1,721,216 research outputs found
Marine invasion genetics: from spatio-temporal patterns to evolutionary outcomes
No full textOver the last 15 years studies on invasion genetics have provided important insights to unravel cryptic diversity, track the origin of colonizers and reveal pathways of introductions. Despite all these advances, to date little is known about how evolutionary processes influence the observed genetic patterns in marine biological invasions. Here, firstly we review the literature on invasion genetics that include samples from European seas. These seas constitute a wide array of unique water masses with diverse degrees of connectivity, and have a long history of species introductions. We found that only a small fraction of the recorded introduced species has been genetically analysed. Furthermore, most studies restrict their approach to describe patterns of cryptic diversity and genetic structure, with the underlying mechanisms involved in the invasion process being largely understudied. Secondly, we analyse how genetic, reproductive and anthropogenic traits shape genetic patterns of marine introduced species. We found that most studies reveal similar genetic diversity values in both native and introduced ranges, report evidence of multiple introductions, and show that genetic patterns in the introduced range are not explained by taxonomic group or reproductive strategy. Finally, we discuss the evolutionary implications derived from genetic patterns observed in non-indigenous species. We identify different scenarios that are determined by propagule pressure, phenotypic plasticity and pre-adaptation, and the effects of selection and genetic admixture. We conclude that there is a need for further investigations of evolutionary mechanisms that affect individual fitness and adaptation to rapid environmental change
Evolutionaire en ecologische uitdagingen voor de driedoornige stekelbaars.
No full textOrganismen in de vrije natuur overleven tal van gevaren. Deze studie gaa t dieper in op drie belangrijke evolutionaire en ecologische risicos vo or de driedoornige stekelbaars (Gasterosteus aculeatus L.): zoetwa terkolonisatie, parasieten en migratiebarrières. Stekelbaars vormt een wereldwijd voorbeeld van parallelle evolutie; para llelle evolutie illustreert de rol van natuurlijke selectie als evolutie mechanisme. Ons onderzoek toonde aan dat populaties van het Schelde- en Maasbekken na de Laatste IJstijd onafhankelijk ontstaan zijn uit een mar iene voorouder. Kolonisatie van het zoetwatermilieu gaat gepaard met ste rke divergerende selectie op lichaamsbepantsering (beenplaatjes en steke ls) en op sommige genen die hiermee in verband staan. Dit toont aan dat de wereldwijde parallelle morfologische evolutie van stekelbaarzen stoel t op een uniforme genetische basis. De driedoornige stekelbaars is tevens een belangrijk model voor de evolu tie van immuniteit. We bestudeerden de ecologische en evolutionaire inte ractie tussen stekelbaarzen en ectoparasieten van het genus Gyro dactylus (Monogenea). Hieruit bleek dat samenlevende driedoornige en tiendoornige stekelbaarzen (Pungitius pungitius L.) hun Gy rodactylus-fauna delen. De populatiedynamiek van Gyrodactylus kon verklaard worden door gastheerdensiteit en de mobiliteit va n de parasieten, twee factoren die aan de basis liggen van gastheerspeci ficiteit. We onderzochten ook in welke mate de intieme interactie tussen de driedoornige stekelbaars en Gyrodactylus gasterostei besc houwd kan worden als een voorbeeld van co-evolutie. Enerzijds werd de in fectiedynamiek sterk bepaald door de slagkracht van de gastheer, overeen komstig de belangrijke rol voor transmissie in de ecologie van Gyrodactylus. Dit zou kunnen wijzen op de afwezigheid van co-evol utie. Anderzijds vertoonden parasieten een lagere virulentie ten opzicht e van lokale gastheren, wat net op co-evolutie wijst. De verspreiding van stekelbaarzen langsheen de kustgebieden van het noor delijk halfrond overlapt grotendeels met de meest verstedelijkte gebiede n ter wereld. Stekelbaars is daarom ideaal voor de studie van de impact van antropogene verstoring op de omgeving. Door het modelleren van genet ische diversiteit en genmigratie in een rivierstelsel toonden we aan dat kunstmatige migratiebarrières de natuurlijke genetische structuur van s tekelbaarspopulaties aantasten. Deze barrières vormen op lange termijn e en gevaar voor elke riviervis. Tenslotte is de integratie van een ecologische en ruimtelijke dimensie i n evolutionair onderzoek belangrijk voor een beter begrip van snelle soo rtvorming, gastheer-parasiet interacties, en de impact van menselijke in vloeden op natuurlijke systemen.status: Publishe
Genomische variatie in zeebaars: van SNP ontdekking in ESTs tot genoomscan.
