cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10513209
title: Supplementary files and data Files for "Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?" Zoological journal of the Linnean society, 2024, vol 1, issue 4. https://doi.org/10.1093/zoolinnean/zlae098
title: Archive3_Buchnera&MitochondrialGenomes.tar
title: Archive1-AphidMitochondrialData&Phylogeny
title: Supplementary_Tables
title: Archive4_Buchnera_Data&Phylogeny
title: TextS1_Protocole_addition
title: Archive2_AphidnuclearData&Phylogeny
title: FigureS1_workflow
title: FigureS2_DnDs

description: This repository comprises



a file with all supplementary Tables  (Supplementary_Tables). Table S1: Collection details and voucher ID for aphid samples from the CBGP-Inrae collection, data origin is given for other specimens. Table S2: Amplification success of long range DNA fragments from mitochondrial genomes . Table S3: Primers used for fluidigm aplification of nuclear genes and sequencing success. Table S4. Genomic features of newly sequenced Buchnera aphidicola with aphid taxonomic affiliation. Table S5: Summary of models used for each ML analysis  and corresponding log-likelihood score of the best tree.Table S6: Output of RERConverge analyses.

two Supplementary  figures: Figure S1: Workflow of phylogenetic analyses as implemented on each dataset. Figure S2: Plot depicting the genome-wide pattern of molecular evolution (dN/dS) between disymbiotic (n = 15) and monosymbiotic aphid (n = 45) branches across the ML phylogeny (horizontal bars indicate 95% CI of the means). P value was calculated by using Wilcoxon Rank test.

a word file (Text S1) with :  Details of protocol for obtaining mitochondrial genomes through long-range DNA amplifications and Illumina sequencing, and two-step PCR protocole.

an archive (archive1) with the mitochondrial AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses ; 




an archive (archive2) with the nuclear AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses

an archive (archive 3) with the twelve new Buchnera genome drafts.

 an archive (archive4) with the Buchnera AA matrices and alternative topologies
DOI: 10.34740/kaggle/dsv/9266391
title: World Weather Repository ( Daily Updating )
DOI: 10.15468/dl.226ncd
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ITA.19_1",
 "TaxonKey is Parnassius apollo (Linnaeus, 1758)",
 "Year 2024-2024"
 ]
}

 The dataset includes 15 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106257-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2nwrxg
title: Occurrence Download

description: A dataset containing 24942220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2019",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 24942220 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106251-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sffdcd
title: Occurrence Download

description: A dataset containing 572 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oryx leucoryx (Pallas, 1777)"
 ]
}

 The dataset includes 572 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106258-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5wz9j
title: Occurrence Download

description: A dataset containing 739 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ficus virens Aiton"
 ]
}

 The dataset includes 739 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106259-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5285/a798f69cb13e4c219e735f96a7c33faa
title: OpenCLIM - Urban Flood Impacts : 1km gridded outputs for five GB cities

description: This dataset contains output datasets from the OpenCLIM_UrbanFlood Workflow. These runs were part of the NERC funded OpenCLIM (Open CLimate IMpacts modelling framework) project. This data can be used for the continued analysis of climate impacts and for comparison with future studies.

The data has been generated using the OpenCLIM_UrbanFlood workflow available on DAFNI (https://www.dafni.ac.uk/) and focuses on the cities of Newcastle, Norwich, Bath, Inverness and Swansea. The workflow was run for five cities across GB to analyse changes in flood risk for a large range of urban and climate futures. The workflow uses output datasets from the Urban Development Model (described below) to generate future urban landscapes. 

A second model transformed the population density data into new urban form maps including building footprints. Passed through the 2-D hydrodynamic model CityCAT, a range of future storm events with varying intensities were modelled to capture changes in flow and water depths across the domain. Damages incurred as a result of flood waters were calculated and aggregated to the 1km grid level along with the number of commercial and residential buildings affected. The code for each model in the workflow is available within the OpenCLIM GitHub repository (linked in Related Documents).

