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2,399 results for “fragmentation”
Comprehensive analysis of commercial fragment libraries.
<p><strong>Description of the files</strong></p> <p>Fragments from libraries:</p> <ul> <li><strong>allFragments_annotations.sdf:</strong> SDF file containing the 3D conformation of all unique 512284 fragments. <ul> <li>Descriptors present on the file: Library type (type), Library size (size) and the number of times the fragment is present in the ensemble of libraries (Frequency).</li> </ul> </li> <li><strong>unique_nonbiased_MW_logP_PBF.sdf:</strong> SDF file containing the ensemble of unique fragments from the non-chemically biased libraries. <ul> <li>Descriptors present on the file: Canonical Smiles (Canonical_Smiles), Molecular Weight (MW), Partition logarithm (ALogP) and Plane of best fit value (PBF).</li> </ul> </li> <li><strong>unique_nonbiased_principal_descriptors.tsv:</strong> TSV file containing the ensemble of unique fragments from the non-chemically biased libraries with the descriptors that were explicitely used in the article. <ul> <li>Descriptors present on the file: Canonical Smiles (Canonical_Smiles), molecular weight (MW), partition logarithm (ALogP) and plane of best fit value (PBF), number of heavy atoms (HAC), number of hydrogen bond acceptors and donors (HBA and HBD), number of rotatable bonds (NRot), number of violations of the rule of three (Ro3_Vio) and quantitative estimate of<strong> </strong>drug-likeness (QED).</li> </ul> </li> <li><strong>unique_nonbiased_descriptors.tsv:</strong> TSV file containing the ensemble of unique fragments from the non-chemically biased libraries with all the calculated descriptors.</li> </ul> <p>GTM model:</p> <ul> <li><strong>training_set_GTM.sdf: </strong>SDF file containing the set of 6017 fragments used for training the GTM model.</li> <li><strong>Model_IIAB2-4_cycle_Freq_05_m301.xml:</strong> xml file of the generated model allowing the generation of GTM landscapes.</li> </ul> <p>Scaffold data:</p> <ul> <li><strong>scaffold_data.tsv:</strong> TSV file containing the scaffold data. For an easy exploration of the file please refer to: <a href="https://gtmfrag.drugdesign.unistra.fr/">https://gtmfrag.drugdesign.unistra.fr/</a></li> </ul>
Data and code for: Plastic and quantitative genetic divergence mirror environmental gradients among wild, fragmented populations of Impatiens capensis
<p><strong>Premise of the study:</strong> Habitat fragmentation generates molecular genetic divergence among isolated populations but few studies have assessed phenotypic divergence and fitness in populations where the genetic consequences of habitat fragmentation are known. Phenotypic divergence could reflect plasticity, local adaptation, and/or genetic drift.</p> <p><strong>Methods:</strong> We examined patterns and potential drivers of phenotypic divergence among 12 populations of jewelweed (<em>Impatiens capensis </em>Meerb.) that show strong molecular genetic signals of isolation and drift among fragmented habitats. We measured morphological and reproductive traits in both maternal plants within natural populations and their self-fertilized progeny grown together in a common garden. We also quantified environmental divergence between home sites and the common garden.</p> <p><strong>Key results: </strong>Populations with less molecular genetic variation expressed less maternal phenotypic variation. Progeny in the common garden converged in phenotypes relative to their wild mothers but retained among-population differences in morphology, survival, and reproduction. Among-population phenotypic variance was 3-10x greater in home sites than in the common garden for 6 of 7 morphological traits measured. Patterns of phenotypic divergence paralleled environmental gradients in ways suggestive of adaptation. Progeny resembled their mothers less as the environmental distance between their home site and the common garden increased.</p> <p><strong>Conclusions: </strong>Despite strong molecular signatures of isolation and drift, phenotypic differences among these <em>Impatiens </em>populations appear to reflect both adaptive quantitative genetic divergence and plasticity. Quantifying the extent of local adaptation and plasticity and how these covary with molecular and phenotypic variation help us predict when populations may lose their adaptive capacity. </p>
Railing fragment with standing figure from Andhra, profile drawing of British Museum 1955,1017.1
<p>Railing fragment with standing figure from Andhra, profile drawing of British Museum 1955,1017.1</p>
Visualizations of fragment ancient Egyptian coffin based on MS PLD recordings
<p><strong>Detail on a fragment of an Egyptian coffin (Theban, end 22nd or early 25th Dynasty, © Archaeological Collections Faculty of Arts, KU Leuven). A: photograph with white light; B: green-induced infrared luminescence (523nm radiation); C: red-induced infrared luminescence (623nm radiation); D: normalmap (surface relief estimations) of isolated Egyptian blue, based on result in C.</strong></p>
Sappho Fragment 44. Hektor i Andromacha. Wesele w Troi.
