Sibship reconstruction for inferring mating systems, dispersal and effective population size in headwater brook trout (Salvelinus fontinalis) populations

Abstract

Brook trout Salvelinus fontinalis populations have declined in much of the native range in eastern North America and populations are typically relegated to small headwater streams in Connecticut, USA. We used sibship reconstruction to infer mating systems, dispersal and effective population size of resident (non-anadromous) brook trout in two headwater stream channel networks in Connecticut. Brook trout were captured via backpack electrofishing using spatially continuous sampling in the two headwaters (channel network lengths of 4.4 and 7.7 km). Eight microsatellite loci were genotyped in a total of 740 individuals (80-140 mm) subsampled in a stratified random design from all 50 m-reaches in which trout were captured. Sibship reconstruction indicated that males and females were both mostly polygamous although single pair matings were also inferred. Breeder sex ratio was inferred to be nearly 1:1. Few large-sized fullsib families ([3 individuals) were inferred and the majority of individuals were inferred to have no fullsibs among those fish genotyped (family size = 1). The median stream channel distance between pairs of individuals belonging to the same large-sized fullsib families ([3 individuals) was 100 m (range: 0-1,850 m) and 250 m (range: 0-2,350 m) in the two study sites, indicating limited dispersal at least for the size class of individuals analyzed. Using a sibship assignment method, the effective population size for the two streams was estimated at 91 (95%CI: 67-123) and 210 (95%CI: 172-259), corresponding to the ratio of effectiveto-census population size of 0.06 and 0.12, respectively. Both-sex polygamy, low variation in reproductive success, and a balanced sex ratio may help maintain genetic diversity of brook trout populations with small breeder sizes persisting in headwater channel networks.

Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events

“…In the present study, we implemented siblingship tests for the first time, which led to an increase in the accuracy and confidence of assignment of the salmon escapees back to their farm(s) of origin. The identification of the relationships among siblings, either those that share 1 (half sibling) or both (full sibling) parents, has formerly been utilised to address a wide variety of questions in biology and ecology, such as elucidating fine-scale patterns of larval dispersal for a rocky reef fish on the open coast (Schunter et al 2014), determining individual variability in reproductive success (Hudy et al 2008, Liu & Ely 2009 and dispersal (Hudy et al 2008), providing some insight into the mating systems by inferring genotypes of unknown parents (Wang 2004, Kanno et al 2011) and tracing market product to the farm of origin in the event of detection of disease or toxins in the market fish (Hayes et al 2005).…”

Simulation and empirical analysis of novel sibship-based genetic determination of fish passage

“…S1 2 ). In particular, pedigree reconstruction could be used to assign juveniles to parents from the same sites (Kanno et al 2011(Kanno et al , 2014. Known parental locations, ideally based on individual-based tagging information close to the time of reproduction, could be used to help identify movement direction of juveniles relative to estimated parent locations (Kanno et al 2014).…”

“…Examples of point distributions of reproduction include salmonid (Einum et al 2008) and lamprey (Nika and Virbickas 2010) redds or sculpin (Fiumera et al 2002) and stream salamander (Bruce 2005) nests. Dispersal of siblings from these point sources can be quantified from a genetic survey and subsequent assignment of individuals (parents and offspring) to family groups (Hudy et al 2010;Kanno et al 2011). When coupled with a sampling design that includes barrier assessment, family members captured on opposite sides of the potential barrier demonstrate individual passage.…”

Genetic monitoring of trout movement after culvert remediation: family matters

“…However, to confirm appropriate sampling, we used the maximum likelihood estimation in program COLONY (Jones and Wang 2010) to evaluate via pedigree analysis any influence of family structure. Because of its ability to reconstruct sibling families based only on genotypes from a single generation (i.e., with no information on parental genotypes), COLONY has been increasingly applied to field studies (Hudy et al 2010;Kanno et al 2011;Read et al 2012). We estimated full-sibling families using the full-likelihood algorithm, updated allele frequencies, an assumption of male polygamy (computational time prohibited assumption of polygyny as well), and no prior for family relationships.…”

“…Under certain scenarios, the program has a tendency to split larger sibling groups (Almudevar and Anderson 2012) and may not accurately estimate very small fullsibling families (Hudy et al 2010;Kanno et al 2011;Wang and Santure 2009), so we undertook a multistep simulation process (Fig. A1) to evaluate the behavior of COLONY based on genetic variation observed in microsatellites markers in our sample populations.…”