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The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology and raw data
<p><strong>Description:</strong> In this work, we deeply sequenced (genome and transcriptome of different organs), assembled, and analyzed the 311-Mbp genome of the terrestrial carnivorous plant <em>U. reniformis</em> (Lentibulariaceae). This project presents great importance to the understanding of genomic, evolutive and functional aspects of<em> U. reniformis</em>, which may, with the next-generation sequencing and computational biology approaches shed light to a better understanding not only for the biology and evolution of <em>Utricularia</em> genus, but also for other genera and lineages of the Lentibulariaceae family. Here we present all the raw data generated, including annotation and gene ontology files.</p> <p><strong>External Information</strong></p> <p><a href="https://genomevolution.org/coge/GenomeInfo.pl?gid=54799">Genome Browser</a> avaliable at CoGe Portal (https://genomevolution.org/coge/GenomeInfo.pl?gid=54799)</p> <p><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">GenBank </a><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">Bioproject</a> (https://www.ncbi.nlm.nih.gov/bioproject/290588) for raw genomic and transcriptomic reads</p> <p><a href="https://bv.fapesp.br/en/auxilios/84264/genomics-and-transcriptomics-of-utricularia-reniformis-lentibulariaceae-an-evolutive-and-function/">FAPESP grant website</a> contaning the project abstract and other information.</p> <p><strong>Papers published related to <em>Utricularia reniformis</em> genome</strong></p> <pre><strong>[1]</strong> Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, MichaelTP, Varani AM. <strong>The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family</strong>. PLoS One. 2016 Oct 20;11(10):e0165176. doi:<strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/27764252">10.1371/journal.pone.0165176</a></strong>. </pre> <pre><strong>[2] </strong>Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. <strong>The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.</strong> PLoS One. 2017 Jul19;12(7):e0180484. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/28723946">10.1371/journal.pone.0180484</a></strong>.</pre> <pre><strong>[3] </strong>Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. <strong>The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity.</strong> Int J Mol Sci. 2019 Dec 18;21(1). pii: E3. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/31861318">10.3390/ijms21010003</a></strong>.</pre> <p><strong>Acknowledgements</strong></p> <p>This work was supported by Sao Paulo Research Foundation FAPESP, Grant ID: [1325164-6]</p> <p> </p> <p><strong>---------------------------------------------------------</strong><br> <strong>FILES DESCRIPTION</strong><br> <strong>---------------------------------------------------------</strong><br> <br> ----------------<br> <strong>ANNOT-vFinal.sql: </strong>MySQL database containing all integrated annotation information of Urenif and Ugibba<br> ----------------<br> <strong>TABLE fields description</strong><br> gene_name gene name generated by EVidence Modeler + PASA<br> length gene lenght<br> status duplicate_gene_classifier status (0:singleton, 1:dispersed, 2:proximal, 3: tandem, 4:WGD)<br> product gene product <br> GOterms Blast2GO/OmicsBox GOterms<br> GO_mapping Blast2GO/OmicsBox GOterms derived from direct mapping (UniProt)<br> GO_annotation Blast2GO/OmicsBox annotated GOterms<br> GO_interpro Blast2GO/OmicsBox derived from InterProScan<br> EC Blast2GO/OmicsBox EC number<br> EC_name Blast2GO/OmicsBox enzyme name<br> NOG_annot EggNOG annotation description<br> NOG_EC EggNOG EC number<br> NOG_GO EggNOG GOterms<br> NOG_class EggNOG COG/KOG classfication<br> KEGG_Pathway EggNOG KEGG pathyways<br> KEGG_ko EggNOG KEGG ko<br> CAZy EggNOG CAZy enzymes<br> TAIR_gene Closest A. thaliana gene name (homologous) TAIR database lasted version<br> TAIR_annot Closest A. thaliana gene product (homologous) TAIR database lasted version <br> ortho MCL clustering among Vvinifera, Athaliana, and Slycopersicum (S:singleton, C: clustered, Y: shared)<br> ortho_two MCL clustering among Urenif and Ugibba (S:singleton, C: clustered, Y: shared)<br> -<br> -<br> ----------------<br> <strong>CEGs.zip </strong> 336 shared and concatenated CEGs from Urenif, U. gibba, Genlisea nigrocaulis, G. hispidula, G. aurea, G. pygmaea, and G. repens.