Genetic diversity of Atlantic salmon (Salmo salar) and European whitefish (Coregonus lavaretus) in the Baltic Sea

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers.

Kymijoen vaelluskalojen nousureittien avaamisen kustannusten ja hyötyjen arviointi

The objective of this thesis is to evaluate different means of increasing natural reproduction of migratory fish, especially salmon, in the river Kymijoki. The original stocks of migratory fish in Kymijoki were lost by the 1950s because of hydropower plants and worsened quality of water in the river. Nowadays the salmon stocks is based on hatchery-reared fish, even though there is significant potential of natural smolt production in the river. The main problem in the natural reproduction is that the migratory fish cannot ascend to the reproduction areas above the Korkeakoski and Koivukoski hydropower plants. In this thesis alternative projects which aim to open these ascencion routes and their costs and benefits are evaluated. The method used in the evaluation is social cost-benefit analysis. The alternative projects evaluated in this thesis consist of projects that aim to change the flow patterns between the eastern branches of Kymijoki and projects that involve building a fish ladder. Also different combinations of these projects are considered. The objective of this thesis is to find the project that is the most profitable to execute; this evaluation can be done in comparing the net present values of the projects. In addition to this, a sensitivity analysis will be made on the parameter values that are most uncertain. We compare the net present values of the projects with the net present values of hatchery-reared smolt releases, so we can evaluate, if the projects or the smolt releases are more socially profitable in the long term. The results of this thesis indicate that especially the projects that involve building a fish ladder next to the Korkeakoski hydropower plant are the most socially profitable. If this fish ladder would be built, the natural reproduction of salmon in the Kymijoki river could become so extensive, that hatchery-reared smolt releases could even be stopped. The results of the sensivity analysis indicate that the net present values of the projects depend especially on the initial smolt survival rate of wild salmon and the functioning of the potential fish ladder in Korkeakoski. Also the changes of other parameter values influence the results of the cost-benefit analysis, but not as significantly. When the net present values of the projects and the smolt releases are compared, the results depend on which period of time is selected to count the average catches of reared salmon. If the average of the last 5 years catches is used in counting the net benefits of smolt releases, all the alternative projects are more profitable than the releases. When the average of the last 10 years is used, only building of the fish ladder in Korkeakoski and all the project combinations are more profitable than the smolt releases.

Bayesian fisheries stock assessment: integrating and updating knowledge

In this thesis the use of the Bayesian approach to statistical inference in fisheries stock assessment is studied. The work was conducted in collaboration of the Finnish Game and Fisheries Research Institute by using the problem of monitoring and prediction of the juvenile salmon population in the River Tornionjoki as an example application. The River Tornionjoki is the largest salmon river flowing into the Baltic Sea. This thesis tackles the issues of model formulation and model checking as well as computational problems related to Bayesian modelling in the context of fisheries stock assessment. Each article of the thesis provides a novel method either for extracting information from data obtained via a particular type of sampling system or for integrating the information about the fish stock from multiple sources in terms of a population dynamics model. Mark-recapture and removal sampling schemes and a random catch sampling method are covered for the estimation of the population size. In addition, a method for estimating the stock composition of a salmon catch based on DNA samples is also presented. For most of the articles, Markov chain Monte Carlo (MCMC) simulation has been used as a tool to approximate the posterior distribution. Problems arising from the sampling method are also briefly discussed and potential solutions for these problems are proposed. Special emphasis in the discussion is given to the philosophical foundation of the Bayesian approach in the context of fisheries stock assessment. It is argued that the role of subjective prior knowledge needed in practically all parts of a Bayesian model should be recognized and consequently fully utilised in the process of model formulation.

Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Kannan, kasvatusympäristön ja ehdollistamisen vaikutus lohenpoikasten pedonvälttämiskäyttäytymiseen

Istutetut kalat selviävät luonnonoloissa usein huomattavasti luonnossa kasvaneita lajikumppaneitaan heikommin. Laitosten kasvatusaltaissa kasvavilla kaloilla ei ole ennen istutusta tarvetta oppia luonnossa välttämättömiä taitoja. Jos istutuskalat ovat sukupolvi sukupolven jälkeen laitoskalojen jälkeläisiä, voi myös kalojen perimä laitostua, kun perimään kertyy luonnossa selviytymisen kannalta haitallisia ja laitosoloissa hyödyllisiä ominaisuuksia. Suomessa hyvä esimerkkilaji istutuskaloista ja niiden ongelmista on lohi (Salmo salar). Yksi istutusten tuloksellisuudelle merkityksellisistä kalojen taidoista on pedonvälttämiskäyttäytyminen eli se, kuinka hyvin kalat välttävät saaliksi jäämistä. Sekä laitosoloissa kasvamisen että perimän laitostumisen on todettu voivan muuttaa kalojen pedonvälttämiskäyttäytymiseen liittyviä käyttäytymispiirteitä. On myös saatu näyttöä perimältään laitostuneiden kalojen luonnonkantaisia kaloja suuremmasta riskistä jäädä petojen saaliiksi. Luonnonkalojen ja laitoskalojen väliset erot sopeutuvuudessa luonnonoloihin ovat poikineet runsaasti tutkimuksia, joissa on selvitetty, miten laitoskalojen pedonvälttämiskäyttäytyminen saataisiin muistuttamaan enemmän luonnonkalojen käyttäytymistä. Tärkeimpiä samankaltaistamiskeinoja ovat laitosten kasvatusaltaiden muuttaminen virikkeellisiksi eli enemmän luonnonoloja vastaaviksi ja laitoskalojen kouluttaminen ennen istutusta. Tutkin kokeissani perimän laitostumisen, virikkeellisen kasvatusympäristön ja klassisen ehdollistamisen vaikutuksia yksivuotiaiden lohenpoikasten pedonvälttämiskäyttäytymiseen. Käytössäni oli Simojoen populaation lohenpoikasia neljästä eri kanta-kasvatusympäristö-käsittelystä: perinteisissä kasvatusaltaissa kasvatettuja luonnonkannan kaloja, virikkeellisissä kasvatusaltaissa kasvatettuja luonnonkannan kaloja, perinteisissä kasvatusaltaissa kasvatettuja laitostuneen kannan kaloja ja virikkeellisissä kasvatusaltaissa kasvatettuja laitostuneen kannan kaloja. Ensimmäisessä kokeessani vertailin eri käsittelyjen kalojen poistumisnopeutta ns. lähtölaatikosta sekä uintikäyttäytymistä kaukalossa, jossa ne eivät olleet aiemmin olleet. Toisessa kokeessa tarkkailin, miten ns. hälyaine vaikutti rohkeuskokeessa olleiden kalojen käyttäytymiseen, kun niitä uitettiin uudestaan samoissa kaukaloissa. Kolmannessa kokeessa ehdollistin molempien laitoskantaisten käsittelyjen kaloja hauen hajulle hälyaineen avulla. Ehdollistamisen jälkeen tarkkailin, kuinka poikaset käyttäytyvät kaukaloissa, joihin johdettiin hauen hajua. Tein myös selviytymiskokeen, jossa vapautin saman ehdollistamiskäsittelyn läpikäyneitä kaloja altaisiin, joissa hauet saivat saalistaa poikasia ja joihin oli kasattu poikasille suojapaikaksi kiviröykkiö. Odotin luonnonkantaisten, virikkeellisesti kasvatettujen ja ehdollistettujen kalojen olevan muita varovaisempia ja hauilta paremmin selviytyviä. Virikkeellinen kasvatus lisäsi monella käyttäytymismuuttujalla mitattuna kalojen varovaisuutta tai arkuutta. Joillain muuttujilla mitattuna virikkeellisyys vaikutti varovaisuutta tai arkuutta lisäten vain luonnonkantaisiin kaloihin Siten myös kalan kannalla oli merkitystä. Yhdessä käyttäytymismuuttujassa kannalla oli lisäksi kasvatusympäristöstä riippumatonkin vaikutus. Hälyaine vaikutti kaloihin lähinnä niiden liikkumista vähentäen. Ehdollistamisen vaikutus kaukalomuuttujiin riippui kasvatusympäristöstä: ehdollistaminen lisäsi virikkeellisissä oloissa kasvatettujen ja vähensi tavallisissa altaissa kasvatettujen uimista. Ehdollistamisella tai kasvatusympäristöllä ei ollut vaikutusta kalojen selviytymiseen haukien saalistukselta. Tulokset herättivät myös mahdollisia uusia tutkimuskysymyksiä. Tulosten perusteella voin sanoa, että kasvatuksessa käytetyt yksinkertaiset ja edulliset virikkeet ja ehdollistamismenetelmät voivat vaikuttaa kalojen käyttäytymiseen muuttamalla sitä varovaisemmaksi ja sopeutuvammaksi eli mahdollisesti joiltain osin luonnonmukaisemmaksi tai luonnossa selviytymistä auttavaksi. Erot virikkeellisen kasvatuksen vaikutuksissa luonnonkantaisiin ja laitoskantaisiin kaloihin voivat kertoa siitä, kuinka tärkeää oli, että kokeissa oli mukana molempien kantojen kaloja. Tulosten soveltamismahdollisuudet ovat lupaavat, koska tämä oli yksi ensimmäisistä koejärjestelyistä, joissa virikkeellistettyjen kasvatusaltaiden kalatiheydet olivat samaa luokkaa kuin kalankasvatuslaitoksissa tavallisesti käytetyt tiheydet.

Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy.

The autosomal recessive kidney disease nephronophthisis (NPHP) constitutes the most frequent genetic cause of terminal renal failure in the first 3 decades of life. Ten causative genes (NPHP1-NPHP9 and NPHP11), whose products localize to the primary cilia-centrosome complex, support the unifying concept that cystic kidney diseases are "ciliopathies". Using genome-wide homozygosity mapping, we report here what we believe to be a new locus (NPHP-like 1 [NPHPL1]) for an NPHP-like nephropathy. In 2 families with an NPHP-like phenotype, we detected homozygous frameshift and splice-site mutations, respectively, in the X-prolyl aminopeptidase 3 (XPNPEP3) gene. In contrast to all known NPHP proteins, XPNPEP3 localizes to mitochondria of renal cells. However, in vivo analyses also revealed a likely cilia-related function; suppression of zebrafish xpnpep3 phenocopied the developmental phenotypes of ciliopathy morphants, and this effect was rescued by human XPNPEP3 that was devoid of a mitochondrial localization signal. Consistent with a role for XPNPEP3 in ciliary function, several ciliary cystogenic proteins were found to be XPNPEP3 substrates, for which resistance to N-terminal proline cleavage resulted in attenuated protein function in vivo in zebrafish. Our data highlight an emerging link between mitochondria and ciliary dysfunction, and suggest that further understanding the enzymatic activity and substrates of XPNPEP3 will illuminate novel cystogenic pathways.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. © 2013 Petersen et al.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. © 2013 Petersen et al.

Stato della salute orale in pazienti istituzionalizzati affetti da patologie neuropsichiatriche

