Chapman, Abbie S.; Beaulieu, Stace E.; Colaço, Ana; Gebruk, Andrey V.; Hilario, Ana; Kihara, Terue C.; Ramirez-Llodra, Eva; Sarrazin, Jozée; Tunnicliffe, Verena; Amon, Diva J.; Baker, Maria C.; Boschen-Rose, Rachel E.; Chen, Chong; Cooper, Isabelle J.; Copley, Jonathan T.; Corbari, Laure; Cordes, Erik E.; Cuvelier, Daphne; Duperron, Sébastien; Du Preez, Cherisse; Gollner, Sabine; Horton, Tammy; Hourdez, Stéphane; Krylova, Elena M.; Linse, Katrin; LokaBharathi, P. A.; Marsh, Leigh; Matabos, Marjolaine; Mills, Susan W.; Mullineaux, Lauren S.; Rapp, Hans Tore; Reid, William D.K.; Rybakova (Goroslavskaya), Elena; Thomas, Tresa R.A.; Southgate, Samuel James; Stöhr, Sabine; Turner, Phillip J.; Watanabe, Hiromi K.; Yasuhara, Moriaki; Bates, Amanda E.
Published Jul 30, 2020
on Dryad.
https://doi.org/10.5061/dryad.cn2rv96
Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait-based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep-sea chemosynthesis-based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global-scale trait database for deep-sea hydrothermal-vent fauna - sFDvent (sDiv-funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: i) capture the performance of vent species and their influence on ecosystem processes, and ii) compare trait-based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal-vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we typify the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow-marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross-ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique doi. 646 vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid-ocean ridges and 6 back-arc spreading centres. sFDvent includes information on deep-sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every five years. Deep-sea hydrothermal-vent fauna with species-level identification present or in progress. .csv and MS Excel (.xlsx)
sFDvent trait database for deep-sea hydrothermal-vent species, v.1.0
This file is the processed, ‘ready-to-use’ version of the sFDvent trait dataset that we recommend for use. The sFDvent database comprises species-level trait scores for deep-sea hydrothermal-vent species across the globe, as contributed by experts using their observations on research cruises and in laboratories, as well as published literature. ‘Taxon’ refers to the taxonomic identity assigned by contributors, while ‘UniqueID’ is an identifier created using letters from the taxon and the entry number, to make it easier to work with the data and reference a taxon. A glossary, describing the traits and modalities, is provided with the paper that accompanies this dataset. We would recommend that users check these data are processed in line with criteria and thresholds appropriate for their research question and/or analytical approach and make adjustments where required, as no dataset will be fit for all purposes. Nevertheless, to ensure this dataset is as user-friendly and ‘ready-to-use’ as possible, we only include traits in this version of the dataset that meet thresholds for certainty and coverage, with more than 50% of species scored and/or an average certainty score of more than 2.3 (of a maximum score of 3). References have been assigned numeric identifiers, which can be matched to the references provided in the paper that accompanies this dataset. If more than one reference is provided to support a score, the reference identifiers are separated by a semi-colon (;). Please note that species with UniqueID 'Aus74' should not have 'Lau Basin' listed as a location. This has been corrected since publication and will be updated in future versions of the sFDvent database.
Table_S4.2_Recommended_References_As_Numbers.csv
Table_S4.1_Glossaries
These glossaries can be used to check the definitions of the traits and modalities in the sFDvent database.
Table_S4.3_Raw
Table S4.3 is a copy of raw data contributions, compiled from the personalised files sent to each sFDvent contributor. This version of the dataset is provided for transparency and as metadata for users wanting to refer to raw contributions and/or data provided by specific contributors. This dataset includes traits that were removed from the error-checked, quality-controlled dataset due to lack of coverage and would require appropriate processing for each user’s research question before it could be used in an analysis. A glossary to support the traits and modalities given in Table S4.3 is provided in Table S4.1.
Table_S4.4_CleanedRaw
Table S4.4 is a cleaned version of Table S4.3, processed according to the decision rules documented in Table S4.5. We refer users to the Supporting Information accompanying the manuscript for further information about this, and other, files.
Table_S4.5_Metadata
Here, we document the decision rules used to clean / process the data provided in Table S4.3 (raw data). We refer users to the Supporting Information accompanying the manuscript, as well as the manuscript itself, for further information.
Table_S4.2_Recommended_References_As_Numbers_v1
This file is the processed, ‘ready-to-use’ version of the sFDvent trait dataset that we recommend for use. The sFDvent database comprises species-level trait scores for deep-sea hydrothermal-vent species across the globe, as contributed by experts using their observations on research cruises and in laboratories, as well as published literature. ‘Taxon’ refers to the taxonomic identity assigned by contributors, while ‘UniqueID’ is an identifier created using letters from the taxon and the entry number, to make it easier to work with the data and reference a taxon. A glossary, describing the traits and modalities, is also available on Dryad (Table S4.1). We would recommend that users check these data are processed in line with criteria and thresholds appropriate for their research question and/or analytical approach and make adjustments where required, as no dataset will be fit for all purposes. Nevertheless, to ensure this dataset is as user-friendly and ‘ready-to-use’ as possible, we only include traits in this version of the dataset that meet thresholds for certainty and coverage, with more than 50% of species scored and/or an average certainty score of more than 2.3 (of a maximum score of 3). References have been assigned numeric identifiers, which can be matched to the references provided in the paper that accompanies this dataset. If more than one reference is provided to support a score, the reference identifiers are separated by a semi-colon (;).
Video_S4.1_Tutorial
Video S4.1 is a copy of a narrated tutorial sent to all contributors as part of the online, personalised Google Sheets populated to create Table S4.3. This video could be used as a guide by future contributors to the database.
Video B.3.1.mov
