Florida Fish and Wildlife Conservation Commission - Florida Imperiled Fish Species Investigation - 2001-2004

Study Extent

Geographic extent: Perdido Bay, Pensacola Bay and Choctawhatchee Bay drainages of northwestern Florida; Apalachicola Bay to Suwannee River drainages of northern Florida; St. Johns River system and other drainages of peninsular Florida Temporal extent: 2001 - 2004

Sampling

Sampling techniques appropriate to the target species and their habitats were selected, and included boat electrofishing, backpack electrofishing, seining, gill netting, dip netting, and visual observations. Specific sampling sites were developed from existing literature and expertise from Florida Fish and Wildlife Conservation Commission staff and other knowledgeable biologists (e.g. Gilbert 1992, Hoehn 1998, Lee et al. 1980). Sample results and location descriptions were incorporated into the Florida Fish and Wildlife Conservation Commission biological database. Target species were divided into two categories: Primary species were those officially classified as protected by the state of Florida. Secondary species were those known or suspected to be rare or imperiled by knowledgeable biologists (e.g. Gilbert 1992). Target species were the focus of this project. Fishes that were already subject to intensive studies, or currently monitored by other agencies, were not sought by this project (e.g. Atlantic sturgeon, Okaloosa darter). Species that require special efforts to capture (e.g. alligator gar, rivulus, etc.) were not targeted, but were recorded if observed or taken incidentally. References: Gilbert, C. R. 1992. Rare and Endangered Biota of Florida. Volume II. Fishes. University Press of Florida, Gainesville, Florida. 247 pp. Hoehn, T. 1998. Rare and Imperiled Fish Species of Florida: A Watershed Perspective. Florida Fish and Wildlife Conservation Commission, Tallahassee, Florida. 60 pp. Lee, D. S., C. R. Gilbert, C. H. Hocutt, R. E. Jenkins, D. E. McAllister, J. R. Stauffer, Jr. 1980. Atlas of North American Freshwater Fishes. North Carolina State Museum of Natural History, Raleigh, North Carolina. 854 pp.

