Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
14,185
datasets available to search
ShareScore release 0.9.0
Dataset results
14,185 results for “phylogenies”
Fig. 17.5 in Chapter 17: Gigantism, Dwarfism, and Cope's Rule: "Nothing in Evolution Makes Sense without a Phylogeny"
Fig. 17.5. Three examples of bodysize evo
Fig. 1 in Plesiosoricids from early Oligocene fissure fillings in South Germany, with remarks on plesiosoricid phylogeny
Fig. 1. Sketch map with the location of the Möhren site.
Fig. 7 in Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)
Fig. 7 Bayesian, ultrametric, unrooted circle tree for 16S. Format and labeling as in Fig. 4
Alignment and tree files for archaeal NusA2 phylogeny
<p>These are the data underlying the phylogenetic analysis of archaeal NusA2 in Figure 3D in our manuscript:</p> <h1><strong>Archaeal NusA2 is the evolutionary ancestor of ribosomal protein eS7 in eukaryotes</strong></h1> <p>Duy Khanh Phung, Simona Pilotto, Dorota Matelska, Fabian Blombach, Nikos Pinotsis, Ladislav Hovan, Francesco Luigi Gervasio, and Finn Werner</p> <p>(under revision)</p>
Supporting Information and Data from: A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and 'archaic' South American ungulates
<p>This is the Supporting Information and Data from: H. P. Püschel, S. L. Shelley, T. E. Williamson, F. A. Perini, J. R. Wible, S. L. Brusatte. 2024. A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and ‘archaic’ South American ungulates. It contains the following files:</p> <p>Table S1: OCCURENCES OF LITOPTERNS BY SALMAS</p> <p>Supplementary Information File S1: OTHER EARLY UNGULATES OF INTEREST</p> <p>Supplementary Information File S2: TAXON SAMPLING AND TAXONOMIC COMMENTS</p> <p>Supplementary Information File S3: CHARACTER LIST</p> <p>Supplementary Information File S4: NEXUS FILE WITH H1 MATRIX AND SCRIPTS FOR REPLICATING THE ANALYSES IN MRBAYES</p> <p>Supplementary Information File S5: NEXUS FILE WITH H2 MATRIX AND SCRIPTS FOR REPLICATING THE ANALYSES IN MRBAYES</p> <p>Supplementary Information File S6: SALMAS’/STAGES’ LOWER AND UPPER LIMITS IN MA </p> <p>Supplementary Information File S7: LIST OF SYNAPOMORPHIES AND AUTAPOMORPHIES</p> <p>Supplementary Information File S8: ADDITIONAL TIP-DATED BAYESIAN PHYLOGENETIC ANALYSES RESULTS</p>
Table 2 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
<p>Table 2. Parenthetical notation of the seven cladograms most parcimonious obtained using equal and implied weighting with k values from 1-10.</p><table><tbody><tr><th>Cladograms from equal weighting from implied weighting (<i>K</i> values)</th><th>Correspondent cladograms</th><th>Parenthetical notation</th></tr></tbody><tbody><tr><th>*Cladogram 1</th><td><i>K</i> 3, <i>K</i> 4, <i>K</i> 5, <i>K</i> 6, <i>K</i> 7, <i>K</i> 8,and <i>K</i> 10</td><td>(( <i>Ce. capitata</i> (<i>D.teretrura</i> (<i>S.crassitibia</i> (<i>I.setiventris, L.sahlbergiana</i> )))) (<i>Ca.personata</i> (<i>Ca.aczeli</i> (<i>Ca.bernardii, Ca.miliaria</i> ))))</td></tr><tr><th>Cladogram 2</th><td>(( <i>Ce. capitata</i> (<i>D.teretrura</i> (<i>S.crassitibia</i> (<i>I.setiventris, L.sahlbergiana</i> )))) (( <i>Ca.personata, Ca.aczeli</i>),(<i>Ca.bernardii, Ca.miliaria</i> )))</td><td></td></tr><tr><th>Cladogram 3</th><td><i>K</i> 