Contorta (Pinus contorta) är ett barrträdslag som naturligt finns i västra Nordamerika och är inplanterat främst i norra Sverige. Syftet med detta arbete är att utvärdera hur långt och i vilken omfattning contorta spridit sig från äldre bestånd i södra Sverige. Resultatet skulle kunna användas vid bedömning om det finns en spridningsrisk i södra Sverige. De tre bestånden som användes vid detta arbete ligger i södra Östergötland och norra Småland. Datainsamlingen utfördes i tre steg i respektive bestånd: 1. Bedömning om contorta kan spridas och etableras från bestånd i södra Sverige. 2. Inventering av contortaplantor i subjektivt valda ytor. 3. Kvantitativ inventering av contortaplantor i systematiskt utlagda linjer, 2 meter breda och 250 meter långa, i fyra riktningar utgående från beståndskant. I inventeringen av subjektivt utvalda ytor hittades contortaplantor 350 meter från contortabestånd och i den kvantitativa inventeringen 50 meter från contortabestånd. Totalt hittades 27 contortaplantor (motsvarande 450 st/ha) i subjektivt utlagda ytor och 18 contortaplantor (45 st/ha) hittades i den kvantitativa inventeringen. Alla funna contortaplantor hittades på störd mark och där trädkronans täckning var noll, dvs. där ljustillgången var högst. Det är däremot inte möjligt att, utifrån denna studie, säga vilken faktor som är primär för contortaplantornas etablering, markstörning eller ljustillgång. / Contorta (Pinus contorta) is a coniferous tree species from western North America that has been introduced mainly in northern Sweden. The purpose of this work was to evaluate how far and to what extent (number of self-dispersal seedlings/ha) Contorta has spread from older populations in southern Sweden. The result can be used in assessing the risk of spreading in southern Sweden. The three forest stands used for this work were located in southern Östergötland and northern Småland, Sweden. The data collection was done in three stages in each stand: 1. Assessment if contorta can be disseminated and established from stocks in southern Sweden. 2. Subjective inventory of Contorta plants in selected areas. 3. Quantitative inventory of contorta plants along defined corridors, 2 meters wide and 250 meters long, in four directions from the edge of the stock. In the inventory of subjectively selected areas, contorta plants were found 350 meters from a contorta stand and in the objective inventory 50 meters from a contorta stand. A total of 27 contorta plants (equivalent to 450 plants/ha) was found in subjectively inventory and 18 contorta plants (45 plants/ha) were found in the quantitative inventory. All Contorta seedlings were found on disturbed ground and where the canopy cover of trees was zero, i.e. where the access to light was highest. On the other hand, based on this study, it is not possible to say which factor is most important for the establishment, field disturbance or light supply.

La question de la coexistence entre espèces est cruciale dans le contexte des changements globaux, où certaines espèces colonisent de nouveaux écosystèmes, tel le cas des espèces invasives. Dans les habitats discontinus, la coexistence entre espèces invasives et natives gagne à être considérée à la lumière de la théorie des métacommunautés, et en particulier en examinant séparément les processus de dispersion et les interactions locales afin de déterminer leurs effets relatifs. Les approches observationnelles en milieux naturels permettent par ailleurs la prise en compte de la complexité des relations possibles. C’est le travail abordé dans cette thèse à travers l’exemple de l’effet de l’invasion de l’écrevisse de Louisiane sur les amphibiens natifs dans des réseaux de mares. La densité des larves et la distribution des amphibiens ont montré la conccurrence avec l’écrevisse dans les mares. Grâce à la génétique du paysage, la dispersion de l’écrevisse s’est révélée fortement contrainte par le caractère discontinu des habitats, contrairement à celle des amphibiens, bien qu’elle ait été variable parmi les trois espèces étudiées. Les analyses d’isotopes stables ont montré que malgré sa position centrale dans les réseaux trophiques, l’écrevisse n’avait pas de fortes interactions trophiques avec les amphibiens, tout au plus un effet indirect par la modification de l’habitat. Sur la base des mécanismes considérés ici, la coexistence entre les amphibiens natifs et l’écrevisse invasive semble ainsi envisageable. Des suites de ce travail sont envisageables à l’échelle des communautés grâce à l’ADN environnemental. / The question of species coexistence is crucial in the context of global changes, where some species colonize new ecosystems, such as the case of invasive species. In patchy habitats, the coexistence between invasive and native species gains at being considered in the light of the metacommunity theory, and particularly by examining separately the processes of dispersal and local interactions to determine their relative effects. Besides, observational approaches in natural habitats allow to account for the complexity of the possible relationships. It is the work tackled in this thesis through the example of the effect of the red swamp crayfish on native amphibians in pond networks. The density of larvae and the distribution of native amphibians showed the co-occurrence with the crayfish in ponds. Owing to landscape genetics, the dispersal of crayfish was shown to be highly constrained by the patchy nature of habitats, contrary to that of amphibians, although it was variable among the three species considered. The stable isotope analyses showed that, despite its central position in the food webs, the crayfish did not have strong trophic interactions with amphibians, all the more an indirect effect through habitat modification. On the basis of the mechanisms considered here, the coexistence between native amphibians and the invasive crayfish seem possible. Perspectives from this work are envisaged at the community scale using environmental DNA.

