cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.331rwa
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Diospyros littorea (R.Br.) Kosterm.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 354 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016404-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mks8pp
title: Occurrence Download

description: A dataset containing 591 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sarcocapnos crassifolia (Desf.) DC."
 ]
}

 The dataset includes 591 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0225590-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3bkuq
title: Occurrence Download

description: A dataset containing 55083 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Zea mays L."
 ]
}

 The dataset includes 55083 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003936-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8wafdg
title: Occurrence Download

description: A dataset containing 785 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Halcyon pileata (Boddaert, 1783)"
 ]
}

 The dataset includes 785 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256046-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qmj7vp
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Apistogramma arua Römer & Warzel, 1998)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049560-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.55c2gm
title: Occurrence Download

description: A dataset containing 385963 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Denmark",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 385963 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237458-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swoci2
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhodostemonodaphne capixabensis Baitello & Coe-Teix."
 ]
}

 The dataset includes 76 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016404-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qh2xcm
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rinorea ramiziana Glaz. ex Hekking"
 ]
}

 The dataset includes 19 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180191-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.decjq7
title: Occurrence Download

description: A dataset containing 2413 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Literature based species occurrence data of birds of North-East India"
 ]
}

 The dataset includes 2413 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260687-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdsnrn
title: Occurrence Download

description: A dataset containing 395 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Mexico",
 {
 "or" : [
 "Issue is Elevation min max swapped",
 "Issue is Geodetic datum assumed WGS84"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Sideroxylon capiri (A.DC.) Pittier",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 395 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016404-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zgppkx
title: Occurrence Download

description: A dataset listing the 34398 species recorded in GBIF matching the query:
{
 "Country" : [
 "is Morocco"
 ]
}

 The dataset's 34398 records were derived from 836 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002000-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9asyw
title: Occurrence Download

description: A dataset containing 6413 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Poecile atricapillus (Linnaeus, 1766)",
 "Year 2011-2018"
 ]
}

 The dataset includes 6413 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237448-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.943b8p
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anura)",
 "Country is one of (Brazil)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011470-210819072339941/datasets/export for details.
DOI: 10.15468/dl.bsxbce
title: Occurrence Download

description: A dataset containing 12572 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Togo National Herbarium Database"
 ]
}

 The dataset includes 12572 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263568-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4he5w4
title: Occurrence Download

description: A dataset containing 4937 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 4937 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0193427-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.azc0fx
title: Occurrence Download

description: A dataset containing 1131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Excoecaria agallocha L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1131 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016405-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.88u7wm
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "TaxonKey is Elaphoglossum herminieri (Bory ex Fée) T.Moore",
 "TaxonKey is Acrostichum herminieri Bory ex Fée"
 ]
 }
 ]
}

 The dataset includes 486 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237461-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdb9sk
title: Occurrence Download

description: A dataset containing 304964 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Equisetaceae"
 ]
}

 The dataset includes 304964 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270276-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fbtwy
title: Occurrence Download

description: A dataset containing 4937 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 4937 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0193447-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.djufe2
title: Occurrence Download

description: A dataset containing 2077 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Philopedon plagiatum (Schaller, 1783)"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2077 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016405-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kj6upu
title: Occurrence Download

description: A dataset containing 55223 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onopordum acanthium L."
 ]
}

 The dataset includes 55223 records from 430 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0268468-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y59xyc
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thamnodynastes ramonriveroi Manzanilla & Sánchez, 2005"
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005845-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ghftvr
title: Occurrence Download

description: A dataset containing 346 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Mexico",
 {
 "or" : [
 "Issue is Elevation min max swapped",
 "Issue is Geodetic datum assumed WGS84"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Tabebuia chrysantha (Jacq.) Nicholson",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 346 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016405-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdjwtn
title: Occurrence Download

description: A dataset containing 1030 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bombus dahlbomii Guérin-Méneville, 1835"
 ]
}

 The dataset includes 1030 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029883-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6cvzv
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Glyphonycteris sylvestris Thomas, 1896"
 ]
}

 The dataset includes 118 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155527-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evda9p
title: Occurrence Download

description: A dataset containing 6905468 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Victorian Biodiversity Atlas",
 "Year is less than or equal to 3000"
 ]
}

 The dataset includes 6905468 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289427-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ae2ji4
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis scopaeus (Lynch, Ruiz-Carranza & Ardila-Robayo, 1996)"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016406-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3nd3j
title: Occurrence Download

description: A dataset containing 599893 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Samanea tubulosa (Benth.) Barneby & J.W.Grimes, Sambucus nigra L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 599893 records from 1136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155509-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xbtvtt
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepidotrigla dieuzeidei Blanc & Hureau, 1973",
 "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 25 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041295-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78y4hm
title: Occurrence Download

description: A dataset containing 1645 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Athene noctua (Scopoli, 1769)"
 ]
}

 The dataset includes 1645 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041296-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jsgk9g
title: Occurrence Download

description: A dataset containing 604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepophidium brevibarbe (Cuvier, 1829)",
 "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 604 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041297-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j339a9
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepophidium entomelan Robins, Robins & Brown, 2012",
 "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 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041299-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aqgxng
title: Occurrence Download

description: A dataset containing 14331 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trema orientale (L.) Blume"
 ]
}

 The dataset includes 14331 records from 307 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041298-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2p6362
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepophidium jeannae Fowler, 1941",
 "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 34 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041300-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15129/c69e5f63-2c84-4fed-ad37-39b9cde4c5b5
title: Data for "Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2"

description: Data is organized as follows:

In the main folder, there are three subfolders with the following data contained within:

1. For small molecules synthesised, NMR, High Resolution Mass spectrometry (HRMS) and IR data are included where appropriate. NMR data was recorded and processed using MestReNova. Mass spectrometry data is provided in pdf format. The data for each compound is contained within a folder numbered with the compound number from the paper/SI. Folder name: Characterisation data-Purines, Characterisation data-Purines-part2, Characterisation data-Pyrimidines, Characterisation data-Pyrimidines-part2.

2. Conversion data of starting materials to products, which were used in the calculation of nucleosides is provided as pdf files of each HPLC analysis carried out. Folder name: Conversion data.

3. Wild-type plasmid sequence in FASTA format used for protein expression for x-ray crystallography is provided in .txt format. Folder name: Crystallography
DOI: 10.5281/zenodo.11108968
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:

* 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/).