<p>This animation depicts the poet Sappho, one of the most influential poets of ancient Greece. You see her performing the surviving fragment of one of her poems – fragment 44, a prequel to the Trojan War, in which the Trojan Prince, Hector, arrives home with his new bride, Andromache. The animation was created from a vase made in Athens in the 6th century BCE (now in the National Museum in Warsaw, in Poland, number 142333). The figures that Sappho creates with her music are made in an older pottery style. The music that she plays is the tune that the poem would have been sung to in ancient Greece.</p> <p>Polish version.</p>
Sappho Fragment 44 , Hector and Andromache. A Wedding at Troy
<p>This animation depicts the poet Sappho, one of the most influential poets of ancient Greece. You see her performing the surviving fragment of one of her poems – fragment 44, a prequel to the Trojan War, in which the Trojan Prince, Hector, arrives home with his new bride, Andromache. The animation was created from a vase made in Athens in the 6th century BCE (now in the National Museum in Warsaw, in Poland, number 142333). The figures that Sappho creates with her music are made in an older pottery style. The music that she plays is the tune that the poem would have been sung to in ancient Greece.</p>
Sappho Fragment 44 Set to Music. Hector and Andromache, A Wedding at Troy
<p>Aliki Markantonatou performs the surviving fragment of the ancient Greek poet Sappho's poem, ‘A Wedding at Troy’. The tune that it is performed to is the tune that would have accompanied the poem when it was sung in ancient Greece. Sappho's poem is a prequel to the Trojan War, recalling the time when Trojan Prince Hector arrived home with his new wife, Andromache.</p> <p>This recording was made to accompany the Panoply Vase Animation Project's vase animation 'Sappho 44: Hector and Andromache – A Wedding at Troy' <a href="https://www.youtube.com/watch?v=ZSn63s88InI&t=0s">https://youtu.be/ZSn63s88InI</a>, and the documentary 'About Sappho' <a href="https://www.youtube.com/watch?v=r_IWSbE1T9o&t=0s">https://youtu.be/r_IWSbE1T9o</a>.</p>
Nanopore sequencing of plasmid cleavage fragments produced with type III CRISPR-associated nucleases NucC, Can1 and Can2
<p>Included datasets were generated in the study "<strong>Sequence-specific capture and concentration of viral RNA </strong><strong>by type III CRISPR system enhances diagnostic"</strong> by Nemudraia et al., 2022</p> <p> </p> <p>For questions contact: Artem Nemudryi (artem.nemudryi@gmail.com) or Blake Wiedenheft (bwiedenheft.com)</p>
Data from: Plant Community Structure in Tropical Rain Forest Fragments of the Western Ghats, India
<p><strong>DESCRIPTION</strong></p><p>This dataset includes vegetation plot data on trees, lianas, understorey plants, and regeneration, and related data and species name matching files in five rainforest sites collected in 2003 as part of the following study:</p><p>MUTHURAMKUMAR, S., AYYAPPAN, N., PARTHASARATHY, N., MUDAPPA, D., RAMAN, T. R. S., SELWYN, M. A. & PRAGASAN, L. A. 2006. <a href="http://doi.org/10.1111/j.1744-7429.2006.00118.x">Plant community structure in tropical rain forest fragments of the Western Ghats, India</a>. <i>Biotropica</i> 38: 143–160. DOI: 10.1111/j.1744-7429.2006.00118.x</p><p>The regeneration data were analysed and presented in the following publication and related dataset:</p><p>OSURI, A. M., CHAKRAVARTHY, D., MUDAPPA, D., RAMAN, T. R. S., AYYAPPAN, N., MUTHURAMKUMAR, S. & PARTHASARATHY, N. 2017. Successional status, seed dispersal mode and overstorey species influence tree regeneration in tropical rain-forest fragments in Western Ghats, India. <i>Journal of Tropical Ecology</i> 33(4): 270-284. DOI: <a href="http://doi.org/10.1017/S0266467417000219">10.1017/S0266467417000219</a></p><p>OSURI, A. M., CHAKRAVARTHY, D., MUDAPPA, D., RAMAN, T. R. S., AYYAPPAN, N., MUTHURAMKUMAR, S. & PARTHASARATHY, N. 2017. <a href="http://doi.org/10.5061/dryad.vd0nn">Data from: Successional status, seed dispersal mode and overstorey species influence tree regeneration in tropical rain-forest fragments in Western Ghats, India</a>, Dryad, Dataset, https://doi.org/10.5061/dryad.vd0nn</p><p><br><strong>CONTACTS</strong></p><p>CONTACT #1<br>1. Name: <a href="https://orcid.org/0000-0002-1347-3953">T. R. Shankar Raman</a><br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Work Phone: +91 821 