Fishscape: A database of fish habitat associations

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Meta-data for the Global Fish Habitat Use Database

CJ Brown, Andrew Broadley 15 May 2017


This is a database of fish associations with their habitats. It is a long-form database, where each row corresponds to one observation of a fish habitat association. A single paper can have multiple rows if for instance it reports on multiple species, or it has measured fish-habitat relationships for a single species in multiple different ways. “Fish” includes bony and cartilaginous fish and fished invertebrates.

We include peer-reviewed and grey literature.

Data entry process

Keep track of time taken and number of pubs and species entered (e.g. time yourself from start to finish). We will use this info to decide when to stop adding species! Choose unentered species from “priority-fish-stocks.xlsx” Focus on benthic/demersal species for now. We still need to work out how to code pelagic habitats. Find publications on web. Download pdf. Unentered pdfs can be saved in that folder. Copy citation info from google scholar and insert into bibtex library. Rename pdf using bibtex cite-key. Enter data into database. Add new field codes if neccessary. Please use all lower case in field entries, including for taxonomic names. Check species off in “priority-fish-stocks.xlsx”

Associated files

Also included in this folder are: /pubs a folder which contains pdfs of publications that have been entered. file names should be the same as the bibtex cite-key. /pubs-not-entered a folder which contains pdfs of publications to check/enter. fish-hab-db-refs.bib bibtex library with citation info. priority-fish-stocks priority fish species and stocks for data entry. Try to get every species. If you see multiple studies for the same species in different areas, try to get the different fish stocks. You can annotate this with species entered to keep track of what is happening. However, if you happen across other species in study, please enter them too. RAM-Legacy-spreadsheet-snapshot-20110815.xlsx copy of the 2011 RAM legacy stock assessment database. We are focussing on stocks in this database initially. list of resources to check for data.



This should match the cite-key in the bibtex library. pdfs should have the same name as their entry to the bibtex cite-key.


Latitude of approximate study site (or centre of region). Use decimal degrees, and -ve values for degrees south. If using study centre, make sure it is in the ocean. You can convert from degrees minutes here:


Longitude of approximate study site (or centre of region). Use decimal degrees, and -ve values for degrees west. If using study centre, make sure it is in the ocean.


Taxonomic Class Fields: [actinopterygii, chondrichthyes ]


Family of the fish species.


Fish species. If species unknown, or includes multiple species then just genus. Leave blank if family known but genus unknown, or species were grouped.


Does the observation included multiple species grouped together? Fields: [y, n] (leave blank if N)


Species that have a wide geographic distribution and migrate for food and reprodcution of vast distances both inside and outside of a countries exclusive economic zone. Fields: [y, n] (leave blank if N)


Species broad habitat zone type. Fields: [benthic, benthopelagic, neritic, epipelagic, mesopelagic…] Benthic rests on the bottom (e.g. stingrays) benthopelagic moves near the bottom (e.g. cod) neritic is the shallow coastal zone before drop-off to continental shelf epipelagic from the surface to 200m mesopelagic 200m to 1000m Use fishbase entry for environment if unsure.


Life stage of the fish species. Leave blank if multiple grouped. Fields: [adult, juvenile, post-larvae, larvae, egg, spawning] post-larvae refers to settlement habitats.


Type of habitat. Seperate multiple entries with ; Fields: [seagrass, mangroves, coral, reef, soft-sediment, sand, mud, macroalgae, rock, …] soft-sediment is a generalisation of sand and mud mixed (if unknown) Seperate multiple fields with a semi-colon (;). e.g. to record a species associated with a rocky reef you would enter.


Lowest taxonomic ID of habitat if available (genus, species etc…)


If known, how does the fish species use the habitat? Fields: [NA, pred-refuge, food, shelter, physiochem, other] NA refers to not described in this study. pred-refuge refers to refuge from predation Where shelter refers to sheltering functions other than avoiding predation. physiochem refers to physiochemical properties (e.g. desired temperature)


if known, type of micro-habitat used by a species.


How did the researchers identify this habitat association? Fields: [direct, catch-survey, catch, e-tag, stomach, isotopes, experimental …] direct refers to direct observation ie you saw it there while diving. catch-survey refers to catching a fish in a habitat using scientific surveys catch refers to catch in commercial/recreational fisheries. experimental refers to preference studies in the lab.

e-tag is an electronic tag. Stomach means habitat was inferred from dietry analysis. Similar for isotopes.


Depth zone of habitat association. Fields: [intertidal, <20, <50, <100, <150, <200, >200, >50, <500, <1000; <3000; mesophotic ,…].


If known, approx. area that was surveyed Fields: [<10m2, <100m2, <1000m2, <1ha, <10ha, <100ha, >100ha].


Flag to indicate that the study reported that a change in the habitat had an impact on a fishery. Fields: [y, n] (leave blank if unknown)


If known, indicates if there is a change fish stock because of a change in habitat. Fields: [decline, increase, stable] (leave blank if unknown)


Describe the reason for a change in the fish-stock. Fields: [climate change, artificial habitat] (leave blank if unknown)


Any notes relating to an impact on a fishery.


Any other notes