Standardized data to support conservation prioritization for sharks and batoids (Elasmobranchii)

We collated and synthesized information on 1,226 Elasmobranch species (i.e., sharks, rays, and skates) globally from a wide range of sources. We obtained curated and standardized data from online databases, legal documents, press releases, and websites. All data were standardized according to the taxonomic nomenclature described in the Catalogue of Life. We grouped data into five categories: 1) biological information, 2) conservation status, 3) management opportunities, 4) use, and 5) inclusion in international conventions and treaties. For species biological information, we included migration, habitat, species characteristics such as length & body weight, their threat to humans, life-history trait data availability from FishBase, whether the species was listed on the Global Register of Migratory Species, the presence of occurrence data from the Global Biodiversity Information Facility (GBIF), information on genomics from GenBank, and species evolutionary distinctiveness scores. For conservation status, we recorded threat status from the International Union for Conservation of Nature Red List of Threatened Species™ and inclusion in the Alliance for Zero Extinction (AZE). For management opportunities, we identified species under human care in zoos and aquariums in the Species360 network, species under management in studbooks from the European Association of Zoos and Aquaria (EAZA), the American Association for Zoos and Aquariums (AZA), and the Zoo and Aquarium Association Australasia (ZAA), as well as data on recovery, management, and action plans at the class, family, and species levels. For use, we collated species-level data on international trade levels from the CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) Trade Database, as used in aquaculture, as bait, and as gamefish, recording the purpose of the trade according to the IUCN Red List and the global catches reported to the FAO (Food and Agriculture Organization of the United Nations). Finally, we collated information from seven international conventions and treaties: CITES, UNCLOS (the United Nations Convention for the Law of the Sea), CMS (the Convention on the Conservation of Migratory Species of Wild Animals), Shark MoU (the Memorandum of Understanding on the Conservation of Migratory Sharks), BERN (the Convention on the Conservation of European Wildlife and Natural Habitats), OSPAR (Protecting and conserving the North-East Atlantic and its resources), and the Barcelona Convention for the Protection of the Marine Environment and the Coastal Region of the Mediterranean. Our data are comparable across databases and will assist further research on in-situ and ex-situ population management for sharks and batoids. Our data can be of use to international policy makers, aquarium curators, management authorities, conservation practitioners, and scientists interested in prioritizing Elasmobranchs for conservation.


a b s t r a c t
We collated and synthesized information on 1,226 Elasmobranch species (i.e., sharks, rays, and skates) globally from a wide range of sources. We obtained curated and standardized data from online databases, legal documents, press releases, and websites. All data were standardized according to the taxonomic nomenclature described in the Catalogue of Life. We grouped data into five categories: 1) biological information, 2) conservation status, 3) management opportunities, 4) use, and 5) inclusion in international conventions and treaties. For species biological information, we included migration, habitat, species characteristics such as length & body weight, their threat to humans, life-history trait data availability from FishBase, whether the species was listed on the Global Register of Migratory Species, the presence of occurrence data from the Global Biodiversity Information Facility (GBIF), information on genomics from GenBank, and species evolutionary distinctiveness scores. For conservation status, we recorded threat status from the International Union for Specifications Table   Subject Management, Monitoring, Policy and Law Specific subject area Species-level data on Elasmobranchs to support conservation prioritization Type of data Table  Figure Chart How data were acquired Open-access online databases, legal documents, press releases, and websites.

Data format
Raw, Analyzed and Filtered Parameters for data collection We collated data on all Elasmobranchs (i.e., sharks and batoids) described in the Catalogue of Life (1,226 species). We collated data into five categories: 1) biological information, 2) conservation status, 3) management opportunities, 4) use, and 5) inclusion in international conventions and treaties. Description of data collection Most datasets were downloaded from online sources in 2019 and 2020 (links provided in Table 1). For species not yet included in online databases, we used press releases. We standardized species names according to the Catalogue of Life and completed all data collation, processing, and analysis in the open-source software R.
( continued on next page ) R. Oegelund Nielsen, R.

Value of the Data
• This is a comprehensive collection of datasets on Elasmobranch species (i.e., sharks and batoids), comprising their biological traits, occurrence, migration, body characteristics, habitat, genomics, conservation status, trade patterns, threat to humans, fishery catches, catching methods, and inclusion in seven international conventions, treaties, and prioritization schemes. • These data will provide key foundational information for the conservation of Elasmobranchs globally. • These data can be re-used to support decision making for ex-situ and in-situ conservation, for example by aquariums (e.g., collection planning and captive management), conservation organizations, governments, and global conventions and treaties. • The dataset identifies salient knowledge gaps and conservation and research opportunities for the Elasmobranchs.

