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Koljonen et al. 2013. Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland

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Abstract

In order to create a management strategy for the sea trout in the Gulf of Finland area, all potential brown trout populations in the area were analysed together with Russian populations from the neighbouring area. In all, 3430 individual brown trout samples from 70 locations and from 34 river systems were analysed from Finnish and Russian rivers. The analysis was based on variation in 16 DNA microsatellite gene loci in these samples. From all samples, the overall diversity, mean allelic richness and effective population size, as well as the number of full-sib families and mean relatedness was assessed. Genetic differentiation was first analysed within rivers systems and in several stages over all the data. The anadromous and resident populations were also analysed separately. A subpopulation structure was observed in seven river systems (Kiskonjoki, Karjaanjoki, Siuntionjoki, Espoonjoki, Vantaanjoki, Summanjoki and Virojoki). In general, diversity differences were very large. No statistically significant differences could be detected between the river sample pairs Aurajoki – Fiskarsinjoki, Ingarskilanjoki – Koskenkylänjoki, Vantaanjoki, Palojoki – Koskenkylänjoki or Isojoki – Kymijoki. In all cases, similarity was a result of hatchery releases of known origin. In general, the genetic distances between the anadromous stocks followed the geographical distances between the river mouths and the form of the coastline. Anadromous populations could be grouped into six main groups: 1) the Uskelanjoki group, 2) Aurajoki group, 3) Isojoki group, 4) Ingarskilanjoki group, 5) Bay of Vyborg group and 6) the group of Russian rivers, mainly the Karelian Isthmus rivers. Two of the groups were influenced by stocked fish: the Aurajoki and Isojoki groups. The releases of these hatchery stocks should be limited to agreed rivers and for sea ranching purposes. Local genetic material for three coastal areas was still available. For southwest Finland, or Varsinais-Suomi, the diversity levels were lower than in other areas, but local genetic material is still left in the Uskelanjoki group rivers (Uskelanjoki, Paimionjoki and Purilanjoki). For the Uusimaa area, the most diverse and valuable populations are in the Ingarskilanjoki group (Ingarskilanjoki, Koskenkylänjoki, Sipoonjoki, Mankinjoki and Vantaanjoki). For the southeastern part of the coast, local genetic material is still available in the border rivers draining into the Bay of Vyborg, and especially in the River Mustajoki population, from which a broodstock has already been founded. Other rivers for that area are Rakkolanjoki, Santajoki, Kilpeenjoki, and Urpalanjoki and Finnish Virojoki, with Saarasjärvenoja belonging to the same group. Recommendations for the management of brown trout populations of the whole Finnish coastal area and also of individual rivers were provided.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and
Russian sea trout populations in
the Gulf of Finland area
Marja-Liisa Koljonen, Aki Janatuinen, Ari Saura and Jarmo Koskiniemi
The content of the publication reflects the authors views and the Managing Authority cannot be held liable for the information
published by the project partners.
Finnish Game and Fisheries Research Institute, Helsinki 2013
10 Ingarskilanjoki AO
18 Koskenkylanjoki AI
15 Sipoonjoki AO
12 Mankinjoki AO
14 Vantaanjoki Lower reaches AI
14 Vantaanjoki Middle reaches AI
19 Kymijoki AI
20 Summanjoki Main stream AI
13 Espoonjoki AM
1 Aurajoki AI
7 Kiskonjoki Latokartanonkoski AM
8 Fiskarsinjoki AI
7 Kiskonjoki Perniönjoki AO
2 Paimionjoki AO
5 Uskelanjoki AO
3 Purilanjoki AO
9 Karjaanjoki Mustionjoki AO
11 Siuntionjoki AO
26 Mustajoki FIN-RUS AO
26 Mustajoki Kananoja 2006 FIN-RUS AO
27 Kilpeenjoki FIN-RUS AO
23 Santajoki FIN-RUS AO
25 Rakkolanjoki FIN-RUS AO
21 Virojoki AO
24 Vilajoki FIN-RUS AM
29 Inojoki RUS AO
32 Kuokkalanpuro RUS AO
28 Notkopuro RUS AO
30 Pikkuvammeljoki RUS AO
31 Vammeljoki RUS AO
33 Rajajoki RUS AO
34 Luga RUS AO
22 Urpalanjoki FIN-RUS AO
Finnish-Russian border rivers
Bay of Vyborg
Ingarskilanjoki
group
Isojoki
hatchery group
Aurajoki
hatchery group
Uskelanjoki
group
The Karelian Isthmus
Publisher:
Finnish Game and Fisheries Research Institute
Helsinki 2013
ISBN 978-952-303-067-1 (Web)
ISSN 1799-4756 (Web)
FGFRI 2013
Description
Authors
Marja-Liisa Koljonen, Aki Janatuinen, Ari Saura and Jarmo Koskiniemi
Title
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
Year
2013
Pages
100
ISBN
978-952-303-067-1
Unit/research program
Research and Expert Services, Habitats and biodiversity
Accepted by
Nina Peuhkuri
Abstract
In order to create a management strategy for the sea trout in the Gulf of Finland area, all potential brown
trout populations in the area were analysed together with Russian populations from the neighbouring area. In
all, 3430 individual brown trout samples from 70 locations and from 34 river systems were analysed from
Finnish and Russian rivers. The analysis was based on variation in 16 DNA microsatellite gene loci in these
samples.
From all samples, the overall diversity, mean allelic richness and effective population size, as well as the
number of full-sib families and mean relatedness was assessed. Genetic differentiation was first analysed
within rivers systems and in several stages over all the data. The anadromous and resident populations were
also analysed separately. A subpopulation structure was observed in seven river systems (Kiskonjoki,
Karjaanjoki, Siuntionjoki, Espoonjoki, Vantaanjoki, Summanjoki and Virojoki). In general, diversity differences
were very large. No statistically significant differences could be detected between the river sample pairs
Aurajoki Fiskarsinjoki, Ingarskilanjoki Koskenkylänjoki, Vantaanjoki, Palojoki Koskenkylänjoki or Isojoki
Kymijoki. In all cases, similarity was a result of hatchery releases of known origin. In general, the genetic
distances between the anadromous stocks followed the geographical distances between the river mouths and
the form of the coastline. Anadromous populations could be grouped into six main groups: 1) the Uskelanjoki
group, 2) Aurajoki group, 3) Isojoki group, 4) Ingarskilanjoki group, 5) Bay of Vyborg group and 6) the group of
Russian rivers, mainly the Karelian Isthmus rivers. Two of the groups were influenced by stocked fish: the
Aurajoki and Isojoki groups. The releases of these hatchery stocks should be limited to agreed rivers and for
sea ranching purposes. Local genetic material for three coastal areas was still available. For southwest Finland,
or Varsinais-Suomi, the diversity levels were lower than in other areas, but local genetic material is still left in
the Uskelanjoki group rivers (Uskelanjoki, Paimionjoki and Purilanjoki). For the Uusimaa area, the most diverse
and valuable populations are in the Ingarskilanjoki group (Ingarskilanjoki, Koskenkylänjoki, Sipoonjoki,
Mankinjoki and Vantaanjoki). For the southeastern part of the coast, local genetic material is still available in
the border rivers draining into the Bay of Vyborg, and especially in the River Mustajoki population, from which
a broodstock has already been founded. Other rivers for that area are Rakkolanjoki, Santajoki, Kilpeenjoki, and
Urpalanjoki and Finnish Virojoki, with Saarasjärvenoja belonging to the same group. Recommendations for the
management of brown trout populations of the whole Finnish coastal area and also of individual rivers were
provided.
