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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project follows to Calendar Versioning.

v21.12: Pyu Ancient Cities [Unreleased]

Added

Ancient Metagenome: Host Associated

  • Kazarina 2021b 10.1016/j.jasrep.2021.103213

Ancient Single Genome: Host Associated

Ancient Metagenome: Environmental

Ancient Metagenome: Anthropogenic

Changed

  • FellowsYates2021: Corrected typo in longitude 85.53 > -85.53

Removed

v21.09: Taputapuātea

Added

Ancient Metagenome: Host Associated

  • Ottoni 2021 10.1073/pnas.2102116118
  • Rampelli 2021b 10.1016/j.isci.2021.102816
  • Brealey 2021 10.1016/j.cub.2021.08.010

Ancient Single Genome: Host Associated

  • Susat 2021 10.1016/j.celrep.2021.109278
  • Guzmán-Solis 2021 10.7554/eLife.68612

Ancient Metagenome: Environmental

  • De Dios 2021 10.1016/j.isci.2021.103021
  • Campos 2021 10.1371/journal.ppat.1009714
  • Wu 2021 10.1371/journal.ppat.1009886

Ancient Metagenome: Environmental

  • Moguel 2021 10.1038/s41598-021-92981-8

Ancient Metagenome: Anthropogenic

Misc

Changed

  • Corrected H. pylori having taxonomic domain to bacteria from virus
  • Ferrari2020: Corrected typo in accession ERS3935829
  • BravoLopez2020: Corrected typo in site name Inmaculate Conception > Immaculate Conception

Removed

v21.06: Côa Valley and Siega Verde

Added

Ancient Metagenome: Host Associated

  • Wibowo 2021 10.1038/s41586-021-03532-0
  • Fellows Yates 2021 10.1073/pnas.2021655118
  • Farrer 2021 10.1038/s41598-021-86100-w

Ancient Single Genome: Host Associated

  • Seguin-Orlando 2021 10.1016/j.isci.2021.102383
  • Haller 2021 10.1016/j.isci.2021.102419
  • Guellil 2020 10.1073/pnas.2009677117
  • Danneels 2021 10.1016/j.cub.2021.03.049

Ancient Metagenome: Environmental

  • Wibowo 2021 10.1038/s41586-021-03532-0
  • Schulte 2021 10.1111/1755-0998.13311
  • Lammers 2021 10.1038/s42003-021-01710-4
  • Liang 2021 10.1186/s40168-021-01057-2

Ancient Metagenome: Anthropogenic

Misc

Changed

  • Changed collection_date column to sampling_date to clarify this is when drilling, or sub-sampling for DNA analysis was performed
  • Corrected date for GLZ001 from Yu et al. (2020) from 4400 to 4600 based on the re-calibrated reported date in the paper (doi: 10.1016/j.cell.2020.04.037)

Removed

v21.03: Town of Provins

Added

  • #348: Interactive GeoJSON maps rendered with GitHub
  • #349: No spaces allowed in archive_accession column.

Ancient Metagenome: Host Associated

  • Philips 2017 10.1186/s12864-020-06810-9
  • Kazarina 2021 10.3390/genes12020309
  • Seguin-Orlando 2021 10.1016/j.cub.2020.12.015
  • Rampelli 2021 10.1038/s42003-021-01689-y
  • Witt 2021 10.1038/s41598-021-82362-6

Ancient Single Genome: Host Associated

  • Philips 2020 10.1186/s12864-020-06810-9
  • Kılınç 2021 10.1126/sciadv.abc4587

Ancient Metagenome: Environmental

  • Rampelli 2021 10.1038/s42003-021-01689-y

Ancient Metagenome: Anthropogenic

Misc

  • Added project accession column to all tables to help finding other samples from same project

Changed

  • Cutibacterium acnes (deDios2020, 10.1016/j.meegid.2020.104209) changed from eukaryota to bacteria.
  • Corrected publication_doi and sample_age_doi for Jacobson2020 (10.1098/rstb.2019.0586)
  • Corrected overwritten new SRA information for Weyrich 2017 (10.1038/nature21674)
  • Corrected date DOI spreadsheetdragging error for Armbrecht 2020 (10.1111/1755-0998.13162)