Re-creation and building new small freshwater habitats belong among the important management activities within the Protected Landscape Area Kokořínsko - Máchův kraj (Czech Republic) for almost two decades. These pools keep the water within the landscape and serve as the habitats for vulnerable species of amphibians and invertebrates, which I have studied within this thesis. Most studies focusing on studying metacommunities of small water bodies have been based on the data from one or two seasons, and thus completely neglect the development of composition of these metacommunities over longer periods of time. This thesis builds on previous research on the species composition of small ponds in the Kokořínsko Protected Landscape Area, which had been done in 2005 and 2006. In 2009 and 2017, sampling in the same ponds continued. I investigated the influence of spatial and environmental variables of individual ponds on the species composition of ostracods, copepods and molluscs in specific years and how has the representation of individual species changed among those years. With one exception, I have not observed any new incoming species of copepods and ostracods since 2006; the number of species had in fact decreased. In the case of molluscs, there was a significant exchange of species between individual...

The population dynamics of small mammal populations in Punda Maria, Kruger National Park, South Africa was investigated with respect to community size and structure, seed predation and dispersal of several trees. Species populations, community structure and habitat attributes were measured at six sites comprising of 3 habitat types (2 sites per habitat); namely Acaciagrassland, North-facing and South-facing sloped sites. Seasonal variation was investigated at the Acacia sites during late summer (April) and winter months (July). Five habitat attributes were measured; percentages of total cover and herbage, plant litter depth (cm), height of dominant vegetation type measured (m) and edaphic condition were recorded at 15 randomly selected traps per site. Almonds (Prunus dulcis), baobabs (Adansonia digitata), mopane (Colophospermum mopane), and Acacia tortilis seeds were used in the predation and dispersal experiment. North- and South-facing sites were dominated by Aethomys sp. while Acacia sites were dominated by Mastomys natalensis. Seed predation was high at the North-facing slopes, with a significant difference in predation on A. tortilis seeds. Seed dispersal activity was low; no , scatter hoarding was identified; only larder hoarding was observed by Aethomys sp. and M. natalensis at North-facing sites and Acacia sites respectively. Trampling by megaherbivore activity impacted vegetation structure and has negatively affected rodent population and ground activity, particularly at the Acacia sites.

Cotula coronopifolia is a short-lived plant that originates from South Africa and Namibia. It has been present in Europe since the 18th century. This study includes a monitoring inventory of two C. coronopifolia populations on Öland, Sweden, which has taken place continuously four consecutive years (2018-2021). It also includes a climate suitability model projected over Europe.  The monitoring inventory gives a picture of the population’s yearly dynamic in terms of spread, expansion and densities. The population density has decreased during these four years and the expansion speed has shifted from over 370 m/year between 2018 and 2019 to a contraction of -20 m/year thereafter. The decreasing densities seem to be due to lower grazing intensities in the last two years. It is also possible that C. coronopifolia have occupied most of the possible habitat available at these two locations.  The model was made to visualize the potential geographic range of C. coronopifolia based on contemporary climate variables such as temperature and precipitation. Predicted suitable habitat was extensive in the coastal regions of western Europe but surprisingly low in the eastern parts of Europe. The most important variable in the model turned out to be “the annual range between maximum temperature and minimum temperature” and that range is generally smaller in coastal climates. That, together with the fact that most of the occurrence records comes from the western parts of Europe (which may reflect the introduction history of the species rather than the climate and/or a geographic reporting bias), should be considered as alternative explanations for the difference in suitability between eastern and western Europe. However, the model seems to give a plausible picture over the contemporary potential distribution range in Sweden where the reporting effort is generally high. This study shows that C. coronopifolia is a species suitable for modelling. Future, refined models should include dispersal mechanisms, propagule pressure and future climate scenarios to predict plausible population spread.