Method steps

1. Field work methods by Florida Fish and Wildlife Conservation Commission staff for fish surveys: A two-person crew sampled areas known, or suspected to harbor desired species, and related fish collected to specific habitats and ambient water quality. Photographs were taken of sampling sites, and locations were obtained with Garmin handheld GPS units (ETrex Legend or GPSMAP 76S) and recorded using the default WGS 84 datum. Where possible, fish were collected with standardized techniques (timed electrofishing, electrofishing-distance transects, standard haul seines, etc.) to allow repeat collections, or for future collectors to monitor species abundances. Collection methods used included: Backpack Electrofisher (CM001), Boat Electrofisher (CM002), Concussion (CM003), Rotenone (CM004), Dip net (CM005), Seine (CM006), Gill net (CM007), Hook & Line (CM008), Cast net (CM009), Going dredge (CM010), Crayfish trap (CM011). Where feasible, collectors determined relative abundance of imperiled fishes within resident fish assemblages. Some of the fish that may have been collected during sampling for the fish survey were provided to the Florida Museum of Natural History.
2. Florida Fish and Wildlife Conservation Commission database with project results: A CD entitled Florida Imperiled Fish Database was included with the study report. The disc contained detailed information regarding each collection. This information is also is available from the Florida Fish and Wildlife Conservation Commission database. Comprehensive information in the database includes latitude-longitude of locations, site descriptions, basic physical and chemical water quality, and other species collected. The disc contains a copy of the Florida Imperiled Fishes Species Investigations database and associated site images, a copy of the final report, and a GIS shapefile that the database can be linked to. The database was created in Microsoft Access 2000 and has hyperlinks to the images contained in the “FWC Site Pictures” folder. A data field description is contained within the database as a report button. The site coordinates were obtained by Garmin handheld GPS units (ETrex Legend or GPSMAP 76S) and recorded using the default WGS 84 datum. The data can be linked to the following GIS datasets: National Hydrologic Dataset 1:100,000 scale (NHD) via the reachcode, Hydrologic Unit Code Basins (8 digit USGS Codes), and DEP_Basin_97 shapefile (developed by the Florida Department of Environmental Protection and linked via the pk_basin).
3. Flattening of the database and processing of resulting dataset by U.S. Geological Survey staff for submission to BISON and GBIF: FWC staff provided a copy of the CD with the Florida Imperiled Fish Database to U.S. Geological Survey (USGS) staff for sharing of the dataset with Biodiversity Information Serving Our Nation (BISON) and the Global Biodiversity Information Facility (GBIF). USGS staff processed the provided Access database with R by extracting relevant fields and corresponding values into a flat text file and formatting the flattened dataset according to BISON/GBIF data formats. During this process, USGS staff removed from the resulting dataset dead specimens, unknown or unidentified species, and entries with missing geographic coordinates or year fields. USGS staff also added some fields to the dataset (indicated below) and reformatted some values to help standardize the data.
4. Fields included in dataset resulting from data processing by USGS staff: • occurrenceID - Field added and populated by USGS staff. Value was developed based on concatenation of FWCCollectionNumber, SampleNumber and Sequence in the original FWC database, plus a consecutive number added by USGS staff to represent different species/taxa that had the same FWCCollectionNumber-SampleNumber-Sequence. All records extracted from the original FWC Access database had a SampleNumber of 1, and only a few records for certain species/taxa had a Sequence greater than 1, with Sequence in this dataset concatenated as a 2-digit number starting with 0 if the Sequence was less than 10. • basisOfRecord - Field added and populated by USGS staff with controlled term suggested in DarwinCore. • eventDate - Based on 'verbatimEventDate' (CollectionDate in original FWC database) but reformatted with an ISO date format. • year - Extracted by USGS staff from the CollectionDate in original FWC database. • verbatimEventDate - Based on CollectionDate in original FWC database. • eventID - Based on FWCCollectionNumber in original FWC database. • samplingProtocol - Based on CollectionMethodID in original FWC database. • samplingEffort - Based on concatenation of SampleEffort and EffortUnits in original FWC database. Records that were blank in the original FWC database for either SampleEffort or EffortUnits or both, are shown in this dataset with an ‘NA’ where the corresponding value would have been if it would have been provided in the original database. • habitat - Based on concatenation of SystemTypeID and RiparianZoneTypeID in the original FWC database. For records where RiparianZoneTypeID was blank in the original FWC database, an ‘NA’ is shown after the SystemTypeID in this dataset. • eventRemarks - Based on concatenation of various fields associated with a collection event in the original FWC database. To concatenate these fields, USGS staff added the field label and a colon followed by the value from the original FWC database. The fields were separated with a pipe symbol in this dataset to convey that each field came from a different column of the original FWC database. An ‘NA’ is included as a value for those records that were blank for the respective field. The following fields (with a description) were concatenated to generate the eventRemarks field of this dataset. FWCCollectionNumber - ID of the collection sampling event. CollectionDayNight - when collection was conducted. CanopyCover - Open; Lightly shaded (11-45%), Moderately shaded (46-80%), or Heavily shaded (>80%). CurrentVelocity - Current velocity at site in m/s; a current velocity listed as 0.9999 or 0.999 indicates no data on current velocity were recorded. AverageStreamWidth - Average stream width at collection site in meters. AverageStreamDepth - Average stream depth at collection site in meters. SubstrateType - type of substrate at site. DO - Dissolved oxygen at the site, specified in parts per million. PH - pH at the site. Conductivity - Conductivity at the site. Salinity - Salinity at the site in ppt. WaterTemperature - temperatue of water at site in degrees Celsius. • scientificName - the scientificName listed