Project
Quantifying abundance and recruitment in a re-establishing lake trout population by close-kin mark-recapture
Effective fisheries management and restoration requires reliable estimates of abundance and population trajectories through time. However, absolute population estimates are extremely difficult to obtain in large systems due to the prohibitively high sample sizes required by most approaches. Close-kin mark-recapture (CKMR) is a new technique that can obviate this hurdle by using the observed kinship within a sample to estimate the true adult population. Our project aimed to develop a CKMR model for lake trout (Salvelinus namaycush) and apply it understand the ongoing re-establishment of Lake Champlain’s wild population by estimating the abundance of individuals contributing to wild recruitment. To do so we 1) developed and validate a flexible, efficient amplicon sequencing-based microsatellite panel that will enable us to identify the parent-offspring and half-sibling pairs necessary for CKMR. 2) created a CKMR abundance model for lake trout that combines parent-offspring and half-sibling kinship information. 3) applied the resultant modeling framework to assess contributions of stocked and wild parents to the ongoing restoration of wild lake trout in Lake Champlain. 4) adapted the analytical code to create an accessible, flexible, and well-documented estimation pipeline that can be applied to a wide range of species and sampling scenarios.
Project Datasets
High resolution microsatellite genotypes for Lake Champlain Lake trout
These data consist of high-resolution microsatellite genotypes (131 loci, see Marcy-Quay et al. in review for marker and protocol information) for 1500 lake trout (S. namaycush) captured in Lake Champlain from 2015-2022. Each row represents an individual fish, with a unique ID code that related to other Lake Champlain datasets. Each locus is represented by a column, with a diploid genotype provided in the format “[haplotype #1] | [haplotype #2]”. Missing values are represented as NAs.
Survey data and individual fish metrics for Lake Champlain Lake trout
This dataset contains survey information (date, location, gear type, etc.) and individual metrics (length, weight, age, sex, etc.) for 1500 lake trout (S. namaycush) captured in Lake Champlain from 2015-2022. Each row represents an individual fish, with a unique ID code that related to other Lake Champlain datasets. Metrics are represented by individual columns. Missing values are represented as NAs.