Elkhorn Slough Estuarine Research Reserve long-term crab monitoring database
Data files
Jun 18, 2025 version files 2.80 MB
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elkhorn_crab_data.csv
2.77 MB
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README.md
20.59 KB
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trap_days_elkhorn_crabs.csv
8.02 KB
Abstract
The purpose of the long term crab monitoring program at Elkhorn Slough Reserve, 1994-2024 was three-fold. First, we wanted to assess the trajectories of the native crab populations, primarily the Oregon mud crab, Hemigrapsus oregonensis, the Lined shore crab, Pachygrapsus crassipes, and various cangrid crab species (mostly Cancer antennarius and Cancer productus). Secondly, we wanted to assess the population trajectory of the newly invading (at the time) European green crab, Carcinus maenas. Last, we wanted to optimize the probability of early detection of any new invasive crab species at Elkhorn Slough. Secondarily, we recorded any fish species, that went into the traps as by-catch. We used regular minnow traps, minnow traps with an enlarged opening in one end, and Fukui fish traps. All traps were baited (usually with anchovies), deployed at zero tidal height (relative to mean low water) and soaked for 24 hours. Upon retrieval, individuals were identified to species, and sexed and measured (carapace width in mm) when possible. Trapping was conducted throughout Elkhorn Slough over the years, but not all sites were trapped in all years. The two most frequently trapped sites were Kirby Park and South Marsh, which were trapped annually in fall. For analysis purposes, a "set" of one small minnow, one large minnow, and one collapsible trap should be used as one unit within one can calculate "crabs per trap" whenever possible. Overall we have found for abundances of native crabs that H. oregonensis is highest, followed by Cancer spp. and then P. crassipes. It should be noted that P. crassipes does not readily go into traps, so our population estimate of that species is most likely a significant underestimate. We also found that abundance of the invasive European green crab peaked in the early 2000s, then declined over the next few years to have a smaller peak around 2011. Since then, European green crab abundance has been declining. The most common fish speices to appear in crab traps is Staghorn Sculpin.
Dataset DOI: 10.5061/dryad.0p2ngf2cg
Description of the data and file structure
This dataset was for monitoring of native and non-native crabs at Elkhorn Slough, 1994-2003.
Consistent trapping methods were used (minnow traps, and collapsible Fukui fish traps. Sites varied over the years, but the most consistently trapped sites were Kirby Park and South Marsh, surveyed annually in fall (October or November).
Contact Elkhorn Slough Reserve's Research coordinator Kerstin.wasson@gmail.com for further information.
Files and variables
File: elkhorn_crab_data.csv
Description:
Important note:
In order to calculate crabs per trap, one needs to know how many traps were set on a given day. This information is found in the file: trap_days_elkhorn_crabs_csv that contains the following variables:
Date (sampling date), Month (sampling month), Collapsible fukui (numbers of that trap type set in Elkhorn Slough, on that date as a sum of all sites trapped that day). Large minnow (numbers of that trap type set in Elkhorn Slough, on that date as a sum of all sites trapped that day). Small minnow (numbers of that trap type set in Elkhorn Slough, on that date as a sum of all sites trapped that day). Seine (numbers of seines conducted in Elkhorn Slough, on that date as a sum of all sites seined that day). Shrimp pot (numbers of that trap type set in Elkhorn Slough, on that date as a sum of all sites trapped that day). Notes (notes from that date in case traps were lost or in case traps were deployed for more than the regular 24 hrs. Null indicates there were no notes on a given day). Hence, if a person wishes to calculate crabs per trap on a given day, they would use the number of crabs caught at all sites found in the main data set "elkhorn crab data" and then they would look of the number of traps in the "trap days elkhorn crabs" file, and divide the number of crabs by the number of traps. Alternatively, one could also use the "trap #" in column K, in combination with "trap type" in column L in "elkhorn crab data" to deduce the total number of traps set on a given day. However, it is easier to look up the trap number in the "trap days elkhorn crabs" cvs file instead. If all traps ever set were entered, and if "empty" was entered in the species name if a trap came up empty, it would not be necessary to know the crabs per trap, but this is not how all data were entered.