3, <i>K</i> 4, <i>K</i> 5, <i>K</i> 6, <i>K</i> 7, <i>K</i> 8,and <i>K</i> 10</td><td>(( <i>Ce. capitata</i> (<i>S.crassitibia</i> (<i>L.sahlbergiana</i> (<i>I.setiventris, D.teretrura</i> )))) (<i>Ca.personata</i> (<i>Ca.aczeli</i> (<i>Ca.bernardii, Ca.miliaria</i> ))))</td></tr><tr><th>Cladogram 4</th><td><i>K</i> 3, <i>K</i> 4, <i>K</i> 5, <i>K</i> 6, <i>K</i> 7, <i>K</i> 8, <i>K</i> 9,and <i>K</i> 10</td><td>(( <i>Ce. capitata</i> (<i>S.crassitibia</i> (<i>I.setiventris</i> (<i>L.sahlbergiana, D.teretrura</i> )))) (<i>Ca.personata</i> (<i>Ca.aczeli</i> (<i>Ca.bernardii, Ca.miliaria</i> ))))</td></tr><tr><th>Cladogram 5</th><td>(( <i>Ce. capitata</i> (<i>S.crassitibia</i> (<i>L.sahlbergiana</i> (<i>I.setiventris, D.teretrura</i> )))) (( <i>Ca.personata, Ca.aczeli</i>),(<i>Ca.bernardii, Ca.miliaria</i> )))</td><td></td></tr><tr><th>Cladogram 6</th><td>(( <i>Ce. capitata</i> (<i>S.crassitibia</i> (<i>I.setiventris</i> (<i>L.sahlbergiana, D.teretrura</i> )))) (( <i>Ca.personata, Ca.aczeli</i>),(<i>Ca.bernardii, Ca.miliaria</i> )))</td><td></td></tr><tr><th>Cladogram without correspondent in equal weighting analysis <i>K</i> 1, <i>K</i> 2 and <i>K</i> 3</th><td>(( <i>Ce. capitata</i> (<i>D.teretrura</i> (<i>L.sahlbergiana</i> (<i>I. setiventris, S.crassitibia</i> )))) (<i>Ca.personata</i> (<i>Ca.aczeli</i> (<i>Ca.bernardii, Ca.miliaria</i> ))))</td><td></td></tr></tbody></table><p><b>Number of cladogram using equal weighting: six cladograms. Number of cladogram using implied weighting with <i>K</i> 1: 1 cladogram; <i>K</i> 2: 1 cladogram; <i>K</i> 3: 4 cladograms; <i>K</i> 4- <i>K</i> 8: three cladograms;</b> <b><i>K</i> 9: 1 cladogram; and <i>K</i> 10: three cladograms, total of 25 cladograms. Number of cladograms using equal and implied weighting 31 cladograms, distributes in seven different hypothesis. *Cladogram</b> selected to represents the phylogeny of Carrerapyrgota.</p>
Table 1 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
<p>Table 1. Matrix of Morphological Characters used for <i>Carrerapyrgota</i> and outgroups.</p><table><tbody><tr><th>Taxon/Character</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th><th>10</th><th>11</th><th>12</th><th>13</th><th>14</th><th>15</th><th>16</th><th>17</th><th>18</th><th>19</th><th>20</th><th>21</th><th>22</th></tr></tbody><tbody><tr><th><i>Ceratitis capitata</i></th><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>1</td><td>1</td><td>0</td><td>1</td><td>3</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>1</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Descoleia teretrura</i></th><td>0</td><td>0</td><td>0</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>—</td><td>0</td><td>0</td><td>0</td><td>3</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td></tr><tr><th><i>Stenopyrgota crassitiba</i></th><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>2</td><td>1</td><td>1</td><td>—</td><td>0</td><td>0</td><td>—</td><td>1</td><td>1</td><td>0</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>—</td></tr><tr><th><i>Idiopyrgota setiventris</i></th><td>0</td><td>0</td><td>0</td><td>0</td><td>—</td><td>2</td><td>1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>0</td><td>2</td><td>1</td><td>0</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><th><i>Leptopyrgota sahlbergiana</i></th><td>0</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>?