Minutes - 4th Project Group Meeting - KO197 MINUTES 4th PROJECT GROUP MEETING – 3. - 5. December 2012 Venue: Kevo Subarctic Research Station, Finland Participants: Sergey Prusov, Elena Samoylova – PINRO, Eero Niemelä, Jorma Kuusela - FGFRI, Juha-Pekka Vähä, Mikhail Ozerov, Rogelio Diaz Fernandez, Kristiina Haapanen - UTU-Kevo, Vidar Wennevik – IMR, Bente Christiansen (chair), Tiia Kalske (referent) - FMFI. Absent: Martin Svenning, Morten Falkegård – NINA. 1.- 2. Opening of the meeting and adoption of the agenda Bente Christiansen opened the meeting at c. 18 o’clock, on 3rd of December. Agenda was adopted without any changes. Last meeting minutes have been circulated and agreed upon earlier on e-mail. 3. Project work plan: status and reports on the project actions implemented in 2012 3.1 Sampling: coastal, estuary and rivers – status and numbers Norway – coastal samples Eero Niemelä highlighted the coastal sampling in northern Norway and the status for scale analysis and ecological work implemented by FGFRI. Number of fishermen in 2012: Nordland – 5, Troms – 10 and Finnmark – 38 (total: 53). Better coverage of the outermost coastal line in 2012 than in 2011 – however some challenges with obtaining optimal spatial and temporal sampling for Tanafjord and inner parts of mid Troms County. Old recaptures from marking studies indicates where Tana salmon is caught – seems to correspond with the very, very preliminary assignments shown by Juha-Pekka Vähä from UTU-Kevo. Number of obtained samples in 2012; Finnmark 6699 wild + 560 (=8%) escaped salmon. Troms: 3183 salmon and Nordland: 754 salmon; altogether 11 196 salmon. FGFRI have visited most of the fishermen in Finnmark, controlling and advising in the sampling and also documenting the fishery. FGFRI was also active in fishing and sampling with Bugøynes fishermen in cooperation with researchers from PINRO (one week in June). Figures for the sea age structure and ‘migratory pattern’ for salmon caught in Finnmark were also highlighted. The noted sea lice numbers are an absolute minimum, due to handling of the catch (nets and in the boat). Russia – coastal samples Sergey Prusov highlighted the sampling and numbers in Russia. PINRO staff has obtained samples from adults from following places; Murmansk region – Kola Bay and Big Eina estuary (Barents Sea) and Chapoma tonya, Ponoi estuary, Umba west, Chavangatonya, Koshevskaya tonya and Vazuga estuary (White sea). Archangelsk and NAO region – Pechora estuary and S. Dvina estuary. In total 1385 samples. Ageing is in progress, FGFRI and PINRO will also discuss the possibilities for PINRO staff to work again at Utsjoki research station in spring 2013. Norway – baseline samples Eero Niemelä highlights the rivers and sample numbers collected by FGFRI in 2012. The rivers (sample nr): Sjåbuselva (50), Østre Risfjordelva (17), Storelva Berlevåg (105), Julelva Tanafjord (5), Iversfjordelva Tanafjord (11), Risfjordelva Tanafjord (190), Tømmervikelva Laksefjord (100), Botneelva Altafjord (50) and Sandfjordelva Hamningberg (1) – altogether 529 samples. The samples are sent to analyses at UTU-Kevo. FGFRI also collected baseline for the special study on effects of escaped salmon into juvenile genomes) for Øystein Skaala (IMR) in 2012 – altogether 1944 fish (Neiden; 451, Vestre Jakobselv; 445, Altaelva; 421, Reisaelva; 326 and Målselva; 301). Russia – baseline samples and archival scales Sergey Prusov highlighted the sample numbers in Russia. PINRO has sampled following rivers for baseline; Murmansk region – Klimkovka, Zarubikha (Kildin), Tipunkova, Vaenga, Bolshaya Tyuva (Barents Sea) and Pulonga, Likhodeevka, Babya (White Sea). Komi Republic – Pechora tributaries Shcugor, Podcherem, Verknya Pechora and Unya (Barents Sea). Karelia – Gridina and Keret. Archangelsk – Nyukcha, Pyshnetsa (S. Dvina tribs) and Ema (Soyana trib). In total 1300 samples. In addition archival scales from following rivers; Archangelsk region – Kyma (Mezen trib), Zimnyaya Zolotitsa, Mudyga, Padoma, Emtsa and Vaenga (all three S. Dvina tribs), Megra, Soyana (Kuloy trib) and Zolotitsa. Komi – Shuchugor and Podcherem (Pechora tribs). In total 957 archival scales. 