2515601<br>4. Email address: trsr@ncf-india.org<br>5. ORCID: https://orcid.org/0000-0002-1347-3953</p><p>CONTACT #2<br>1. Name: <a href="https://orcid.org/0000-0001-9708-4826">Divya Mudappa</a><br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Work Phone: +91 821 2515601<br>4. Email address: divya@ncf-india.org<br>5. ORCID: https://orcid.org/0000-0001-9708-4826</p><p>CONTACT #3<br>1. Name: <a href="https://orcid.org/0000-0001-9909-5633">Anand M. Osuri</a><br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Work Phone: +91 821 2515601<br>4. Email address: aosuri@ncf-india.org<br>5. ORCID: https://orcid.org/0000-0001-9909-5633</p><p>CONTACT #4<br>1. Name: <a href="https://orcid.org/0000-0003-4383-557X">N. Ayyappan</a><br>2. Work Address: French Institute of Pondicherry, No. 11, Post Box No. 33, Saint Louis Street, Pondicherry – 605 001, India.<br>3. Work Phone: + 91- 413-2231616<br>4. Email address: ayyappan.n@ifpindia.org<br>5. ORCID: https://orcid.org/0000-0003-4383-557X</p><p>CONTACT #5<br>1. Name: <a href="https://orcid.org/0000-0002-7791-8499">S. Muthuramkumar</a><br>2. Work Address: V.H.N.S.N. College, 3/151-1, College Road, Virudhunagar - 626001, Tamil Nadu, India.<br>3. Work Phone: + 91-4562-280154<br>4. Email address: muthuramkumar@vhnsnc.edu.in<br>5. ORCID: https://orcid.org/0000-0002-7791-8499</p><p>CONTACT #6<br>1. Name: <a href="https://orcid.org/0000-0002-4172-5441">N. Parthasarathy</a><br>2. Work Address: Department of Ecology and Environmental Sciences, Pondicherry University, R Venkat Raman Nagar, Kalapet, Pondicherry 605014, India<br>3. Work Phone: + 91-413-2654326<br>4. Email address: parthapu@yahoo.com<br>5. ORCID: https://orcid.org/0000-0002-4172-5441</p><p><br><strong>KEYWORDS</strong></p><p>Anamalai hills; biodiversity hotspot; disturbance; endemics; fragmentation; lianas; plant conservation; tree diversity; tropical rain forest; understory plants.</p><p><br><strong>GEOGRAPHIC COVERAGE</strong></p><p>1. Location/Study Area: Valparai Plateau, Tamil Nadu, India; Anamalai Tiger Reserve, Tamil Nadu, India</p><p>2. GPS coordinates: Valparai Plateau (10°15'- 10°22'N, 76°52' - 76°59'E); Anamalai Tiger Reserve (10°12' - 10°35'N, 76°49' - 77°24'E)</p><p><br><strong>TEMPORAL COVERAGE</strong></p><p>1. Begins: 2003-03-01 (Year, Month, Day)<br>2. Ends: 2003-04-30 (Year, Month, Day)</p><p><br><strong>METHODS</strong></p><p>Methods involved systematic vegetation plots for trees, lianans and understorey plants as described in Muthuramkumar et al. 2006 (<i>Biotropica</i> 38: 143–160. DOI: 10.1111/j.1744-7429.2006.00118.x) and for tree and woody regeneration as described in Osuri et al. 2017 (<i>Journal of Tropical Ecology</i> 33(4): 270-284. DOI: 10.1017/S0266467417000219). The vegetation sampling methods are briefly described below.</p><p>The present study was conducted in five tropical wet evergreen forest fragments located on the Valparai plateau (Fig. 1): Akkamalai (AK, 2600 ha), Upper Manamboli (UM, 100 ha), Lower Manamboli (LM, 100 ha), Tata Finlay (TF, 32 ha), and Injipara (IP, 18 ha).</p><p>In each site, vegetation was sampled in randomly placed noncontiguous plots of 20 × 20 m located at least 50 m apart and at least 20 m into the fragment interior from the edges, major trails, or roads. We sampled 20 plots each in IP, TF, and LM, and 25 plots each in UM and AK. Within each plot, all trees ≥30cm girth at breast height (gbh, at 1.3 m; corresponding to DBH of 9.55 cm) and lianas ≥1 cm diameter at breast height (DBH) were identified to species, counted, and their girth/diameter measured. For multi-stemmed trees bole girths were measured separately, basal area calculated and summed. Each 20 x 20 m plot was divided into four 10 × 10 m quarters.</p><p>For understory plants, 2 × 2 m quadrats were laid at the four corners of the 20 × 20 m plot (one in each of the corresponding four quarters) and all shrubs, undershrubs, herbs, ferns, and small twiners found within the quadrats were enumerated and identified. The regeneration sampling was done in a 5 × 5-m plot (0.0025 ha) placed at the outer corner of the first (south-west) quarter of the 20 x 20 m plot. Within each regeneration plot, we identified, counted and measured all tree saplings >1 cm diameter at breast height (dbh, at 1.3 m) and <9.55 cm dbh (equivalent to <30 cm girth at breast height, gbh). Woody shrubs of 1–9.55 cm dbh were alsorecorded in the regeneration plots (but these were excluded in the Osuri et al. 2017 analysis).