No full textEuropean sea bass (Dicentrarchus labrax) is an economically important marine species in European aquaculture. Althou gh sea bass population structure is well known, aquaculture does not benefit fr om selection programs, sea bass production being nearly completely based on wild-caught fishes reproducing in semi-controlled conditions. More knowl edge on the sea bass genome would help the breeding progress in this species, th e study of natural populations and their evolution as well as the management of fisheries. The generation of large collections of Expr essed Sequence Tags (ESTs) would provide genomic resources for discovering new genes and new markers, identifying intron-exon boundaries and studying genes expression profiles. In this thesis, efforts were concentrated on the di scovery of Single Nucleotide Polymorphisms (SNPs) within ESTs. SNPs are the most abundant source of variation in most eukaryotic and prokaryotic genomes and can have applications both in aquaculture and natural popula tions. Approximately 30,000 ESTs from 14 libraries of five sea bass individuals have been sequenced. This large EST collection was described and compared to a similar set of ESTs generated for gilthead sea bream (S parus aurata), another economically important marine species. The processin g of ESTs led to the generation of 17,716 and 18,198 sea bass and sea bream u nique sequences, of which less than a third were common to both species. Autom atic annotation indicated that more protein coding sequences were generated f or sea bass than for sea bream. This was further confirmed by the prediction of Open Reading Frames (ORFs) and by the GC content of sea bass and sea bream un ique sequences. Gene Ontology (GO) annotation showed that the same categories were represented for both species. Six SNP discovery tools were used on sea bass ESTs and their performance was assessed by validating around 10% of the SNP candidates. This analysis demonstrated that the selection of redundant candidate SNPs (mismatches detected at least twice in the ESTs) was a good mean of improving SNP di scovery performance. The selection of SNP candidates with a minimum allele frequency greater or equal to 0.3 further enhanced SNP discovery performance although reducing the number of SNP candidates. Finally the selection of SNP candidates detect ed by several tools and the exclusion of indels were also good means of reduci ng the number of false positive candidate SNPs. Transition SNP candidates appea red to be less reliable than transversion SNP candidates due to the presence of RNA editing sites in EST collections. High quality of EST assembly and of th e flanking regions of SNP candidates revealed to be essential for an efficient SNP discovery. These conclusions led to the development of a pipeline integrating the six tes ted SNP discovery tools. This efficient and easy to use pipeline allows the detection of SNPs in any EST dataset , the selection of SNP candidates according to redundancy and/or minimum allel e frequency and the comparison of SNP candidates according to SNP discovery tool. It has been used successfully on EST collections of the fishes Dicentra rchus labrax, Sparus aurata, Anguilla anguilla and the waterflea Daphnia magna. The use of the six SNP discovery tools identified 1,072 unique SNP candidates of which a subset was validated. A total of 360 SNPs were discovered in introns and ESTs, proving that resequencing the conti gs predicted to be polymorphic was an efficient way of discovering SNPs. The nucleotide diversity of sea bass was estimated to one SNP every 137 bp and was high er in introns than in ESTs. The Mendelian inheritance was checked on 17 SNPs polymorphic on the Venezia Fbis family used to produce sea bass linkage maps. Four of them did not follow Mendelian inheritance, suggesting the presence of null alleles. Finally, 22 wild sea bass populations were successfully genotyped at 49 SNPs. This set of SNPs sufficed to confirm the established sea bass popu lation structure, namely the differentiation of Atlantic and Mediterranean samp les. Adriatic samples were shown to be genetically distinct from Western and Eastern Mediterranean samples. Selection analyses pointed to a locus that could be under natural selection in the Atlantic Ocean. In conclusion, a bioinformatic approach to discover SNPs was proven to be very valuable. Meanwhile SNP genotyping technologi es have evolved, allowing the validation of SNP candidates on the samples to be investigated.status: Publishe
Evolutionaire consequenties van een katadrome levensstrategie op de genetische structuur van Europese paling (Anguilla anguilla L.).