Keywords
Sea trout, Salmo trutta, DNA microsatellites, genetic diversity, management
Publications internet address
http://www.rktl.fi/www/uploads/pdf/uudet%20julkaisut/tyoraportit/healfish_report.pdf
Contact
Marja-Liisa Koljonen, marja-liisa.koljonen@rktl.fi
Additional information
This work was part of the Central Baltic INTERREG IV A Programme 2007-2013, project HEALFISH 20102013
Kuvailulehti
Tekijät
Marja-Liisa Koljonen, Aki Janatuinen, Ari Saura ja Jarmo Koskiniemi
Nimeke
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area,
Suomalaisten ja venäläisten, Suomenlahteen laskevien jokien taimenkantojen geneettinen rakenne
Vuosi
2013
Sivumäärä
100
ISBN
978-952-303-067-1
Yksikkö/tutkimusohjelma
Tutkimus- ja asiantuntijapalvelut/Elinympäristöt ja monimuotoisuus
Hyväksynyt: Nina Peuhkuri
Tiivistelmä
Suomenlahden alueen meritaimenkantojen hoitostrategian luomiseksi selvitettiin sekä suomalaisten että
venäläisten Suomenlahteen laskevien jokien taimenkantojen geneettinen rakenne. Kaikkiaan tutkittiin 3 430
yksittäistä taimennäytettä, 70 populaatiosta ja 34 vesistöstä. Analyysi perustuu 16 DNA mikrosatelliittigeeni-
lokuksen muunteluun. Kaikista näytteistä analysoitiin kokonaisdiversiteetti, alleelirikkaus, geneettisesti tehollinen
populaatiokoko, täyssisarperheiden määrä ja keskimääräinen sukulaisuusaste. Perinnöllinen erilaistuminen ana
lysoitiin ensin saman vesistön eri populaatoiden välillä. Vaeltavat ja paikalliset populaatiot analysoitiin myös erik
seen. Seitsemässä vesistössä havaittiin populaatioiden välistä erilaistumista eri jokihaarojen tai koskien popu
laatioiden välillä. Nämä vesistöt olivat Kiskonjoki, Karjaanjoki, Siuntionjoki, Espoonjoki, Vantaanjoki, Summan joki
ja Virojoki. Koko aineistossa geneettisen diversiteetin määrän erot olivat jopa kolminkertaiset vähiten ja eniten
muuntelevien populaatioiden välillä. Tilastollisesti merkittävää eroa ei voitu havaita viiden jokinäyteparin välillä:
Aurajoki Fiskarsinjoki, Ingarskilanjoki Koskenkylänjoki, Vantaanjoki, Palojoki - Koskenkylänjoki, ja Isojoki
Kymijoki. Kaikissa tapauksissa samankaltaisuuden selittivät tunnetut poikasistutukset. Runsaista istutuksista
huolimatta meritaimenkantojen perinnölliset etäisyydet vastasivat edelleen varsin hyvin niiden maantietteellisiä
etäisyyksiä ja rannikon rakennetta. Meritaimenkannat ryhmittyivät kuuteen pääryhmään: 1) Uskelanjoki, 2)
Aurajoki, 3) Isojoki, 4) Ingarskilanjoki, 5) Viipurinlahti ja 6) Venäläiset joet (Karjalan kannas). Näistä ryhmistä kaksi
oli sellaisia, joissa oli selvää istutuskantojen vakutusta: Aurajoki ja Isojoki. Näiden laitostaimenkantojen siirtäminen
ja istuttaminen tulisi rajoittaa sovittuihin jokiin ja merialueen istutuksiin. Paikallista perinnöllistä aineista oli
olemassa edelleen kolmelle alueelle. Varsinais-Suomen alueen alkuperäisimmät meritaimenkannat ovat Uskelan-
joen, Paimionjoen ja Purilanjoen taimenet. Tämän alueen kantojen geneettinen diversiteetti oli alhaisempi kuin
muiden alueiden, pienten populaatiokokojen vuoksi. Uudenmaan alueen taimenkantojen arvokkain, alkuperäinen
geneettinen materiaali on parhaiten säilynyt Ingarskilajoen taimenen lisäksi Koskenkylänjoen, Sipoonjoen, Man
kinjoen ja Vantaanjoen taimenpopulaatioissa. Kaakkois-Suomen alueen taimenkantojen geneettinen mate riaali
on säilynyt Viipurinlahteen laskevien rajajokien populaatioissa. Näistä tärkein on Mustajoki, josta on jo perustettu
emokalasto. Muita rajajokia ovat Urpalanjoki, Rakkolanjoki, Santajoki ja Kilpeenjoki. Myös kokonaan Suomen puo
lella oleva Virojoen Saarasjärvenoja kuuluu geneettisesti tähän ryhmään. Hoitosuositukset on annettu paitsi koko
Suomen rannikolle, myös kaikille taimenkannoille erikseen.
Asiasanat
Meritaimen, DNA mikrosatelliitti, perinnöllinen monimuotoisuus, hoitostrategia
Julkaisun verkko-osoite
http://www.rktl.fi/www/uploads/pdf/uudet%20julkaisut/tyoraportit/healfish_report.pdf
Yhteydenotot
Marja-Liisa Koljonen, marja-liisa.koljonen@rktl.fi
Muita tietoja
Tämä työ on osa Central Baltic INTERRED IV A - ohjelmaan kuuluvaa HEALFISH-projektia (2010-2013)
Contents
1. Introduction 7
2. Material and Methods 9
2.1. DNA methods 9
2.2. Statistical analyses 10
2.3. Brown trout samples 10
3. Results 17
3.1. Genetic diversity within populations 17
3.2. Effective population size and the relatedness within populations 19
3.3. Genetic differentiation among populations 22
3.4. Genetic distances among populations 27
4. Regional results and management recommendations 32
4.1. ELY Centre for Southwest Finland 32
4.1.1. Aurajoki 32
4.1.2. Paimionjoki 34
4.1.3. Purilanjoki 36
4.1.4. Halikonjoki 37
4.1.5. Uskelanjoki 39
4.1.6. Punassuon Lohioja 42
4.1.7. Kiskonjoki 43
4.2. ELY Centre for Uusimaa 48
4.2.1. Fiskarsinjoki 48
4.2.2. Karjaanjoki 50
4.2.3. Ingarskilanjoki 55
4.2.4. Siuntionjoki 57
4.2.5. Mankinjoki 59
4.2.6. Espoonjoki 62
4.2.7. Vantaanjoki 64
4.2.8. Sipoonjoki 69
4.2.9. Mustijoki 71
4.2.10. Porvoonjoki 73
4.2.11. Koskenkylänjoki 75
4.3. ELY Centre for Southeast Finland. 76
4.3.1. Kymijoki 76
4.3.2. Summanjoki 77
4.3.3. Virojoki 79
4.3.4. Urpalanjoki 82
4.3.5. Santajoki 83
4.3.6. Vilajoki 83
4.3.7. Rakkolanjoki 84
4.3.8. Mustajoki (Juustilanjoki) 84
4.3.9. Kilpeenjoki 85
4.4. Russian rivers 86
4.4.1. Notkopuro 86
4.4.2. Inojoki 86
4.4.3. Pikkuvammeljoki 86
4.4.4. Vammeljoki 86
4.4.5. Kuokkalanpuro 87
4.4.6. Rajajoki, Siestarjoki 87
4.4.7. Laukaanjoki, Luga 87
4.5. Hatchery stocks for comparison 88
4.5.1. Lapväärtin-Isojoki 88
4.5.2. Rautalamminreitti 89
4.5.3. Luutajoki 89
4.5.4. Sweden, Gotland 89
4.5.5. Denmark, Kolding 90
5. Discussion 90
5.1. Diversity levels 90
5.2. Genetic structure 91
5.3. Management 93
6. References 96
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
7
1. Introduction
The EU and international organizations (UN, FAO, IUCN, ICES, NASCO, and HELCOM) all recognize the crucial
need to conserve genetic diversity as a fundamental part of biodiversity, which is rapidly being depleted
due to human activities. The loss of genetic diversity reduces the level of local adaptation and the ability of
species to adapt to continued changes in the environment, and results in an irreversible loss of genetic
resources and a reduction in the overall evolutionary potential of species.