</p><p>For vegetatively propagating plants a clump of stems that is basally connected was considered as one individual. Canopy height was measured with a range finder and canopy closure was measured using a spherical densiometer. Vouchers were identified with regional flora and confirmed with the Western Ghats collections available in the herbarium of Salim Ali School of Ecology, Pondicherry University, from our previous works in the region.</p><p> </p><p><strong>ACKNOLWEDGEMENTS</strong></p><p>Funders and other supporters of the research are acknowledged in the original publications. The compilation and publication of this dataset was carried out as part of an NCF project supported by Fondation Franklinia.</p><p><br><strong>FILES INCLUDED</strong></p><p>Besides the 00_README.txt file that contains this metadata, the dataset includes the following 11 files, whose details and contents are explained below.</p><p><br><strong>01_all_sites.csv</strong></p><p><i>Description</i>: The file contains details of the five study sites (three continuous forest and two forest fragment sites).<br> <br><i>Note</i>: Current Name of TF (Tata Finlay) site is Old Valparai, current name of Akkamalai (AK) is Iyerpadi-Akkamalai complex. Sites and codes correspond to the Muthuramkumar et al. 2006 paper (https://doi.org/10.1111/j.1744-7429.2006.00118.x).</p><p><i>Column names and descriptions:</i><br>eventDate: Date range when sampling was carried out in the sites<br>old_sitename: Name of the site as used in the Muthuramkumar et al. (2006) paper (https://doi.org/10.1111/j.1744-7429.2006.00118.x)<br>sitecode: Site code as used in the Muthuramkumar et al. (2006) paper (https://doi.org/10.1111/j.1744-7429.2006.00118.x)<br>site: Site name as at present and used in this dataset<br>decimalLatitude: latitude in decimal degrees North<br>decimalLongitude: longitude in decimal degrees East<br>geodeticDatum: Geodetic Datum WGS 84<br>coordinateUncertaintyInMeters: Uncertainty in metres of the GPS location (as only one location available for entire site where points were distributed)<br>type: Indicates whether site was continuous rainforest or rainforest fragment<br>Area_ha: Area in hectares<br>Altitude_min_m: Minimum altitude in metres of sampled plots<br>Altitude_max_m: Maximum altitude in metres of sampled plots<br>Ownership: Whether site is in privately owned land or within state-protected reserve<br>Average_canopy_height_m: average canopy height in metres<br>Canopy_closure_%: estimated canopy closure in percentage<br>Nearby_plantations: Adjoining plantations</p><p><br><strong>02_all_trees_adult_data.csv</strong></p><p><i>Description</i>: The file contains records of all adult trees >= 30 cm girth at breast height of 1.3 m (gbh) recorded within 20 m x 20 m plots across three continuous forests and two forest fragments.</p><p><i>Note</i>: Same as in the Osuri et al. (2017) dataset (https://doi.org/10.5061/dryad.vd0nn), with <i>Tithonia diversifolia</i> added back in Injipara and data from one additional site (Manamboli Lower) added back from the original dataset corresponding to the Muthuramkumar et al. 2006 paper (https://doi.org/10.1111/j.1744-7429.2006.00118.x).<br> <br><i>Column names and descriptions:</i><br>x: Row index<br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m adult tree plot within each site<br>q_no: An unique number assigned to each of four 10m x 10m quarters within each adult plot<br>t_no: An unique number assigned to each individual tree within each site.<br>old_code: Species codes used at the time of data collection (refer to Appendix A of the main paper for full species names, and the 06_all_species_names.csv file with this dataset)<br>osuri_code: Revised species codes used in the Osuri et al. 2017 paper in <i>Journal of Tropical Ecology</i> 33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn)<br>current_code: Species codes used at present<br>gbh_1 to gbh_16: Girth at breast height of single- (gbh_1) and multi-stemmed (gbh_2 – gbh_16) individuals, measured in centimetres (cm)<br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>03_all_liana_data.csv</strong></p><p><i>Description</i>: The file contains records of all lianas >= 1 cm diameter at breast height of 1.3 m (dbh) recorded within 20 m x 20 m plots across three continuous forests and two forest fragments.