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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.

1. Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. 2. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement, akin to an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. 3. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. Use of a population dynamics model allowed robust interpolation of expected catch composition at areas and times with no genetic observations. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses: incorporation of prior information about stock abundance and movement resulted in more plausible and precise estimates of mixture compositions in time and space. 4. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.

The genetic consequences and gene flow of pikeperch (Sander lucioperca) stocking were assessed in three boreal lakes based on admixture model analysis and comparison of the pre- and post-release patterns of genetic variability at 9 DNA microsatellite loci in the recipient populations. In two out of the three cases, the releases of fish from foreign populations caused significant changes in the genetic structure of the recipient population. The largest changes were observed in Lake Oulujrvi, where the post-release sample was almost identical to the released Lake Vanajanselk population, and about 90% of the catch was composed of the released population. The genetic composition of Lake Lohjanjrvi pikeperch also shifted markedly towards that of the released Lake Vanajanselk population, and about half of the later catch was of released Vanajanselk origin. In Lake Vanajanselk, in contrast, releases of pikeperch from lakes Painio and Averia had only a small impact on the genetic structure of the pikeperch population. These results indicate that the current stocking practices create an effective artificial gene flow that may strongly shape and reduce the genetic differentiation among the remaining native pikeperch populations. A common feature of all three cases was the lack of prior appraisal of the potential genetic and ecological risks in relation to the expected benefits of the release programmes.

Microsatellite DNA based analysis of the pattern of genetic diversity among three coastal and five freshwater populations of pikeperch Sander lucioperca in the northern part of the Baltic Sea drainage basin indicated marked genetic differentiation between the coastal and lake populations. The Fst between these population groups was as high as 0.25 and Rst=0.32. In general, the lake populations showed higher genetic diversity than the coastal ones. In terms of genetic distance, the three coastal populations (Vanhankaupunginlahti, Västanfjärd and Taivassalo) grouped tightly together. The freshwater samples formed a looser group, in which the northern Lake Kemijärvi showed greater distance from the southern lakes than these did from each other. The two lake populations originally established through stockings (Lakes Painio and Averia) grouped near to their source population of Lake Lohjanjärvi and their diversity level was nearly the same. Safeguarding the unique Baltic coastal populations of S. lucioperca against gene flow from increasing hatchery releases using freshwater S. lucioperca should be a high management priority.

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers. Tutkimuksessa kuvattiin Itämeren alueella olevien historiallisten ja nykyisten lohikantojen (Salmo salar L.) sekä eri siikakantojen (Coregonus lavaretus) ja siikamuotojen geneettistä muuntelua DNA tason mikrosatelliittimerkkien avulla. Lisäksi pyrittiin arvioimaan ihmisen toiminnan vaikutusta lohi- ja siikakantoihin. Verrattuna Atlantin itärannikon kantoihin Itämeren alueen lohikannoissa havaittiin keskimäärin hieman vähemmän geneettistä muuntelua. Itämeren alueella olevat järvilohikannat (Vänern, Saimaa, Ääninen ja Laatokka) olivat puolestaan merkitsevästi vähemmän muuntelevia kuin alueen merilohikannat. Lohikantojen geneettinen rakenne oli hierarkkinen. Perinnöllisten erojen perusteella Itämeren alueen lohikannat ryhmittyivät kolmeen ryhmään: pohjoiseen (Pohjanlahden alueen kannat), itäiseen (Suomenlahden kannat ja itäisen pääaltaan kannat) ja eteläiseen (läntiset pääaltaan kannat) ryhmään. Tämän jako kuvastaa mahdollisesti kehityslinjaeroja ajalta, jolloin lohi on asuttanut Itämeren alueen jokia viimeisen jääkauden jälkeen. Kun verrattiin useitten sukupolvien ajan laitoskasvatuksen kohteena olleita lohikantoja (Iijoki ja Oulujoki) samoista joista peräisin oleviin historiallisiin näytteisiin alkuperäisistä villeistä kaloista, havaittiin että alleelifrekvenssit olivat muuttuneet laitoskasvatetuissa kannoissa, ja geenimuotoja oli hävinnyt. Vastaavana ajanjaksona Tenojoen suuressa villissä luonnonkannassa ei ollut tapahtunut juurikaan muutoksia. Vaikka todettiinkin että geneettinen monimuotoisuus oli laitoskasvatuksessa hieman vähentynyt, on laitoskasvatuksen avulla silti onnistuttu säilyttämään suuri osa menetettyjen historiallisten lohikantojen monimuotoisuudesta. Tutkittujen eri siikamuotojen välinen geneettinen erilaistuminen oli vähäistä. Tämä havainto tukee teoriaa siitä että Fennoskandian alueen siiat kuuluvat samaan lajiin. Eri siikamuodoista kaikkein omaleimaisin oli pohjasiika (C.l.fera). Siikamuotojen väliset erot kvantitatiivisissa ominaisuuksissa, kuten siivilähampaitten määrässä, ovat siten joko kehittyneet riippumatta mahdollisesta kehityslinjasta, tai sitten eri linjat ovat sekoittuneet ajan kuluessa, ja erot ovat syntyneet myöhemmin elinympäristön ja erilaisten valintapaineiden vuoksi. Suomen rannikon siikakantojen väliset geneettiset erot olivat hyvin pieniä, erityisesti Pohjanlahden alueella. Kun verrattiin villejä ja laitoskasvatettuja kantoja toisiinsa, havaittiin että villit kannat olivat geneettisesti hieman monimuotoisempia kuin vastaavien jokien laitoskasvatetut kannat.