Because the financial resources and the means to preserve genetic resources are limited, efficient
strategies are needed to maximize the overall maintenance of genetic diversity in each situation. A key
question is thus the definition of management units for each management activity and geographical level.
The valuation, choice and priorisation of populations according to their genetic characteristics are also
essential for conservation strategies.
With genetic markers, it is possible to measure diversity levels and the amount of genetic
differentiation, estimate current gene flow levels between populations, as well as to analyse the similarity
between hatchery stocks and natural stocks as an indication of the influence of hatchery-released fish.
Genetic markers also allow estimates of genetically effective population sizes, and levels of inbreeding or
mixing of populations. With this information, it is possible to define population borders and hierarchical
population structures, and as a conclusion define management units of different levels (Koljonen 2001).
There are currently about 101 rivers or brooks draining into the Gulf of Finland from Finland, Russia or
Estonia in which there is an anadromous trout population (Salmo trutta L.). From these populations, 85 can
be regarded as native wild stocks (ICES 2013). The remaining populations have been supported by hatchery
releases. For about one-third of the anadromous trout populations, the conservation status is very poor, as
for 29 populations the current smolt production level is less than 5% of the potential smolt production level
of the river. In addition, the conservation status is weak and uncertain for another 30 populations.
According to a threat factor analysis for the whole Gulf of Finland, including Russian and Estonian
rivers, the most common threat to the sea trout stock was overexploitation (for 47 river populations),
followed by habitat degradation (for 45 populations), while for 27 populations the threat was pollution, and
for 15 cases its was dam construction (ICES 2013).
In the Finnish Red Data Book, the anadromous trout is listed as Critically Endangered, because natural
reproduction is unstable in most Finnish Baltic Sea populations due to intensive fishing, which also targets
immature fish, migration obstructions and highly alternating water flow levels in rivers (Kaukoranta et al.
2000, Kallio-Nyberg et al. 2001, Heinimaa et al. 2007, Urho et al. 2010). In Russia, a declaration of trout
preservation is in force so that no legal trout fishing should occur. However, despite many of the rivers
being situated in the border zone, poaching is a threat. In Finland, the legal minimum catch size of sea trout
has been 50 cm, but will be increased to 60 cm at the beginning of 2014. In addition, in 2013, the legal
minimum catch size of sea trout was increased in the Finnish governmentally ruled offshore sea area of the
Gulf of Finland from 50 cm to 65 cm.
In Finland, dam construction has been especially active and several sea trout stocks have been
destroyed (Kallio-Nyberg et al. 2001). Depending on the distance of the first dam from the river mouth,
different types of more or less artificially isolated populations have remained in the river systems (Kallio-
Nyberg et al. 2010). In the current HEALFISH project, restoration plans exist for five Finnish rivers
(Hitolanjoki, Ingarskilanjoki, Vantaanjoki, Koskenkylänjoki and Vaalimaanjoki).
In order to compensate for the decreased population abundance and production levels, artificial
reproduction in hatcheries and the release of reared fish or eggs into rivers with the aim of re-establishing
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
8
extinct or enhancing weak populations are commonly practiced. In addition, hatchery releases to improve
sea trout catches have also been widely used along the coastal area. However, this may have resulted in
irreversible changes in the genetic composition of local, native populations due to the direct effects of
releases or indirect impacts of hatchery fish ascending from the sea to spawn in native rivers.
Even if the released hatchery fish originate from the same river, non-natural selective pressures in
hatcheries, termed the domestication effect, or the loss of genetic variation through genetic drift and
inbreeding due to the restricted population sizes in hatcheries may compromise local adaptations and
decrease the overall diversity of the native populations. These may also pose a threat to the maintenance
of genetic diversity. The potential genetic changes may reduce the conservation value of the trout stocks.
In all, 293 000 smolts were released into the Gulf of Finland in 2012. The majority (74%, i.e., 216 000
smolts) were from Finnish releases, 22% (64 000 smolts) from Russia and 4% (13 000 smolts) were from
Estonian releases (ICES 2013). Estonia has announced an end to its trout releases in 2013. The profitability
of hatchery releases for fishing purposes has been low. The recapture rate of Carlin-tagged, released sea
trout has followed a continuously decreasing trend for more than 20 years in the Gulf of Finland (ICES
2013).
Some mixing of anadromous trouts in the sea is known to occur, as tagging experiments have shown in
general about 510% of the trout tagged in Finland to be returned from the Estonian coast and some also
from Russia. Correspondingly, sea trout tagged in Estonia have partly been recaptured in Finnish coastal
waters. The coastal sea trout catch in 2012 in Estonia was 13 300 kg, and in Finland 15 900 kg. In addition,
Finland announced a total catch of 3 800 kg from rivers (ICES 2013).
In Russia, wild sea trout populations are found in at least 40 rivers or streams. The majority are
situated in the northern coast of the Gulf of Finland, but the rivers with the highest smolt production are in
the southern area. Average densities are in general below ten 0+ parr per 100 m2. The total smolt
production of Russian rivers has been estimated to be at least 10 00015 000 smolts. Smolt trap
experiments indicate that between 2000 and 8000 sea trout smolts of natural origin annually migrate to
the sea from the Luga, the largest Russian trout river. Six Russian rivers, in addition to border rivers, were
included in the current analyses to enable a comparison with native wild stocks and describe the level of
differentiation in general. Part of the earlier analyzed data on Russian populations (EU Interreg IIIA project
ISKALT 20032007) was updated for 16 DNA microsatellite loci and used for the analysis of pooled data
sets.
Watershed-based analyses of the genetic structure of Finnish brown trout populations have also
previously been conducted (Koljonen 1989, Marttinen and Koljonen 1989, Koljonen et al. 1992, Koljonen
and Saura 1992, Koskiniemi 2005, Koskiniemi 2007, Koskiniemi 2008, Koskiniemi 2009a,b,c, Aaltonen 2009,
Koskiniemi 2010, Aaltonen 2011, Koskiniemi 2012, Nuotio and Koskiniemi 1995, Saura 2005b), but this was
the first analysis covering the whole southern coastal area. In addition, research teams from other Baltic
Sea countries have studied some restricted areas or river systems of Baltic Sea drainage basin by using
allozyme, mtDNA and microsatellite markers (Ryman 1983, Hansen and Mensberg 1998, Hindar et al. 1991,
Luczynski et al. 1997, Laikre et al. 2002, Was and Wenne 2002, Wlodarczyk and Wenne 2001, Lehtonen et
al. 2009, Samuiloviene et al. 2009).