</p><p><i>Note</i>: Lianas were not included in the Osuri et al. (2017) dataset (https://doi.org/10.5061/dryad.vd0nn).</p><p><i>Column names and descriptions:</i><br>x: Row index<br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m adult tree plot within each site<br>q_no: An unique number assigned to each of four 10m x 10m quarters within each adult plot<br>t_no: An unique number assigned to each individual tree within each site.<br>old_code: Species codes used at the time of data collection (refer to Appendix A of the main paper for full species names, and the 06_all_species_names.csv file with this dataset)<br>osuri_code: Indicated as NA since these data were not used in the Osuri et al. 2017 paper in <i>Journal of Tropical Ecology</i> 33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn)<br>current_code: Species codes used at present<br>dbh_1 to dbh_11: Diameter at breast height of single- (dbh_1) and multi-stemmed (dbh_2 – dbh_11) individuals, measured in centimetres (cm) <br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>04_all_herbs_data.csv</strong></p><p><i>Description</i>: The file contains records of all understorey plants (shrubs, undershrubs, herbs, ferns, and small twiners) recorded in 2 m × 2 m quadrats laid at the four corners of each 20 m × 20 m plot in three continuous forests and two forest fragments.</p><p><i>Note</i>: Understorey plants were not included in the Osuri et al. (2017) dataset (https: //doi.org/10.5061/dryad.vd0nn).</p><p><i>Column names and descriptions:</i><br>x: Row index<br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m plot within each site<br>corner_no: An unique number assigned to each of four 2 m x 2 m quadrat laid at the four corners of the 20 m x 20 m plot<br>t_no: A number assigned to each individual species recorded within the corner plot.<br>old_code: Species codes used at the time of data collection (refer to Appendix A of the main paper for full species names, and the 06_all_species_names.csv file with this dataset)<br>osuri_code: Indicated as NA since these data were not used in the Osuri et al. 2017 paper in <i>Journal of Tropical Ecology</i> 33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn)<br>current_code: Species codes used at present<br>count: Number of individuals counted (for vegetatively propagating plants a clump of stems that was basally connected was considered as one individual)<br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>05_all_regeneration_data.csv</strong></p><p><i>Description</i>: The file contains records of woody seedlings and saplings (1-5 cm diameter at breast height at 1.3 m, dbh) and larger-stemmed trees (>5 cm dbh) recorded within single 5 m x 5 m regeneration plots nested within 20 m x 20 m plots. Plots were located in three continuous forests and two forest fragments. Data were filtered during analysis in Osuri et al. (2017, <i>Journal of Tropical Ecology</i>) to retain only seedling and saplings, defined as individuals with effective diameter <=5 cm.</p><p><i>Note</i>: Same as in the Osuri et al. (2017) dataset, with <i>Tithonia diversifolia</i> added back in Injipara from original dataset; and data from one additional site (Manamboli Lower) added back from the Muthuramkumar et al. 2006 dataset.<br> <br><i>Column names and descriptions:</i><br>x: Row index<br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m adult tree plot within each site<br>q_no: The 5 m x 5 m plot was placed in the SW corner of the 20 m x 20 m plot in this q_no which indicates one of the four 10 m x 10 m quarters of the 20 m x 20 m plot, where each quarter was given a unique number in each site<br>t_no: An unique number assigned to each individual seedling, sapling or tree within each site.<br>old_code: Species codes used at the time of data collection (for full species names refer to 06_all_species_names.csv file with this dataset)<br>osuri_code: Revised species codes used in the Osuri et al. 2017 paper in <i>Journal of Tropical Ecology </i>33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn)<br>current_code: Species codes used at present<br>dbh_1 to dbh_12: Diameter at breast height of single- (dbh_1) and multi-stemmed (dbh_2 – dbh_12) individuals, measured in centimetres (cm) <br>eff_dbh: Effective diameter at breast height (cm)- calculated as ((dbh)^2 +(dbh_1)^2 +...