No full textMariene organismen vertonen over het algemeen een meer homogene populati estructuur en geringere differentiatie t.o.v. zoetwater organismen. Subt iele genetische verschillen in tijd en ruimte worden nochtans waargenome n. De katadrome paling (Anguilla anguilla L.) staat tijdens zijn l ange levenscyclus onder invloed van heel wat externe invloeden, met bela ngrijke gevolgen voor zijn biologische populatiegrootte (sterke daling s inds 1960) en zijn genetische populatiestructuur. Verder is genetische v ariabiliteit cruciaal voor de overleving van organismen; ze bepaalt de m ogelijkheid om in de toekomst te kunnen evolueren en voldoende fitness t e behouden. Mariene soorten bezitten echter een hoge genetische last die bij een daling in populatiegrootte (flessenhals), de populatie des te s terker kan treffen. Deze thesis beschrijft de veelzijdige evolutionaire consequenties van een katadrome levensstrategie op de genetische structu ur van de Europese paling. De resultaten vallen in drie luiken uiteen: Gepubliceerde gegevens gebaseerd op microsatelliet DNA toonden aan dat d e Europese paling een subtiele genetische structuur vertoonde volgens ee n isolatie door afstand model. Maar aangezien vermoed wordt dat er genet ische introgressie gebeurt vanuit de Amerikaanse paling, en dit vooral i n Noord-Europa, werden eerst betrouwbare testen ontwikkeld om de soortst atus van Europese individuen te karakteriseren. De interspecifieke toepa sbaarheid van onze microsatelliet merkers werd getest op verwante paling soorten om de statistische kracht voor soortenonderscheid te testen. Ver volgens werd deze kennis toegepast op Noord-Atlantische palingsoorten do or IJslandse en Europese stalen te toetsen op introgressie door de Ameri kaanse paling. Indicaties voor ongelijke, maar beperkte hybridisatie wer den gevonden. Ze worden in stand gehouden door middel van selectie tegen hybriden en het behoud van migratierichting. In een tweede luik werd de genetische variabiliteit en differentiatie tu ssen verschillende glasaal- en zilveraalpopulaties vergeleken over een u itgestrekte geografische schaal (van IJsland tot Marokko; Spanje tot Tur kije) met temporele replicatie. Vooreerst werd aan de hand van allozymat ische merkers een patroon van isolatie-door-afstand (IDA )gevonden in de Europese volwassen populaties. Na een uitgebreide staalname in tijd en ruimte, kon de stabiliteit van dit patroon niet aangetoond worden, waarb ij het grootste deel van de genetische differentiatie tussen populaties te wijten was aan temporele verschillen. Door het bemonsteren van glasaa l cohortes over een driejarige periode, werd uiteindelijk een sterkere g enetische differentiatie gevonden tussen temporeel gescheiden stalen. In ter-annuële verschillen waren veel hoger dan ruimtelijke verschillen. De populatiegenetische structuur van paling wordt mogelijks bepaald door e en dubbel proces: (1) een patroon van isolatie-door-tijd (IDT) van repro ducerende cohorten op grote schaal en (2) een verschil in reproductief s ucces van volwassenen, waarschijnlijk het gevolg van de heersende oceani sche en klimatologische condities. In een derde luik werd de relatie tussen multi-locus heterozygositeit (M LH) en fitness componenten nagegaan. Indien er een verband bestaat tusse n genetische variabiliteit en fitness kenmerken, is het nog belangrijker om de populatiegrootte van paling te bewaren. De sterke achteruitgang v an de palingpopulatie zou hierdoor nog kunnen versneld worden, met uitst erven tot gevolg. In door zware metalen vervuilde palingen werd een duid elijke negatieve correlatie gevonden tussen MLH en bioaccumulatie. Bij p alingen uit een vetmesterij werd een positieve correlatie gevonden tusse n MLH en groeiratio. In beide studies werd dit effect hoofdzakelijk op m etabolische enzymen waargenomen, die instaan voor de energiecyclus, waar bij polymorfisme op functionele merkers van cruciaal belang blijkt te zi jn. Samenvattend kunnen we stellen dat 1) genetische introgressie voorkomt v anuit de Amerikaanse paling in Europa (vooral in IJsland); 2) het ruimte lijke patroon van genetische differentiatie veel lager is dan temporele variatie tussen jaren en levensstadia, en reproducerende cohorten een is olatie-door-tijd patroon volgen en dat 3) het individuele genetisch patr oon van paling van belang is voor overleving in situaties van stress of competitie. De gevolgen van dit onderzoek situeren zich op het vlak van de visserij en de aquacultuur. De visserij op jonge glasaal en zilverpal ing moet teruggeschroefd, rivieren moeten vrije toegang bieden tot