cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11108967
title: Code and Data for manuscript "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes"

description: Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation

--------

This repository contains all the R code used in the manuscript:

* Title: "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation"

* Authors: Anais Gibert, Schatz Bertrand, Buscail Roselyn, Dominique Nguyen, Baguette Michel, Bartes Nicolas and Joris Bertrand

* Year of publication: 2024

* doi: https://doi.org/10.1101/2024.03.21.586062

 

Synopsis of the study

--------





Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape.




Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation.




We identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor.




This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes.



 

Running the code

--------

Here we present the data and code for carrying out the analyses, as well as the figures and tables from the article and the supplementary material. Once you have installed the necessary packages, run the commands in 'analysis_share.R'. This script uses several functions available in the '/R' directory.

Figures and tables are produced in a 'manuscript/figures' and 'manuscript/tables' directory. The `/data' directory contains the data used in the analyses (data/input or data/output), but also the resulting datasets produced by the code (data/RData/).
DOI: 10.5281/zenodo.14524901
title: Code and Data for manuscript "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes"

description: Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation

--------

This repository contains all the R code used in the manuscript:

* Title: "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation"

* Authors: Anais Gibert, Schatz Bertrand, Buscail Roselyn, Dominique Nguyen, Baguette Michel, Bartes Nicolas and Joris Bertrand

* Year of publication: 2024

* doi: https://doi.org/10.1101/2024.03.21.586062

 

Synopsis of the study

--------





Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape.




Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation.




We identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor.




This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes.



 

Running the code

--------

Here we present the data and code for carrying out the analyses, as well as the figures and tables from the article and the supplementary material. Once you have installed the necessary packages, run the commands in 'analysis_share.R'. This script uses several functions available in the '/R' directory.

Figures and tables are produced in a 'manuscript/figures' and 'manuscript/tables' directory. The `/data' directory contains the data used in the analyses (data/input or data/output), but also the resulting datasets produced by the code (data/RData/).
DOI: 10.15468/dl.c8xu9g
title: Occurrence Download

description: A dataset containing 2119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Megaceryle lugubris (Temminck, 1834)"
 ]
}

 The dataset includes 2119 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041301-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nc5tk
title: Occurrence Download

description: A dataset containing 882 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptagonus decagonus (Bloch & Schneider, 1801)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 882 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041303-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9ckq9
title: Occurrence Download

description: A dataset containing 54223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is one of (Sweden, Finland, Estonia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fucus vesiculosus L."
 ]
}

 The dataset includes 54223 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041302-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyt447
title: Occurrence Download

description: A dataset containing 1842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptoclinus maculatus (Fries, 1838)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1842 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041304-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10358541
title: Unexpected and unexplained variabilities in Euromomo z-score reporting

description: In this entry we provide the materials and code for the short communication entitled "Unexpected and unexplained variabilities in Euromomo z-score reporting" that is to be submitted to the journal Public Health.

Samples of z-score time series downloaded from the web archive copies of the site euromomo.org
python code used to compute the variances
graphical abstract
submission information
DOI: 10.5281/zenodo.10367747
title: Unexpected and unexplained variabilities in Euromomo z-score reporting

description: In this entry we provide the materials and code for the short communication entitled "Unexpected and unexplained variabilities in Euromomo z-score reporting" that is to be submitted to the journal Public Health.

Samples of z-score time series downloaded from the web archive copies of the site euromomo.org
python code used to compute the variances
graphical abstract
submission information
DOI: 10.5281/zenodo.10594048
title: paper submitted to public health

description: In this entry we provide the materials and code for a short communication entitled  submitted to the journal Public Health.



Samples of z-score time series downloaded from the web archive copies of the site euromomo.org

python code used to compute the variances

graphical abstract

submission information

the message from the editorial board discarding the paper without peer review
DOI: 10.5281/zenodo.10644804
title: unexpected and unexplained variations in euromomo all cause mortality z-score reports detected from web archive retrospective study

description: In this entry we provide the materials and code for a short communication entitled  submitted to the journals Public Health and MDPIs Healthcare.



Samples of z-score time series downloaded from the web archive copies of the site euromomo.org

python code used to compute the variances

graphical abstract

submission information

the messages from the editorial boards discarding the paper without peer review
DOI: 10.5281/zenodo.10358540
title: unexpected and unexplained variations in euromomo all cause mortality z-score reports detected from web archive retrospective study

description: In this entry we provide the materials and code for a short communication entitled  submitted to the journals Public Health and MDPIs Healthcare.



Samples of z-score time series downloaded from the web archive copies of the site euromomo.org

python code used to compute the variances

graphical abstract

submission information

the messages from the editorial boards discarding the paper without peer review
DOI: 10.5281/zenodo.14524938
title: unexpected and unexplained variations in euromomo all cause mortality z-score reports detected from web archive retrospective study

description: In this entry we provide the materials and code for a short communication entitled  submitted to the journals Public Health and MDPIs Healthcare.