<br> ----------------</p> <p><strong>ProcessRepeats_mod</strong> Modified version of RepeatMasker, ProcessRepeats script for detection of plant evolutionary lineages<br> ----------------</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia gibba</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Ugibba</strong><strong>-no-masked.fa </strong> Ugibba genome excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ugibba-softmasked.fa</strong> Ugibba genome RepeatMasker softmasked and excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ug.collinearity </strong> MCScanX collinearity file<br> <strong>Ug-duplicates.txt</strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ug.gene_type </strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ug.tandem </strong> Ugibba tandem genes generated by MCScanX tool<br> <strong>Ugibba_annot.annot </strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) <strong>Ugibba_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong><strong> </strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Ugibba</strong><strong>.cDNA</strong> Ugibba cDNAs fasta file<br> <strong>Ugibba</strong><strong>.CDS </strong> Ugibba CDSs fasta file<br> <strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Ugibba GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Ugibba GFF3 file fully annotated (genes only)<br> <strong>Ugibba_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Ugibba_fasta.fasta</strong> Blast2GO/OmicsBox Ugibba fasta proteins containg annotation (product and GO terms)<br> <strong>ugibba_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>ugibba_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>ugibba_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)</p> <p><strong>Ugibba_GAF.txt</strong> GAF file<br> <strong>Ugibba</strong><strong>.gene</strong> Ugibba gene fasta file<br> <strong>Ugibba_GOstat.txt </strong> GOstat file<br> <strong>Ugibba</strong><strong>-PASA-assemblies.fasta </strong> Ugibba PASA assemblies<br> <strong>Ugibba</strong><strong>-PASA.stats </strong> Ugibba annotation STATS<br> <strong>Ugibba</strong><strong>.</strong><strong>prot</strong><strong> </strong> Ugibba protein fasta file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff </strong> Ugibba RepeatMasker gff file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff3 </strong> Ugibba RepeatMasker gff3 file<br> <strong>Ugibba</strong><strong>-RepeatMasker.tbl </strong> Ugibba RepeatMasker results<br> <strong>Ugibba</strong><strong>-RepeatMasker-v2.gff3</strong> Ugibba RepeatMasker gff3 second version file<br> <strong>Ugibba</strong><strong>-RNAseq-assembled.fasta </strong> Ugibba RNAseq assembled transcriptome (Trinity)<br> <strong>Ugibba_TEs_DANTE_2019.fa </strong> Ugibba TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Ugibba_WEGO.txt </strong> WEGO file</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia reniformis</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Urenif</strong><strong>-no-masked.fa </strong> Urenif genome excluding organellar genomes<br> <strong>Urenif</strong><strong>-</strong><strong>softmasked</strong><strong>.fa</strong> Urenif genome RepeatMasker softmasked and excluding organellar genomes<br> <strong>Ur.collinearity </strong> MCScanX collinearity file<br> <strong>Ur-duplicates.txt </strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ur.gene_type</strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ur.tandem</strong> Urenif tandem genes generated by MCScanX tool<br> <strong>Urenif_annot.annot</strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim)<br> <strong>Urenif_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Urenif</strong><strong>.cDNA</strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>.CDS </strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Urenif GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Urenif GFF3 file fully annotated (genes only)<br> <strong>Urenif_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Urenif_fasta.fasta</strong> Blast2GO/OmicsBox Urenif fasta proteins containg annotation (product and GO terms)<br> <strong>urenif_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>urenif_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>urenif_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)<br> <strong>Urenif_GAF.txt </strong> GAF file<br> <strong>Urenif</strong><strong>.gene</strong> Urenif gene fasta file<br> <strong>Urenif_GOStat.txt </strong> GOstat file<br> <strong>Urenif</strong><strong>-PASA-assemblies.fasta</strong> Urenif PASA assemblies<br> <strong>Urenif</strong><strong>-PASA.stats </strong> Urenif annotation STATS<br> <strong>Urenif</strong><strong>.</strong><strong>prot</strong><strong> </strong> Urenif protein fasta file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff </strong> Urenif RepeatMasker gff file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff3 </strong> Urenif RepeatMasker gff3 file<br> <strong>Urenif</strong><strong>-RepeatMasker.tbl </strong> Urenif RepeatMasker results<br> <strong>Urenif</strong><strong>-RepeatMasker-v2.gff3 </strong> Urenif RepeatMasker gff3 second version file<br> <strong>Urenif</strong><strong>-RNAseq-assembled.fasta </strong> Urenif RNAseq assembled transcriptome (Trinity)<br> <strong>Urenif_TEs_DANTE_2019.fa </strong> Urenif TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Urenif_WEGO.txt </strong> WEGO file<br> <strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong></p>