trekk ende paling en de vervuiling van rivierslib moet dringend krachtdadiger aangepakt worden. Transfers van jonge paling tussen rivierbekkens en zel fs continenten zijn uit den boze. Ondanks zijn bijnaam als rivierpaling , is de Europese paling een mariene soort die op globale Europese schaa l beheerd dient te worden en niet lokaal zoals nu het geval is. De palin g aquacultuur zelf moet efficiënter jonge glasaal opkweken en liefst op termijn overgaan tot kweek van paling in plaats van jonge dieren af te v angen. Enkel dan is het voortbestaan van paling mogelijk. In de toekomst , zou meer aandacht besteedt moeten worden aan oceanische factoren die d e populatiestructuur van Anguillidae kunnen beïnvloeden en aan de analys e van volwassen dieren met gekende leeftijd, om de stabiliteit van het I DT patroon na te gaan.status: Publishe
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Seascape genetics in support of sustainable fisheries management of flatfish
Full text linkIn 1883, Thomas Huxley put forward that all the great sea fisheries are inexhaustible. This illustrates the classical notion that marine environments tend to be demographically open without any chance of complete extinction. Such belief was based on the wide distribution of many marine species with extensive larval and adult dispersal, and large population sizes, even after heavy exploitation. However, the classical view of inexhaustible fisheries has proven incorrect after major declines in many world fisheries the last decades, prompting for a better understanding of fishery stock demography and connectivity using multidisciplinary approaches. Fisheries research has gained from the integration of genetic studies showing the various mechanisms explaining the evolution of population structure in the ocean. The resilience of fish populations and the maintenance of genetic diversity has important implications for the viability and stability of entire ecosystems under heavy exploitation.In this thesis, I aim at integrating novel knowledge on the genetic composition of flatfish stocks with fisheries management tools. Therefore, the genetic structure was investigated of the flatfish turbot and brill, in the Northeast Atlantic Ocean. A combination of conventional population genetic analyses and multivariate statistics was used to assess how environmental factors influence the genetic variation at various spatio-temporal scales. The focus was on several flatfish species with a synchronic sampling design. The seascape genetic approach made it possible to identify the interaction between oceanography and species-specific traits, and their effect on the true dispersal of the species. In the case of turbot, the combination of anonymous and gene-based nuclear markers proved useful for elucidating potential population units as each shows a different level of differentiation. This approach is highly valuable from a conservation perspective, as it allows one to infer the effect of community-wide fragmentation. Common geographic patterns were identified in the genetic structure. However, differences in sensitivity to gene flow barriers were reported. This discrepancy was driven by species-specific traits, particularly reproductive behavior. Within the Northeast Atlantic Ocean, I could distinguish two large groups: one comprising the Skagerrak-Kattegat area and a second along the Irish shelf. For turbot, another population might even be present in the Baltic Sea. Seascape genetic analyses based on putatively selective markers suggest an additional gene flow barrier within the North Sea, linked to the Friesian frontal zone. For a species like turbot, with a wider distribution range in the North Sea than flatfish such as sole and brill, the identification of this barrier has an important implication for the delineation of management units. At present, the incorporation of genetic data into statistical fisheries models has been limited. This is mainly because genetic research draws inferences about populations on an evolutionary time scale, while fisheries management is more interested in short-term demographic independence. Fisheries models usually lead management instruments towards short-term gains. But the long-term vision of sustainable fisheries management also needs to take evolutionary consequences into account. Our findings suggest that turbot could serve as a so-called umbrella species, i.e. a vulnerable species whose environmental requirements encapsulate the needs of most other species. It represents a foundation for appropriately managing seascapes in order