The aim of this study was to describe the genetic structure and measure the level of genetic
differentiation and diversity levels of brown trout stocks in watersheds draining into the Gulf of Finland and
Archipelago Sea from Finland and Russia to create a management plan for Finnish sea trout stocks. The plan
should utilize all the available genetic resources and potential breeding areas.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
9
The goals of this research have been:
1. To reveal the intraspecific genetic population structure of southern Finnish and Russian brown
trout populations in the Gulf of Finland area;
2. To measure the levels of genetic diversity, differentiation and relatedness between and within all
populations;
3. To estimate the effective population sizes of the river populations;
4. To assess the impact of hatchery releases and small population sizes on the population genetic
structure of Finnish anadromous brown trout stocks;
5. To compare Finnish sea trout stocks with native Russian stocks;
6. To study the formation of the population genetic structure in re-established and/or enhanced sea
trout populations;
7. To prepare proposals for conservation and management for individual Finnish seat trout rivers.
In this report, the main goal is to describe the fine-level population structure of Finnish trout populations in
the coastal river systems, as this information is especially valuable in management decision making at the
local level. In practice, each sample was intially analysed separately to examine how the overall picture has
been built and to check whether any clear distinction occurs among samples from separate tributaries. This
might indicate a subpopulation structure resulting from isolation caused by migration barriers, natural
differences in migration behaviour or the genetic effects of hatchery releases. The pooling of samples for
the final calculations was carried out according to this preliminary analysis and it is also reported here. This
work was financed by EU Interreg IV A Programme and project HEALFISH (Healthy fish stocks indicators of
successful river basin management) (20102013).
2. Material and Methods
2.1. DNA methods
Total genomic DNA was extracted from scale or tissue samples in 95% alcohol using the DNeasy Blood &
Tissue Kit method (Qiagen). From each sample, 400 µl of liquid DNA was obtained. Variation was
determined at 16 microsatellite loci (Table 1). For each sample, two multiplex PCR reactions were
performed using the Qiagen Type-it Microsatellite kit in a 10 µl reaction volume with 3 µl of extracted DNA,
5 µl of kit master mix and primers with concentrations and dyes as presented in Table 1. PCR reactions
were carried out PTC200 Thermal Cyclers (MJ Research), and the temperature profile of the PCR program
was suggested in the Type-it Microsatellite kit manual. The annealing temperature was 56 °C.
Microsatellite genotypes were detected with an Applied Biosystems ABI 3130 automated DNA
sequencer and analysed with GENEMAPPER Analysis Software version 4.0, with the size standard of Applied
Biosystems GeneScan 500LIZ. Automatic outputs were manually checked.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
10
Table 1. Microsatellite loci used for brown trout analysis. References, multiplexes, dyes and primer
concentrations are also indicated.
Locus
Reference
Multiplex
plate
Dye
Primer
concentration
1
BS131
Estoup et al., 1998
MP 1
VIC
0.03 µM
2
OneU9
Schribner et al., 1996
MP 2
VIC
0.03 µM
3
SSa197
O'Reilly et al., 1996
MP 1
NED
0.02 µM
4
SSa289
McConnell et al., 1995
MP 1
PET
0.30 µM
5
Ssa407
Cairney et al., 2000
MP 1
NED
0.15 µM
6
SSa85
McConnell et al., 1995
MP 2
VIC
0.02 µM
7
Ssosl311
Slettan et al., 1995
MP 2
NED
0.07 µM
8
SSosl417
Slettan et al., 1995
MP 1
PET
0.04 µM
9
SSosl438
Slettan et al., 1996
MP 2
VIC
0.07 µM
10
SSsp1605
Patterson et al., 2004
MP 2
NED
0.04 µM
11
SSsp2201
Patterson et al., 2004
MP 1
6-FAM
0.03 µM
12
Str15INRA
Estoup et al., 1993
MP 1
6-FAM
0.05 µM
13
Str60lNRA
Estoup et al., 1993
MP 2
PET
0.04 µM
14
Str73lNRA
Estoup et al., 1993
MP 1
VIC
0.04 µM
15
Str85lNRA
Presa & Guyomard 1996
MP 2
6-FAM
0.40 µM
16
Strutt58
Poteaux 1995
MP 2
6-FAM
0.30 µM
2.2. Statistical analyses
The allele frequencies, genotype distributions and pairwise FST values (Weir and Cockerham 1984) were
calculated with Genepop software, version 4.0.7 (Raymond and Rousset 1995, Rousset 2008)
(http://kimura.univ-montp2.fr/~rousset/Genepop.htm). The diversity measures, i.e. the number of alleles,
allelic richness, mean diversities and FIS values, were calculated with FSTAT version 2.9.3.2. (Feb. 2002)
(Goudet 1995, Goudet 2001) (http://www2.unil.ch/popgen/softwares/fstat.htm). Analysis of the
differences between samples was based on allele frequency differences, and was tested with FSTAT, which
includes Bonferroni correction for multiple tests. Genetic diversity and allelic richness were compared
between the stock groups with the two-sided randomization test of FSTAT.
Genetic distances between samples were calculated using Nei’s DA distances (Nei et al. 1983).
Phylogenetic trees were constructed using a neighbour-joining (NJ) algorithm (Saitou and Nei 1987,
Takezaki 1998) with Populations 1.2.32 sofware (http://bioinformatics.org/~tryphon/populations/).
Bootstrapping with 1 000 replicates was used to test the statistical strength of the branches. The trees were
drawn with TreeView version 1.6.1 (Page 2000) (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html).
The effective population size (Ne), and the number of fullsib families were calculated with COLONY
software (version 2, May 2008) (Wang 2004, Wang and Santure 2009). The average pairwise relatedness
was calculated with COANCESTRY software (version 1.0, December 1, 2008) (Wang 2007).
2.3. Brown trout samples
In all, 39 watersheds and 3430 individuals were analysed in the current work (Figure 1, Table 2). The
samples included both anadromous and resident populations of each watershed to more closely examine
the substructure within each river system and to invesitigate the potential isolation level between resident
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
11
and anadromous parts of the populations. In some cases, isolation had been artificially created by dams,
but in other cases it had occurred naturally and was a cause of differentiating evolution.
Most of the river systems (21) were on the Finnish coast. Six of the rivers crossed the border with
Russia, such that the upper reaches of the rivers were located in Finland and the lower parts in Russia.
Seven rivers were relatively native rivers on the Russian side. In addition, five hatchery stocks were
analysed. These have either been used or are suspected to have been used in hatchery releases in the area,
and might thus have caused gene flow into the local stocks (Table 2). The Russian samples were collected in
the Interreg projects ISKALT and ISKALT II (Saulamo et al. 2007), as well as some previous Finnish samples,
and this part of the data was updated here for 16 DNA microsatellite loci, from the previous 10 loci data
sets. The Finnish population samples were obtained from rivers discharging into either the nearby
Archipelago Sea or into the Gulf of Finland.
The sampled river basins in Finland are located in the Varsinais-Suomi, Uusimaa, Kymenlaakso or Etelä-
Karjala, which represent three Centres for Economic Development, Transport and the Environment (ELY
Centres): 1. ELY Centre for Southwest Finland (Varsinais-Suomi), 2. ELY Centre for Uusimaa (Uusimaa) and
3) ELY Centre for Southeast Finland (Kymenlaakso and Etelä-Karjala). Some extensive river systems were
located in two ELY Centre areas.
The rivers are listed and numbered from west to east along the coast (Table 2). The data also include
current information on migratory behaviour, and the populations have been classified as either
anadromous or resident. In addition, the preliminary information has been used to classify the populations
according to their level of originality as original (native), mixed by stockings or introduced, depending on
their stocking history. The most interesting and valuable populations from the management point of view
are those that are genetically diverse, anadromous and original. The size of the river systems varies
considerably, and thus they were all initially treated separately to support river system-based management
and to allow substructure analysis within each river system. Samples were then pooled according to the
differentiation level within the river systems. For part of the analysis, only anadromous populations were
included.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
12
Figure 1. The sampled brown trout rivers in Finland and Russia. The colour of the river indicates its quality as a
spawning site and potential environment for brown trout. Red: river is closed; blue: irregular reproduction occurs; and
green: open river with regular natural production of brown trout populations. The following names and numbering of
the rivers is the same as in Table 2: 1) Aurajoki, 2) Paimionjoki, 3) Purilanjoki, 4) Halikonjoki, 5) Uskelanjoki, 6)
Punassuon Lohioja, 7) Kiskonjoki, 8) Fiskarsinjoki, 9) Karjaanjoki, 10) Ingarskilanjoki, 11) Siuntionjoki, 12) Mankinjoki,
13) Espoonjoki, 14) Vantaanjoki, 15) Sipoonjoki, 16) Mustijoki, 17) Porvoonjoki, 18) Koskenkylänjoki, 19) Kymijoki, 20)
Summanjoki, 21) Virojoki, 22) Urpalanjoki, 23) Santajoki, 24) Vilajoki, 25) Rakkolanjoki, 26) Mustajoki, 27) Kilpeenjoki,
28) Notkopuro, 29) Inojoki, 30) Pikkuvammeljoki, 31) Vammeljoki, 32) Kuokkalanpuro, 33) Rajajoki (Siestarjoki) and 34)
Luga.
