DOI: 10.5281/zenodo.4072959
title: All Fish catch data at the SAFE project 2011-2019

description: <b>Description: </b>All fish catch data of all methods across all streams sampled at the SAFE project, Danum Valley and surrounding oil palm areas. Please note this is the raw dataset and may contain errors that need correcting/editing. I have tried to correct the majority of errors, but all were corrected in seperate files prior to analysis, so please see specific datasets in relation to specific papers already published. All changes are detailed in the notes column or listed here if more general. <br><br>All Rasbora caught in 2013 are labelled as cf. sumatrana as they were not differentiated from R. hubbsi. All Systomus changed to Barbodes. All Tor labelled as T. tambra, with no differentiation between tambra and tambroides. From 2018 onwards, all R. sumatrana have been renamed as R. pycnopeza. New captures were not pit tagged. Fish mortality are tracked in the data. <br><br>In 2018, some sites were sampled twice. <br><br>In this version, several changes and new spreadsheets have been added on top of previous versions. This includes: 1. Electrofishing setup - the voltage used in electrofishing corresponding to the conductivity measured; 2. Stream _variables along transect- detailed environmental data collect along transect at each site; 3. Riparian survey, with data on the riparian surveys along the fishing transect. The sheet "Data" has been renamed Capture_Data. Environmental data 2017 sheet has been renamed and updated to Environmental Data site level, to include summarized data by site and by year.<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Composition and abundance of tropical freshwater vertebrate communities across a land use gradient</b><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: RawDataFish_with_Riparian_V3.0.xlsx<b>RawDataFish_with_Riparian_V3.0.xlsx</b>This file contains dataset metadata and 6 data tables:<b>Capture_Data</b> (described in worksheet Capture_Data)Description: Fish catch data Number of fields: 18Number of data rows: 18994Fields: <b>Date</b>: Date that stream was sampled (Field type: date)<b>Stream</b>: Which stream was sampled (Field type: location)<b>RA.</b>: Which research assistant helped do the work? (Field type: comments)<b>Researcher</b>: Which researcher conducted the work? (Field type: categorical)<b>Method</b>: What method was used to catch the fish (Field type: categorical)<b>Cast_or_Trap_Numer</b>: The cast or trap numer that the fish was caught at (Field type: numeric)<b>Distance</b>: The distance along the transect in which the fish was caught (Field type: numeric)<b>Taxon</b>: Species sampled (Field type: taxa)<b>N</b>: The number of fish caught at that stream, location and date (Field type: numeric)<b>Pittagnumber</b>: The 10 digit pit tag number (Field type: id)<b>Recapture</b>: Has this fish been caught before? (Field type: categorical)<b>Length</b>: Total length of fish (Field type: numeric)<b>Weight</b>: Weight of fish (Field type: numeric)<b>Specimen</b>: Was this fish taken as a specimen? (Field type: categorical)<b>Stable_isotope_Fin</b>: Number of the stable isotope sample of all fin clips if they were taken (Field type: numeric)<b>Stable_isotope_Muscle</b>: Number of the stable isotope sample of all muscle samples if they were taken (Field type: numeric)<b>Notes</b>: Notes, includes any data changes, fish deaths etc. (Field type: comments)<b>Mortality</b>: Mortality - fish deaths (Field type: categorical)<b>Electofishing_Setup</b> (described in worksheet Electofishing_Setup)Description: The voltage and conductivity used for electrofishingNumber of fields: 7Number of data rows: 60Fields: <b>Stream</b>: Which stream was sampled (Field type: location)<b>Date</b>: Date that stream was sampled (Field type: date)<b>Conductivity_of_stream</b>: Stream conductivity (Field type: numeric)<b>Stream_temperature</b>: Stream water temperature (Field type: numeric)<b>RunNum</b>: Which electrofishing pass (run) (Field type: numeric)<b>Voltage</b>: Voltage set on the electrofishing kit (Field type: numeric)<b>Electrofisher</b>: Data collectors (Field type: id)<b>Stream_Variables along transect</b> (described in worksheet Stream_Variables along transect)Description: Stream environmental data along fishing transect of each site. Data from 2018 onwardsNumber of fields: 13Number of data rows: 131Fields: <b>Stream</b>: Which stream was sampled (Field type: location)<b>Date</b>: Date measured (Field type: date)<b>Landuse</b>: Landuse of the stream sampled (Field type: categorical)<b>Distance_on_stream</b>: Distance of measured stream variables along transect (Field type: numeric)<b>Flow</b>: Average flow of the stream (Field type: numeric)<b>Wetted_width</b>: wetted width of the stream (Field type: numeric)<b>Depth</b>: Average stream depth (Field type: numeric)<b>sand</b>: Stream substrate (Field type: numeric)<b>gravel</b>: Stream substrate (Field type: numeric)<b>pebbles</b>: Stream substrate (Field type: numeric)<b>large_rocks</b>: Stream substrate (Field type: numeric)<b>bedrock</b>: Stream substrate (Field type: numeric)<b>Notes</b>: Notes, includes any data changes, fish deaths etc. (Field type: comments)<b>Riparian survey along transect</b> (described in worksheet Riparian_survey_along_transect)Description: Riparian surveys of each stream along the 500m transect. Data from 2018 onwardsNumber of fields: 15Number of data rows: 352Fields: <b>Stream</b>: Which stream was sampled (Field type: location)<b>Date</b>: Sampling date (Field type: date)<b>Landuse</b>: Landuse of the stream sampled (Field type: categorical)<b>Distance</b>: Distance on the stream from first RT plot point (Field type: numeric)<b>Upstream</b>: Canopy openness (Field type: numeric)<b>away_from_stream</b>: Canopy openness (Field type: numeric)<b>downstream</b>: Canopy opennes (Field type: numeric)<b>Towards_river</b>: Canopy openness (Field type: numeric)<b>Average_total_area_not_occupied</b>: Average reading across the 4 (Field type: numeric)<b>Percent_area_not_occupied</b>: Percent overhead area not occupied by canopy (Field type: numeric)<b>Overstory_density_</b>: Overstory density - area occupied (Field type: numeric)<b>Vine_cover</b>: Estimation of vine cover (Field type: numeric)<b>Forest_quality_score</b>: Visual assessment of the forest quality (Field type: numeric)<b>Notes</b>: Notes or remarks (Field type: comments)<b>Ras</b>: Data collectors (Field type: id)<b>EnvironmentalData_sitelevel</b> (described in worksheet EnvironmentalData_sitelevel)Description: Averaged data of streams on a site levelNumber of fields: 23Number of data rows: 51Fields: <b>Stream</b>: Which stream was sampled (Field type: location)<b>Year</b>: Sampling year (Field type: date)<b>Landuse</b>: Landuse of the stream sampled (Field type: categorical)<b>Turbidity</b>: Stream water turbidity (Field type: numeric)<b>Flow</b>: Average flow of the stream (Field type: numeric)<b>Wetted_width</b>: Average wetted width of the stream (Field type: numeric)<b>Depth</b>: Average stream depth (Field type: numeric)<b>sand</b>: Average stream substrate (Field type: numeric)<b>gravel</b>: Average Stream substrate (Field type: numeric)<b>pebbles</b>: Average stream substrate (Field type: numeric)<b>large_rocks</b>: Average stream substrate (Field type: numeric)<b>bedrock</b>: Average stream substrate (Field type: numeric)<b>Littoral.leaf.litter.cover</b>: Average leaf litter on stream bed (Field type: numeric)<b>pH</b>: Stream pH (Field type: numeric)<b>Temperature</b>: Stream water temperature (Field type: numeric)<b>O2</b>: Dissolved oxygen (Field type: numeric)<b>Conductivity</b>: Stream conductivity (Field type: numeric)<b>Canopy.openness</b>: Averaged canopy openness above the stream, average from upstream, downstream, left and right bank measurements (Field type: numeric)<b>Sedimentation</b>: Is there sediment within the stream? Yes or No (Field type: categorical)<b>CanopyOpennessRiparian</b>: Average canopy openness in the riparian, average from upstream, downstream, away from the stream and towards the stream measurements (Field type: numeric)<b>Vine</b>: Average % vine cover (Field type: numeric)<b>FQ</b>: Average SAFE project forest quality score (0-5) (Field type: numeric)<b>Tree</b>: Average density of trees (Field type: numeric)<b>Riparian_OP 2017</b> (described in worksheet Riparian_OP 2017)Description: Averaged data by stream of all measured environmental variables for OP streams in 2017Number of fields: 24Number of data rows: 20Fields: <b>Stream</b>: Which stream was sampled (Field type: location)<b>Landuse</b>: Landuse of the stream sampled (Field type: categorical)<b>Turbidity</b>: Stream water turbidity (Field type: numeric)<b>Flow</b>: Average flow of the stream (Field type: numeric)<b>Wetted_width</b>: wetted width of the stream (Field type: numeric)<b>Depth</b>: Average