+(dbh_12)^2)^(1/2),<br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>06_all_canopy_readings.csv</strong></p><p><i>Description</i>: The file contains canopy-related measurements taken in each 20 m × 20 m plot in three continuous forests and two forest fragments.</p><p><i>Note</i>: Units of light meter reading were not recorded</p><p><i>Column names and descriptions:</i><br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m adult tree plot within each site<br>reading: A number assigned to the 1 to 4 readings taken in each plot<br>light: Light measurement taken with a light meter in the plot<br>canopy_openness: Canopy openness (scored from 0-100%) using a spherical densiometer (Canopy cover = 100 - canopy openness)<br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>07_all_extracanopy_trees_data.csv</strong></p><p><i>Description</i>: The file contains records of additional trees outside the 5 x 5 m plot whose canopy was overhead of the plot.</p><p><i>Note</i>: Species codes are used to denote presence (not count of stems) of that species in the overhead canopy.</p><p><i>Column names and descriptions:</i><br>site: Name of forest site<br>plot_no: An unique plot number assigned to each 20m x 20m adult tree plot within each site<br>q_no: The 5 m x 5 m plot was placed in the SW corner of the 20 m x 20 m plot in this q_no which indicates one of the four 10 m x 10 m quarters of the 20 m x 20 m plot, where each quarter was given a unique number in each site<br>old_code: Species codes used at the time of data collection (for full species names refer to 06_all_species_names.csv file with this dataset)<br>osuri_code: Revised species codes used in the Osuri et al. 2017 paper in J<i>ournal of Tropical Ecology </i>33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn)<br>current_code: Species codes used at present<br>P_ID: Unique plot ID created by combining columns site and plot_no</p><p><br><strong>08_all_species_names.csv</strong></p><p><i>Description</i>: This file provides species codes and species scientific names as originally used in the Muthuramkumar et al. 2006 paper (https://doi.org/10.1111/j.1744-7429.2006.00118.x), and as matched with the Global Biodiversity Information Facility (GBIF) species name matching tool</p><p><i>Note</i>: For plots that had no species occurrences (old_code = No herbs, Noliana), NA has been used for other columns</p><p><i>Column names and descriptions:</i><br>group: Code indicating main dataset group where species occurs (tree and regeneration data, liana data, understorey plants data)<br>old_code: Species codes used at the time of data collection (refer to traits data file for full species names)<br>osuri_code: Revised species codes if used in the Osuri et al. 2017 paper in <i>Journal of Tropical Ecology</i> 33: 270-284 (https://doi.org/10.1017/S0266467417000219) and related dataset (https://doi.org/10.5061/dryad.vd0nn) or else indicated as NA<br>current_code: Species codes used at present<br>original_name: Scientific name of plant species as used at the time of the original publication (Muthuramkumar et al. 2006)<br>original_fullname: Scientific name and authorship of plant species as used at the time of the original publication (Muthuramkumar et al. 2006)<br>original_family: Family of the plant species as used at the time of original publication<br>GBIFname: Scientific name as matched by GBIF species name matching tool<br>key: GBIF name matching tool key number<br>matchType: Type of match<br>confidence: Confidence returned by name matching tool<br>status: Whether accepted name or synonym<br>rank: Taxanomic rank (level) to which identified<br>kingdom: Taxonomic Kingdom<br>phylum: Taxonomic Phylum<br>class: Taxonomic Class<br>order: Taxonomic Order<br>family: Taxonomic Family<br>genus: Taxonomic Genus<br>species: Taxonomic Species<br>canonicalName: Canonical part of scientific name matched by GBIF<br>authorship: Authorship of scientific name matched by GBIF<br>scientificName: Current scientific name (from species, genus, or family columns)</p><p><br><strong>09_tabula_Biotropica_appendix1.csv</strong></p><p><i>Description</i>: This file contains tabled values extracted from Appendix 1 of Muthuramkumar et al. 2006 paper in Biotropica (DOI: 10.1111/j.1744-7429.2006.00118.x); extraction from PDF carried out using Tabula software (https://tabula.technology/)</p><p><i>Note</i>: Last 5 columns contain total abundance (count of individuals/stems) in the corresponding site.