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Best practices for the provision of prior information for Bayesian stock assessment
No full textThis manual represents a review of the potential sources and methods to be applied when providing prior information to Bayesian stock assessments and marine risk analysis.
The manual is compiled as a product of the EC Framework 7 ECOKNOWS project (www.ecoknows.eu).
The manual begins by introducing the basic concepts of Bayesian inference and the role of prior information in the inference. Bayesian analysis is a mathematical formalization of a sequential learning process in a probabilistic rationale. Prior information (also called ”prior knowledge”, ”prior belief”, or simply a ”prior”) refers to any existing relevant knowledge available before the analysis of the newest observations (data) and the information included in them. Prior information is input to a Bayesian statistical analysis in the form of a probability distribution (a prior distribution) that summarizes beliefs about the parameter concerned in terms of relative support for different values.
Apart from specifying probable parameter values, prior information also defines how the data are related to the phenomenon being studied, i.e. the model structure. Prior information should reflect the different degrees of knowledge about different parameters and the interrelationships among them.
Different sources of prior information are described as well as the particularities important for their successful utilization. The sources of prior information are classified
into four main categories: (i) primary data, (ii) literature, (iii) online databases, and (iv) experts. This categorization is somewhat synthetic, but is useful for structuring the process of deriving a prior and for acknowledging different aspects of it.
A hierarchy is proposed in which sources of prior information are ranked according to their proximity to the primary observations, so that use of raw data is preferred where possible. This hierarchy is reflected in the types of methods that might be suitable – for example, hierarchical analysis and meta-analysis approaches are powerful, but typically require larger numbers of observations than other methods. In establishing an informative prior distribution for a variable or parameter from ancillary raw data, several steps should be followed. These include the choice of the frequency distribution of observations which also determines the shape of prior distribution, the choice of the way in which a dataset is used to construct a prior, and the consideration related to whether one or several datasets are used. Explicitly modelling correlations between parameters in a hierarchical model can allow more effective use of the available information or more knowledge with the same data. Checking the literature is advised as the next approach. Stock assessment would gain much from the inclusion of prior information derived from the literature and from literature compilers such as FishBase
(www.fishbase.org), especially in data-limited situations. The reader is guided through the process of obtaining priors for length–weight, growth, and mortality parameters from FishBase. Expert opinion lends itself to data-limited situations and can be used even in cases where observations are not available. Several expert elicitation tools are introduced for guiding experts through the process of expressing their beliefs and for extracting numerical priors about variables of interest, such as stock–recruitment dynamics, natural mortality, maturation, and the selectivity of fishing gears. Elicitation of parameter values is not the only task where experts play an important role; they also can describe the process to be modelled as a whole.
Information sources and methods are not mutually exclusive, so some combination may be used in deriving a prior distribution. Whichever source(s) and method(s) are chosen, it is important to remember that the same data should not be used twice. If the 2 | ICES Cooperative Research Report No. 328 plan is to use the data in the analysis for which the prior distribution is needed, then the same data cannot be used in formulating the prior.
The techniques studied and proposed in this manual can be further elaborated and fine-tuned. New developments in technology can potentially be explored to find novel ways of forming prior distributions from different sources of information. Future research efforts should also be targeted at the philosophy and practices of model building based on existing prior information. Stock assessments that explicitly account for model uncertainty are still rare, and improving the methodology in this direction is an important avenue for future research. More research is also needed to make Bayesian analysis of non-parametric models more accessible in practice. Since Bayesian stock assessment models (like all other assessment models) are made from existing
knowledge held by human beings, prior distributions for parameters and model structures may play a key role in the processes of collectively building and reviewing those
models with stakeholders. Research on the theory and practice of these processes will
be needed in the future
Poikasistutukset Atlantin lohen suojelukeinona
Get PDFWild salmon stocks in the northern Baltic rivers became endangered in the second half of the 20th century, mainly due to recruitment overfishing. As a result, supplementary stocking was widely practised, and supplementation of the Tornionjoki salmon stock took place over a 25 year period until 2002. The stock has been closely monitored by electrofishing, smolt trapping, mark-recapture studies, catch samples and catch surveys. Background information on hatchery-reared stocked juveniles was also collected for this study. Bayesian statistics was applied to the data as this method offers the possibility of bringing prior information into the analysis and an advanced ability for incorporating uncertainty, and also provides probabilities for a multitude of hypotheses.
Substantial divergences between reared and wild Tornionjoki salmon were identified in both demographic and phenological characteristics. The divergences tended to be larger the longer the duration spent in hatchery and the more favourable the hatchery conditions were for fast growth. Differences in environment likely induced most of the divergences, but selection of brood fish might have resulted in genotypic divergence in maturation age of reared salmon. Survival of stocked 1-year old juveniles to smolt varied from about 10% to about 25%. Stocking on the lower reach of the river seemed to decrease survival, and the negative effect of stocking volume on survival raises the concern of possible similar effects on the extant wild population. Post-smolt survival of wild Tornionjoki smolts was on average two times higher than that of smolts stocked as parr and 2.5 times higher than that of stocked smolts. Smolts of different groups showed synchronous variation and similar long-term survival trends. Both groups of reared salmon were more vulnerable to offshore driftnet and coastal trapnet fishing than wild salmon. Average survival from smolt to spawners of wild salmon was 2.8 times higher than that of salmon stocked as parr and 3.3 times higher than that of salmon stocked as smolts.
Wild salmon and salmon stocked as parr were found to have similar lifetime survival rates, while stocked smolts have a lifetime survival rate over 4 times higher than the two other groups. If eggs are collected from the wild brood fish, stocking parr would therefore not be a sensible option. Stocking smolts instead would create a net benefit in terms of the number of spawners, but this strategy has serious drawbacks and risks associated with the larger phenotypic and demographic divergences from wild salmon.