in this dataset is the standardized valid scientific name followed by the Integrated Taxonomic Information System (ITIS) [https://www.itis.gov/]. USGS staff used the provided Taxonomic Serial Number (TSN) that was included in the original FWC database to look up the valid ITIS scientific names that are included in this dataset field. The scientific names provided in the original FWC database are included in this dataset in the taxonRemarks field. Species name changes as a result of providing the ITIS valid scientific name rather than the providedScientificName in this field of the dataset resulted in the following name replacements: Macrhybopsis replaces Macrhybopsis n. sp. cf aestivalis, Moxostoma replaces Moxostoma n.sp.cf poecilurum, Fundulus olivaceus replaces Fundulus olivaceous, Etheostoma replaces Etheostoma bifascia, Petroscirtes anolius replaces Petroscrites anolius, Gobionellus boleosoma replaces Gobionellus bolesoma, and Fundulus rubrifrons replaces Fundulus rubifrons. • kingdom - Field added and populated by USGS staff. • taxonRank - Field added by USGS staff but based on fields included in the original FWC database. • scientificNameAuthorship - Field added and populated by USGS staff based on valid scientific names provided by the Integrated Taxonomic Information System (ITIS). • vernacularName - based on providedCommonName from the original FWC database. • taxonRemarks - Based on concatenation of providedScientificName, providedCommonName, and Category from the original FWC database. To concatenate these fields, USGS staff added a label for each concatenated field and a colon followed by the value from the original FWC database. The fields were separated with a pipe symbol in this dataset to convey that each field came from a different column of the original FWC database. Description of the field Category: Category represents predominant occurrence - M (marine including estuarine and euryhaline species), F (freshwater), E (exotic), A (anadromous), C (catadromous) as provided by FWC. • taxonID - Field added and populated by USGS staff. It is the URL for the ITIS valid scientific name. • scientificNameID - Field added and populated by USGS staff. It is the LSID for the ITIS valid scientific name. • acceptedNameUsageID - Field added and populated by USGS staff with the Taxonomic Serial Number (TSN) of ITIS scientific names. • verbatimLatitude - Based on Latitude in original FWC database. • verbatimLongitude - Based on Longitude in original FWC database. • verbatimCoordinateSystem - Field added by USGS staff based on type of values provided in the Latitude and Longitude fields of the original FWC database. • decimalLatitude - Based on Latitude in original FWC database. • decimalLongitude - Based on Longitude in original FWC database. • geodeticDatum - Based on GeoposDatumID in original FWC database. • georeferenceProtocol - Based on GeoposMethod field in original FWC database. A value of ‘GO’ corresponds to ‘GeoposMethodName = GPS – Other’ and to ‘GeoposMethodDescription = Location derived through the use of an unspecified GPS device’. A value of ‘I1’ corresponds to ‘GeoposMethodName = Interpolation – Map’ and to ‘GeoposMethodDescription = Location derived from a paper or other non-digital map’. • higherGeographyID - Based on concatenation of three fields in original FWC database. To concatenate these fields, USGS staff added the field label and a colon followed by the value from the original FWC database. The fields were separated with a pipe symbol in this dataset to convey that each field came from a different column of the original FWC database. An ‘NA’ is included as a value for those records that were blank for the respective field. The following fields (with a description) were concatenated to generate the higherGeographyID field of this dataset. HUC - USGS Hydrologic Unit 8-digit Code. Rch_code - Unique reach code used to link data to the National Hydrologic Dataset (NHD). PkBasin - Unique drainage basin code that links to the Florida Department of Environmental Protection "drainage basin 1997" (DEP_Basin_97) GIS coverage. • continent - Field added and populated by USGS staff with controlled term suggested in DarwinCore. • country - Field added and populated by USGS staff based on data contents of the FWC database. • countryCode - Field added and populated by USGS staff based on ISO country code. • stateProvince - Field added and populated by USGS staff based on data contents of the FWC database. • county - Based on CollectionCounty in original FWC database. For standardization of the values in this field, USGS staff replaced in this dataset the values that were provided originally for 4 samples to conform to fully spelled county names provided for the rest of samples in the database. Therefore, for FWCCollectionNumber FWC0280 and FWC0281, a value of “sa” was replaced with “Santa Rosa”, for FWCCollectionNumber FWC0297 a value of “colul” was replaced with “Columbia”, and for FWCCollectionNumber FWC0298 a value of “collu” was replaced with “Columbia”. • verbatimLocality - Based on CollectionLocation in original FWC database. • verbatimDepth - Based on AverageStreamDepth in original FWC database, which represents the average stream depth at collection site in meters. • type - Field added and populated by USGS staff with controlled term suggested in DarwinCore. • language - Field added and populated by USGS staff with controlled term suggested in DarwinCore. • license - Field added and populated by USGS staff based on access provided by FWC. • associatedReferences - Field added and populated by USGS staff based on documents included with original FWC database provided to USGS. • institutionID - Field added and populated by USGS staff with URL of FWC’s website. • datasetID - Field added and populated by USGS staff with URL to the metadata for this dataset. • institutionCode - Field added and populated by USGS staff with the acronym of the data provider’s organization. • recordedBy - Based on Collector in original FWC database. • individualCount - Based on Number in original FWC database, which represents the number of individuals of a species/taxon collected as listed in a Sequence of a given FWCCollectionNumber event. A value of 0 for individualCount as provided in the original FWC database indicates the species/taxon was observed and identified during the sampling event but was not collected. • occurrenceStatus - Field added by USGS staff as a global value with controlled term suggested in DarwinCore. This field was added to avoid it being inferred from individualCount by the Global Biodiversity Information Facility.