The Urban Development Model (Newcastle University) presents plausible realisations of future urban change. These are initiated from the 2017 Ordnance Survey urban-rural land use ('UDMbaseline') and projected into the future using attractors and constraints based on the UK's Shared Socio-ecconomic Pathways (SSPs).
DOI: 10.15468/dl.nzbr5j
title: Occurrence Download

description: A dataset containing 18886 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Spain",
 "TaxonKey is Anthus berthelotii Bolle, 1862",
 "Year 2019-2024"
 ]
}

 The dataset includes 18886 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106260-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.20383/103.01021
title: Atmospheric Chemistry Experiment SciSat Level 2 Processed Data, v4.1/v4.2

description: The Atmospheric Chemistry Experiment is a satellite-based mission that has been probing the Earth's atmosphere via solar occultation since February 2004. The solar occultation approach provides global coverage over the order of a few months, with up to 30 occultations over limited latitude ranges on a given day. Instruments on board include a high-resolution Fourier transform spectrometer (ACE-FTS) measuring in the infrared (750-4400 cm-1) and a pair of filtered imagers operating at 1.02 and 0.525 µm. Level 2 data on a 1-km altitude grid from ACE-FTS processing version v4.1/4.2, spanning February 2004 to July 2024, are provided in this data set. This processing version added seven new molecules and three new subsidiary isotopologues compared to v3.5/3.6, for a total of 44 molecules and 24 isotopologues. V4.1/4.2 fixed problems encountered from saturation of CO2 lines in the pressure-temperature retrieval in v4.0, along with removing spikes that occurred in v4.0 in the presence of polar stratospheric clouds. For the imagers, forward model calculations were changed to a 100 m altitude grid (rather than a 1 km grid) in version 4 processing. ACE SciSat Level 2 Processed Data, v4.1/4.2. Temperature, Pressure and Volume Mixing Ratio (VMR) profiles as a function of altitude for many atmospherically relevant molecules: H2O, O3, N2O, CO, CH4, NO, NO2, HNO3, HF, HCl, OCS, N2O5, ClONO2, HCN, CH3Cl, CF4, CFC-12 (CCl2F2), CFC-11 (CCl3F), COF2, COCl2, COClF, C2H6, C2H2, HCFC-22 (CHClF2), HCOOH, SF6, HO2NO2, H2O2, H2CO, CH3OH, CCl4, N2, O2, CFC-113 (Cl2FC-CClF2), HCFC-141b (Cl2FC-CH3), HCFC-142b (ClF2C-CH3), HFC-134a (F3C-CFH2), PAN (CH3C(O)OONO2), CHF3, acetone (C3H6O), SO2, CH3CN, ClO, CO2, as well as isotopologues for some of these molecules. Imager (IMG) and geolocation (GLC) data are also included. C. Boone, et al. Version 4 retrievals for the atmospheric chemistry experiment Fourier transform spectrometer (ACE-FTS) and imagers, 106939, 2020; doi:10.1016/j.jqsrt.2020.106939.
DOI: 10.15468/dl.93n76x
title: Occurrence Download

description: A dataset containing 18459 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Anthus trivialis (Linnaeus, 1758)",
 "Year 2019-2024"
 ]
}

 The dataset includes 18459 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106261-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6urwr2
title: Occurrence Download

description: A dataset containing 22163 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Schinus terebinthifolia Raddi"
 ]
}

 The dataset includes 22163 records from 430 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013472-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7crcm
title: Occurrence Download

description: A dataset containing 556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Grus japonensis (Statius Muller, 1776)"
 ]
}

 The dataset includes 556 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106263-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nvd7zs
title: Occurrence Download

description: A dataset containing 209500 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nucifraga caryocatactes (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 209500 records from 211 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106256-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13963752
title: Rawdata and Code of 'Efficient and sustained optogenetic control of sensory and cardiac systems'

description: This is the rawdata and code of the publication "Efficient and sustained optogenetic control of sensory and cardiac systems".
DOI: 10.5281/zenodo.13963753
title: Rawdata and Code of 'Efficient and sustained optogenetic control of sensory and cardiac systems'

description: This is the rawdata and code of the publication "Efficient and sustained optogenetic control of sensory and cardiac systems".
DOI: 10.5281/zenodo.14364282
title: Rawdata and Code of 'Efficient and sustained optogenetic control of sensory and cardiac systems'