2
1
5
4
7
8
9
10 11 1213
21
Helsinki
Tallin
St. Petersburg
Gulf of Finland
0 15 30 60 90 120
km
FINLAND
ESTONIA RUSSIA
Bay of Vyborg
Karelian
Isthmus
Vyborg
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
13
Table 2. Analyzed brown trout samples from Finland and Russia. The brown trout juvenile samples,
sampled river, tributary or area, country of origin, origin of samples and number of samples used for
microsatellite analysis are presented. The migration behaviour, either anadromous or resident
(freshwater), and the known stocking history are also indicated.
No
River
Country
Tributary
Year
N
Migr.
Originality
ELY Centre for Southwest Finland
1
Aurajoki
FIN
2006
37
Anad.
Introduced
2
Paimionjoki
FIN
Vähäjoki, Karhunoja
2004,
2008
22
Anad.
Original
3
Purilanjoki
FIN
2011
15
Anad.
Original
4
Halikonjoki
FIN
Main stream, Kuusjoki, Somer-oja
2008
30
Anad./Resid.
Original
5
Uskelanjoki
FIN
Pitkäkoski, Kaukolankoski,
Haukkalankoski
2007
19
Anad.
Original,
Introduced
Uskelanjoki
Hitolanjoki, Myllykoski
2007
15
Anad.
Original,
Introduced
Uskelanjoki
Hitolanjoki, Satakoski
2007
16
Resid.
Original,
Introduced
Uskelanjoki
Terttilänjoki
2007
7
Anad.
Original,
Introduced
6
Punassuon Lohioja
FIN
2011
16
Resid.
Original
7
Kiskonjoki
FIN
Latokartanonkoski
2010
29
Anad.
Mixed
Kiskonjoki
Myllyjoki
2010
15
Resid.
Mixed
Kiskonjoki
Aneriojoki, Varesjoki-Huhdanoja,
Koorlan Lohioja
2010
42
Resid.
Original
Kiskonjoki-
Perniönjoki
Juottimenoja-Piilioja, Pakapyölin
Lohioja
2008
50
Anad.
Original
Kiskonjoki-
Perniönjoki
Kylmässuonoja-Metsänoja
2008
25
Resid.
Original
Table 2 continues on the next page.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
14
Table 2. Continued.
Table 2 continues on the next page.
No
River
Country
Tributary
Year
N
Migr.
Originality
ELY Centre for Uusimaa
8
Fiskarsinjoki
FIN
Main branch
2010
50
Anad.
Introduced
Risslaån
2010
20
Resid.
Introduced
9
Karjaanjoki
FIN
Mustionjoki;
Mossabäcken
2001
23
(Anad.)
Original
Karjaanjoki
Nummenjoki,
Pitkiönjoki; Myllykoski,
Santsillanoja,
Pajasillanoja, Kivanoja
2001
59
Resid.
Original,
Mixed
Karjaanjoki
Nummenjoki,
Pusulanjoki, Räpsänjoki
2003
26
Resid.
Original,
Mixed
Karjaanjoki
Nuijajoki; Käyräkoski,
Jyrkänkoski,
Porraskoski,
Korkeakoski
2003
63
Resid.
Mixed,
Introduced
Karjaanjoki
Karjaanjoki, Saavajoki
2003
57
Resid.
Mixed,
Introduced
Karjaanjoki
Vihtijoki
2004
58
Resid.
Original,
Mixed
Karjaanjoki
Vihtijoki, Hiiskula
2006
50
Resid.
Original,
Mixed
Karjaanjoki
Vihtijoki,
Tammerkoskenoja
2009, 2010
55
Resid.
Original,
Mixed
10
Ingarskilanjoki
FIN
Main
stream,Pärthyvelbäcken
, Krämars
2005
192
Anad.
Original
11
Siuntionjoki
FIN
Kirkkojoki, Lempansån
2010
54
Anad.
Resid.
Original
Siuntionjoki
Passilankoski
2010
16
Anad.
Original
12
Mankinjoki
FIN
Espoonkartanonkoski
2008, 2010
24
Anad.
Original
Mankinjoki
Gumbölenjoki;
Mynttilänkoski
2005, 2010,
2011
70
Anad.
Original
Mankinjoki
Gumbölenjoki;
Myllykoski,
Karhusuonpuro (2 ind.)
2008
39
Anad.
Original
Espoonjoki
FIN
Glomsinjoki,
Espoontienkoski, Kehä
III, Myllykoski
2008, 2010
66
Anad.
Original
Espoonjoki
Ryssänniitunoja
2008
21
Resid.
Original
Espoonjoki
Glimsinjoki, Espoonjoki
main stream (3 ind.)
2008
9
Anad.
Original
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
15
No
River
Country
Tributary
Year
N
Migr.
Originality
14
Vantaanjoki, lower reaches
FIN
Vantaankoski,
Pitkäkoski, Ruutinkoski
2010
62
Anad.
Mixed,
Introduced
Vantaanjoki, middle reaches
Nukarinkoski
2010
88
Anad.
Mixed,
Introduced
Vantaanjoki, upper reaches
Toromäenkoski,
Käräjäkoski
2010
101
Resid.
(Anad.)
Original
Vantaanjoki, tributary 1
Longinoja
2010
57
Anad.
Introduced
Vantaanjoki, tributary 2
Palojoki/Rannikonmäki
2010
53
Anad.
Introduced
Vantaanjoki, tributary 2
Palojoki, Juvankoski
2011
54
Anad.
Introduced
Vantaanjoki, tributary 3
Lepsämänjoki/
Myllypuro
2011
55
Resid.
Original,
Introduced
Vantaanjoki, tributary 4
Luhtajoki, Matkunoja
2011
14
Resid.
Original
Vantaanjoki, tributary 5
Epranoja
2001
38
Resid.
Original
15
Sipoonjoki
FIN
Ritobäcken, Byabäcken
2010
46
Anad.
Original
16
Mustijoki
FIN
Kalkinoja
2011
31
(Anad.)
Resid.
Original
17
Porvoonjoki
FIN
Vähäjoki, Ylösjoki
2010
51
Resid.
Original
18
Koskenkylänjoki
FIN
Hammarfors, Kvarnfors,
Käkikoski, Sahakoski,
Seppäläishuopinkoski
2010
31
Anad.
Introduced
ELY Centre for Southeast Finland
19
Kymijoki
FIN
Kyminkartanonkoski,
Kokonkoski, Pykinkoski,
Koivukoski, Kotokoski,
Martinkoski
2006, 2010
26
Anad.
Mixed
20
Summanjoki
FIN
Mainstream
2008
22
Anad.
Introduced
Summanjoki
Kelkanjoki
2010
73
Resid.
Introduced
Summanjoki
Sippolanjoki
2004
50
Resid.