Target species that were the focus of this project included those officially classified as protected by the state of Florida, and also those known or suspected to be rare or imperiled by knowledgeable biologists. Target species are listed below. Fishes that were already subject to intensive studies, or were monitored by other agencies, were not sought by this project (e.g. Atlantic sturgeon, Okaloosa darter). Species that required special efforts to capture (e.g. alligator gar, rivulus, etc.) were not targeted, but were recorded if observed or taken incidentally.

1. Cyprinella callitaenia
   common name: Bluestripe shiner rank: species
2. Hybognathus hayi
   common name: Cypress minnow rank: species
3. Luxilus chrysocephalus isolepis
   common name: Southern striped shiner rank: subspecies
4. Luxilus zonistius
   common name: Bandfin shiner rank: species
5. Lythrurus atrapiculus
   common name: Blacktip shiner rank: species
6. Macryhybopsis n. sp. cf aestivalis
   common name: Florida chub rank: species
7. Nocomis leptocephalus bellicus
   common name: Southern bluehead chub rank: subspecies
8. Notropis baileyi
   common name: Rough shiner rank: species
9. Notropis melanostomus
   common name: Blackmouth shiner rank: species
10. Pteronotropis welaka
    common name: Bluenose shiner rank: species
11. Moxostoma carinatum
    common name: River redhorse rank: species
12. Moxostoma sp.
    common name: Grayfin redhorse rank: species
13. Ameiurus brunneus
    common name: Snail bullhead rank: species
14. Ameiurus serracanthus
    common name: Spotted bullhead rank: species
15. Umbra pygmaea
    common name: Eastern mudminnow rank: species
16. Menidia conchorum
    common name: Key silverside rank: species
17. Fundulus blairae
    common name: Southern starhead topminnow rank: species
18. Fundulus jenkinsi
    common name: Saltmarsh topminnow rank: species
19. Cyprinodon variegatus hubbsi
    common name: Lake Eustis pupfish rank: subspecies
20. Enneacanthus chaetodon
    common name: Blackbanded sunfish rank: species
21. Micropterus notius
    common name: Suwannee bass rank: species
22. Micropterus cataractae
    common name: Shoal bass rank: species
23. Crystallaria asprella
    common name: Crystal darter rank: species
24. Etheostoma histrio
    common name: Harlequin darter rank: species
25. Etheostoma olmstedi maculaticeps
    common name: Southern tessellated darter rank: subspecies
26. Etheostoma parvipinne
    common name: Goldstripe darter rank: species
27. Etheostoma proeliare
    common name: Cypress darter rank: species
28. Etheostoma stigmaeum
    common name: Speckled darter rank: species
29. Percina austroperca
    common name: Southern logperch rank: species
30. Percina vigil
    common name: Saddleback darter rank: species

Project phases: Phase 1 (2001 - 2002) - Survey of Perdido Bay, Pensacola Bay and Choctawhatchee Bay drainages of northwestern Florida; Phase 2 (2002 -2003) - Survey of the Apalachicola Bay to Suwannee River drainages of northern Florida; and Phase 3 (2003 - 2004) - Survey of the St. Johns River system and other drainages of peninsular Florida.