Samples of z-score time series downloaded from the web archive copies of the site euromomo.org

python code used to compute the variances

graphical abstract

submission information

the messages from the editorial boards discarding the paper without peer review
DOI: 10.15468/dl.w5swp5
title: Occurrence Download

description: A dataset containing 1604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptocottus armatus Girard, 1854",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1604 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041305-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.745kcq
title: Occurrence Download

description: A dataset containing 522 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Forsythia ovata Nakai"
 ]
}

 The dataset includes 522 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041307-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9thx5
title: Occurrence Download

description: A dataset containing 24313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Alcedo atthis (Linnaeus, 1758)"
 ]
}

 The dataset includes 24313 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041306-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ufh7h
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lestidiops ringens (Jordan & Gilbert, 1880)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 36 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041308-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2hxtsj
title: Occurrence Download

description: A dataset containing 1497 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lesueurigobius friesii (Malm, 1874)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1497 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041309-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gb5nfh
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lesueurigobius sanzi (de Buen, 1918)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 32 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041310-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c6qg63
title: Occurrence Download

description: A dataset containing 1932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Testulea gabonensis Pellegr., Champluviera nuda (C.B.Clarke) I.Darbysh. & T.F.Daniel, Eugenia ogoouensis Amshoff, Chaetocarpus gabonensis Breteler, Baphia megaphylla Breteler, Chlamydocarya soyauxii Engl., Citropsis letestui Pellegr., Diospyros cleistantha O.Lachenaud & G.E.Schatz, Diospyros subargentea O.Lachenaud, Dauby & G.E.Schatz, Paropsia gabonica Breteler, Psychotria neurosticta O.Lachenaud, Begonia anisosepala Hook.fil., Carapa batesii C.DC., Dichapetalum rabiense Breteler, Mapania chevalieri (Nelmes) Lye, Microdesmis afrodecandra Floret, A.M.Louis & J.M.Reitsma, Mocquerysia distans Breteler, Pleiocarpa robusta O.Lachenaud, Octoknema klaineana Pierre, Renealmia stenostachys K.Schum., Rinorea abbreviata Achound. & Bos, Rinorea soyauxii M.Brandt, Salacia diplasia N.Hallé)"
 ]
}

 The dataset includes 1932 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041313-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgv43x
title: Occurrence Download

description: A dataset containing 27659 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nicotiana tabacum L."
 ]
}

 The dataset includes 27659 records from 601 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041312-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pncww5
title: Occurrence Download

description: A dataset containing 3208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Regulus regulus (Linnaeus, 1758)"
 ]
}

 The dataset includes 3208 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041314-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcfe7a
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lesueurigobius suerii (Risso, 1810)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 50 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041315-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8zrrn
title: Occurrence Download

description: A dataset containing 940 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-25.6277 18.11967,48.3733 18.11967,48.3733 67.03559,-25.6277 67.03559,-25.6277 18.11967))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Donacilla cornea (Poli, 1791)"
 ]
}

 The dataset includes 940 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041316-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11395083
title: Data for "Influence of Deposition Parameters on the Plasmonic Properties of Gold Nanoantennas Fabricated by Focused Ion Beam Lithography"

description: This is the dataset for the manuscript "Influence of Deposition Parameters on the Plasmonic Properties of Gold Nanoantennas Fabricated by Focused Ion Beam Lithography".

Datasets were recorded by TEM, AFM and XRD.

Files .emd and .dm4 contain the raw data from TEM measurements. They can be opened, for example, in Velox software (.emd files) and Digital Micrograph software (.dm4 files).Files .ras contain the raw data from XRD measurements in Rigaku XRD RAS Format.Files .gwy contain the raw data from AFM measurements. They can be opened in Gwyddion software.

The original datasest .emd, .dm4, .ras and .gwy are exported to open format data as .tiff, .png, or .txt, too.
DOI: 10.15468/dl.vb6vux
title: Occurrence Download

description: A dataset containing 292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucoraja circularis (Couch, 1838)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 292 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041317-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9zatcr
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucoraja fullonica (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 58 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041318-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2h3t5a
title: Occurrence Download

description: A dataset containing 352692 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Plantae of Costa Rica (INBio)"
 ]
}

 The dataset includes 352692 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041311-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8mmgj
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucoraja lentiginosa (Bigelow & Schroeder, 1951)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 27 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041319-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28055189.v1
title: Santos et al. The association of Mediterranean plant species with herbivorous arthropods and its effect on pest abundance in organic vineyards

description: Non-crop plant resources, such as hedgerows and adjacent woodland areas, may impact the distribution of pest species in the crop. Knowledge on the associations between plants and arthropods, as well as their impact on pest distribution, is thus key to adequately manage agroecosystems. We selected a number of native Mediterranean plant species located around organic vineyards in Southern Portugal and determined their associations with speciesofAuchenorrhyncha and phytophagous tetranychid and tenuipalpid mites, including the main vineyard pests in the area. We also tested if the abundance of vineyard pests is affected by the distance to the edge and to the species of plants present. Most non-crop plants and ground cover vegetation harbored very low numbers of leafhopper pests. <i>Rubus ulmifolius </i>and<i> Tamarix africana </i>proved to be a repository of non-pest Auchenorrhyncha species, with the former also serving as winter repository of the leafhopper pest<i> Jacobiasca lybica</i>.<i> Rosa canina </i>and<i> Fraxinus angustifolia </i>hosted abundant populations of<i> </i>the spider mite <i>Tetranychus urticae</i>.Still, plots next to plant biodiverse margins harbored fewer numbers of <i>T. urticae</i>, when compared with plots next to other vineyards. Furthermore, pest abundance in vineyards increased with growing distance to plant biodiverse margins. Our results highlight the benefits of biodiverse margins in reducing pest abundance and point to the importance of a good selection of plant species when managing and planning these non-crop plant resources.