There is a kmz file at Elkhorn Slough reserve, in the folder Research/Monitor/Crabs/Maps which shows the exact locations of some of the odd sites trapped in 2006-2008 and 2025-2017
Variables
- Date Collected: date traps were retrieved
- Month: month traps were retrieved
- Season: season traps were retrieved
- Year: year traps were retrieved
- Region: region of Elkhorn Slough where traps were set and retrieved
- Subregion: sub region of Elkhorn Slough where traps were set and retrieved. If a subregion is not designate for a site, the value appears as "n/a"
- Area: area of Elkhorn Slough where traps were set and retrieved. If an area is not designate for a site, the value appears as "n/a"
- Subarea: subarea region of Elkhorn Slough where traps were set and retrieved. If a subarea is not designate for a site, the value appears as "n/a"
- Site: specific site where traps were set and retrieved. If a site is in the data set, but does not appear in this table, it means that we don't know where that site was, other than it was definitely in Elkhorn Slough.
| Site Key | ||
|---|---|---|
| Site Code | Site Description | Site Location |
| BSL | Bennett Slough | Bennett Slough, on the E side of Bennett, when walking north from Jetty Rd |
| BH | Battilaria Heaven | North of Hummingbird Island |
| COY | Coyote Marsh | Coyote Marsh is on the W side of the railroad near the S end of North Marsh |
| FBR | Footbridge | Footbridge on South Marsh Loop Trail on the reserve |
| H1 | Hester phase 1 | Hester Marsh, main channel but near Dave's tree, was restricted in summer of 2021 |
| HI | Hummingbird Island, by the main channel on west side of island | The Hummingbird Island site is where the shoreline that faces a mid-channel island off the Reserve, near a grove of eucalyptus |
| HL | Hudson Landing, at Batillaria transect | Hudson Landing - where Elkhorn Road crosses the slough, close to the head of the slough |
| HP | Hidden Pond | Small Pond between Whistlestop and North Marsh, just south of Coyoto Marsh |
| JRD | North Harbor | Jetty Rd, on the south side of the culverts/bridge across Bennett Slough at Jetty Rd |
| JRN | North Harbor | Jetty Rd, on the north side of the culverts/bridge across Bennett Slough at Jetty Rd |
| KP | Kirby Park, left side of dock (if you are facing the water) | Kirby Park |
| KPS | Kirby Park, south of boat ramp | |
| KP2 | Kirby Park, north of boat ramp, about 200 north of point where trail starts from parkinglot | |
| MLHM | Moss Landing Harbor, south, muted flow = MLS for water quality | Moss Landing Harbor, muted - Moro Cojo |
| MLHF | Moss Landing Harbor, north, full flow, = MLN for water quality | Moss Landing Harbor, full flow, north side |
| MLWA | Moss Landing wildlife Area | Moss Landing Wildlife Area, by the old invertebrate transects |
| NML | North Marsh Tide Gate, left side (RR track side) of gate; High tidal flow | Site on reserve, south of Kirby Park |
| NMR | North Marsh Tide Gate, right side (water testing side) of gate; Muted tidal flow | Site on reserve, south of Kirby Park |
| PAC | Packard Dock | On the Packard property, by the dock formerly used for launching kayaks(?), on kmz map |
| PO | Parsons Overlook | On the reserve, on the trail along Long Canyon |
| PTR | Porter Marsh, muted | Porter Marsh is on the east side of Elkhorn Rd, across from Hudson Landing on the west side of Elkhorn Rd |
| RBR | Reserve Bridge Rocky | Footbridge on South Marsh Loop Trail on the reserve |
| RBS | Reserve Bridge Sandy (Footbridge on South Marsh Loop Trail) | Footbridge on South Marsh Loop Trail on the reserve |
| PRN | Portrero Road North | |
| VB | Vierras, along beach | At the Hwy 1 Bridge, crossing Elkhorn Slough |
| WSL | Whistle Stop Lagoon, left side of road (if you are facing RR Tracks/Hummingbird Island); High tidal flow | Whistlestop Lagoon is the souther-most finger of South Marsh on the reserve |
| WSR | Whistle Stop Lagoon, right side of road (if you are facing RR tracks/Hummingbird Island); Muted tidal flow | Whistlestop Lagoon is the northern-most finger of South Marsh on the reserve |
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Tidal Regime: full unobstructed tidal flow or muted flow behind tide gates. If site location is unknown, the tidal regime was recorded as "unknown" too.