</td></tr><tr><th><i>C.aczeli</i></th><td>0</td><td>1</td><td>1</td><td>1</td><td>—</td><td>2</td><td>1</td><td>1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><th><i>C.bernardii</i></th><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>2</td><td>1</td><td>1</td><td>2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td></tr><tr><th><i>C.miliaria</i></th><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>2</td><td>1</td><td>1</td><td>2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td></tr><tr><th><i>C.personata</i></th><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>2</td><td>1</td><td>1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>3</td><td>1</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>—</td></tr></tbody></table>
Table 3 in Fig. 11. Left G 1 s in Tuerkayana latens, a New Species of Land Crab from French Polynesia, with a Discussion on the Phylogeny of the Genus (Crustacea: Decapoda: Brachyura: Gecarcinidae)
<p><b>Table 3.</b> The frequency of contribution of environmental variables in predicting the clades geographic distribution models</p><table><tbody><tr><th>Environmental variable (unit)</th><th>Clade <i>I</i></th><th>Clade <i>III</i></th></tr></tbody><tbody><tr><th>Temperature Mean</th><td>39.8</td><td>56.8</td></tr><tr><th>Temperature Range</th><td>25.7</td><td>4.9</td></tr><tr><th>Phytoplankton Mean</th><td>15.3</td><td>5.9</td></tr><tr><th>Salinity Mean</th><td>5.5</td><td>1.4</td></tr><tr><th>Salinity Range</th><td>3.9</td><td>6.2</td></tr><tr><th>Current Velocity Mean</th><td>2.7</td><td>3.7</td></tr><tr><th>Current Velocity Ltmax</th><td>2</td><td>0</td></tr><tr><th>Dissolved oxygen Range</th><td>1.9</td><td>1.6</td></tr><tr><th>Phosphate Mean</th><td>1.6</td><td>5.3</td></tr><tr><th>Current Velocity Min</th><td>1</td><td>14.2</td></tr><tr><th>Current Velocity Max</th><td>0.6</td><td>0</td></tr></tbody></table>
Table 2 in Fig. 11. Left G 1 s in Tuerkayana latens, a New Species of Land Crab from French Polynesia, with a Discussion on the Phylogeny of the Genus (Crustacea: Decapoda: Brachyura: Gecarcinidae)
<p><b>Table 2.</b> Pairwise estimates of <i>COI</i> genetic divergence (Φ ST) for <i>Amphibalanus amphitrite</i> among five biogeographical areas. The significance of ΦST values was tested by a permutation test with 1000 replicates</p><table><tbody><tr><th></th><th>MK(PG)</th><th>TH(PG)</th><th>GU(GO)</th><th>CH(GO)</th><th>JS(GO)</th></tr></tbody><tbody><tr><th>MK(PG)</th><td>0</td><td></td><td></td><td></td><td></td></tr><tr><th>TH(PG)</th><td>0.00748</td><td>0</td><td></td><td></td><td></td></tr><tr><th>GU(GO)</th><td>0.00728</td><td>0.03051*</td><td>0</td><td></td><td></td></tr><tr><th>CH(GO)</th><td>0.03196*</td><td>0.00921</td><td>0.01027</td><td>0</td><td></td></tr><tr><th>JS(GO)</th><td>0.01838</td><td>0.00420</td><td>0.00528</td><td>0.02062</td><td>0</td></tr></tbody></table><p>* <i>p</i> <0.05.</p>
Fig. 1 in Fig. 11. Left G1s in Tuerkayana latens, a New Species of Land Crab from French Polynesia, with a Discussion on the Phylogeny of the Genus (Crustacea: Decapoda: Brachyura: Gecarcinidae)
Fig. 1. Map of the sampling localities.