Aquaculture facilities involve mooring a large amount of artificial structures in offshore areas, which are colonised by a wide group of marine organisms, forming characteristic fouling communities. Many studies have focused on determining what sessile organisms are able to settle on nets, ropes and buoys, owing to the specific problems they cause and their economic cost to the aquaculture industry. Although sessile fouling communities are well-studied from the point of view of controlling this community on aquaculture facilities, little is known about the epifaunal mobile species inhabiting these artificial structures. This thesis addresses the study of crustacean amphipods, which have been scarcely studied regarding their species composition and relation to the habitats created by the sessile species and despite being detected in high abundances. After the general introduction, which sets the study framework, Chapter 1 is a preliminary study on the composition of fouling assemblages on aquaculture facilities in the Mediterranean Sea, comparing them with others such as those in harbours or offshore structures. Therein, it is shown that fouling communities are made up of mainly bivalves, algae, hydroids and bryozoans and amphipods usually represent more than 80 % of motile fauna associated with these organisms. Moreover, amphipod assemblages are characterised by seven frequent and dominant species: Elasmopus rapax, Jassa marmorata, Jassa slatteryi, Ericthonius punctatus, Stenothoe tergestina, Caprella equilibra and Caprella dilatata. A quantitative study of amphipod densities is carried out in Chapter 2, where mean amphipod densities observed in fish farm fouling amounted to 176,000 ind.m-2 and reached maxima up to 1,000,000 ind.m-2. There, the role of the macro- and microhabitat in supporting such amphipod communities is explored. The effect of the modification of marine currents on pelagic communities due to the introduction of coastal infrastructures is analysed in Chapter 3. Therein, it was detected a retention effect on planktonic amphipods near such facilities, noticeable in the increased abundance of hyperiids and migrating amphipods from different benthic and floating habitats. The influence of fouling amphipods on other habitats is analysed in Chapters 4 and 5, it is shown that fish-farm fouling acts as a source population of amphipods dispersing towards both defaunated sediments in soft-bottoms and surrounding floating habitats. Finally, in the last chapter, based on the possibility of using wild fauna already growing in fish farms, the applicability of amphipods as an accessory culture is tested in an offshore integrated multi-trophic aquaculture (IMTA) system with finfish as main fed species. Throughout this thesis it has been shown that fish-farming activities affect the amphipod assemblage in several ways such as the establishment of high population densities or the intimate connectivity between different subpopulations. As a result, a new potential commercial application arises from the possibility of using them as biofilters of aquaculture wastes, within an off-coast integrated multitrophic aquaculture system, promoting a more sustainable development of aquaculture in the marine environment. / Las estructuras artificiales que conforman las instalaciones de acuicultura en mar abierto suelen ser colonizadas por multitud de organismos marinos, que forman comunidades de fouling características en estas estructuras. Muchos estudios se han centrado en la descripción de los organismos sésiles que se desarrollan sobre cabos, redes y boyas de las instalaciones de acuicultura, debido a los problemas que generan para el cultivo y los costes adicionales que significan para la industria derivados de su necesaria eliminación. Sin embargo, aunque las comunidades de fouling sésiles han sido bien estudiadas desde el punto de vista de su control en las instalaciones de acuicultura, poco se sabe sobre la epifauna que habita estas estructuras artificiales. Esta tesis se centra en el estudio de los crustáceos anfípodos, los cuales aún no han sido estudiados en cuanto a la composición de especies y a su relación con los hábitats creados por los organismos sésiles, a pesar de haber sido detectados en grandes abundancias en las instalaciones de acuicultura. Después de una introducción general, que establece el marco de estudio, el capítulo uno es un estudio preliminar sobre las comunidades de fouling de las instalaciones de acuicultura en el Mediterráneo, comparándolas con las desarrolladas en otras estructuras artificiales como puertos o plataformas petrolíferas. En este capítulo, se demuestra que las comunidades de fouling están compuestas principalmente por bivalvos, algas, hidrozoos y briozoos y que más de un 80% de la fauna asociada a estos organismos son anfípodos. Además el poblamiento se caracteriza por la presencia