3.2. Ecology: Scales – status and numbers of analysed scales Minutes - 4th Project Group Meeting - KO197 Finnmark adult scales Eero Niemelä highlighted the number of analysed and measured scales. Scales from 2008, 2009 and 2011 are measured for juvenile, smolt and sea face ages. After assignments growth increment data can be merged with river/ region of origin. Scale samples from Finnmark 2012 are now in the process for digital photographing and measurements. Escaped salmon are also easy to recognise in the scale analysis, due to their scale structure. Norway juvenile scales – status Eero Niemelä highlights the number of analysed juvenile scales. All 2011 material is age determined and growth measured in 2012. Material from 2012 age determination and scale growth increments from 2472 fish will be ready in late January 2013. All old materials (2009-2010) baseline scale material are aged and measured. In total 57 rivers from Finnmark and 27 rivers in Troms has been sampled by the FGFRI (see annex 1). The data will be used in a comparison study on growth patterns between the rivers. Altogether 12 039 juvenile salmon has been sampled (7108 for KO197 and 4931 for IMR/ KO197). 3.3. Genetics: Baseline and adult salmon scales – status and analysed samples + assignments Developing the baseline Vidar Wennevik highlights the status for the baseline. So far 147 distinct units in the material (not rivers, see Annex 2 for the river map). Archangelsk samples from earlier – bad quality. PINRO has/ will re-sample parts/ archival scales. Finnmark baseline is complete, Troms and Kola has good coverage. Structure of the baseline shows three divisions; Eastern rivers (shift at Ponoi), Northern rivers (shift at North Troms) and Western rivers. Tana and Varangerfjord bottom (Bergebyelva) also show shifts in structure. In western rivers it is harder to see patterns. Repeat samples also confirm that both labs get the same results – reassuring. IMR will have completed all lab analyses of baseline in the end of January. Further work: last Russian rivers to be added, maybe to include estuary samples from adults S. Dvina and Pechora as proxy for the baseline, to evaluate stability – add more temporal samples. Spin-offs: analyse and assign ocean samples from Barents Sea, use the baseline for assignment of northern fish from Faroe Island and Spitsbergen samples. Rogelio Diaz Fernandez highlights the work done in UTU-Kevo laboratory on the baseline samples delivered to them. Almost 3000 samples analysed so far, 1440 passed in the quality control for DNA –fingerprint (37 river/ populations) – quality control still ongoing. Additional ~500 samples arrived – to be analysed spring 2013. Adult genetics – status for analyses and prognosis Rogelio Diaz Fernandez highlights current status for the analyses of coastal samples 2011 and 2012. Aim for 2011 was 6000 samples, 7300 are analysed (133 % of aim). 6465 good quality DNA-fingerprint (108% of aim), 5% contamination. Aim for 2012-2013 is 6000 samples – 10 660 in total now, of these 2400 salmon are analysed (40% of aimed number). Juha-Pekka Vähä highlights that UTU Kevo has so far analysed c. 10 000 adult scale samples (2008, 2009 and 2011) with the 31 microsatellite marker system. Some c. 1400 of 2008 samples at IMR (those included in the pilot study) should be analysed with the additional markers – UTU-Kevo and IMR will look at the possibilities for this. Vidar Wennevik – the ~2000 Russian coastal samples will be analysed after the baseline samples are finished. Technical study - SNPs and Microsatellites – accepted paper Mikhail Ozerov highlights the technical study, SNPs vs. Microsatellites. Includes 14 pooled populations, 106 individual genotypes, c. 4000 bi-allelic SNPs, sample cost 90€/ sample. The article Cost- effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) will be published in BMC Genomics. Population structure and assignments using DNA pooling approach – new paper Mikhail Ozerov highlights issues on population structure and assignments. The study contains 23 populations, 2880 SNPs – DNA pooling, 31 microsatellites - individual genotyping. Pooled vs. Individual genotyping; there is god correspondence of genetic diversity values obtained from individual genotyping (STRs) and DNA pooling (SNPs). Diversity and FST values are significantly correlated. Considering simulations and % of correct assignments to the reporting groups depends of the dataset – over 95% correct assignments are achieved using 25-50 SNPs for all populations. Conclusions are that 1) pair wise selection methods for informative markers (pair wise FST or Delta) are preferable, 2) 5-10 highly informative SNPs provide high discrimination power among salmon populations at a large geographical scale, i.e. West/East, 3) population-based level: 100-150 highly informative SNPs are needed to achieve 95% of correct assignment within population and 4) Minutes - 4th Project Group Meeting - KO197 Microsatellites assignment power is as good as of randomly selected SNPs. Plan is to submit the paper in the end of January 2013. Simulation study of baseline Mikhail Ozerov highlights the work done on a baseline simulation study; contains 145 populations, 31 microsatellites, simulated fishery genotypes 100 individuals/ population in 9 reporting groups. The reporting groups are based on geography