Introduced
21
Virojoki
FIN
Saarasjärvenoja
2004, 2005,
2008
80
Anad.
Resid.
Original
Virojoki
FIN
Virojärvi, upper reaches
2008
61
Resid.
Introduced
Border rivers
22
Urpalanjoki
FIN/RUS
2006, 2010
40
Anad.
Original
23
Santajoki
FIN/RUS
2006
19
Anad.
Original
24
Vilajoki
FIN/RUS
Käpylänkoski,
Pappilankoski
2006, 2010
63
Resid.
Introduced,
Mixed
25
Rakkolanjoki
FIN/RUS
2006
13
Anad.
Original
26
Mustajoki
FIN/RUS
2006, 2007,
2008
336
Anad.
Original
Mustajoki Kananoja
FIN/RUS
2006
50
Anad.
Original
27
Kilpeenjoki
FIN/RUS
2006
11
Anad.
Original
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
16
No
River
Country
Tributary
Year
N
Migr.
Originality
Russian rivers
28
Notkopuro
RUS
2006
51
Anad.
Original
29
Inojoki
RUS
2006
25
Anad.
Original
30
Pikkuvammeljoki
RUS
2006
50
Anad.
Original
31
Vammeljoki
RUS
2006
39
Anad.
Original
32
Kuokkalanpuro
RUS
2006
23
Anad.
Original
33
Rajajoki
RUS
2006
21
Anad.
Original
34
Luga
RUS
2006
64
Anad.
Original
Hatchery stocks
1
Lapväärtin-Isojoki
FIN
Laukaa hatchery
20062008
98
Anad.
Hatchery
2
Rautalamminreitti
FIN
Laukaa hatchery
2006
98
Resid.
Hatchery
3
Luutajoki
FIN
Laukaa hatchery
2004
40
Resid.
Hatchery
4
Gotland
SWE
Själsöån,
Lummelundaån, Åland
hatchery
20042005
60
Anad.
Hatchery
5
Denmark
DAN
Kolding hatchery
2011
46
Anad.
Hatchery
Total
3430
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
17
3. Results
3.1. Genetic diversity within populations
The number of actually observed alleles in the brown trout samples varied considerably from 27 in
Purilanjoki to 182 in the Danish hatchery population (Table 3). As the number of observed alleles depends
on the sample size, which varied greatly from 11 for Kilpeenjoki to 336 for Mustajoki, the sample-size-
standardized allelic richness was used to create comparable numbers for allelic diversity. When all
populations were included, allele richness was standardized for 11 individuals, and it then varied from 1.67
to 7.43. For larger samples, a measure for 30 individuals was calculated to increase the range of variation
(2.6210.30). The maximum value of allele richness was recorded for the Danish population from the
Kolding hatchery (7.43 for 11 individuals and 10.30 for 30 individuals). It has been suspected that this type
of trout was released into Finnish rivers in the 1960s, and because of this it has been included as a
reference sample.
The highest allele richnesses in Finnish populations (over 6.0 alleles for 11 individuals) were measured
in mixed populations, such as Fiskarsinjoki, the middle and upper reaches of the River Vantaanjoki and the
upper reaches of Summanjoki. Into the next category (over 5.0 alleles for 11 individuals) belonged
populations from the rivers Aurajoki, Kiskonjoki-Latokartanonkoski, Kiskonjoki-Perniönjoki, Karjaanjoki-
Nummenjoki branch, Mankinjoki, the lower reaches of Vantaanjoki, Kymijoki, and the main branch of
Summanjoki in Finland. Four out of seven native Russian populations belonged to this relatively high
diversity class: Notkopuro, Inojoki, Vammeljoki and Kuokkalanpuro. The hatchery reference samples from
the Isojoki and Rautalamminreitti populations, as well as the Swedish population from Gotland additionally
belonged to this category.
The lowest allelic richness values were measured for two populations in the rivers of Varsinais-Suomi:
Purilanjoki (1.67, minimum) and Punasuon Lohioja. Low values were also observed for populations in the
rivers Mustijoki and Virojoki-Saarasjärvenoja. These all are small populations that only occur at restricted
sites.
The mean diversity (heterozygosity) within populations varied from 0.22 to 0.72, with a mean of 0.62.
This is also a very marked range, being more than three times greater for the most diverse populations than
for the least diverse ones. The diversity levels correlated well with the allelic richness estimates and were
highest for the same populations. Further pooling of samples from the same river systems would probably
increase the values for some cases. The presented pooling of samples was based on information migration
obstacles and on river system analysis described below.
When the diversity levels for the population groups classified as anadromous or resident were
compared, no differences in their diversity levels could be seen. The hatchery stocks were excluded from
this analysis. The mean diversity for both groups was 0.61, and the allelic richness estimates were 4.6 (for
11 individuals) and 6.0 (for 30 individuals) for the anadromous and 4.5 (for 11 individuals) and 5.9 (for 30
individuals) for the resident group.
When the five geographical river groups were compared, there was a tendency of increasing genetic
diversity towards the east. However, the only statistically significant differences were between group 1 (ELY
Centre for Southwest Finland, Varsinais-Suomi) and the two other groups. Group 1 had on average a lower
genetic diversity (0.56) than group 2 (0.65, ELY Centre for Uusimaa, P-value 0.0003), and group 5 (0.65,
Russian rivers, P-value 0.02). Group 1 mainly consisted of small native populations, most of which were also
geographically isolated.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
18
In general, the sampled populations were not always in Hardy-Weinberg equilibrium for known
reasons, which was seen as FIS deviations (Table 3). Population borders in the water systems were not
known, and fish from different breeding populations might therefore have been pooled in sampling,
presumably causing a deficiency of heterozygosity. Stocking and mixing of populations in the wild
temporarily causes an excess of heterozygosity and thus an excess of heterozygotes when compared to the
equilibrium situation. Therefore, in the testing of population differentiation, a Hardy-Weinberg equilibrium
was not assumed, but the test was conducted by randomizing genotype distributions. Interestingly, there
were fewer deviations from the H-W equilibrium in the native Russian populations.
Table 3. Diversity within sampled Finnish and Russian brown trout populations. The number in front of the
river name denotes the watershed number. The mean number of individuals analysed over 16 DNA
microsatellite loci, number of observed alleles (N), allelic richness for 11 and 30 individuals, mean diversity
(DIV), FIS, and its significance are presented.
Population
Mean
N/
locus
N all
All Rich
for 11 ind.
All Rich
for 30 ind.
