v21.09: Taputapuātea

Fifth major release of AncientMetagenomeDir

Release v21.09 includes 9 new publications, representing 122 new ancient host-associated metagenome samples, 13 new ancient microbial genomes, and 12 new ancient environmental samples.

This brings the repository to a total of 132 publications, 1038 new ancient host-associated metagenome samples, 368 ancient microbial genomes, and 375 new ancient environmental samples.

Corrections were made to 3 publications.

Thanks to the following contributors and reviewers: @Jesser11 @ivelsko @pheintzman @bbartholdy @MeriamOs

Thanks to the following authors of added publications for answering queries: Jaelle Brealey, Miriam Bravo-López, and Barbara Moguel.

The full changelog is below.

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

Taputapuātea

Taputapuātea on Ra’iātea Island is at the centre of the ‘Polynesian Triangle’, a vast portion of the Pacific Ocean, dotted with islands, and the last part of the globe to be settled by humans. The property includes two forested valleys, a portion of lagoon and coral reef and a strip of open ocean. At the heart of the property is the Taputapuātea marae complex, a political, ceremonial and funerary centre. It is characterized by several marae, with different functions. Widespread in Polynesia, the marae were places where the world of the living intersected the world of the ancestors and the gods. Taputapuātea is an exceptional testimony to 1,000 years of mā'ohi civilization.

Description used under license CC-BY-SA IGO 3.0

v21.06: Côa Valley and Siega Verde

Release Description

Fourth major release of AncientMetagenomeDir

Release v21.06 includes 10 new publications, representing 142 new ancient host-associated metagenome samples, 33 new ancient microbial genomes and 11 new ancient environmental samples.

This brings the repository to a total of 916 ancient host-associated metagenome samples, 355 ancient microbial genomes, and 363 ancient environmental samples.

Corrections were made to 1 publications.

The full changelog is below.

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
• Added new feature (sea coast)
• 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

Prehistoric Rock Art Sites in the Côa Valley and Siega Verde

The two Prehistoric Rock Art Sites in the Côa Valley (Portugal) and Siega Verde (Spain) are located on the banks of the rivers Agueda and Côa, tributaries of the river Douro, documenting continuous human occupation from the end of the Paleolithic Age. Hundreds of panels with thousands of animal figures (5,000 in Foz Côa and around 440 in Siega Verde) were carved over several millennia, representing the most remarkable open-air ensemble of Paleolithic art on the Iberian Peninsula.

Description is available under license CC-BY-SA IGO 3.0 from UNESCO

v21.03: Town of Provins

Release Description

Third major release of AncientMetagenomeDir.

Release v21.03 includes 8 new publications, representing 228 new ancient host-associated metagenome samples, 3 new ancient microbial genomes and 14 new ancient environmental samples.

This brings the repository to a total of 774 ancient host-associated metagenome samples, and 322 ancient microbial genomes and 352 ancient environmental samples.

Corrections were made to 4 publications. New functionality includes an interactive geoJSON map rendered on GitHub, which can be accessed here

The full changelog is below.

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

Provins, Town of Medieval Fairs

The fortified medieval town of Provins is situated in the former territory of the powerful Counts of Champagne. It bears witness to early developments in the organization of international trading fairs and the wool industry. The urban structure of Provins, which was built specifically to host the fairs and related activities, has been well preserved.

v20.12: Ancient City of Nessebar

Release Description

Second major release of AncientMetagenomeDir.

Release v20.12 includes 20 new publications, representing 42 new ancient host-associated metagenome samples, 46 new ancient microbial genomes and 23 new ancient environmental samples.

This brings the repository to a total of 546 ancient host-associated metagenome samples, and 319 ancient microbial genomes and 338 ancient environmental samples.

Corrections were made to 9 publications. New functionality includes auto-generated images of sample location maps, sample count histograms and publication count timelines on each new merge. These can be found under assets/live/images.

The full changelog is below.

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

Ancient City of Nessebar

Situated on a rocky peninsula on the Black Sea, the more than 3,000-year-old site of Nessebar was originally a Thracian settlement (Menebria). At the beginning of the 6th century BC, the city became a Greek colony. The city’s remains, which date mostly from the Hellenistic period, include the acropolis, a temple of Apollo, an agora and a wall from the Thracian fortifications. Among other monuments, the Stara Mitropolia Basilica and the fortress date from the Middle Ages, when this was one of the most important Byzantine towns on the west coast of the Black Sea. Wooden houses built in the 19th century are typical of the Black Sea architecture of the period. Description is available under license CC-BY-SA IGO 3.0 from https://whc.unesco.org/en/list/217/

v20.09.1: Ancient Ksour of Ouadane

This is the first point release of AncientMetagenomeDir!

• Fixes missing table in ZIP file

Release Description
First major release of AncientMetagenomeDir of Host associated meta- and single-genomes samples older than 1950.

Release v20.09 includes 87 publications since 2011, representing 443 ancient host-associated metagenome samples, 269 ancient microbial genomes and 312 sediment samples and spans 49 countries.

Ancient Ksour of Ouadane, Chinguetti, Tichitt and Oualata
Founded in the 11th and 12th centuries to serve the caravans crossing the Sahara, these trading and religious centres became focal points of Islamic culture. They have managed to preserve an urban fabric that evolved between the 12th and 16th centuries. Typically, houses with patios crowd along narrow streets around a mosque with a square minaret. They illustrate a traditional way of life centred on the nomadic culture of the people of the western Sahara. Description is available under license CC-BY-SA IGO 3.0 from https://whc.unesco.org/en/list/750/

v20.09: Ancient Ksour of Ouadane

This is the first release of AncientMetagenomeDir!

Release Description
First major release of AncientMetagenomeDir of Host associated meta- and single-genomes samples older than 1950.

Release v20.09 includes 87 publications since 2011, representing 443 ancient host-associated metagenome samples, 269 ancient microbial genomes and 312 sediment samples and spans 49 countries.

Ancient Ksour of Ouadane, Chinguetti, Tichitt and Oualata
Founded in the 11th and 12th centuries to serve the caravans crossing the Sahara, these trading and religious centres became focal points of Islamic culture. They have managed to preserve an urban fabric that evolved between the 12th and 16th centuries. Typically, houses with patios crowd along narrow streets around a mosque with a square minaret. They illustrate a traditional way of life centred on the nomadic culture of the people of the western Sahara. Description is available under license CC-BY-SA IGO 3.0 from https://whc.unesco.org/en/list/750/

Second pre-release for Zenodo DOI

This allows citability for mostly-complete Microbiome (host-associated) papers list

Pre-release for Zenodo DOI

Pre-release to allow registration with Zenodo