084/m9.figshare.4579162
title: Data from: Fire and plant diversity at the global scale

description: Data and maps from:<br>Pausas J.G. & Ribeiro E. (2017). Fire and plant diversity at the global scale. <i>Global Ecology and Biogeogragphy</i> doi: 10.1111/geb.12596<br>There are 3 files:<br>1) A .csv file with the data for each ecoregion, including biome, diversity, mean NDVI mean, spatial variability of NDVI, temporal variability of NDVI, fire activity, radiative power, and seasonality in temperature.<br>2) A .zip file with the global maps of fire activity and plant diversity (for each ecoregion) in shape (GIS) format.<br>3) A .jpg file (image) with the same maps as 2). It corresponds to Fig. 1 of the paper.<br><br>
DOI: 10.6084/m9.figshare.4579096
title: Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity

description: Oligouridylate binding protein 1b (UBP1b), a marker protein of plant stress granules (SGs), plays a role in heat stress tolerance in plants. A previous microarray analysis revealed that the expression of several ABA signaling-related genes is higher in <i>UBP1b</i>-overexpressing <i>Arabidopsis</i> plants (<i>UBP1b</i>-ox) subjected to both non-stressed and heat stress conditions. Root elongation and seed germination assays demonstrated that <i>UBP1b</i>-ox exhibited hypersensitivity to ABA. RT-qPCR analysis confirmed that mitogen-activated protein kinase (MAPK) cascade genes, such as <i>MPK3, MKK4</i>, and <i>MKK9</i> were upregulated in <i>UBP1b</i>-ox plants. ABA receptor genes, including <i>PYL5</i> and <i>PYL6</i>, were also upregulated in <i>UBP1b</i>-ox plants. mRNA of <i>WRKY33</i> – a downstream gene of MPK3 and an upstream gene of ethylene biosynthesis, exhibited high levels of accumulation, although the level of endogenous ABA was not significantly different between <i>UBP1b</i>-ox and control plants. In addition, RNA decay analysis revealed that <i>WRKY33</i> was more stable in <i>UBP1b</i>-ox plants, indicating that the mRNA of <i>WRKY33</i> was protected within UBP1b SGs. Collectively, these data demonstrate that UBP1b plays an important role in plant response to ABA.
DOI: 10.6084/m9.figshare.4579096.v1
title: Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity

description: Oligouridylate binding protein 1b (UBP1b), a marker protein of plant stress granules (SGs), plays a role in heat stress tolerance in plants. A previous microarray analysis revealed that the expression of several ABA signaling-related genes is higher in <i>UBP1b</i>-overexpressing <i>Arabidopsis</i> plants (<i>UBP1b</i>-ox) subjected to both non-stressed and heat stress conditions. Root elongation and seed germination assays demonstrated that <i>UBP1b</i>-ox exhibited hypersensitivity to ABA. RT-qPCR analysis confirmed that mitogen-activated protein kinase (MAPK) cascade genes, such as <i>MPK3, MKK4</i>, and <i>MKK9</i> were upregulated in <i>UBP1b</i>-ox plants. ABA receptor genes, including <i>PYL5</i> and <i>PYL6</i>, were also upregulated in <i>UBP1b</i>-ox plants. mRNA of <i>WRKY33</i> – a downstream gene of MPK3 and an upstream gene of ethylene biosynthesis, exhibited high levels of accumulation, although the level of endogenous ABA was not significantly different between <i>UBP1b</i>-ox and control plants. In addition, RNA decay analysis revealed that <i>WRKY33</i> was more stable in <i>UBP1b</i>-ox plants, indicating that the mRNA of <i>WRKY33</i> was protected within UBP1b SGs. Collectively, these data demonstrate that UBP1b plays an important role in plant response to ABA.
DOI: 10.6084/m9.figshare.4579072
title: Input data for 2017_ms_immunostim

description: Please note that this information accompanies the github code that explains the complete analysis, found at: https://github.com/bensutherland/2017_ms_immunostim<br><br>Input data files are to be put in the '02_raw_data' folder of the above git repo, and they include: 1) Physiology and lice count data: immunostim_data-jan21-15.csv<br>2) Lice qPCR input datanew-together_formatted-notdouble.txt<br><br>3) Salmon qPCR input datasalmon_qpcr-oct23-14-longform.csv<br><br>Interpretation files are to be put into the '00_archive' folder of the above git repo and they include:1) The interpretation file for the microarray analysis:Targets_2color_immunostim.csv<br><br>2) The control spots file for the microarray analysis:SpotTypes<br><br>3) The short form annotation file for the microarray analysis:koop_Lsal38K_2010-02-25b-short.txt<br><br>