description: This is the rawdata and code of the publication "Efficient and sustained optogenetic control of sensory and cardiac systems".
DOI: 10.5281/zenodo.14532216
title: Rawdata and Code of 'Efficient and sustained optogenetic control of sensory and cardiac systems'

description: This is the rawdata and code of the publication "Efficient and sustained optogenetic control of sensory and cardiac systems".
DOI: 10.5281/zenodo.15210800
title: Rawdata and Code of 'Efficient and sustained optogenetic control of sensory and cardiac systems'

description: This is the rawdata and code of the publication "Efficient and sustained optogenetic control of sensory and cardiac systems".
DOI: 10.15468/dl.qq72ts
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Inversodicraea ledermannii Engl."
 ]
}

 The dataset includes 97 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021813-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive130228.20221219.7.1
title: Paraburkholderia diazotrophica (Sheu et al. 2013) Sawana et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130229.20220920.7
title: Paraburkholderia dilworthii (De Meyer et al. 2014) Sawana et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130229.20221219.7.1
title: Paraburkholderia dilworthii (De Meyer et al. 2014) Sawana et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130230.20220920.7
title: Paraburkholderia eburnea (Kang et al. 2014) Sawana et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130230.20221219.7.1
title: Paraburkholderia eburnea (Kang et al. 2014) Sawana et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130231.20220920.7
title: Paraburkholderia aspalathi (Mavengere et al. 2014) Sawana et al. 2017

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130231.20221219.7.1
title: Paraburkholderia aspalathi (Mavengere et al. 2014) Sawana et al. 2017

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130232.20220920.7
title: Paraburkholderia insulsa (Rusch et al. 2015) Dobritsa and Samadpour 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130232.20221219.7.1
title: Paraburkholderia insulsa (Rusch et al. 2015) Dobritsa and Samadpour 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130233.20220920.7
title: Ralstonia sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130233.20221219.7.1
title: Ralstonia sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130234.20220920.7
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130234.20221219.7.1
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130235.20220920.7
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130235.20221219.7.1
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130236.20220920.7
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130236.20221219.7.1
title: Ralstonia syzygii subsp. indonesiensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130237.20220920.7
title: Ralstonia syzygii subsp. celebesensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130237.20221219.7.1
title: Ralstonia syzygii subsp. celebesensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130238.20220920.7
title: Ralstonia syzygii subsp. celebesensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130238.20221219.7.1
title: Ralstonia syzygii subsp. celebesensis Safni et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130239.20220920.7
title: Campylobacter coli (Doyle 1948) Véron and Chatelain 1973

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130239.20221219.7.1
title: Campylobacter coli (Doyle 1948) Véron and Chatelain 1973

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130240.20220920.7
title: Phenylobacterium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130240.20221219.7.1
title: Phenylobacterium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130241.20220920.7
title: Pseudactinotalea suaedae (Zhao et al. 2015) Cho et al. 2017

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130241.20221219.7.1
title: Pseudactinotalea suaedae (Zhao et al. 2015) Cho et al. 2017

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130242.20220920.7
title: Chlamydia pecorum Fukushi and Hirai 1992

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130242.20221219.7.1
title: Chlamydia pecorum Fukushi and Hirai 1992

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130243.20220920.7
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130243.20221219.7.1
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130244.20220920.7
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130244.20221219.7.1
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130245.20220920.7
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130245.20221219.7.1
title: Clostridium sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130246.20220920.7
title: Clostridium boliviensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130246.20221219.7.1
title: Clostridium boliviensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130247.20220920.7
title: Clostridium sulfatireducens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130247.20221219.7.1
title: Clostridium sulfatireducens

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130248.20220920.7
title: Clostridium algifaecis Wu et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130248.20221219.7.1
title: Clostridium algifaecis Wu et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130249.20220920.7
title: Clostridium swellfunianum Liu et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130249.20221219.7.1
title: Clostridium swellfunianum Liu et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130250.20220920.7
title: Clostridium oryzae Horino et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive130250.20221219.7.1
title: Clostridium oryzae Horino et al. 2015

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.