stream depth (Field type: numeric)<b>sand</b>: Stream substrate (Field type: numeric)<b>gravel</b>: Stream substrate (Field type: numeric)<b>pebbles</b>: Stream substrate (Field type: numeric)<b>large_rocks</b>: Stream substrate (Field type: numeric)<b>bedrock</b>: Stream substrate (Field type: numeric)<b>Littoral.leaf.litter.cover</b>: leaf litter on stream bed (Field type: numeric)<b>pH</b>: Stream pH (Field type: numeric)<b>Temperature</b>: Stream water temperature (Field type: numeric)<b>O2</b>: Dissolved oxygen (Field type: numeric)<b>Conductivity</b>: Stream conductivity (Field type: numeric)<b>Canopy.openness</b>: Canopy openness above the stream, average from upstream, downstream, left and right bank measurements (Field type: numeric)<b>Sedimentation</b>: NA (Field type: categorical)<b>CanopyOpennessRiparian</b>: Canopy openness in the riparian, average from upstream, downstream, away from the stream and towards the stream measurements (Field type: numeric)<b>Vine</b>: % vine cover (Field type: numeric)<b>FQ</b>: Average SAFE project forest quality score (0-1) (Field type: numeric)<b>Tree</b>: Density of trees (Field type: numeric)<b>DateOPplanted2</b>: Years since oil palm was planted (compared to 2017 sampling date) (Field type: numeric)<b>Average500_2bank</b>: Average width of riparian buffers as the sum of both sides of the river. Averaged over 11 locations measured on GIS, but with the width of the river removed. (Field type: numeric)<b>Date range: </b>2011-09-19 to 2020-02-18<b>Latitudinal extent: </b>4.5000 to 5.0700<b>Longitudinal extent: </b>116.7500 to 117.8200<b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets. - Animalia <br> - - Chordata <br> - - - Amphibia <br> - - - Actinopterygii <br> - - - - Synbranchiformes <br> - - - - - Mastacembelidae <br> - - - - - - <i>Mastacembelus</i> <br> - - - - - - - <i>Mastacembelus unicolor</i> <br> - - - - - - <i>Macrognathus</i> <br> - - - - - - - <i>Macrognathus keithi</i> <br> - - - - Anguilliformes <br> - - - - - Anguillidae <br> - - - - - - <i>Anguilla</i> <br> - - - - - - - <i>Anguilla borneensis</i> <br> - - - - - - - <i>Anguilla marmorata</i> <br> - - - - Siluriformes <br> - - - - - Bagridae <br> - - - - - - <i>Hemibagrus</i> <br> - - - - - - - <i>Hemibagrus baramensis</i> <br> - - - - - - - <i>Hemibagrus fortis</i> <br> - - - - - Clariidae <br> - - - - - - <i>Clarias</i> <br> - - - - - - - <i>Clarias anfractus</i> <br> - - - - - - - <i>Clarias teysmanni</i> <br> - - - - Cypriniformes <br> - - - - - Balitoridae <br> - - - - - - <i>Protomyzon</i> <br> - - - - - - - <i>Protomyzon borneensis</i> <br> - - - - - - - <i>Protomyzon griswoldi</i> <br> - - - - - - - <i>Protomyzon whiteheadi</i> <br> - - - - - - <i>Homalopteroides</i> <br> - - - - - - - <i>Homalopteroides stephensoni</i> <br> - - - - - - <i>Parhomaloptera</i> <br> - - - - - - - <i>Parhomaloptera microstoma</i> <br> - - - - - - <i>Gastromyzon</i> <br> - - - - - - - <i>Gastromyzon ingeri</i> <br> - - - - - - - <i>Gastromyzon lepidogaster</i> <br> - - - - - - - <i>Gastromyzon umbrus</i> <br> - - - - - Nemacheilidae <br> - - - - - - <i>Nemacheilus</i> <br> - - - - - - - <i>Nemacheilus olivaceus</i> <br> - - - - - Cyprinidae <br> - - - - - - <i>Cyclocheilichthys</i> <br> - - - - - - <i>Luciosoma</i> <br> - - - - - - - <i>Luciosoma pelligrinii</i> <br> - - - - - - <i>Barbonymus</i> <br> - - - - - - - <i>Barbodes collingwoodi</i> <br> - - - - - - - <i>Barbonymus balleroides</i> <br> - - - - - - <i>Rasbora</i> <br> - - - - - - - <i>Rasbora pycnopeza</i> <br> - - - - - - - <i>Rasbora elegans</i> <br> - - - - - - - <i>Rasbora hubbsi</i> <br> - - - - - - <i>Hampala</i> <br> - - - - - - - <i>Hampala sabana</i> <br> - - - - - - <i>Crossocheilus</i> <br> - - - - - - - <i>Crossocheilus elegans</i> <br> - - - - - - <i>Leptobarbus</i> <br> - - - - - - - <i>Leptobarbus melanotaenia</i> <br> - - - - - - <i>Lobocheilos</i> <br> - - - - - - - <i>Lobocheilos erinaceus</i> <br> - - - - - - - <i>Lobocheilos unicornis</i> <br> - - - - - - <i>Anematichthys</i> <br> - - - - - - - <i>Anematichthys repasson</i> (as synonym: <i>Cyclocheilichthys repasson</i>)<br> - - - - - - <i>Nematabramis</i> <br> - - - - - - - <i>Nematabramis borneensis</i> <br> - - - - - - - <i>Nematabramis everetti</i> <br> - - - - - - <i>Osteochilus</i> <br> - - - - - - - <i>Osteochilus chini</i> <br> - - - - - - - <i>Osteochilus ingeri</i> <br> - - - - - - <i>Tor</i> <br> - - - - - - - <i>Tor tambra</i> <br> - - - - -&e