Understanding the role of structural variants such as chromosomal inversions in local adaptation among small, isolated populations is an important addition to robust conservation strategies, as most studies investigating inversions to date have been conducted on high gene flow systems. Brook Trout (Salvelinus fontinalis), an economically important top sportfish, is extremely vulnerable to thermal stress. Local adaptation with respect to this trait warrants investigation as climate change accelerates the loss of cold-stream ecosystems. We performed low-coverage whole genome sequencing (lcWGS) on N=192 Brook Trout from nine small, isolated streams in Nova Scotia, Canada. Using the indirect structural variant detection framework, we detected four potential chromosomal inversions in the three westernmost populations which differ from all other streams in water temperature, streamflow, and surficial geology. These genomic regions exhibited high linkage disequilibrium (LD) and principal component analyses (PCA) revealed the presence of three karyotypes (inverted and non-inverted homokaryotype, and heterokaryotype). Heterozygosity was lowest among inverted homokaryotypes, providing further support of the presence of inversions. Mitogenome analyses suggest that a single glacial lineage recolonized the region. The mtDNA haplotypes of individuals carrying potential inversions were shared among individuals with two copies of non-inverted chromosomal regions, suggesting these inversions were derived post-recolonization. These novel inversions comprised genes involved in different biological processes including thermal adaptations.

Although efforts to estimate Ne, Nc, and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how representative many estimates may be. Answering this question requires studies of long-term population dynamics. We non-lethally sampled N=5400 brook trout (Salvelinus fontinalis) from seven populations during 6 consecutive years (2014-2019) and genotyped them at 33 microsatellites to examine variation in Ne, Nc and their ratio. Nc was estimated by Mark-Recapture (Nc(MR)) (2014-2018) as well as by Close-Kin-Mark-Recapture (Nc(CKMR)) (2015-2017). Within populations, annual variation in Ne (max/min Ne) ranged from 1.6-fold to 58-fold. Over all 7 populations, median annual variation in Ne was 5-fold. These results reflect important interannual changes in reproductive success variance. Within population Nc(MR) varied by a median of 2.7. Thus, Ne varied nearly twice as much as did Nc(MR) . Our results suggest that, at least in small populations, any single annual estimate of Ne is unlikely to be representative of long-term dynamics. At least 3-4 annual estimates may be required for an estimate of contemporary Ne to be representative. For five of the seven populations, Nc(MR) was indistinguishable from Nc(CKMR). The two populations with discordant estimates exhibited the largest annual Ne variation (58-fold and 35.4-fold). These results suggest sampling effort in these two streams may have been insufficient to capture the genetic diversity of the entire population. Our study demonstrates how knowledge of temporal variation in Ne can be used to identify potential biases in Nc(CKMR).