Data Description
The presented data cover 1,226 Elasmobranchs (i.e., sharks, rays, and skates) described in the Catalogue of Life [1] . We used the Catalogue of Life as a standardized taxonomy to access information across a range of open-source data repositories ( Table 1 ). The supplementary dataset Supplementary File S3 is a list of species' scientific names used for the following datasets: Catalogue of Life (CoL), FishBase, IUCN Red List, CITES, and ZIMS (Species360 Zoological Information Management System). This data file can be used as a taxonomic translation table among datasets. We further cross-matched the species taxonomy from CoL with the taxonomy from the World Register of Marine Species (WoRMS) which is available from the Supplementary File S1. The Supplementary File S1 shows merged data for the following five categories: 1) biological information, 2) conservation status, 3) management opportunities, 4) use, and 5) inclusion in international conventions and treaties. The Supplementary File S2includes explanations of all data, variables, their sources and original column names.

Biological information
This category summarizes information available in open-source repositories on species biological traits, migratory status, occurrence data, species characteristics, habitat, genomics, and evolutionary distinctiveness. We merged data from FishBase, the Global Register of Migratory Species (GROMS), the Global Biodiversity Information Facility (GBIF), the IUCN Red List, GenBank, the Vertebrate Genome Project (VGP), and evolutionary distinctiveness scores from the EDGE of Existence database [3] . We included two types of data retrieved from Fishbase, 1) whether or not biological traits are available from FishBase [4] in the following categories: reproduction, photo identification, ecology, food, maturity, maximum size, spawning, length and weight, eggs, diet, growth, genetics, predators, mortality and hatchlings ( Table 2 ). We assumed that data existed for a given category if at least one of the parameters was available for that species. 2) Data on common names, habitat, body shape, water zone, migration, depth ranges and common depth ranges, longevity, price category, length, body weight, resilience to fishery, their electrogenic abilities, threat to humans, vulnerability to fishery and trophic level. More details on each Table 1 The number of Elasmobranch species assessed in each dataset, with data types and sources. We also quantify overlap with species described in the Catalogue of Life (CoL). Comparing the second and third columns shows how many species will be lost when merging datasets with the Catalogue of Life taxonomy. Further data sources for management opportunities are described in Table 7 . Note: For the data from the IUCN Red List Advanced search we show the number of different species in each of the corresponding data files under the Title column. Additionally, please note that some databases contain data used in more than one category even though the database is only listed under one of the categories in this table (refer to the category column in the Supplementary File S1).   Table 5 . For references on these, we refer to Fishbase.org. Additionally we included data on country distribution, threats, stressors, generation length, and migration patterns from the IUCN Red List of Threatened Species TM Advanced Search.
We assessed sequence data from GenBank to identify the type of information available for each species in each of nine sequence types: 1) gene sequences (GEN), 2) genomic survey sequence (GSS), 3) nuclear marker (NM), 4) mitochondria (mtDNA), 5) pseudogene (PG), 6) RNA sequences (RNA), 7) whole genome sequence (WGS) or 8) other genetic sequences (Other). We found 736 species with records on any of the nine categories. In Supplementary File S1, we list for each species how many records were reported for each sequence type. Fig. 1 summarizes the number of species for which different sequence types were reported for sharks and batoids separately.
For primary biodiversity data, we found 1,017 species of sharks and batoids with occurrence data on the GBIF website between 20 0 0 and April 2020. In Table 3 , we show the number of observations for each taxonomic level (e.g., family, genus, species, subspecies, or unknown). For each Elasmobranch order, we display the number of records for: fossils, human observations, living specimens, machine observations, material samples, observations, preserved specimens, and unknown [6] . We filtered the data and counted the total number of observations for each species over the period 2009-2019 for 1) All observation types and 2) only for human observations, machine observations and observations.

Conservation status
Conservation status was assessed with IUCN Red List extinction risk assessments and the Alliance for Zero Extinction (AZE) [7] . In the Supplementary File S1 , we list the two batoids in AZE and the current IUCN Red List threat status, the Red List criteria used, the year of assessment, and the species population trend (i.e., declining, stable, increasing, or unknown). For all records, we included a Red List species ID that can be used to merge the data with other IUCN data. In Table 4 , we show the number of sharks and batoids that are threatened with extinction (i.e., listed as Vulnerable, Endangered, or Critically Endangered) and break down species in ZIMS, CITES (Appendices I, II, or III), and the Catalogue of Life by threat status. We also indicate the number of species present in those datasets but not assessed by IUCN.

