Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar

Abstract

This study assesses whether the effective number of breeders (N ) can be estimated using a time and cost-effective protocol using genetic sibship reconstruction from a single sample of young-of-the-year (YOY) for the purposes of Atlantic salmon Salmo salar population monitoring. N was estimated for 10 consecutive reproductive seasons for S. salar in the River Nivelle, a small population located at the rear-edge of the species distribution area in France, chronically under its conservation limit and subjected to anthropogenic and environmental changes. Subsampling of real and simulated data showed that accurate estimates of N can be obtained from YOY genotypes, collected at moderate random sampling intensity, achievable using routine juvenile electrofishing protocols. Spatial bias and time elapsed since spawning were found to affect estimates, which must be accounted for in sampling designs. N estimated in autumn for S. salar in the River Nivelle was low and variable across years from 23 (95% C.I. 14-41) to 75 (53-101) and was not statistically correlated with the estimated number of returning adults, but it was positively correlated with the estimated number of YOY at age 9 months. N was found to be lower for intermediate levels of redd aggregation, suggesting that the strength of the competition between males to access females affects reproductive success variance depending on redd spatial configuration. Thus, environmental factors such as habitat availability and quality for spawning and YOY development predominate over demographic ones (number of returning adults) in driving long-term population viability for S. salar in the River Nivelle. This study showcases N as an integrated parameter, encompassing demographic and ecological information about a reproductive event, relevant to the assessment of both short-term effects of management practices and long-term population conservation status.

Effects of spatial aggregation of nests on population recruitment: the case of a small population of Atlantic salmon

“…The negative trend between the number of breeders and the aggregation of nests is consistent with the negative effect of aggregation on the number of effective breeders at low aggregation found by Bacles et al (2018) in the same population. The negative trend between the number of breeders and the aggregation of nests is consistent with the negative effect of aggregation on the number of effective breeders at low aggregation found by Bacles et al (2018) in the same population.…”

“…Aggregation of nests increased at low adult density, something expected under ideal distributions. The negative trend between the number of breeders and the aggregation of nests is consistent with the negative effect of aggregation on the number of effective breeders at low aggregation found by Bacles et al (2018) in the same population. Our results indicate that when few individuals are present, they all fit in the best patches, whereas they have to spill out to lower quality patches when density increases.…”

“…In addition to the effects of aggregation on demographic processes, aggregation of nests may also modify genetic diversity within populations (Falcy 2015, Lara-Romero et al 2016, Tentelier et al 2016, Winandy et al, 2017, Bacles et al 2018. Indeed, some individuals could have most of their nests destroyed within aggregates due to scouring or nest superimposition, future offsprings of conspecifics being able to colonize empty habitats (Gharrett et al 2013).…”

Fast sequence-based microsatellite genotyping development workflow

“…Selection criteria included allele size smaller than 300 bp to ensure that sequencing reads can span the entire allele length including library construction and absence of sequences complementarity between primers tested using Multiplex Manager (Holleley and Geerts 2009). In the second strategy, we chose to sequence a set of 15 microsatellites (Supporting Table S1) that are routinely amplified in a single multiplexed PCR and genotyped using electrophoresis-based capillary sequencers (Bacles et al, 2018;Lepais et al, 2017).…”

Understanding fish populations

“…Salmonids in the form of S. salar reappeared again within the theme of Tools for Understanding Fish Populations as the study species in a genetics-based investigation of the feasibility of estimating the effective number of adult breeders from single samples of young individuals reported by Bacles et al (2018), with the discussion paper of Paris et al (2018) addressing the wider subject under five main approaches of tagging and telemetry, molecular tools, survey tools, statistical and modelling tools, and tissue analyses. Fish in a Changing World is represented by specific and more generic studies.…”