Processed data supporting the manuscript "Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution"
<div><strong>Processed data supporting the manuscript: </strong>Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution</div> <div> </div> <div><strong>By:</strong> Diego de S. Souza 1, 2, Rowan L. K. French 3, José O. Silva Júnior 4, Eugenio H. Nearns 5, Luciane Marinoni 4, Ian P. Swift 6, Kelly B. Miller 7, Felix A. H. Sperling 2 & Marcela L. Monné 1</div> <div> </div> <div>1 Department of Entomology, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.</div> <div>2 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.</div> <div>3 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.</div> <div>4 Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil.</div> <div>5 National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.</div> <div>6 California State Collection of Arthropods, Sacramento, California, USA.</div> <div>7 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.</div> <div> </div> <div>Corresponding author: Diego de S. Souza, dsouza@fieldmuseum.org. Current affiliation: Field Museum of Natural History, Chicago, Illinois, USA.</div> <div> </div> <div> </div> <div><strong>List of Contents: </strong></div> <div> </div> <div><strong>Onciderini_concat_matrix.phy</strong></div> <div>Concatenated matrix (cox1, Wg and CPS) used for the phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini). </div> <div> </div> <div><strong>PartitionFinder_AICc_best_scheme.txt</strong></div> <div>Results from PartitionFinder v2.1.1, containing the best partitioning scheme for the concatenated matrix of Onciderini, identified using the corrected Akaike Information Criterion (AICc), with model definitions for use in the phylogenetic analyses.</div> <div> </div> <div><strong>RAxML_Onciderini_concat_matrix (zip file)</strong></div> <div>- Onciderini_concat_matrix.phy: concatenated matrix (cox1, Wg and CPS) used in the RAxML phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini).</div> <div>- Partitions_AICc_RAxML.txt: partitioning scheme used in the RAxML analysis as predefined by PartitionFinder v2.1.1 using the corrected Akaike Information Criterion (AICc).</div> <div>- RAxML_bestTree.Onciderini_concat_matrix_ML: best-scoring maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini.</div> <div>- RAxML_bipartitions.Onciderini_concat_matrix_final: bipartitions (clades) of the maximum likelihood tree inferred by RAxML with support values estimated from 1,000 pseudoreplicates.</div> <div>- RAxML_bipartitionsBranchLabels.Onciderini_concat_matrix_final: final maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini, with labeled branches showing bootstrap support values.</div> <div>- RAxML_bootstrap.Onciderini_concat_matrix_bootstrap: bootstrap trees generated from a non-parametric bootstrap analysis in RAxML based on 1,000 pseudoreplicates.</div> <div>- RAxML_info.Onciderini_concat_matrix_bootstrap: log file containing details of the bootstrap analysis, including the settings and parameters used in the non-parametric bootstrap runs in RAxML.</div> <div>- RAxML_info.Onciderini_concat_matrix_final: log file summarizing the RAxML analysis, including settings and convergence statistics for the final maximum likelihood tree.</div> <div>- RAxML_info.Onciderini_concat_matrix_ML: log file containing details of the maximum likelihood tree search, including the parameters and models applied during the maximum likelihood analysis conducted by RAxML.</div> <div>- RAxML_log.Onciderini_concat_matrix_ML: log file of the maximum likelihood tree search for the concatenated matrix of Onciderini.</div> <div>- RAxML_parsimonyTree.Onciderini_concat_matrix_ML: parsimony starting tree used by RAxML during the maximum likelihood analysis for the concatenated matrix of Onciderini.</div> <div>- RAxML_result.Onciderini_concat_matrix_ML: maximum likelihood tree inferred by RAxML from the concatenated matrix of Onciderini, summarizing the tree topology and likelihood score for the best tree obtained.</div> <div> </div> <div><strong>BI_AICc_Onciderini_concat_matrix (zip file)</strong></div> <div>- BI_AICc_Onciderini_concat_matrix.nex: nexus file containing the concatenated matrix of Onciderini used for Bayesian Inference (BI), including the best-fit model scheme identified by PartitionFinder and MCMC parameters for running the analysis in MrBayes.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex_r1_r2_combined_consensus.tree: consensus tree from two combined independent Bayesian Inference (BI) runs based on the concatenated matrix of Onciderini, after discarding the first 25% of initial generations as burn-in.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run1.p: log file containing parameter values and likelihood scores from the first run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run2.p: log file containing parameter values and likelihood scores from the second run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_lognormal (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_lognormal.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- BEAST2_Onciderini_BD_lognormal_run[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_exponential (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_exponential.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- BEAST2_Onciderini_BD_exponential_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_uniform (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_uniform.