to preserve diversity. Using turbot for that purpose has two advantages: 1) the impact of environmentally driven connectivity is most straightforward in turbot, and 2) turbot seems most vulnerable to the negative effects of fisheries and can therefore serve as the proverbial canary in the coal mine an indicator of declining environmental quality. This implies that policymakers will have to make trade-offs to serve all marine stakeholders in the best possible way without jeopardising the long-term gains. Scientists can help to address these trade-offs. They can meet the needs of the stakeholders by communicating scientific results on all administrative levels as well as informing policy-makers of these results and the impact they may have on the ecosystem. Scientific research results are normally communicated via peer-reviewed publications and participation in conferences. At the same time, scientists must communicate through their national fisheries institutes, because these institutes play a key role in communicating between politicians, stakeholders and scientists. Such a communication strategy would not only transfer knowledge but will also help to tackle the problems related to a mismatch between the knowledge produced and the knowledge that policymakers actually need. Finally, it has become clear in recent years that unexpected management outcomes stem from human behavior related to uncertainty. The ecosystem is not yet sufficiently understood, and it shall never be completely understood because of its inherent variability and associated uncertainties. To address and reduce uncertainty, managers will have to incorporate information about resource user behavior provided by the social sciences. Such information depends largely on improved interdisciplinary communication among scientists. Often uncertainty in scientific results is reduced via the peer review process for high-level journals, usually restricted to a specific field. By expanding research to involve other disciplines and increasing efforts to improve communication between scientists and other actors, more and better knowledge will be produced and uncertainty will be further reduced. The ICES structure and workflow play a crucial role in creating an atmosphere for trans- and multi-disciplinary research. Working in a transnational context to stimulate interdisciplinary research and communication will encourage rapid and sure progress towards improved sustainability of sea fisheries. <w:latentstyles deflockedstate="false" defunhidewhenused="true" <w:lsdexception="" locked="false" priority="0" semihidden="false" status: Publishe
Medición de distancias genéticas en poblaciones de camarón blanco litopenaeus vannamei en la costa ecuatoriana
Full text linkCon el fin de determinar la estructura poblacional en el camarón blanco, un total de 560 individuos de Litopenaeus vannamei fueron colectados durante dos épocas (agosto 2002 y mayo 2003) en 7 zonas del litoral ecuatoriano. Para determinar diversidad genética, distancia y estructura poblacional entre estos puntos de muestreo, se emplearon 8 locitipo microsatélites. Los resultados revelan un 100% de polimorfismo para todos los loci. El indice de diversidad, expresado como heterocigocidad esperada, fluctuó entre 0,71 y 0,83 con un promedio de He=0,80+-0,02, mientras que la heterocigocidad observada fue Ho=0,50+-0,05. El promedio de alelos por loci fue de 12,2+-0,78. El equilibrio de Hardy-Weinberg se desvio significativamente en todos los loci (p<0,0001), debido a baja heterocigocidad, posiblemente por la presencia de alelos nulos. Se encontró diferenciación genética moderada entre las zonas estudiadas (Fst=0,0576).To determine the population structure of white shrimp, a total of 560 individuals of Litopenaeus vannamei were collected during two seasons (August 2002 and May 2003) in seven coastal areas of Ecuador. Eight microsatellite loci were used to determine genetic diversity, distance, and population structure between these sampling points. The results revealed 100% polymorphism for all loci. The diversity index, expressed as expected heterozygosity, ranged from 0.71 to 0.83, with an average of He = 0.80 +/- 0.02, while the observed heterozygosity was Ho = 0.50 +/- 0.05. The average number of alleles per loci was 12.2 +/- 0.78. Hardy-Weinberg equilibrium deviated significantly at all loci (p<0.0001) due to low heterozygosity, possibly due to the presence of null alleles. Moderate genetic differentiation was found between the studied areas (Fst=0.0576)
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