Management opportunities
Data for ex-situ management include species holdings and total population size across aquariums in the Species360 network (ZIMS) and whether species are included in a captive breeding program by a regional association. Of the 1,226 species described in the Catalogue of Life, 159 were represented in ZIMS and 18 were managed in regional associations. Of these 18 species, five species were managed only by the European Association of Zoos and Aquaria (EAZA), five species were managed by both the EAZA and the American Association of Zoos and Aquariums (AZA), seven species were managed only by the AZA, and one species was managed by both the AZA and the Aquarium Association Australasia (ZAA).
For in-situ management, we included information on conservation strategies from the IUCN Species Survival Commission (SSC) Shark Specialist Group (SSG) and recovery or action plans under the Australian or Canadian Government, which were the only countries with action plans that were found during the search, either at the family or species level. Additionally, we included national and regional plans both historically and in use from IPOA Sharks [8] which provides an overview of when, and in which countries the action plans are either adopted, drafted, non-official or in progress, though these data do not provide scientific names of species under protection. Further, we included if there is an active recovery plan in place for species and if the habitat lies partly or completely within a protected area according to the IUCN Red List.

Use
This category summarizes information available on the use of the species (e.g., economic, cultural, or medicinal). We included information on international trade in Elasmobranchs between 20 0 0 and 2018 at the species or genus level from the UNEP-WCMC (United Nations Environment Programme World Conservation Monitoring Centre), CITES Trade Database and global catches from the FAO from 20 0 0 to 2017. The dataset in Supplementary File S1 includes CITES information on importing and exporting countries, the origin and source of the species of concern, the purpose of the transaction and quantities, and the terms the species was traded under. We also note the CITES Appendix under which each species is listed. In Table 5 we list terms and purposes of trade. For global FAO catches (20 0 0-2017), we included quantities caught at the species, genus, family and order levels. Catches recorded at the order, the family, or the genus level were divided by the number of species within that taxon to get an overview of which species are possibly caught and at which quantities. We estimated the total catch at the species level as the sum of catches recorded at the order, the family, the genus and the species level for each species. These estimations gave us an overview of which species are possibly caught and at which quantities [9] . Out of the 1,226 species in the Catalogue of Life, six species were listed on CITES Appendix I, 41 on Appendix II, 23 on Appendix III, and 142 were listed on FAO fisheries catches.
We also included data from the IUCN Red List indicating any purposes of trade for the focal species (e.g human food, sport hunting, medicine, research, jewelry or accessories, chemicals or as pets or display animals). From Fishbase we collated data on catch methods and if the species is used in aquariums, as bait, in aquaculture or as a gamefish.

Conventions and treaties
We collated and standardized the information of seven legal instruments (i.e., international, and/or regional conventions and treaties) protecting or managing Elasmobranchs. In Supplementary File S1, we include if the species is listed in the following international or regional conventions or treaties: CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) both internationally and in the EU, UNCLOS (the United Nations Convention for Yes. We mention the original column names from the Advanced Search data files "countries", "threats", "usetrade" and "all_other_fields" in the description column in the Supplementary File S2.  Fig. 2 (sharks) and Fig. 3 (batoids) summarize the overlap between the seven conventions or treaties, the IUCN Red List, and species holdings in aquariums (ZIMS). Nine shark or batoid species ( < 1%) are not included in the visualizations as their taxonomy did not match across databases ( Table 1 ). We also provide a list of migratory species that can be used to support decision making.

Experimental Design, Materials, and Methods
To collate data across the 31 open-source repositories, databases, and documents, we standardized the Elasmobranch taxonomy using the Catalogue of Life [1] with the R package taxize  Table 1 for definitions of all other abbreviations of datasets and conventions or treaties. This plot was generated with the UpSetR package (doi:10.1093/bioinformatics/btx364) in the open-source software R [10] . [ 10 , 11 ], which automatically retrieves species names. When the accepted names were not automatically standardized, we conducted manual checks. Six species on the IUCN Red List were not found in the Catalogue of Life. We retained those in the dataset but list them as NA under the Catalogue of Life (CoL) column. To create the Supplementary File S3, we cross-referenced databases by combining the Catalogue of Life, FishBase, ZIMS, and CITES data into a taxonomic translation table.
Furthermore, we cross-referenced the species taxonomy from CoL with the taxonomy from the World Register of Marine Species (WoRMS) by using the WoRMS Taxon Match Tool available at http://www.marinespecies.org/aphia.php?p=match . We added the scientific name, the taxon status (if taxon is accepted or not according to WoRMS) and the internal taxon ID from WoRMS to the Supplementary File S1. We divided the data by taxonomic orders into sharks: Hexanchiformes, Squaliformes, Carcharhiniformes, Pristiophoriformes, Heterodontiformes, Lamniformes, Orectolobiformes, Squatiniformes and batoids: Rhinopristiformes, Rajiformes, Myliobatiformes, Torpediniformes [1] .

