Genetic diversity, admixture, and hatchery influence in Brook Trout (Salvelinus fontinalis) throughout western New York State

Abstract

Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non‐native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation‐decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% ( q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.

Genetic Characteristics of Brook Trout Salvelinus fontinalis (Mitchill, 1848) Broodstocks from Hatcheries in Bosnia and Herzegovina

“…However, across all loci, the number of alleles and genotypes was low. Except for some loci in DJA brood, the allele count per locus was four or less, which is in concordance with the findings of Beer et al (2019) who examined the genetic diversity of three brook trout strains in two hatcheries in New York State, USA. Just as population bottleneck is inevitable when establishing the breeding stock, genetic drift and population size fluctuation are likely to follow.…”

“…While mtDNA provides invaluable insight into migration and colonization patterns as well as possible interspecies hybridization, neutral nuclear markers such as microsatellites are better indicators of recent events at the population level. Investigations of North American populations of brook trout revealed extensive genetic diversity of this species (Bernatchez and Danzmann, 1993;Beer et al, 2019;Bruce et al, 2019). However, there are significant differences in genetic structure between hatchery stock and feral populations (Shikano et al, 2008).…”

“…However, these stocking efforts proved to be futile as no findings of sustainable population of brook trout in the wild have been reported in this millennium. Previous studies showed that in natural environments, farmed brook trout tended to exhibit lower survival rates (Fraser, 1981;Beer et al, 2019) and lower reproductive abilities (Araki et al, 2007(Araki et al, , 2008. On the other hand, this is beneficial for the native fish community as alien species can pose a threat to the autochthonous and endemic gene pool either through hybridization, competition for habitat and food or direct predation.…”

Complete mitochondrial genome of Mahachai betta, Betta mahachaiensis (Teleostei: Osphronemidae)

“…The large biodiversity of betta is currently being lost more rapidly than at any time in the past several million years, with the invasion of alien species or hybrids introduced into the wild leading to genetic admixture (Beer et al. 2019 ). This is a very serious problem in the context of conservation biology and genetics and needs to be resolved as a matter of urgency.…”

Next-generation sequencing yields complete mitochondrial genome assembly of peaceful betta fish, Betta imbellis (Teleostei: Osphronemidae)

“…This betta fish inhabits still and sluggish waters including rice paddies, swamps, roadside ditches, streams, and ponds. Artificial selection activities for ornamental and aquarium trade purposes have resulted in inbreeding and outbreeding depression with an adverse effect on the genetic integrity of wild populations (Beer et al 2019). Here, a complete mitochondrial genome (mitogenome) of B. imbellis collected from Nakhon Si Thammarat, Thailand (8.4325 N,99.9599 E), was assembled, annotated, analyzed, and stored in the Thailand Natural History Museum (no.…”