Mean
DIV
FIS
1AurajokiA
36.8
121
5.9
7.3
0.68
0.025
2Paimionjo
18.8
79
4.3
-
0.59
-0.097**
3Purilanjo
14.9
27
1.7
-
0.22
-0.166*
4Halikonjo
29.8
88
4.6
-
0.63
0.028
5Uskelanjo
55.6
109
4.3
5.8
0.50
0.068***
6Punassuon
16.0
39
2.4
-
0.39
0.001
7KiskoLato
28.8
98
5.0
-
0.65
0.019
7KiskoMyll
14.8
67
4.0
-
0.61
0.023
7KiskoKooR
38.1
65
3.4
4.0
0.51
0.138***
7KiskoPern
49.4
99
4.3
5.6
0.56
0.132***
7KiskPerMe
24.6
106
5.7
-
0.71
-0.001
Mean Southwest
29.8
81.6
4.1
5.7
0.55
8FiskarsAI
66.6
139
6.0
7.7
0.70
0.040**
9KarjaMust
23.0
53
3.0
-
0.52
-0.159***
9KarNumRO
84.7
131
5.6
7.1
0.69
0.068***
9KarNuiRM
63.0
114
4.9
6.2
0.64
0.032*
9KarjaSaav
56.7
108
4.9
6.1
0.61
0.090***
9KarjaViht
157.3
98
4.3
5.1
0.61
0.099***
10Ingarski
186.4
97
4.5
5.2
0.64
0.043***
11SiuntKir
53.6
82
4.2
4.8
0.66
-0.041*
11SiuntPas
14.9
79
4.7
-
0.68
0.068*
12Mankinjo
129.9
121
5.2
6.4
0.69
0.018
13Espoonjo
72.0
95
4.8
5.6
0.64
-0.009*
12EspooRys
24.0
57
3.1
-
0.48
-0.001
14LoVantaa
117.8
156
5.9
7.7
0.71
0.061***
14MiVantaa
87.5
144
6.0
7.6
0.72
0.019
14UpVantaa
207.0
147
6.3
7.9
0.73
0.145***
14PaVantaa
106.8
97
4.5
5.4
0.63
0.034*
15SipooAO
45.9
59
3.0
3.5
0.55
-0.274***
16Mustijok
31.0
42
2.4
2.6
0.39
-0.303***
17Porvoonj
51.0
93
4.4
5.4
0.64
-0.033
18Koskenky
30.9
80
4.2
5.0
0.62
-0.005
Mean Uusimaa
80.5
99.6
4.6
5.8
0.63
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
19
Table3. Continued.
Population
Mean N/
locus
N all
All Rich for
11 ind.
All Rich for
30 ind.
Mean
DIV
FIS
19Kymijoki
25.9
121
5.9
-
0.70
0.038
20SummaMai
43.0
110
5.3
6.6
0.68
0.056***
20SummUppb
99.0
147
6.1
7.8
0.72
0.051***
21Virojoki
80.0
62
2.9
3.4
0.48
-0.046*
21ViroUppR
61.0
81
4.3
4.9
0.63
-0.071***
Mean Southeast
61.8
104.2
4.9
5.7
0.64
22UrpalaFI
39.8
134
6.2
7.9
0.73
0.001
23Santajok
19.0
76
4.4
-
0.62
-0.063*
24Vilajoki
62.6
93
4.3
5.3
0.64
-0.028
25Rakkolan
13.0
54
3.3
-
0.52
-0.107*
26Mustajoki
375.9
127
4.7
5.7
0.63
0.009
27Kilpeenjoki
11.0
58
3.6
-
0.50
-0.265***
Mean Border rivers
86.9
90.3
4.4
6.3
0.61
28Notkopuro
50.5
121
5.6
7.0
0.67
0.016
29InojokiR
24.9
109
5.7
-
0.68
-0.018
30Pikkuvam
49.2
109
4.9
6.3
0.60
0.038*
31Vammeljo
38.9
116
5.4
6.9
0.66
0.000
32Kuokkala
22.8
106
5.5
-
0.67
0.036
33Rajajoki
20.2
82
4.5
-
0.64
0.072*
34LugaRUSA
58.8
112
4.9
6.2
0.65
0.051**
Mean Russia
37.9
107.9
5.2
6.6
0.65
ISOJOKIANA
97.9
143
5.8
7.6
0.68
0.061***
LUUTAJOKIR
40.0
81
4.1
4.9
0.58
0.017
DENMARK
46.0
182
7.4
10.3
0.77
0.019
RAUTALAMMI
97.9
157
5.5
7.4
0.64
0.023*
GOTLANDSWE
59.9
128
5.6
7.1
0.70
-0.027
All over
62.5
100.0
4.7
6.2
0.62
Min
11.0
27
1.7
2.6
0.22
Max
375.9
182
7.4
10.3
0.77
3.2. Effective population size and the relatedness within populations
The genetically effective population sizes of the populations understandably varied because of the varying
sample sizes, but were rarely over 50, which is the recommended minimum size for individual populations
in hatchery breeding. Effective sizes over 50 were only observed for populations of the rivers Vantaanjoki
(lower section), Kymijoki, Summanjoki (upper section), Mustajoki and Russian Notkopuro (Table 4).
The sample size independent Ne/N ratio was used as an indirect measure of the relatedness within
populations. It is commonly known to be usually less than one in wild populations, often being roughly
about half of the actual size, and it can be increased with organized mating or mixing of populations. It can
be maximally two, when the effective size is twice the true size. Low Ne/N values of less than 0.4 indicated
high relatedness in populations of the rivers Purilanjoki, Karjaanjoki-Mustijoki, Karjaanjoki-Vihtijoki,
Ingarskilanjoki, Mankinjoki, Espoonjoki, Upper Vantaanjoki, Vantaanjoki-Palojoki, Sipoonjoki, Mustijoki,
Porvoonjoki, Virojoki-Saarasjärvenoja, Vilajoki and Mustajoki.
For the Russian populations, the Ne/N ratio was always above 0.4 and even as high as 1.15 on average.
Among these populations, the Luga River was an exception, as its Ne/N ratio was only 0.41. For ordinary
hatchery stocks the ratio was also close to 1 as result of organized mating, except for the trout population
from Gotland, for which the founder number has probably been small.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
20
The estimated number of full-sib families in the samples can also be used to assess the width of the
genetic background in the population. In cases where sampling has been representative, the number of
families gives an idea of the true situation in the river. The number of families was often less than 20, and
in some cases even less than ten (Purilanjoki, Karjaanjoki-Mustionjoki, Rakkolanjoki and Kilpeenjoki). For
Purilanjoki and Mustionjoki, the Ne/N ratio was also low, so there were hardly more families involved in the
population. For the Russian rivers Rakkolanjoki and Kilpeenjoki, the Ne/N ratio was relatively high so the
small family number was probably explained by the small sample sizes, which were both under 15 fish. The
newly founded Mustajoki broodstock had as many as 258 families, although the Ne/N ratio was only 0.35.
For Finnish rivers, sampling was more likely to be representative for the whole population, whereas for
Russian rivers, sampling was more random and the sampled fish may represent only a fraction of the
spawning stock.
The mean relatedness is 0.5 for full-sibs, 0.25 for half-sibs, 0.125 (1/8) for first cousins and 0.031
(1/128) for second cousins. The relatedness of two populations exceeded that of the first cousin level
(Purilanjoki, Espoonjoki-Ryssänniitunoja). Values over 0.10 were, however, also observed for four other
populations: Karjaanjoki-Mustionjoki, Kiskojoki-Perniönjoki branch, Mustijoki and the Russian Vilajoki.
Almost equally high relatedness was also observed in samples from the rivers Halikonjoki, Virojoki-
Saarasjärvenoja and Kilpeenjoki. For the native Russian populations, the mean relatedness was 0.045, with
the River Luga population having the highest value of 0.062. Excluding the River Luga, the mean was only
0.042, which indicates the level in the wild state for these relatively small rivers.
Table 4. The actual sample size (N) and effective size (Ne) with its 95% confidence interval (95% CI), the
Ne/N ratio and the number of full-sib families in the brown trout samples from Finnish and Russian rivers
draining into the Gulf of Finland and Archipelago Sea.