Biological information
We retrieved two types of data from FishBase, 1) we collected the data on biological traits available for the following variables: ecology, food, diet, predators, spawning, maturity, eggs, hatchlings, growth, mortality, length and weight, maximum size, genetics, or photo identification from the Fishbase Information Gaps webpage [5] and, 2) we automatically retrieved data on the species common names, habitat, body shape, water zone, migration, depth . We indicate which species has been observed between 20 0 0 and April 2020. Additionally, we filtered the data and counted the total number of observations for each species in the time period 2009 and 2019 for 1) All observation types and 2) only for human observations, machine observations and observations [13] . For references and definitions, we refer to the Biodiversity Information Standards Darwin Core quick reference guide [6] .
To retrieve genomic information from GenBank, we used the R package taxize [11] and obtained a text file with gene descriptions. For simplicity, we classified the data extracted from GenBank into the following sequences 1) gene sequences (GEN), 2) genomic survey sequence (GSS), 3) nuclear marker (NM), 4) mitochondria (mtDNA), 5) pseudogene (PG), 6) RNA sequences (RNA), 7) whole genome sequence (WGS) or 8) other genetic sequences (Other). In Table 6 , we list the terms used to search for sequence descriptions in Genbank. We listed all the species with full genome sequences by searching the species list of the Vertebrate Genome Project (VGP; https://vertebrategenomesproject.org/ways-to-help-1 ). We obtained Evolutionary Distinctiveness (ED) scores for each species from the EDGE of Existence webpage [3] .
We gathered data on the species country distribution, generation length range, movement patterns, threats and stressors from the IUCN Red List Advanced Search version 2020-2 using the "country", "threat" and "all other fields" files.

Conservation status
We retrieved IUCN Red List assessments from the IUCN Red List of Threatened Species TM version 2020-1 from their website using the taxonomy function, selecting the 12 Elasmobranch orders. We downloaded information from the Alliance for Zero Extinction (AZE) data from the Global AZE map 2018 [7] .

Management opportunities
We submitted a request for species holdings data to the Zoological Information Management System (ZIMS) managed by Species360. The species holdings files contain a list of species in Species360-member aquariums globally, the number of adult individuals alive at the time of data extraction and their sex (May 2019).
We obtained the lists of species managed under a breeding program in a studbook from the websites of three regional associations: the European Association of Zoos and Aquaria (EAZA), the American Association of Zoos and Aquariums (AZA), and the Zoo and Aquarium Association Australasia (ZAA).
EAZA reports two types of breeding programs: the European Endangered species Program (EEP) and the European Studbook (ESB). AZA reports on the Species Survival Plan (SSP) as a part of the Marine Fishes Taxon Advisory Group (TAG). ZAA reports on the Australasian Species Management Program (ASMP).
We used the IUCN Species Survival Commission Shark Specialist Group's webpage to gather information on shark and batoid families with a conservation strategy. We assumed that every species under a family with a conservation strategy would have higher in-situ conservation opportunities than those without one. We gathered data on if there is an active recovery plan in place for species and if the habitat lies partly or completely within a protected area from the IUCN Red List Advanced Search version 2020-2 and used the "all other fields" file.
To find action plans at the species level, we used the search engine Google and the keywords: "action plan rays", "recovery plan rays", "management plan rays", "recovery plan sharks", "action plan sharks", "management plan sharks", "management plan Elasmobranchii", and "action plan Elasmobranchii". We did not include plans labelled as inactive. The list of species with a recovery, management, or action plan is available in Supplementary File S1. During the search, we found two databases with management plans and action plans at the country level (Australia and Canada). In Table 7 , we list all sources used to achieve data on recovery, management, or action plans. Additionally, we included the national and regional plans both historically and in use from other regions of the globe. These were manually retrieved from the interactive map from the FAO International Plan of Action for the Conservation and Management of Sharks [8] .

Use
Data on international trade was retrieved from the UNEP WCMC CITES Trade Database (20 0 0-2018) for Elasmobranchii. We gathered the data from the FAO (2007-2017) on catches in Oceania, Africa, Asia, Europe, and the Americas for inland waters and marine areas. All marine species within the group "sharks, rays, and chimeras" were selected. Catches recorded at the order, the family, or the genus level were divided by the number of species within that taxon according to CoL, to get an overview of which species are possibly caught and at which quantities. We then estimated the total catch at the species level as the sum of catches recorded at the order, the family, the genus, and the species level for each species [9] .
We included the data from the IUCN Red List Advanced Search version 2020-2 indicating the purpose of the trade with the particular species (e.g. human food, sport hunting, medicine, research, jewelry or accessories, chemicals or as pets or display animals), and used the "usetrade" file. To gather data on describing if the species are used: i) in aquariums, ii) as bait, iii) in aquaculture, or iv) as a gamefish and catch methods, we retrieved data from Fishbase using the 'rfishbase' package from the open-source software R [ 10 , 12 ].