Marja-Liisa Koljonen

Maintenance of genetic diversity of Atlantic salmon (Salmo salar) by captive breeding programmes and the geographic distribution of microsatellite variation

Abstract The capability of Finnish Atlantic salmon ( Salmo salar L.) broodstock breeding programmes to maintain genetic diversity was assessed by comparing the levels of microsatellite diversity in wild and hatchery stocks in general, and in wild and hatchery derivatives of the same stock. The effective population sizes ( N e ) of the broodstocks and the ratio of effective size to census size ( N e / N c ) as well as the rate of loss of diversity in captive breeding were assessed. Moreover, the distribution and pattern of genetic diversity among Atlantic salmon stocks in the Baltic Sea, Barents Sea and NW Atlantic were measured. Microsatellite data were also compared with allozyme data of the same salmon stocks. Nine microsatellite loci were amplified: Ssa85, Ssa171, Ssa197, Ssa202, Ssa289, SSOSL85, SSOSL 311, SSOSL417 and SSOSL438 from 11 Atlantic salmon stocks. The effective population sizes of broodstocks were estimated with the method based on temporal allele frequency change. In short-term breeding programmes, the average rate of loss of heterozygosity was 1.4% per generation and the average observed rate of loss of alleles was 4.7% per generation. The estimated N e s for the broodstocks were 32 and 238. The average N e / N c ratio was 0.81. Changes in present-day broodstocks were not alarming and the N e / N c ratios were higher than in wild populations in general. The genetic D A distance between continents was 0.64 ( F ST ( θ )=0.22) and distances about half of that level ( D A distance 0.34, F ST =0.09) were measured between European and Baltic Sea salmon stocks. A nearly diagnostic difference was observed in the SSOSL311 of the North American stocks (Maine 0.982 and Labrador 0.957) for a single allele (SSOSL311 118 ) that did not occur in European populations at all. Microsatellite data showed relatively more genetic differentiation ( F ST =0.040) on a small geographical scale than did allozyme data ( F ST =0.017), indicating the higher discrimination power of this data set.

Extensive immigration from compensatory hatchery releases into wild Atlantic salmon population in the Baltic sea: spatio-temporal analysis over 18 years

Genetic homogenization has been recognized as a serious threat in an increasing number of species, including many salmonid fishes. We assessed the rate and impact of immigration from the main hatchery stocks of Atlantic salmon in the Gulf of Bothnia into one of the largest wild salmon populations in the Baltic Sea, the River Vindelälven, within a temporal framework of 18 years (from 1985–2003). We provide genetic evidence based on mtDNA and microsatellite markers, using mixed-stock analysis, that a large proportion (66%) of fin-damaged spawners (n=181) caught in the Ume/Vindelälven during 1997–2003 originated from the hatcheries in the Rivers Ångermanälven, Luleälven and Ljusnan. The maximum-likelihood estimate of immigration rate from these hatcheries into the wild Vindelälven population was 0.068 (95% CI 0.021–0.128) over the studied time period (1985–2003) and reached up to a quarter (m=0.249, 95% CI 0.106–0.419) of the total population during 1993–2000. This resulted in significant (P<0.01) genetic homogenization trend between the wild Vindelälven population and hatchery stocks of the Ångermanälven and Luleälven. Our results demonstrate extensive straying from geographically distant hatchery releases into wild salmon population and emphasize the genetic risks associated with current large-scale stocking practices in the Baltic Sea.

Genetic changes in Atlantic salmon stocks since historical times and the effective population size of a long-term captive breeding programme

Human-caused genetic changes in two Atlanticsalmon (Salmo salar L.) stocks, from therivers Iijoki and Oulujoki in Finland, wereassessed by comparing the genetic parameters ofthese stocks before and after the hatcherybreeding of several successive generations,corresponding to 40 and 33 years since the wildstate. The changes were also compared withthose observed in a large wild salmon stock inthe River Teno during 56 years. In all, thevariation at seven microsatellite DNA loci wasexamined in 11 Atlantic salmon samplesoriginating from these three rivers. Theeffective population size, Ne, duringbreeding of the Iijoki broodstock and for theTeno salmon was also estimated by the temporalmethod based on allele frequency changes. Forthe Iijoki broodstock, the changes could betracked generation by generation from thefounding of the stock. Statisticallysignificant changes in allele frequencies werecommon in the hatchery stocks (F = 0.029, forIijoki), but not in the wild Teno stock, whichwas temporally very stable (F = 0.007). Allelicrichness decreased statistically significantly(24.8%) in the Oulujoki broodstock, from 62.1to 46.7 alleles at nine loci. On average, therewere 9.7 fewer alleles (15.7%) in thecontemporary broodstocks than in thecorresponding historical stocks. The meanheterozygosity was 6.6% lower in thecontemporary Oulujoki broodstock, but remainedunchanged in the Iijoki broodstock. Theestimated Ne for the Iijoki broodstock wasunder 80 for 4.5 generations from 1962 to 1995and for the wild Teno salmon over 900 for 56years from 1939 to 1995.

