Chapter 2 Early detection assessment planning
These tools should be used during early detection assessment planning and are all geared toward the goal of detecting green crab presence. “Detecting presence” refers to catching at least one green crab or producing at least one eDNA detection.
Necessary effort: If you have a target true capture rate, figure out the effort necessary to detect green crab presence.
Lowest detectable true capture rate: If you already know how many traps you’re setting, figure out the lowest detectable true capture rate.
Note: These tools can be used to help guide effort planning at a site over a relatively short time period. (See section 1.3 for more info).
2.1 Necessary effort
This function helps you identify the effort necessary to detect green crab presence. Navigate to Assessment Planning > Necessary effort. In these sections, we will focus on only trapping efforts.
Refer to section 2.3 for more information about using eDNA in this web app.
2.1.2 Interpreting the plot
Interpret the outputs and plot.
Note that these tools are intended to help planning an effort at a site over a relatively short time period. See section 1.3 for more details.
2.1.3 Trap-adjusted capture rate
The previous necessary effort section assumed all trap types function equally. However, both the type of trap and crab size affect capture rates.
In this section, you can adjust for trap type by using the trap-adjusted capture rate. This rate scales all trapping observations relative to the rate at which fukui traps catch crabs. Head to section 1.2.2 for more information about the trap-adjusted capture rate.
Here, our previous target capture rate input of 4 crabs/100 traps still applies, except now the target is 4 small crabs/100 fukui traps and 4 large crabs/100 fukui traps.
The types of traps used in this section are:
Square fukui fish traps (1.27 cm mesh)
Modified steel minnow traps (2 inch opening, 0.635 cm mesh)
Non-collapsible shrimp traps (1 inch mesh)
If the type of trap you use is not listed here, choose the trap above that functions most similarly to your trap, or contact us at crabteam@uw.edu if you have further questions. Note that one trap set refers to a soak window with one overnight tide (typically a ~16-18 hr time period).
Fill in the inputs for trap-adjusted capture rate. We’ll begin with shrimp traps and large crabs.
Interpret the text and plot to identify the number of shrimp traps necessary to capture at least one large crab when the trap-adjusted capture rate is 4 large crabs/100 fukui traps.
Now toggle to minnow traps and keep the large crab size. Now we can see the number of minnow traps necessary to capture at least one large crab when the trap-adjusted capture rate is 4 large crabs/100 fukui traps.
You can see that shrimp traps are much more effective at detecting large green crab presence! Toggle through the trap types and crab sizes to make more comparisons.
2.2 Lowest detectable capture rate
You can think of this function as a “temper your expectations” function. If you know how many traps you plan to set, what is the lowest capture rate where you can expect to detect green crab presence?
Navigate to Assessment Planning > Lowest detectable capture rate. In these sections, we will focus on only trapping efforts.
Refer to section 2.3 for more information about using eDNA in this web app.
2.2.1 Inputs
Fill in your desired inputs.
The types of traps used in this section are:
Square fukui fish traps (1.27 cm mesh)
Modified steel minnow traps (2 inch opening, 0.635 cm mesh)
Non-collapsible shrimp traps (1 inch mesh)
If the type of trap you use is not listed here, choose the trap above that functions most similarly to your trap, or contact us at crabteam@uw.edu if you have further questions. Note that one trap set refers to a soak window with one overnight tide (typically a ~16-18 hr time period).
Note that these tools are intended to help planning an effort at a site over a relatively short time period. See section 1.3 for more details.
2.2.3 Trap-adjusted capture rate
Although you inputted the number of traps of each type, the previous lowest detectable capture rate section assumed all trap types function equally. However, both the type of trap and crab size affect capture rates.
In this section, you can adjust for trap type by using the trap-adjusted capture rate. This rate scales all trapping observations relative to the rate at which fukui traps catch crabs. Head to section 1.2.2 for more information about the trap-adjusted capture rate.
Here, our previous trap number inputs still apply.
Fill in the input for trap-adjusted capture rate. We’ll begin with small crabs.
Interpret the text and plot to identify the lowest detectable trap-adjusted capture rate of small crabs, given the number and type of traps you plan to set.
Now toggle to the large crab size. Now we can see if the lowest detectable trap-adjusted capture rate of large crabs is different.
2.3 Environmental DNA (eDNA)
This section of the web app is sensitive to eDNA data collection methods. The model underlying this tool was built using eDNA data collected following the protocol in Keller et al. 2022. Water samples collected for eDNA analysis using different protocols may make inference using this web tool less applicable.
The sensitivity of eDNA detection relative to trapping likely depends upon the field collection protocols (i.e. water volume, collection depth) and laboratory protocols (i.e. DNA extraction and purification methods).
Seasonality may also play a role in eDNA sensitivity. Season-specific factors like green crab activity, movement, and molting cycles can affect the rate at which organisms shed eDNA. Also, the presence and density of organic matter in the water may vary seasonally and affect eDNA extraction and PCR inhibition.
However, this tool can be useful if your eDNA protocols are similar those outlined in Keller et al. or if you want to explore how the sensitivity of eDNA samples could potentially compare to trapping.
2.3.1 Necessary effort – Traps & eDNA
This function helps you identify all combinations of trapping and eDNA efforts that would be necessary to detect green crab presence. In this scenario, “detecting presence” means catching a crab or producing one true positive eDNA detection.
2.3.1.2 Interpreting the plot
Interpret the outputs and plot. Here, you will find the combinations of trap and eDNA efforts that, together, will be sufficient to detect green crab presence at your target true capture rate. Note that “detecting presence” refers to catching at least one crab or producing at least one true positive eDNA detection.
Note that one water sample refers one biological replicate with three technical replicates (i.e., qPCR reactions). Refer to Keller et al. 2022 for more information.
2.3.2 Lowest detectable capture rate – Traps & eDNA
If you know how many traps you plan to set and how many eDNA samples you plan to collect, what is the lowest capture rate where you can expect to detect green crab presence?
In this scenario, “detecting presence” means catching a crab or producing one true positive eDNA detection.
Note that one water sample refers one biological replicate with three technical replicates (i.e., qPCR reactions). Refer to Keller et al. 2022 for more information.