Maps of the diversity and distribution of Raunkiær's life forms in European vegetation
<p>This repository contains raster files (TIF format) with a 50 km × 50 km resolution (over UTM grid EPSG:32633), showcasing the diversity and distribution of Raunkiær’s life forms in European vegetation. The maps are based on two key metrics: (i) the proportion (%) of species within each life form and (ii) the diversity of life forms, including richness and evenness.</p> <p>To generate these maps, we averaged plot-level metric values across a comprehensive dataset comprising 546,501 vegetation plots sourced from the European Vegetation Archive (EVA; Project 163; <a href="https://euroveg.org" target="_new">https://euroveg.org</a>). These plots cover diverse habitats, including 173,190 forests, 260,884 grasslands, 52,517 scrubs, and 59,910 wetlands.</p> <p>The maps encompass the entire dataset, offering a visualization of the geographical distribution patterns of life forms across Europe. Additionally, we created habitat-specific maps by subsetting the dataset to explore unique patterns within each habitat type (forest, grassland, scrub, and wetland).</p> <p>Furthermore, we generated additional maps based on standardised effect sizes (SES) of diversity metrics. Through 500 species identity shuffles without replacement, specific to each habitat type, we examined the deviations from random expectations. SES values outside the range of -1.96 to 1.96 indicate significantly lower or higher metric values than expected at random, respectively. </p> <p> </p> <table> <tbody> <tr> <td><strong>Folder name</strong></td> <td><strong>Description of TIF raster values</strong></td> </tr> <tr> <td>full.div</td> <td>Mean richness and evenness of life forms across all habitat types</td> </tr> <tr> <td>full.mean.rel.prop</td> <td>Mean proportion of each life form across all habitat types</td> </tr> <tr> <td>habitat.div</td> <td>Mean richness and evenness of life forms across separate habitat types (forest, grassland, scrub, and wetland)</td> </tr> <tr> <td>habitat.mean.rel.prop</td> <td>Mean proportion of each life form across separate habitat types (forest, grassland, scrub, and wetland)</td> </tr> <tr> <td>SES.full.div</td> <td>Mean richness and evenness of life forms across all habitat types measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.full.mean.rel.prop</td> <td>Mean proportion of each life form across all habitat types measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.habitat.div</td> <td>Mean richness and evenness of life forms across separate habitat types (forest, grassland, scrub, and wetland) measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.habitat.mean.rel.prop</td> <td>Mean proportion of each life form across separate habitat types (forest, grassland, scrub, and wetland) measured with standardized effect sizes (SES)</td> </tr> </tbody> </table> <p><br>Additional information is available in our publication:<br><br>Midolo, G., Axmanová, I., Divíšek, J., Dřevojan, P., Lososová, Z., Večeřa, M., Karger, D. N., Thuiller, W., Bruelheide, H., Aćić, S., Attorre, F., Biurrun, I., Boch, S., Bonari, G., Čarni, A., Chiarucci, A., Ćušterevska, R., Dengler, J., Dziuba, T., Garbolino, E., Jandt, U., Lenoir, J., Marcenò, C., Rūsiņa, S., Šibík, J., Škvorc, Ž., Stančić, Z., Stanišić-Vujačić, M., Svenning, J. C., Swacha, G., Vassilev, K., & Chytrý, M. (2024) Diversity and distribution of Raunkiær’s life forms in European vegetation.<em> Journal of Vegetation Science. </em>Accepted on the 10th of December 2023</p>
BRAIN Journal-Evolving Spiking Neural Networks for Control of Artificial Creatures-Figure 9. A typical artificial life form and circular area around of it
<p>As mentioned the reservoir neural network has been chosen for neural network of the artificial creature as main body structure. Figure 9 illustrates a typical artificial life form and circular area around of it. Maximum seeing of the artificial life form is periphery of the circular area and can't see places that have beyond of periphery of the circular area. The artificial creature by each movement is the center of a circular area so if the creature move to forward direct can see new<br> places and some places are voided of seeing.</p>
Fig. 4 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (Central Bulgarian Black sea coast). Part I. Taxonomic and zoogeographic structure, life forms, habitat and humidity preferences
Fig. 4. Proportions of the subclasses of life forms in the carabid complex (I – class Zoophaga, II – class Mixophytophaga).