Population
N sample
Ne
95% CI
Ne/N
N Fam
Mean
Relatedness %
1Aurajoki
37
34
2258
0.92
28
4.1
2Paimionjoki
22
11
627
0.50
12
7.4
3Purilanjoki
15
5
220
0.33
6
16.7
4Halikonjoki
30
14
831
0.47
14
9.8
5Uskelanjoki
57
39
2361
0.68
47
6.3
6Punassuon
16
19
1043
1.19
14
8.7
7KiskoLatok
29
16
835
0.55
16
6.9
7KiskoMylly
15
21
1048
1.40
15
6.2
7KiskoKooR
42
23
1343
0.55
33
8.3
7KiskoPerniö
50
21
1239
0.42
32
12.4
7KiskPerMet
25
15
834
0.60
17
2.2
Mean Southwest
16.0
0.69
21.3
8.1
Table 4 continues.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
21
Population
N sample
Ne
95% CI
Ne/N
N Fam
Mean Relatedness %
8Fiskarsinjoki
68
45
3072
0.66
47
4.3
9KarjaMust
23
6
320
0.26
8
10.5
9KarjaNumRO
85
35
2256
0.41
45
5.8
9KarjaNuiRM
63
44
2970
0.70
45
5.6
9KarjaSaava
57
23
1342
0.40
28
6.6
9KarjaVihtij
163
40
2762
0.25
105
7.6
10Ingarskilan
192
45
3169
0.23
86
5.7
11SiuntioKirk
54
28
1750
0.52
38
7.4
11SiuntioPas
16
15
737
0.94
15
6.3
12Mankinjoki
133
33
2155
0.25
60
5.8
13Espoonjoki
72
12
726
0.17
22
7.4
12EspoonRyssä
24
13
730
0.54
15
14.1
14LowVantaa
119
86
62119
0.72
91
4.4
14MiddleVantaa
88
50
3477
0.57
67
4.3
14UppVantaa
208
33
2255
0.16
89
6.6
14PaloVantaa
107
32
2153
0.30
48
6.8
15Sipoonjoki
46
11
626
0.24
17
6.3
16Mustijoki
31
6
220
0.19
12
10.7
17Porvoonjoki
51
19
1138
0.37
24
7.6
18Koskenkylänjoki
31
28
1651
0.90
26
4.8
Mean
27.1
0.44
44.4
6.9
19Kymijoki
26
52
29107
2.00
23
2.47
20SummajokiMain
43
28
1750
0.65
27
5.06
20SummUppb
99
61
439
0.62
76
4.42
21Virojoki
80
25
1544
0.31
47
9.51
21ViroUppR
61
40
2765
0.66
53
5.97
Mean
41.2
0.85
45.2
5.5
22Urpalanjoki
40
35
2261
0.88
33
4.1
23Santajoki
19
14
734
0.74
13
7.7
24Vilajoki
63
11
628
0.17
23
10.4
25Rakkolanjoki
13
13
640
1.00
9
7.2
26Mustajoki
382
133
107169
0.35
258
5.1
27Kilpeenjoki
11
8
426
0.73
5
8.9
Mean
35.7
0.64
56.8
7.2
28Notkopuro
51
61
4192
1.20
45
3.6
29Inojoki
25
24
1349
0.96
17
4.3
30Pikkuvammeljoki
50
28
1749
0.56
36
5.3
31Vammeljoki
39
48
3080
1.23
33
4.4
32Kuokkalanpuro
23
44
2699
1.91
20
3.2
33Rajajoki
21
37
2176
1.76
18
4.7
34Luga
64
26
1646
0.41
38
6.2
Mean
38.3
1.15
29.6
4.5
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
22
Table 4.Continued.
Population
N sample
Ne
95% CI
Ne/N
N Fam
Mean Relatedness %
ISOJOKI
98
88
63121
0.90
82
3.8
LUUTAJOKI
40
36
2761
0.90
36
5.7
DENMARK
46
88
57136
1.91
46
2.5
RAUTALAMMINR.
98
102
72137
1.04
89
3.5
GOTLAND SWE
60
19
1138
0.32
37
5.3
Mean
66.6
1.01
58.0
4.2
3.3. Genetic differentiation among populations
Genetic differentiation in allele frequencies among the listed populations (Table 5) was always significant
and often highly significant. After strict Bonferroni correction for multiple tests for the genotype
differentiation, a non-significant difference was only recorded for four pairs of stocks:
Aurajoki Fiskarsinjoki (FST 0.01),
Ingarskilanjoki Koskenkylänjoki (FST 0.01),
Vantaanjoki_Palojoki Koskenkylänjoki (FST 0.01) and
Isojoki Kymijoki (FST 0.01)
The difference was only significant at the 5% nominal level for three other stock pairs,
Paimionjoki Siuntionjoki (FST 0.11),
Kymijoki Summanjoki (FST 0.02) and
Inojoki Kuokkalanpuro (FST 0.02).
In addition, differences were not always significant within river systems. These analyses are reported in
regional results. Despite the frequently significant differences between populations, there were several
stock pairs for which the FST value was low, and even below 0.05 (Table 5). Most of these were cases in
which clear genetic effects of hatchery releases could be assumed (Table 5), as known hatchery releases
were carried out in just these rivers. The Aurajoki trout has been released into the River Fiskarsinjoki,
Koskenkylänjoki has been enhanced with Ingarsilanjoki trout, which explains their identity, and
Ingarskilanjoki trout have also been released into Vantaanjoki, and especially into Palojoki. Isojoki trout
have regularly been released into the River Kymijoki, and they have additionally been released into
Summanjoki. The Russian population pair of the rivers Inojoki and Kuokkalanpuro was the only native
brown trout population pair for which no statistically significant difference could be observed. Thus, they
were similar for natural reasons, either because of common historical reasons or more likely as a result of
currently high gene flow levels.
From the released populations, Ingarskilanjoki had very high similarity with Mankinjoki, the lower parts
of Vantaanjoki, the Vantaanjoki Palojoki tributary and Koskenkylänjoki. Ingarskilanjoki trout are known to
have been released into other rivers, in addition to Mankinjoki (Table 5). Between Mankinjoki and
Ingarskilanjoki, the similarity may simply be a result of a common local history. Isojoki trout had a high
degree of similarity with populations from Fiskarsinjoki, Karjaanjoki-Nummenjoki, Espoonjoki, the lower
and middle reaches of Vantaanjoki, Kymijoki and the mainstream population of Summanjoki. The Luutajoki
hatchery stock had only some similarity with the population in the upper reaches of Summanjoki (FST =
0.08). The Danish trout did not have a very strong similarity with any of the Finnish populations, but
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
23
nevertheless some similarity with many of them. Some of these were rivers into which the Danish trout
have certainly not been released, so no final conclusions could be made on the basis of this analysis. Some
more detailed analytical methods, such as the STRUCTURE program (Pritchard and Wen 2004), might offer
some insight into the case, if actual traces could any longer be found so many generations after the
releases. The previous releases of Danish trout currently have no effect on the management plan or
valuation of Finnish trout populations. The Finnish Rautalamminreitti trout did not show very strong
similarities with the natural stocks, either. The closest was the population inhabiting the upper reaches of
Summanjoki (FST = 0.06). This population also appeared similar to the Swedish trout from the island of
Gotland, but this must be a random event. Ingarskilanjoki and Isojoki are known to be the most commonly
released stocks in southern Finland, so the similarities found with these stocks are to be expected.
Working papers of the Finnish Game and Fisheries Institute 25/2013
Genetic structure of Finnish and Russian sea trout populations in the Gulf of Finland area
24
Table 5. Pairwise FST estimates between brown trout samples. FST values from 0.01 to 0.04 are highlighted in red and from 0.05 to 0.08 in yellow.
Pop
1Aurajok
2Paimion
3Purilan
4Halikon
5Uskelan
6Punassu
7KiskoLa
7KiskoMy
7KiskoKo
7KiskoPe
7KiskPer
8Fiskars
9KarjaMu
9KarNumR
9KarNuiR
9KarjaSa
9KarjaVi
10Ingars
11SiuntK
11SiuntP
12Mankin
13Espoon
12EspooR
14LoVant
14MiVant
14UpVant
14PaVant
15SipooA
16Mustij
2Paimion
0.08
3Purilan
0.33
0.31
4Halikon
0.10
0.18
0.40