Analysis of gene associated tandem repeat markers in Atlantic salmon (Salmo salar L.) populations: implications for restoration and conservation in the Baltic Sea

Patterns of genetic diversity and differentiation among five wild and four hatchery populations of Atlantic salmon in the Baltic Sea were assessed based on eight assumedly neutral microsatellite loci and six gene-associated markers, including four expressed sequence tag (EST) linked and two major histocompatibility complex (MHC) linked tandem repeat markers (micro- and mini-satellites). The coalescent simulations based on the method of Beaumont and Nichols (1996, Proc. R. Soc. Lond. Ser. B – Biol. Sci., 263, 1619–1626) indicated that two loci (MHCIIα and Ssa171, with the lowest and highest overall FST estimates, respectively) exhibited significant departures (P<0.05) from the neutral expectations. Another coalescent-based test for selective neutrality (Vitalis et al. 2001, Genetics, 158, 1811–1823) further supported the outlier status of the Ssa171 microsatellite locus but not of the MHCIIα linked minisatellite. In addition, actin related protein linked microsatellite locus was identified with this test as an outlier in six pairwise population comparisons. All genetic diversity estimates revealed more genetic variation in hatchery stocks than in the small wild salmon populations from the Gulf of Finland. However, the wild populations possessed alleles at gene-associated markers (e.g. MHCI and IGF) not found in the hatchery stocks, which together with moderate genetic differentiation and distinctive environmental conditions justifies the special conservation measures for the last remaining native salmon populations in the Gulf of Finland.

Effect of maternal and paternal line on spatial and temporal marine distribution in Atlantic salmon.

We examined the inheritance of the sea migration pattern of Atlantic salmon, Salmo salar, in a crossing and tagging experiment in the Baltic Sea. Individuals from the parental stocks, Neva and Iijoki, and their reciprocal hybrids were released as 2-year-old smolts, into the same estuary of the Bothnian Sea in 1994. Two thousand smolts from each of the four groups were marked with Carlin tags. The recapture rate of the tags was nearly 10%. We used log-linear models to analyse the marine distribution of the salmon groups from the tag recovery data. The pure stocks and their pooled hybrid groups all showed statistically significant differences between each other in spatial and temporal sea distribution. The Iijoki salmon were more frequently (9%) caught outside the Bothnian Sea than were the Neva salmon (2%). The majority of the Iijoki salmon (55%), but fewer Neva salmon (40%), were caught in the second sea year. In spatial distribution, the hybrids seemed to be intermediate between the parental stocks, with no differences between reciprocal female and male lines. In duration of sea migration and age at maturity, however, the hybrids were very similar to their maternal line, the effect of which was thus clearly stronger than that of the paternal line. Copyright 2000 The Association for the Study of Animal Behaviour.

Divergent trends in life-history traits between Atlantic salmon Salmo salar of wild and hatchery origin in the Baltic Sea

Four Atlantic salmon Salmo salar stocks in the Baltic Sea, varying in their breeding history, were studied for changes in life-history traits over the years 1972-1995. Total length (L(T)) at age of captured (L(TC)) fish had increased throughout the study period, partly due to increased temperature and increased L(T) at release, (L(TR)) but also due to remaining cohort effects that could represent unaccounted environmental or genetic change. Simultaneously, maturation probabilities controlled for water temperature, L(TC) and L(TR) had increased in all stocks. The least change was observed in the River Tornionjoki S. salar that was subject only to supportive stockings originating from wild parents. These results suggest a long-term divergence between semi-natural and broodstock-based S. salar stocks. Increased L(T) at age explained advanced maturation only marginally, and it remains an open question to what extent the generally increased probabilities to mature at early age reflected underlying genetic changes.

Genetic differentiation among European whitefish ecotypes based on microsatellite data

The amount of genetic differentiation at DNA microsatellite loci in European whitefish (Coregonus lavaretus) was assessed among ecotypes, populations and run-timing types. The magnitude of genetic changes potentially caused by hatchery broodstock rearing were also compared with those observed in corresponding natural populations. A total of 35 populations were studied, including 33 Coregonus lavaretus populations and two samples of Coregonus peled. Five of the six whitefish ecotypes in Finland were represented within C. lavaretus populations. Genetic diversity among C. lavaretus populations proved to be high compared to two C. peled populations. The genetic D(A) distance between these two species was as high as 0.86. The genetic differentiation among ecotypes was generally low and thus gives support for the hypothesis of one native European whitefish species in Scandinavia. Among the ecotypes the northern, large sparsely-rakered, bottom-dwelling whitefish was most unique. Thus, observed genetic differences in quantitative traits have either developed independently of phylogenetic lineages, or have mixed and later changed according to environments and selection pressures. Overall genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Populations of this area have been heavily influenced by human activities, and they also have the highest probability of mixing by natural means. In two cases, the Rivers Iijoki and Tornionjoki, statistically significant genetic differences could be observed between summer- and autumn-run spawning-time types. Wild populations had slightly higher allelic diversity than hatchery-reared populations of corresponding rivers. Although some reduction in genetic diversity during hatchery rearing is possible, it is an important aid in maintaining endangered populations.

High level of population genetic structuring in lake-run brown trout, Salmo trutta, of the Inari Basin, northern Finland

Rivers draining into (Lake) Inarijärvi, northern Finland, sustain a number of lake-run brown trout, Salmo trutta, populations but, as with most lake-run S. trutta systems, the level of population genetic structuring among populations is unknown. To address this and to assist fish stock management in the region, the population genetic structure of S. trutta collected from 28 sampling sites in rivers flowing into Inarijärvi was studied using 13 microsatellite loci. Populations were clustered into three separate groups, largely corresponding to geographic regions, with between-region F(ST) values ranging from 0·11 to 0·16. The significant differentiation observed between most populations within each region also implies that individual populations should be recognized as separate management units and actions to improve, and subsequently maintain, conditions for natural spawning should be prioritized. The results of this study further indicate that the trout from each of these regions may have different biological characteristics, such as local-lake feeding behaviour among the western populations and strong isolation among the northern stocks. As a consequence, further research is warranted to better understand the level of ecological uniqueness of lake-run S. trutta populations.

Coastal and freshwater pikeperch (Sander lucioperca) populations differ genetically in the Baltic Sea basin

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 F(st) between these population groups was as high as 0.25 and R(st) =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.

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%).