Le patologie di pertinenza odontostomatologica in pazienti adulti istituzionalizzati affetti da disabilità neuropsichiatrica presentano un’alta prevalenza; scopo del presente lavoro è stato la valutazione della prevalenza di carie (DMFT, SIC) e lo stato di igiene orale (OHI-S) in un gruppo di 103 (72 maschi, 31 femmine, età media 51) pazienti degli Istituti del P.O. Corberi e della RSD Beato Papa Giovanni XIII di Limbiate (MB). E’ stato valutata la collaborazione alla visita con la scala di Frankl, si è definito lo stato funzionale del paziente, in base alla Classificazione Internazionale del Funzionamento, della Disabilità e della Salute (ICF) e si è valutata con un questionario la motivazione degli operatori sanitari a stili di salute orale. Lo studio ha evidenziato un DMFT medio pari a 16,14 e SIC pari a 23,8, valori non correlabili con l'età del soggetto. L’OHI-S medio è pari a 3,46, dato che si presenza correlato con il tempo intercorso dall’ultima visita odontoiatrica. Dal confronto con un gruppo di soggetti sani della stessa età risultano significativamente più elevati i valori della componente (M) e (F) del DMFT e di tutte le componenti dell’OHI-S. Il campione è stato diviso in due gruppi a seconda della loro pregressa collaborazione al trattamento odontoiatrico e sono stati confrontati i dati ricavati dalla checklist ICF. Il gruppo collaborante ha mostrato livelli di funzionalità superiori per quanto riguarda le capacità di osservare, parlare e l’assistenza personale. Dalle risposte del personale socio-sanitario ermerge scarsa informazione sulle tecniche di igiene orale domiciliare quotidiana del paziente assistito. I risultati di questo studio confermano l'alta prevalenza di carie e scarsa igiene orale in soggetti istituzionalizzati con disabilità neuropsichiatrica. L'ICF si è dimostrata una utile guida per la valutazione dell�approccio comportamentale più idoneo in fase di trattamento. Infine, si evidenzia l’importanza di una formazione continua degli operatori socio-sanitari.

LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. Humans share many diseases with our canine companions, making dogs an ideal model organism for comparative disease genetics. Using newly developed resources, genome-wide association studies in dog breeds are proving to be exceptionally powerful. Towards this aim, veterinarians and geneticists from 12 European countries are collaborating to collect and analyse the DNA from large cohorts of dogs suffering from a range of carefully defined diseases of relevance to human health. This project, named LUPA, has already delivered considerable results. The consortium has collaborated to develop a new high density single nucleotide polymorphism (SNP) array. Mutations for four monogenic diseases have been identified and the information has been utilised to find mutations in human patients. Several complex diseases have been mapped and fine mapping is underway. These findings should ultimately lead to a better understanding of the molecular mechanisms underlying complex diseases in both humans and their best friend.

LGI2 truncation causes a remitting focal epilepsy in dogs

One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2-10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years), and remits by four months (human eight years), versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy) during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission.

A mutation in the SUV39H2 gene in Labrador Retrievers with hereditary nasal parakeratosis (HNPK) provides insights into the epigenetics of keratinocyte differentiation.

Hereditary nasal parakeratosis (HNPK), an inherited monogenic autosomal recessive skin disorder, leads to crusts and fissures on the nasal planum of Labrador Retrievers. We performed a genome-wide association study (GWAS) using 13 HNPK cases and 23 controls. We obtained a single strong association signal on chromosome 2 (p(raw) = 4.4×10⁻¹⁴). The analysis of shared haplotypes among the 13 cases defined a critical interval of 1.6 Mb with 25 predicted genes. We re-sequenced the genome of one case at 38× coverage and detected 3 non-synonymous variants in the critical interval with respect to the reference genome assembly. We genotyped these variants in larger cohorts of dogs and only one was perfectly associated with the HNPK phenotype in a cohort of more than 500 dogs. This candidate causative variant is a missense variant in the SUV39H2 gene encoding a histone 3 lysine 9 (H3K9) methyltransferase, which mediates chromatin silencing. The variant c.972T>G is predicted to change an evolutionary conserved asparagine into a lysine in the catalytically active domain of the enzyme (p.N324K). We further studied the histopathological alterations in the epidermis in vivo. Our data suggest that the HNPK phenotype is not caused by hyperproliferation, but rather delayed terminal differentiation of keratinocytes. Thus, our data provide evidence that SUV39H2 is involved in the epigenetic regulation of keratinocyte differentiation ensuring proper stratification and tight sealing of the mammalian epidermis.