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KevinSee / ManuscriptSTADEM

Contains the manuscript and supporting R code describing the STADEM package and how it has been used at Lower Granite Dam to generate salmon escapement estimates.
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Which fish are sampled for scales and genetics? #2

Closed KevinSee closed 4 years ago

KevinSee commented 4 years ago

In the paragraph under Method, about the Adult Fish Trap Data, it says, "each fish had scale and genetic tissue samples taken". Is that true, or were those samples taken from a subsample of the fish in the trap?

ryankinzer commented 4 years ago

Good catch...at the time I was thinking of non-clipped fish which I'm fairly certain are 100% sampled. Hatchery-origin fish are sub-sampled.

KevinSee commented 4 years ago

When I'm done reviewing, could one of you (Ryan or Mike) make that change, if you know what the correct description is?

mackerman44 commented 4 years ago

I'll review, today. Currently, all unclipped fish are 100% sampled for scale and tissues. However, in ye olde yonder prehistoric years only every other unclipped fish was sampled, that change was made somewhere around 2011.

Clipped fish are sub-sampled at like 10-20% and that rate can change annually. I'll dig into it...

ryankinzer commented 4 years ago

the weekly summary sheets from IDFG show sub-sampling rates for hatchery clipped fish have varied from 0%-50%. Generally, higher rates are observed for clipped steelhead.

mackerman44 commented 4 years ago

I changed that passage to read:

"For adipose-intact (unclipped) adults, which includes wild and hatchery-no clip individuals, some portion or all of fish trapped had scale and genetic tissue samples taken. Scale samples were used to estimate age [@Wright2015] and genetic tissue samples were used to determine sex [@Campbell2012a] and estimate the origin of wild fish via genetic stock identification (e.g., @Hargrove2019). Starting with adults spawning in 2013, every unclipped Chinook salmon and steelhead trapped at LGR was genotyped to simplify collaborative logistics and better estimate the proportion of phenotypically wild fish of truly hatchery origin. Previous to that, only fish determined to be wild in origin at the trap were sampled for scale and genetics. @Camacho2017 provide further details on trap sample rates and valid sample selection. Prior to release, all non-PIT tagged fish with an intact adipose fin (i.e., putatively wild) received a PIT tag. Final determination of wild, hatchery, and hatchery no-clip origins were assigned using a post-hoc analysis of marks and tags, including genetic parentage-based tags [@Steele2013; @Steele2019]."

But I kind of feel like I made it worse, especially since we don't include any sex results and no information on how much the wild and hatchery no-clip estimates were changed by including PBT results. Tell me if I missed the mark and I can take another stab at it.

KevinSee commented 4 years ago

I re-arranged your 2 sentences about pre- and post-2013 sampling, but otherwise I think it addresses what we need it to. There is some mention in the discussion about how sex and age information from the trap can be used in conjunction with DABOM escapement to look at productivity.