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Trap #: the numerical identifier for given trap on a given day
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Trap Type: the type of trap used.
Trap Key Trap Code Trap Description Minnow Unknown if large or small minnow Small Minnow Unmodified Minnow trap: Conically shaped white plastic trap, 44cm tall, 16cm diameter at the ends and 21cm diameter in the middle. The opening in either end is 2.5 cm. Large Minnow Modified Minnow trap: Conically shaped, white plastic trap, 44cm tall, 16cm diameter at the ends and 21cm diameter in the middle. One end has a 5 cm diameter opening the other opening is 2.5 cm Collapsible Fukui Trap Box trap (Fukui fish trap): 45cm x 60 cm x 20 cm Seine 30 ft beach seine. Mesh size = [insert here] Pitfall Small Bucket Small plastic bucket, 24 cm tall, 24 cm in diameter Shrimp Pot commercial shrimp pod Pitfall Tennisball Can Tennis ball can with holes drilled in bottom - pitfall trap -
Species1: species identities of specimens found upon trap retrieval
Species Key Species Code Common names Genus species (if known) AA Top smelt Atherinops affinis AG Arrow goby Clevelandia ios AF Yellowfin goby Acanthogobius Flavimanus BA Batillaria Batillaria attramentaria BAT Bat ray Myloibatis Californica BG Bubble snail Bulla gouldiana CA, RA Rock crab Cancer antennarius, Romaleon antennarium CAN Rock crab Cancer spp. CG Graceful crab Cancer gracilis CM Green crab Carcinus maenas CP Rock crab Cancer productus CR Crangon spp. Crangon spp. CSP Sanddab Citharichtys spp. EM Anchovy Engraulis mordax FF Flatfish GA Stickleback Gastorosteus aculeatus GM Longjaw mudsucker Gillicthys mirabilis GN Opaleye Girella nigricans GO Goby HC shrimp Heptacarpus spp. HO Mud crab Hemigrapsus oregonensis HN Hemigrapsus Hemigrapsus nudus MC Malacoplax Californiensis Malacoplax Californiensis NX Sea slug Navanax spp. PA Pagarus spp. Pagarus spp. PC Lined shore crab Pachygrapsus crassipes PCH Perch PN Plainfin midshipman Porichthys notatus PP Kelp crab Pugettia productus RC Thornback ray Raja Clavata RF Rockfish SA Brown rockfish Sebastes auricalutus RP Shovelnose guitarfish Rhinobatus productus SA California tonguefish Symphurus atricauda Shrimp Shrimp SL Bay pipefish Syngnathus leptorhyncus SP Shiner surf perch Cymatogaster aggregata SS Staghorn sculpin Leptocottus armatus TS Leopard shark Triakis semifasciata WO Wooly sculpin Clinocottus analis WS Whelk Snail EMPTY Trap closed and baited, but empty NULL Trap empty and open, not baited, missing (include in notes) -
Sex: F = female, J = juvenile, M = male, U = unknown, P = parasitized and thus unknown. If no sex was recorded, "NR" is in the cell
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Size (mm): carapace width of crab or fish length. If no size was recorded, "NR" is in the cell
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Number of individuals (if you only have counts from that day): if individuals were not measured, they were counted instead. n/a means that the individual was measured, so this column doesn't apply to the row entry
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Data Source: Data collector(s)
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Notes: notes
Access information
Data was derived from the following sources:
- Elkhorn Slough Long term monitoring data base