</p><p><i>Column names and descriptions:</i><br>slno: serial number<br>habit: Plant habit indicating trees, lianas, or understorey plants<br>species: species name as used in Appendix 1 of Muthuramkumar et al. 2006<br>asterisk: species endemic to Western Ghats are indicated by an asterisk (∗ ), and invasive species by double asterisk (∗∗ ).<br>voucher_number: voucher number of herbarium specimen deposited in the herbarium of Salim Ali School of Ecology, Pondicherry University, India.<br>family: plant family as in Appendix 1<br>Iyerpadi-Akkamalai: abundance (total number of individuals counted) in this site<br>Manamboli_Upper: abundance (total number of individuals counted) in this site<br>Manamboli_Lower: abundance (total number of individuals counted) in this site<br>Old_Valparai: abundance (total number of individuals counted) in this site<br>Injipara: abundance (total number of individuals counted) in this site</p><p><br><strong>10_Muthuramkumar et al 2006_Abstract and Appendix 1_extract_Biotropica.pdf</strong></p><p>Extracted PDF of first page with Abstract and Appendix 1 of Muthuramkumar et al. 2006 (DOI: 10.1111/j.1744-7429.2006.00118.x).</p><p><br><strong>11_figure_1_Biotropica_paper.jpg</strong></p><p>JPEG image of Figure 1 (map of study area) from the following publication:<br>MUTHURAMKUMAR, S., AYYAPPAN, N., PARTHASARATHY, N., MUDAPPA, D., RAMAN, T. R. S., SELWYN, M. A. & PRAGASAN, L. A. 2006. Plant community structure in tropical rain forest fragments of the Western Ghats, India. Biotropica 38: 143–160. DOI: 10.1111/j.1744-7429.2006.00118.x</p>
Text-fig. 40. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 4"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment with one kind of pollen grain; b) Detail of pollen clump showing densely packed pollen all of the same kind; c) Pollen grains in equatorial (left) and polar (right) views showing the coarse reticulum in the mesocolpium regions, the striate-reticulate tectum over the polar regions, and the microreticulate to foveolate tectum along the aperture margins; d) Detail of pollen wall showing smooth muri supported by long, densely-spaced columellae; e) Detail of broken pollen wall showing long, densely-spaced columellae detached from the thick foot layer. Specimen, Catefica 50-S170386 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d, e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 40. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 4"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment with one kind of pollen grain; b) Detail of pollen clump showing densely packed pollen all of the same kind; c) Pollen grains in equatorial (left) and polar (right) views showing the coarse reticulum in the mesocolpium regions, the striate-reticulate tectum over the polar regions, and the microreticulate to foveolate tectum along the aperture margins; d) Detail of pollen wall showing smooth muri supported by long, densely-spaced columellae; e) Detail of broken pollen wall showing long, densely-spaced columellae detached from the thick foot layer. Specimen, Catefica 50-S170386 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d, e).
Text-fig. 38. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 2"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b, d, e) Pollen grains from stamen fragment in equatorial (b, e) and polar (d) views showing the long colpi with coarsely verrucate aperture membranes and semitectate-microreticulate pollen wall; note small, spherical orbicules scattered on the surface of the tectum (arrows); c) Detail of pollen wall showing smooth muri with very faint transverse striations and a granular to columellate infratectal layer. Specimen, Catefica 153-S105614 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 38. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 2"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b, d, e) Pollen grains from stamen fragment in equatorial (b, e) and polar (d) views showing the long colpi with coarsely verrucate aperture membranes and semitectate-microreticulate pollen wall; note small, spherical orbicules scattered on the surface of the tectum (arrows); c) Detail of pollen wall showing smooth muri with very faint transverse striations and a granular to columellate infratectal layer. Specimen, Catefica 153-S105614 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1 Μm (c).
