Large inter-stock differences in catch size-at-age of mature Atlantic salmon observed by using genetic individual origin assignment from catch data.

Genetic individual assignment of river stock of origin of mixed stock catch fish offers a tool to analyze size differences among river stocks. Data on the genetically identified river stock of origin of individual fish from commercial mixed stock catches were used to compare the catch size-at-age of mature Atlantic salmon catch fish (Salmo salar) from different rivers in the Baltic Sea. In this application of genetic mixed stock modeling, individual assignments of the river stock of origin were analyzed together with length- and weight-at-age data for individual catch fish. The use of four genetic stock identification based methods was compared for defining the length distributions of caught mature salmon in different river stocks. The catch data included information on maturing salmon in the northern Baltic Sea over the years 2000-2013. DNA microsatellite data on 17 loci and information on the smoltification age were used to assign spawners to their stock of origin. All of the compared methods for using probabilistic stock of origin data in our case yielded very similar estimates of the final mean length distributions of the stocks. The Bayesian mixture model yielded slightly more conservative estimates than the direct probability method, threshold method, or the modified probability method. The catch size between spawners of a same sex and age from river stocks differed significantly and the differences were large. The mean catch weight of 1-sea-winter old mature males in different rivers varied from 1.9 kg to 2.9 kg, from 5.1 kg to 7.5 kg for 2-sea-winter old males, from 5.0 kg to 7.2 kg for 2-sea-winter old females, and from 8.2 kg to 10.8 kg for 3-sea-winter-old females. The mean size of caught wild salmon spawners in each year-class was on average smaller than that of the hatchery-reared and sea ranched stocks.

Restored river habitat provides a natural spawning area for a critically endangered landlocked Atlantic salmon population.

Supplementing endangered fish populations with captive bred individuals is a common practice in conservation management. The aim of supplementary releases from hatchery broodstocks is to maintain the viability of populations by maintaining their genetic diversity. Landlocked Lake Saimaa salmon (Salmo salar m. sebago) has been critically endangered for the past half-century. As a result of anthropogenic disturbance, especially construction of hydroelectric power plants, the Lake Saimaa salmon has become completely dependent on hatchery broodstock. Recently, habitat restoration has been done in one of the former spawning rivers with the aim of creating a new natural spawning ground for the critically endangered population. Hatchery fish releases have also been revised so that in addition to juveniles, adult fish from the hatchery and from the wild have been released into the restored river. We assessed here if a restored river stretch can be used as a natural spawning ground and juvenile production area with the aim of improving genetic diversity of the critically endangered Lake Saimaa salmon. By constructing a pedigree of the released adults, and juveniles sampled from the restored river, we found that the majority of the released adults had produced offspring in the river. We also found that wild-caught spawners that were released into the restored river had much higher reproductive success than hatchery-reared parents that were released into the restored river at the same time. We found no significant differences in genetic diversity between the parent and offspring generations. Meanwhile, relatedness among different groups of adults and juveniles varied a lot. For example, while the hatchery-reared females were on average half-siblings, wild-caught females showed no significant relatedness. This highlights the importance of using pedigree information in planning the conservation and management of endangered populations, especially when artificial propagation is involved.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation.

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

Wild Estonian and Russian sea trout (Salmo trutta) in Finnish coastal sea trout catches: results of genetic mixed-stock analysis.

For responsible fisheries management of threatened species, it is essential to know the composition of catches and the extent to which fisheries exploit weak wild populations. The threatened Estonian, Finnish and Russian sea trout populations in the Gulf of Finland are targets of mixed-stock fisheries. The fish may originate from rivers with varying production capacities, from different countries, and they may also have either a wild or hatchery origin. In order to resolve the composition of Finnish coastal sea trout catches, we created a standardized baseline dataset of 15 DNA microsatellite loci for 59 sea trout populations around the Gulf of Finland and tested its resolution for mixed-stock analysis of 1372 captured fish. The baseline dataset provided sufficient resolution for reliable mixture analysis at regional group level, and also for most of the individual rivers stocks. The majority (76-80%) of the total catch originated from Finnish sea trout populations, 6-9% came from Russian and 12-15% from Estonian populations. Nearly all Finnish trout in the catch were of hatchery origin, while the Russian and Estonian trout were mostly of wild origin. The proportion of fish in the Finnish catches that originated from rivers with natural production was at least one fifth (22%, 19-23%). Two different spotting patterns were observed among the captured trout, with a small and sparsely spotted form being markedly more common among individuals of Russian (28%) and Estonian origin (22%) than among fish assigned to a Finnish origin (0.7%).