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- BEAST2_Onciderini_BD_uniform_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>Comparative_analyses (zip file)</strong></div> <div><strong>RawData (folder):</strong> raw morphometric and girdling data, plus tree that was later pruned for downstream comparative analyses; these data were used as input for the OncidHeadDimorphism-DatasetPREP-FINAL.R data cleaning script. </div> <div>- Onciderini_BD_lognormal_run1-run8_consensus.nwk: newick version of TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre (outputted as a newick file by importing the .tre file into FigTree and exporting in newick format).</div> <div>- Measurements_Onciderini_Raw_Final.csv: individual-level raw morphometric data for Onciderini.</div> <div>- Behav_Matrix_2_states_trimmed_2022-12-15.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as girdlers (2 behavioral states across Onciderini species). </div> <div>- Matrix_3_states_trimmed_final.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as facultative girdlers (3 behavioral states across Onciderini species). </div> <div>- Matrix_2_states_trimmed_1LochGirdler_Final.csv: species-level data on girdling status for Onciderini species, with only one Lochmaeocles species (L. tessellatus) classified as a girdler (2 behavioral states across Onciderini species). </div> <div> </div> <div><strong>ProcessedData (folder): </strong>filtered data and pruned trees outputted by the OncidHeadDimorphism-DatasetPREP-FINAL.R script</div> <div>- oncid_f_36spp_clean.csv: dataset of species means and log-ratios for morphometric traits in females, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_m_42spp_clean.csv: dataset of species means and log-ratios for morphometric traits in males, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_sd_35spp_clean.csv: dataset of species means for sexual dimorphism in morphometric traits, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_girdlingbehav_allingroupspp_clean.csv: full dataset of girdling behavior for 56 Onciderini species that are in the phylogenetic tree; includes separate columns for the three alternative girdling classification schemes</div> <div>- oncid_tree_behavfull_56spp.nwk: pruned phylogenetic tree for the full girdling dataset (56 species)</div> <div>- oncid_tree_f_36spp.nwk: pruned phylogenetic tree for the female morphometric dataset (36 species)</div> <div>- oncid_tree_m_42spp.nwk: pruned phylogenetic tree for the male morphometric dataset (42 species)</div> <div>- oncid_tree_mf_43spp.nwk: pruned phylogenetic tree for all species with morphometric data for males or females; used for the stochastic character map next to the heatmap plot (Fig 4)</div> <div>- oncid_tree_sd_35spp.nwk: pruned phylogenetic tree for the sexual dimorphism dataset (35 species)</div> <div> </div> <div><strong>FittedModels (folder): </strong>fitted models (mvgls, model comparison analyses, OUM models, simmaps) outputted by the OncidHeadDimorphism-Analysis-FINAL.R script </div> <div>- MacroModelFits_logRtraits_f_36spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to female morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits_logRtraits_m_42spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to male morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits-SDDI-35spp_2024-10-11.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to sexual dimorphism data across 100 stochastic character maps of girdling behavior</div> <div>- mvgls-results-headsize-mf-2024-10-12.Rdata: fitted mvgls regression models for male and female traits (analyzed separately)</div> <div>- mvgls-results-sddi-2024-10-12.Rdata: fitted mvgls regression models for sexual dimorphism</div> <div>- OUM_headtraits_f_36spp-2024-10-12.Rdata: fitted OUM models and summary statistics for female head traits</div> <div>- OUM_headtraits_m_42spp-2024-10-12.Rdata: fitted OUM models and summary statistics for male head traits</div> <div>- OUM-SDDI-35spp-2024-10-12.Rdata: fitted OUM models and summary statistics for sexual dimorphism in head traits</div> <div>- simmaps_ard_full_2state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - all Lochmaeocles species are classified as girdlers</div> <div>- simmaps_ard_full_3state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with three behavioral states (girdling, non-girdling, or facultative girdling)</div> <div>- simmaps_ard_full_1Loch.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - only one Lochmaeocles species (L. tessellatus) is classified as a girdler</div> <div>- simmaps_ard_m.RDS: stochastic character map for the 42 species used in the analyses of male morphometric traits</div> <div>- simmaps_ard_f.RDS: stochastic character map for the 36 species used in the analyses of female morphometric traits</div> <div>- simmaps_ard.RDS: stochastic character map for the 35 species used in the sexual dimorphism analyses; 2 behavioral states.</div> <div> </div> <div><strong>Rscripts (folder): </strong>R scripts used to process data and run phylogenetic comparative analyses of head size and girdling behavior.</div> <div>- OncidHeadDimorphism-DatasetPREP-FINAL.R: R script used to filter data and prune trees from the RawData folder for downstream phylogenetic comparative analyses; outputs of this script are in the ProcessedData folder.</div> <div>- OncidHeadDimorphism-Analysis-FINAL.R: R script used to analyze data in the ProcessedData folder to answer questions about the origin and evolution of girdling behavior and the relationship between girdling and head size or head size sexual dimorphism; fitted models outputted by this script are in the FittedModels folder</div> <div>- OncidHeadDimorphism-Plots-FINAL.R: R script used to generate plots for the manuscript<br><br></div>
Figure 13. Grades 44 and 46. The philodromids also share a in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 13. Grades 44 and 46. The philodromids also share a common ancestor with the salticids at grade 45.
