Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology

Abstract

The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD‐capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (Nb), as well as the extrapolated minimum number of spawners (Ns), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype‐based pedigree information with length‐at‐age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree‐based Nb and Ns estimates provide a promising and rapid assessment tool for sea lamprey and other species.

Evaluating the utility of effective breeding size estimates for monitoring sea lamprey spawning abundance

“…A bioinformatic pipeline based on Sard et al ( 2020 ) and Weise et al ( 2020 ) was used to process sequencing data. First, reads were oriented with a custom perl script bRAD_flip (originally developed by Paul Hohenlohe, University of Idaho, and modified by Brian Hand and Seth Smith, University of Montana) and demultiplexed using the Stacks 2.0 (Catchen et al, 2013 ) function process_radtags.…”

“…Genomic data and reconstructed pedigrees can provide population‐level inference regarding estimates of the minimum number of spawning adults ( N s ) and the effective number of breeding adults ( N b ), that can be used to fill information gaps in the absence of information on N c and inform management actions for invasive species (Weise et al, 2020). Effective population size ( N e ) is a parameter describing the size of an idealized population that experiences drift or inbreeding at the same rate as the sampled population (Wright, 1931).…”

“…Since N b is estimated for a single reproductive event, it is used to assess species for early detection of population decline or extinction risk (Jay et al, 2014 ; Kamath et al, 2015 ). For invasive species, N b can be used to track the growth and spread of invasive species, or evaluate management intervention (Weise et al, 2020 ). Several methods are used to estimate N b .…”

“…Advances in genotyping technology have allowed large‐scale genetic‐based population assessments with large sample sizes and genome‐wide SNP data, including for sea lamprey (Sard et al, 2020 ; Weise et al, 2020 ). Genomic technologies like restriction site associated DNA sequencing (RADseq; Baird et al, 2008 ) and RAD‐capture sequencing (Ali et al, 2016 ) allow for high‐throughput genotyping.…”

Demographic patterns of walleye (Sander vitreus) reproductive success in a Wisconsin population

“…Genetic tools provide a means of identifying parent‐offspring relationships in natural settings (e.g., Andersson et al., 2017 ; Baetscher et al., 2018 ; Hohenlohe et al., 2018 ). High‐throughput genotyping panels allow high‐resolution genetic data to be efficiently collected at hundreds to thousands of single nucleotide polymorphism (SNP) loci (Meek & Larson, 2019 ), enabling large‐scale pedigrees to be reconstructed in wild populations (Sard et al., 2020 ; Weise et al., 2022 ). The process for developing an effective SNP panel has been detailed by Bootsma et al.…”