Removed

v20.12: Ancient City of Nessebar

Added

Ancient Metagenome: Host Associated

  • Modi 2020 10.1007/s12520-019-00983-5
  • Appelt 2014 10.1128/AEM.03242-13
  • Eisenhofer 2020 10.1098/rstb.2019.0578
  • Jacobson 2020 10.1098/rstb.2019.0589
  • Sabin 2020 10.1098/rstb.2019.0576
  • Williams 2020 10.1128/MRA.00850-20
  • Fotakis 2020 10.1098/rstb.2019.0584

Ancient Single Genome: Host Associated

  • Susat 2020 10.1038/s41598-020-71530-9
  • Eisenhofer 2020 10.1098/rstb.2019.0578
  • Morozova 2020 10.1098/rstb.2019.0569
  • Schuenemann 2018 10.1371/journal.pntd.0006447
  • Ferrari 2020 10.1098/rstb.2019.0572
  • Williams 2020 10.1128/MRA.00850-20
  • Fotakis 2020 10.1098/rstb.2019.0584
  • Marciniak 2016 10.1016/j.cub.2016.10.016
  • Gelabert 2016 10.1073/pnas.1611017113
  • Taubenberger 2005 10.1038/nature04230
  • Lugli 2017 10.1186/s40168-016-0221-y
  • Bravo Lopez 2020 10.1098/rstb.2019.0580

Ancient Metagenome: Environmental

  • Added new metadata columns to improve data reconstructions: sequence_name (e.g. core, transect), depth, feature (e.g. cave, lake), study type.
  • Braadbaart 2020 10.1016/j.jasrep.2020.102468
  • DerSarkissian 2016 10.1111/1755-0998.12679

Ancient Metagenome: Anthropogenic

Misc

  • Added 'live-status' summary images that are displayed on README and updated on every new submission.

Changed

  • Ardelean 2020: Differentiated samples with identical names
  • Ahmed 2018: Updated sample_age and sample_age_doi
  • Graham 2016: Updated sequence_name
  • Wang 2017: Updated sequence_name
  • Pedersen 2016: Updated sequence_name and corrected two typos in depth
  • Armbrecht 2020: fixed broken DOI due to spreadsheet drag-down error
  • de Dios 2019: Standardised coordinates and location name with Gelabert 2016 for accuracy
  • van Dorp 2020: Standardised coordinates and location name with Gelabert 2016 for accuracy
  • Weyrich 2017: Replaced OAGR codes with newly uploaded SRA accession numbers

v20.09: Ancient Ksour of Ouadane

Added

Ancient Metagenome: Host Associated

  • Warinner 2014 10.1038/ng.2906
  • Weyrich 2017 10.1038/nature21674
  • Velsko 2018 10.1186/s40168-019-0717-3
  • Jensen 2019 10.1038/s41467-019-13549-9
  • Fagernäs 2020 10.1016/j.jas.2020.105135
  • Mann 2018 10.1038/s41598-018-28091-9
  • Brealey 2020 10.1093/molbev/msaa135
  • Ozga 2019 10.1038/s41598-019-53802-1
  • Ottoni 2019 10.1038/s41598-019-56074-x
  • Zhou 2018 10.1016/j.cub.2018.05.058
  • Wilman 2018 10.1371/journal.pone.0196482
  • Nieves-Colón 2020 10.1093/molbev/msz267
  • Ozga 2016 10.1002/ajpa.22960
  • Santiago-Rodriguez 2016 10.1093/femsec/fiw182
  • Santiago-Rodriguez 2017 10.3390/genes8110310
  • Maixner 2016 10.1126/science.aad2545
  • Ferrari 2018 10.3390/genes9090436
  • McDonough 2018 10.1093/jmammal/gyy080
  • Campana 2014 10.1186/1756-0500-7-111
  • Bieker 2020 10.1111/1755-0998.13174
    • In addition to new samples, includes re-utilised data from Sánchez-Barreiro 2016 10.1111/1755-0998.12610 and Exposito-Alonso 2018 10.1371/journal.pgen.1007155
  • Neukamm 2020 10.1186/s12915-020-00839-8
  • Eerkens 2018 10.1016/j.ijpp.2018.05.001