Video lecture "Life(less Forms" / "Un-Menschliche Lebensformen" (winter 2021/22, teaser)
<p>Betrachtet werden in der Vorlesung #Spuren und #Verhalten im Umgang mit dem "Leben". Ausgangspunkt ist die Betrachtung von Artefakten, die den Künsten zugeordnet werden, wobei die Vorlesung, wenn man herkömmliche labels verwendet, nicht "Kunstkultur" behandelt, sondern am ehesten wohl mit "natureculture" in Verbindung gebracht werden kann.<br> Die Artefakte (Auswahl kann noch geändert werden):</p> <ul> <li>Guillermo del Toro: "El Laberinto del Fauno" (2006) und "Shape of Water" (2017)</li> <li>Mikhail Bulgakow: "Hundeherz" (1925) / Alberto Lattuada: "Cuore di cane" (1976, <a href="https://youtu.be/USQolIA-v5I)">https://youtu.be/USQolIA-v5I)</a></li> <li>Enki Bilal: "La Foire aux immortels" (1980, graphic novel) / "Immortel (ad vitam)" (2004, Film)</li> <li>Émile Zola: "La Bête humaine" (1890) / Jean Renoir: "La Bête humaine" (1938)</li> <li>Jacques Lob & Jean-Marc Rochette: "Le Transperceneige" (1982) / Bong Joon Ho: "Snowpiercer" (2013)</li> <li>Ridley Scott: "Blade Runner" (1982) / Denis Villeneuve: "Blade Runner 2049" (2017)</li> </ul>
Figure 11 in Hybridization in the evolution of animal form and life-cycle
Figure 11. Four mid-Cambrian species from the Burgess Shale of British Columbia. A, Laggania cambria (= Anomalocaris nathorsti), ventral; B, Anomalocaris canadensis, ventral; C, Amiskwia sagittiformis; D, Nectocaris pteryx. Scale bar = ∼200 mm (A, B), ∼5 mm (C, D). [A, B reproduced with permission from S M Gonn III (from 'The Anomalocarid Bauplan' http://www.geocities.com/goniagnostus/background3.html); C, D, from Marianne Collins in Gould, 1989.]
Figure 9 in Hybridization in the evolution of animal form and life-cycle
Figure 9. Reticulate phylogeny of adults and larvae of extant hemichordates and echinoderms, showing probable sequence of events. Time (horizontal) not to scale. Ord/Sil, Ordovician/Silurian boundary; pres, present; thick black lines, adults; thin black lines, larvae; grey arrows, larval transfers.
Figure 7. Two Cambrian trilobites. A–D in Hybridization in the evolution of animal form and life-cycle
Figure 7. Two Cambrian trilobites. A–D, stages in the development of Sao hirsute: A, protaspis; B–D, early segmented stages. E, adult Agnostus pisiformis. Scale bar = ∼1 mm (A–D from Borradaile et al., 1935; E redrawn after Fortey, 2000.)
Figure 6 in Hybridization in the evolution of animal form and life-cycle
Figure 6. Stages in the development of the branchiopod crustacean Leptestheria syriaca, to different magnifications. (From Gurney, 1942; as Estheria.)
Figure 5. A in Hybridization in the evolution of animal form and life-cycle
Figure 5. A, nauplius of Penaeus sp. (recent Crustacea: Penaeidae). B, C, Martinssonia elongata (upper Cambrian): B, paranauplius II (left first appendage omitted); C, oldest known stage. Scale bar = ∼0.1 mm (A after Gurney, 1942; B, C adapted from Müller & Walossek, 1986b.)
Figure 4 in Hybridization in the evolution of animal form and life-cycle
Figure 4. Enteropneust and pterobranch hemichordates and a planctosphere. A–E, enteropneusta: A, adult Dolichoglossus, B, tornaria larva; C–E, stages in metamorphosis; F, G, Pterobranchia: F, adult Rhabdopleara; G, pterobranch larva. H, Planctosphaeromorpha: adult Planctoshaera pelagica. Scale bar = ∼10 mm (A), ∼1 mm (B–E, G), ∼5 mm (F, H). (Adapted from Borradaile et al., 1935; Hyman, 1959.)
Figure 3. Bryozoan larvae and adult. A in Hybridization in the evolution of animal form and life-cycle
Figure 3. Bryozoan larvae and adult. A, trochophore larva of Alcyonidium; B, cyphonautes larva of Membranipora; C, adult zooid of Electra. (After Williamson, 1992.)
Figure 2 in Hybridization in the evolution of animal form and life-cycle
Figure 2. Examples of overlapping metamorphosis. A, Luidia sarsi (Echinodermata): swimming bipinnaria larva and detached juvenile starfish; B, Polygordius sp. (Annelida): two stages showing segmented polychaete worm protruding from swimming trochophore larva; C, Cerebratulus sp. (Nemertea): juvenile nemertean worm within swimming pilidium larva; D, Doliolum mulleri (Urochordata): juvenile doliolid tunicate within cuticle of tadpole larva. Juvenile stippled in each case. (A, C adapted from Williamson, 1992; B, D adapted from Borradaile et al., 1935.)