Figure 11. Grades 31 and 37 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 11. Grades 31 and 37. The great majority of modern spiders are entelegynes, with separation of copulatory ducts from oviposition ducts (gonopores) of the female epigynum. Entelegynes in turn can be divided into two large groups, one (the RTA clade) distinguished by the presence of a retrolateral tibial apophysis on the male pedipalp.
Figure 10. Grades 27 and 28 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 10. Grades 27 and 28. There are many different mygalomorphs today, characterized by the parallel, parasagittal (orthognath) alignment of their chelicerae. The Theraphosidae is the largest family in the group, including the largest of all spiders. In some countries, these are popularly known as tarantulas, and kept as low-maintenance pets. Filistatids like this Filistata are near the base of araneomorph evolution. Their anterior medial spinnerets have fused to form a cribellum with many small ducts. This produces a kind of kinky silk that entangles prey in the webs of these spiders.
Figure 9. Grades 25 and 26. There are presently 126 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 9. Grades 25 and 26. There are presently 126 living species of whipscorpions (Uropygi) and they have a long fossil history dating back to the Pennsylvanian (Santana et al. 2024). The East Asian Mesothelae represent the most basal group of spiders, with two pairs of book lungs and four pairs of spinnerets at a central position on the underside of the opisthosoma. Note also the prominent tergites on the dorsal opisthosoma of this Liphistius, similar to those seen on Mastigoproctus.
Figure 4. Grades 10 and 11 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 4. Grades 10 and 11. Adult tunicates are usually sessile (some are detached and roll on the sea bottom), but they begin their lives as mobile, planktonic larvae. The Spiralia are diverse, including annelids and molluscs. Many Platyhelminthes (flatworms) are parasitic or aquatic in freshwater and marine environments, but some, like the one shown here, are terrestrial.
Figure 3 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 3. Divergent representatives of two subsequent grades, able to coordinate movement with contractile muscle cells and bioelectric signalling. These are motile, predatory marine organisms.
Figure 7. Grades 19 and 24 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 7. Grades 19 and 24. The Xiphosura have paired book gills under the opisthosoma (thoracetron). Although the group has a long fossil record, there are only 4 living species (Lamsdell 2020). Scorpions, with paired book lungs, chelicerate pedipalps, and an unusual appendage at the rear of the opisthosoma, are now diverse and successful.
Figure 1 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 1. Hypothetical grades of evolution leading to the Salticidae. The estimated time of origin for some of these grades is shown in millions of years (Ma, millions of years ago). Not all sources agree on this arrangement.
Figure 6. Grades 16 and 17 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)
Figure 6. Grades 16 and 17. The Onychophora, or velvet worms, are successful predators with many species in terrestrial, mostly tropical habitats. With flexible legs, they resemble giant tardigrades. The Mandibulata is by far the most successful group of animals, including the myrapods and the pancrustaceans; the latter group includes the insects and a diverse array of crustaceans, mostly marine.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.