Ancient Single Genome: Host Associated

  • Warinner 2014 10.1038/ng.2906
  • Bos 2014 10.1038/nature13591
  • Schuenemann 2013 10.1126/science.1238286
  • Schuenemann 2018 10.1371/journal.ppat.1006997
  • Devault 2017 10.7554/eLife.20983
  • Mühlemann 2018 10.1038/s41586-018-0097-z
  • Düx 2020 10.1126/science.aba9411
  • Andrades Valtueña 2017 10.1016/j.cub.2017.10.025
  • Rasmussen 2015 10.1016/j.cell.2015.10.009
  • Spyrou 2018 10.1038/s41467-018-04550-9
  • Rascovan 2019 10.1016/j.cell.2018.11.005
  • Yu 2020 10.1016/j.cell.2020.04.037
  • Guellil 2018 10.1073/pnas.1807266115
  • Duggan 2016 10.1016/j.cub.2016.10.061
  • de Barros Damgaard 2018 10.1038/s41586-018-0094-2
  • Key 2020 10.1038/s41559-020-1106-9
  • Barquera 2020 10.1016/j.cub.2020.04.002
  • Krause-Kyora 2018 10.7554/eLife.36666
  • Giffin 2020 10.1038/s41598-020-66012-x
  • Feldman 2016 10.1093/molbev/msw170
  • Bar-Gal 2013 10.1002/hep.25852
  • Keller 2019 10.1073/pnas.1820447116
  • Mühlemann 2018b 10.1073/pnas.1804921115
  • Wagner 2014 10.1016/S1473-3099(13)70323-2
  • Bos 2011 10.1038/nature10549
  • Bos 2016 10.7554/eLife.12994.001
  • de-Dios 2020 10.1016/j.meegid.2020.104209
  • Patterson Ross 2018 10.1371/journal.ppat.1006750
  • Vågene 2018 10.1038/s41559-017-0446-6
  • Zhou 2018 10.1016/j.cub.2018.05.058
  • Sabin 2020 10.1186/s13059-020-02112-1
  • Kay 2014 10.1128/mBio.01337-14
  • Devault 2014 10.1056/NEJMoa1308663
  • Kay 2015 10.1038/ncomms7717
  • van Dorp 2020 10.1093/molbev/msz264
  • Worobey 2016 10.1038/nature19827
  • Kerudin 2019 10.1016/j.jas.2019.105035
  • Schuenemann 2011 10.1073/pnas.1105107108
  • deDios 2019 10.1099/mgen.0.000289
  • Duggan 2020 10.1186/s13059-020-02079-z
  • Namouchi 2018 10.1073/pnas.1812865115
  • Spyrou 2016 10.1016/j.chom.2016.05.012
  • Martin 2013 10.1038/ncomms3172
  • Spyrou 2019 10.1038/s41467-019-12154-0
  • Krause-Kyora 2018b 10.1038/s41467-018-03857-x
  • Majander 2020 10.1016/j.cub.2020.07.058
  • Yoshida 2013 10.7554/eLife.00731 (KM117502 and KM117507 not included, no data in the ENA PRJEB1877)
  • Mühlemann 2020 10.1126/science.aaw8977
  • Mendum 2014 10.1186/1471-2164-15-270
  • Neukamm 2020 10.1186/s12915-020-00839-8
  • Eerkens 2018 10.1016/j.ijpp.2018.05.001

Ancient Metagenome: Environmental

  • Ahmed 2018 10.1016/j.quascirev.2017.11.037
  • Gaffney 2020 10.3390/geosciences10070270
  • Slon 2017 10.1126/science.aam9695
  • Smith 2015 10.1126/science.1261278
  • Ardelean 2020 10.1038/s41586-020-2509-0
  • Domain 2020 10.3389/fevo.2020.00218
  • Armbrecht 2020 10.1111/1755-0998.13162
  • Pedersen 2016 10.1038/nature19085
  • Graham 2016 10.1073/pnas.1604903113
  • Wang 2017 10.1111/jbi.13010
  • Seersholm 2016 10.1038/ncomms13389

Ancient Metagenome: Anthropogenic

Changed

  • Fagernäs 2020: Fixed missing sample age DOI
  • Ottoni 2019: Fixed duplicate SRA codes
  • de-Dios 202: Added sample data
  • Schuenemann 2018: dates corrected calculating based on 1950
  • Willman2018: re-list the community_type of tooth samples as skeletal tissue
  • Brealey2020: re-list the community_type of tooth samples as skeletal tissue
  • Maixner2016: collapsed H. pylori genome samples into one
  • Bos2016: Corrected site name
  • Bos2011: changed site name for sample ES_6330 (6330) to Abbey St. Mary Graces after investigation from Monica Green
  • Weyrich 2017: Added missing OAGR accession after consultation with authors
  • Maixner2016: corrected singlegenome_domain

Removed