Figure 1 in Hybridization in the evolution of animal form and life-cycle
Figure 1. Hydroid and medusae of Hebella (Hydrozoa: Thecata). A, gonophores of H. parasitica; B, male and female medusae of H. parasitica; C, medusa of H. furax. (A, B adapted from Boero, 1980; C adapted from Migotto & de Andrade, 2000.)
Figure 10. A in Hybridization in the evolution of animal form and life-cycle
Figure 10. A phylogram of some metazoans, based on 18S rRNA. (From Williamson, 2002; after Michael Syvanen, unpubl. data)
Figure 8 in Hybridization in the evolution of animal form and life-cycle
Figure 8. Larvae of an enteropneust hemichordate and echinoderms. A, tornaria larva of an acorn-worm (Enteropneusta); B, auricularia larva of a sea-cucumber (Holothuromorpha); C, bipinnaria larva of a starfish (Asteromorpha); D, echinopluteus larva of a sea-urchin (Echinomorpha); E, ophiopluteus larva of a brittle-star (Ophiuromorpha); F, doliolaria larva of a sea-lily (Crinomorpha). Scale bar = ∼1 mm (Adapted from Williamson, 1992, 2003.)
Naturalization of introduced plants is driven by life-form-dependent cultivation biases
<p><em>Aims: </em></p> <p>Most naturalized plants are escapees from cultivation. Inventories of cultivated introduced species thus offer unique, still underutilized, opportunities to assess naturalization drivers of introduced plants. We used a comprehensive inventory of 13,718 introduced species cultivated in China's botanical gardens to test which species characteristics distinguish the 739 species that have naturalized.</p> <p><em>Locations:</em> China.</p> <p><em>Methods: </em></p> <p>We used generalized linear models to test whether the naturalization of cultivated introduced plants in China is associated with functional traits, propagule pressure, environmental niche, and introduction history. To test direct and indirect effects of those variables and their relative importance in driving naturalization, we used structural equation models.</p> <p><em>Results: </em></p> <p>We showed that species were more likely to naturalize when they originate from the Americas, are more widely cultivated, and have a longer residence time. Moreover, species were more likely to naturalize if they have a good environmental match, are short-lived herbs, are predominantly propagated from seeds, and, in the case of herbs, are relatively tall compared to other herbs. Part of the latter effects are mediated by how these variables relate to propagule-pressure proxies, and this varies among short-lived herbs, long-lived herbs and woody plants. Main conclusions: Naturalization is partly driven by life-form-dependent cultivation biases.</p>
Naturalization of introduced plants is driven by life-form-dependent cultivation biases
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Data from: Evidence for complex life cycle constraints on salamander body form diversification
Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.
Climate controls plant life form patterns on a high-elevation oceanic island
<p>Aim: Plant life forms characterize key morphological strategies that enable large-scale comparisons of plant communities. This study applies Raunkiær's plant life form concept that was developed for temperate climate to a subtropical island flora, in parts, dominated by summer aridity. We quantify how plant life form patterns as well as patterns of important plant functional traits (PFTs) relate to important climate and topographic characteristics. Location: La Palma, Canary Islands Taxon: Flora of La Palma.</p> <p>Methods: We assigned each native plant species a plant life form, i.e., phanerophyte, chamaephyte, hemicryptophyte, geophyte and therophyte, as well as PFTs (succulence and N-fixer). We used stacked species distribution models to assess occurrence probability for each species using the Atlantis database (500x500 m grid). We related richness and percentage values for each plant life form and PFT to climate and topography.</p> <p>Results: Plant life forms and PFTs showed a clear pattern within geographic but also climate space, while topography had a minor effect. Phanerophytes mainly contributed to the flora in humid areas. Chamaephytes and hemicryptophytes most strongly contributed to the summit scrub flora and, to some degree, also to the arid coastal regions. Geophytes and therophytes were mainly found in dry coastal regions. N-fixers contributed mainly to warm-arid and cool-arid regions, while succulent species were mainly found in arid coastal regions.</p> <p>Main conclusions: Raunkiær's plant life form concept can be comprehensively transferred to a subtropical island flora by adapting to local unfavorable growing conditions, i.e., aridity. Using the strong environmental gradients offered by our study island, we identify substantial climate-driven variation in patterns of plant life forms and PFTs that might be used for large scale comparisons in macroecological studies. The growth strategies reflected in Raunkiær's plant life forms suggest differences in species establishment and coexistence dynamics within different parts of the island's climate space.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.