Supplementation was shown not to be the key factor behind the recovery of the Tornionjoki and other northern Baltic salmon stocks. Instead, a combination of restrictions in the sea fishery and simultaneous occurrence of favourable natural conditions for survival were the main reasons for the revival in the 1990 s.
This study questions the effectiveness of supplementation as a conservation management tool. The benefits of supplementation seem at best limited. Relatively high occurrences of reared fish in catches may generate false optimism concerning the effects of supplementation. Supplementation may lead to genetic risks due to problems in brood fish collection and artificial rearing with relaxed natural selection and domestication. Appropriate management of fisheries is the main alternative to supplementation, without which all other efforts for long-term maintenance of a healthy fish resource fail.Pohjoisen Itämeren luonnonlohikannat liikakalastettiin uhanalaisiksi viime vuosisadan loppupuoliskolla. Lohikantojen suojelemiseksi häviämisriskiltä aloitettiin monilla kutujoilla kalanviljelylaitoksissa kasvatettujen lohenpoikasten istutukset. Väitöstyö arvioi tämän istutustoiminnan tuloksellisuutta. Työ keskittyy Itämeren suurimman lohijoen, Tornionjoen, lohikantaan 1980-luvulta nykyhetkeen. Kantaa tuettiin istutuksilla 25 vuotta vuoteen 2002 saakka. Kannan kehitystä seurattiin koekalastuksilla, merkintätutkimuksilla sekä jokikalastuksen saalisnäytteillä ja saalistilastoinnilla. Istutetut poikaset merkittiin eväleikkauksella, jonka perusteella ne voitiin tunnistaa ja erottaa luonnonkaloista istutuksen jälkeen.
Luontaisesta lisääntymisestä peräisin olevien sekä istutettujen lohien eloonjääntiä, biologisia ominaisuuksia, kannanrunsautta ja kalastusta tutkittiin kalojen eri elämänvaiheissa. Kantaseuranta-aineistoja analysoitiin todennäköisyyspohjaisella ns. Bayesilaisella tilastollisella päättelyllä, jota sovellettiin erityisesti populaatiomalleihin.
Useat istutettujen lohien biologiset ominaisuudet erosivat huomattavasti luonnonlohien ominaisuuksista. Erot kasvoivat sitä suuremmiksi mitä pidempään poikasia kasvatettiin viljelylaitoksessa ja mitä paremmat viljelyolosuhteet olivat kasvulle. Ympäristöolojen erilaisuus (luonto vs. viljelylaitos) oli luultavasti pääsyy eroille, mutta viljelyssä käytettyjen emokalojen valinta saattoi muuttaa geneettisesti lohen sukukypsyysikää. Yksivuotiaista poikasistukkaista säilyi hengissä merivaelluksen alkuun (vaelluspoikaseksi) 10-25 %. Istutus joen alajuoksulle sekä runsaat istutusmäärät heikensivät poikasten selviytymistä. Runsaat istutusmäärät saattavat heikentää myös luonnonpoikasten eloonjääntiä, mikä olisi erittäin haitallista. Merivaelluksen alun eloonjäänti oli luonnonlohilla kaksi kertaa parempi kuin yksivuotiaina jokipoikasina istutetuilla lohilla ja 2,5-kertaa parempi kuin kaksivuotiaina vaelluspoikasina istutetuilla lohilla. Istukkaat joutuivat merikalastuksen saaliiksi helpommin kuin luonnonlohet, mikä kasvatti edelleen eloonjääntieroja kutuvaiheeseen mennessä: luonnonlohien eloonjäänti vaelluspoikasesta kutuloheksi oli 2,8-kertainen yksivuotiaisiin istukkaisiin ja 3,3-kertainen kaksivuotiaisiin istukkaisiin verrattuna. Eloonjäänti mätimunasta kutijaksi oli yksivuotiaana istutetuilla lohilla samaa tasoa, mutta kaksivuotiaina vaelluspoikasina istutetuilla lohilla nelinkertainen suhteessa luonnonlohiin. Kaksivuotiaiksi saakka kasvatetut poikaset poikkeavat kuitenkin biologisilta ominaisuuksiltaan niin paljon, että niiden istuttamiseen luonnonkannan suojelutarkoituksessa liittyy merkittäviä haittoja ja riskejä.
Istutukset eivät merkittävästi vaikuttaneet Tornionjoen ja muiden Pohjanlahden luonnonlohikantojen elpymiseen 1990-luvulla. Sen sijaan voimistunut kalastuksensäätely yhdessä lohen eloonjäännille otollisten ympäristöolosuhteiden esiintymisen kanssa johtivat kantojen elpymiseen.
Väitöstutkimus kyseenalaistaa istutukset luonnonlohikannan suojelukeinona. Istutusten positiiviset vaikutukset kantakehitykseen näyttävät parhaimmillaankin vähäisiltä. Istukkaiden runsas saaliiksi saaminen antaa liian optimistisen kuvan istutusten tuloksellisuudesta. Emokalojen valinta ja keinotekoiset viljelyolosuhteet aiheuttavat geneettisiä riskejä. Toimiva kalastuksensäätely on perusedellytys terveille ja tuottaville kalakannoille ja sen on istutuksia vaarattomampi ja tehokkaampi lohikantojen suojelukeino.ei saavutettav
Tornionjoen lohikannan kasvu on taittunut - Ökningen av Torneälvslaxbeståndet har avstannat
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Early‐season river entry of adult Atlantic salmon: its dependency on environmental factors
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