Text-fig. 37. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 1"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b–d) Pollen grains from stamen fragment in equatorial view showing the long colpi and well-developed, heterobrochate reticulum with very distinct large and small lumina; e) Detail of pollen wall showing orbicules with irregular projections; f) Detail of pollen wall showing smooth muri supported by short, densely spaced columellae. Specimen, Catefica 50-S170419 (a–f). Scale bars = 600 Μm (a), 6 Μm (b–d), 1.5 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 37. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 1"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b–d) Pollen grains from stamen fragment in equatorial view showing the long colpi and well-developed, heterobrochate reticulum with very distinct large and small lumina; e) Detail of pollen wall showing orbicules with irregular projections; f) Detail of pollen wall showing smooth muri supported by short, densely spaced columellae. Specimen, Catefica 50-S170419 (a–f). Scale bars = 600 Μm (a), 6 Μm (b–d), 1.5 Μm (e, f).
Text-fig. 18. Scanning electron microscope (SEM) images of fragmentary flower of Catanthus dolichostemon (a, b) and flower of Saportanthus parvus (c, d); Catefica locality, Portugal. a, b) Fragment of flower bud showing bulky tepals (te) and fleshy stamens (st) in ventral (a) and lateral (b) views; note the long stamen base and small anther with extrorse anther dehiscence (arrows); c, d) Flower in lateral (c) and oblique apical (d) views showing inferior ovary and eight bulky tepals almost completely enclosing the stamens and styles. Specimens, Catefica MM92-P0159 (a, b), Catefica MM285-P0331 (c, d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 18. Scanning electron microscope (SEM) images of fragmentary flower of Catanthus dolichostemon (a, b) and flower of Saportanthus parvus (c, d); Catefica locality, Portugal. a, b) Fragment of flower bud showing bulky tepals (te) and fleshy stamens (st) in ventral (a) and lateral (b) views; note the long stamen base and small anther with extrorse anther dehiscence (arrows); c, d) Flower in lateral (c) and oblique apical (d) views showing inferior ovary and eight bulky tepals almost completely enclosing the stamens and styles. Specimens, Catefica MM92-P0159 (a, b), Catefica MM285-P0331 (c, d). Scale bars = 300 Μm (a–d).
Text-fig. 11. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 2"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains; c) Pollen grain in distal view showing short colpus with irregular margin and aperture membrane covered by irregular verrucae; d) Detail of pollen wall showing tiny spherical orbicules; e) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170389 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 3 Μm (d), 1.5 Μm (e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 11. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 2"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains; c) Pollen grain in distal view showing short colpus with irregular margin and aperture membrane covered by irregular verrucae; d) Detail of pollen wall showing tiny spherical orbicules; e) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170389 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 3 Μm (d), 1.5 Μm (e).
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d).
Text-fig. 12. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 3"; Catefica locality, Portugal. a) Stamen fragment with pollen in situ; b, c) Pollen grains showing the semitectate-reticulate pollen wall and folds (c) indicating a possible monocolpate aperture; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation; e) Detail of pollen wall showing tiny, spherical, finely spiny orbicules. Specimen, Catefica 50-S170449 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d, e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 12. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 3"; Catefica locality, Portugal. a) Stamen fragment with pollen in situ; b, c) Pollen grains showing the semitectate-reticulate pollen wall and folds (c) indicating a possible monocolpate aperture; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation; e) Detail of pollen wall showing tiny, spherical, finely spiny orbicules. Specimen, Catefica 50-S170449 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d, e).
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g).
Text-fig. 10. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 1"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains and tiny orbicules on the inner surface of the anther wall (arrows); c) Pollen grains in distal view showing short colpi with irregular margins and aperture membrane with irregular verrucae; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170387 (a–d). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 10. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 1"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains and tiny orbicules on the inner surface of the anther wall (arrows); c) Pollen grains in distal view showing short colpi with irregular margins and aperture membrane with irregular verrucae; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170387 (a–d). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d).
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h).
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b).
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Annotated Behaviour and Observability Dataset (ABODe)
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