de siete especies de anfípodos que son frecuentes y abundantes: Elasmopus rapax, Jassa marmorata, Jassa slatteryi, Ericthonius punctatus, Stenothoe tergestina, Caprella equilibra y Caprella dilatata. Un estudio cuantitativo de las densidades de estos anfípodos se lleva a cabo en el capítulo 2, donde se encuentra que la densidad media es de 176.000 ind.m-2, con máximos de más de 1.000.000 ind.m-2. Allí se explora también el papel de los macro y microhábitats en mantener dichas poblaciones de anfípodos. El efecto de la modificación de corrientes sobre las comunidades plantónicas debida a la instalación de las piscifactorías se analiza en el capítulo 3. En él, se detectó una retención de los anfípodos planctónicos cerca de las instalaciones, evidenciada por el incremento en las abundancias de hipéridos y de anfípodos migradores desde diferentes hábitats bentónicos flotantes. La influencia de las grandes densidades de anfípodos del fouling sobre otros hábitats se estudia en los capítulos 4 y 5, donde se observó que el fouling actúa como fuente de anfípodos migradores, exportando individuos que colonizan tanto sedimentos defaunados en el fondo marino como otros hábitats flotantes cercanos. Finalmente, en el último capítulo se analiza la posibilidad de aprovechar la producción natural y la conectividad observadas a través del cultivo de anfípodos como parte de un sistema de acuicultura multitrófica integrada (AMTI) en mar abierto con peces como especie principal. A lo largo de esta tesis, se demuestra que la acuicultura influencia las poblaciones de anfípodos marinos, tanto en el establecimiento de grandes densidades de población como en la conectividad entre las diferentes subpoblaciones. Como resultado, surge una nueva aplicación comercial de la posibilidad de usar los anfípodos del fouling como biofiltros, reciclando los residuos de la acuicultura dentro de un sistema de acuicultura multitrófica, garantizando así un desarrollo más sostenible de la acuicultura en el medio marino.

Among tools that are used to fill knowledge gaps on natural systems, ecological modelling has been widely applied during the last two decades. Ecological models are simple representations of a complex reality. They allow to highlight environmental drivers of species ecological niche and better understand species responses to environmental changes. However, applying models to Southern Ocean benthic organisms raises several methodological challenges. Species presence datasets are often aggregated in time and space nearby research stations or along main sailing routes. Data are often limited in number to correctly describe species occupied space and physiology. Finally, environmental datasets are not precise enough to accurately represent the complexity of marine habitats. Can we thus generate performant and accurate models at the scale of the Southern Ocean ?What are the limits of such approaches ?How could we improve methods to build more relevant models ?In this PhD thesis, three different model categories have been studied and their performance evaluated. (1) Mechanistic physiological models (Dynamic Energy Budget models, DEB) simulate how the abiotic environment influences individual metabolism and represent the species fundamental niche. (2) Species distribution models (SDMs) predict species distribution probability by studying the relationship between species presences and the environment. They represent the species realised niche. (3) Dispersal lagrangian models predict the drift of propagules in water masses. Results show that physiological models can be developed for marine Southern Ocean species to simulate the metabolic variations in link with the environment and predict population dynamics. However, more data are necessary to highlight detailed physiological contrasts between populations and to accurately evaluate models. Results obtained for SDMs suggest that models generated at the scale of the Southern Ocean and future simulations are not relevant, given the lack of data available to characterise species occupied space, the lack of precision and accuracy of future climate scenarios and the impossibility to evaluate models. Moreover, model extrapolate on a large proportion of the projected area. Adding information on species physiological limits (observations, results from experiments, physiological model outputs) was shown to reduce extrapolation and to improve the capacity of models to estimate the species realised niche. Spatial aggregation of occurrence data, which influenced model predictions and evaluation was also succefully corrected. Finally, dispersal models showed an interesting potential to highlight the role of geographic barriers or conversely of spatial connectivity and also the link between species distribution, physiology and phylogeny history. This PhD thesis provides several methodological advice, annoted codes and tutorials to help implement future modelling works applied to Southern Ocean marine species. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Coral reef fish are known to have a bipartite life cycle: a dispersive pelagic larval phase (DPL), where larvae ‘travel’ away from their parents to occupy new habitats, and a sedentary reef phase characterized by juveniles and adults. Study of the DPL is an essential prerequisite to understand how persistence, connectivity, and gene flow operate between populations. Clownfish have been the subject of considerably varied fields of research in recent decades, not only due to their economic value, but also because of their ease of maintenance in laboratory settings, regular spawning, and short DPL. Their life cycle is also defined as bipartite, with a DPL lasting around 15 days until settlement, and the fish exhibit a symbiotic relationship with sea anemones. The transitions between phases are associated with a series of morphological, behavioural, genetic, cellular and molecular changes. However, these changes are poorly characterized in some species of clownfish. Therefore, the Red Sea clownfish, Amphiprion bicinctus, was reared to fill the gap in the literature by investigating their i) morphology, ii) swimming abilities, and iii) differential gene expression (DGE) throughout ontogeny. The DPL was characterized in the preflexion, flexion and postflexion stages, according to flexion of the notochord, on 0, 2 and 10 days post hatch (dph), respectively. Metamorphosis was defined by a morphological transition between the DPL and juvenile phases, associated with the appearance of white stripes, on day 10 and until the end of the experiment, on day 14. Additionally, metamorphosis is followed by a behavioural change at 14 dph, called settlement, where larvae transition from free swimming in the water column to associating with the substrate. We also demonstrate that the larvae present active swimming from the moment they hatch, and the swimming speed increases throughout DPL. Overall, the development of A. bicinctus is similar to other clownfish species. This work provides a strong baseline on the development of A. bicinctus, which may open the door to a deeper understanding of the role of dispersal behaviours and enhance our ability to design effective marine reserve networks in the Red Sea.

Mainly because of the problems with species delineation, the biogeography of microscopic organisms is notoriously difficult to elucidate. In this contribution, variable nuclear and mitochondrial DNA markers were sequenced from individual specimens representing the Echiniscus virginicus complex that are morphologically indistinguishable under light microscopy (five populations from the temperate Eastern Nearctic and 13 populations from the subtropical and tropical zone). A range of methods was used to dissect components of variability within the complex (Bayesian inference, haplotype networks, Poisson tree processes, automatic barcode gap discovery delineations, principal components analysis and ANOVA). We found deep divergence between the temperate Eastern Nearctic E. virginicus and pantropical Echiniscus lineatus in all three genetic markers. In contrast, intraspecific genetic variation was very low, regardless of the geographical distance between the populations. Moreover, for the first time, statistical predictions of tardigrade geographical distributions were modelled. The factor determining the allopatric geographical ranges of deceptively similar species analysed in this study is most likely to be the type of climate. Our study shows that widespread tardigrade species exist, and both geographical distribution modelling and the genetic structure of populations of the pantropical E. lineatus suggest wind-mediated (aeolian) passive long-distance dispersal.

Successful bioremediation of polluted soils is often limited by the bioavailability of organic contaminants to degrading bacteria. Recent studies revealed that fungal hyphae have the potential to promote bacterial dispersal, and thus raised the idea of specifically stimulating the establishment of fungal networks in soils to increase contaminant bioavailability. Can such bacterial dispersal networks improve biodegradation performance considerably? If so, how are the improvements affected by abiotic conditions and by the spatial structure of dispersal networks? This doctoral thesis aims at answering these research questions. To this end, laboratory experiments are performed and a bacterial simulation model is developed, incorporating both microbiological and ecological theory. Manifold simulations and analyses of the microbial ecosystems’ spatiotemporal dynamics under different environmental scenarios reveal key factors and processes controlling biodegradation performance and determining benefits from bacterial dispersal networks.