Titel Deelnemers "Korte inhoud" "Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean" "Rosa Van Der Ven, Jean-François Flot, Carol Nathaly Buitrago López, Marc Kochzius" "Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. S. hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa. As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones. Based on microsatellite analyses three groups could be distinguished within the WIO: (1) northern Madagascar, (2) south-west Madagascar together with one site in northern Mozambique (Nacala) and (3) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region." "Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines" "Gabriella Lindgren" "The Estonian Native Horse (ENH) is a medium-size pony found mainly in the western islands of Estonia and is well-adapted to the harsh northern climate and poor pastures. The ancestry of the ENH is debated, including alleged claims about direct descendance from the extinct Tarpan. Here we conducted a detailed analysis of the genetic makeup and relationships of the ENH based on the genotypes of 15 autosomal short tandem repeats (STRs), 18 Y chromosomal single nucleotide polymorphisms (SNPs), mitochondrial D-loop sequence and lateral gait allele in DMRT3. The study encompassed 2890 horses of 61 breeds, including 33 ENHs. We show that the expected and observed genetic diversities of the ENH are among the highest within 52 global breeds, and the highest among 8 related Northern European ponies. The genetically closest breeds to the ENH are the Finn Horse, and the geographically more distant primitive Hucul and Konik. ENH matrilines are diverse and relate to draught and Pontic-Caspian breeds. ENH patrilines relate to draught breeds, and to a unique haplogroup not described before. None of the 33 ENHs carried the ""gait"" mutation, but the mutation was found in 2 Huculs. The study demonstrates that the ENH is a genetically distinct and diverse breed of ancient origin with no notable pressure of selective breeding." "Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology" "K Brudey, JR Driscoll, Leen Rigouts, Unknown [...], Françoise Portaels" "Population genetics of African Schistosoma species" "O. Rey, Bonnie L. Webster, Tine Huyse, D Rollinson, Frederik Van den Broeck, J. Kincaid-Smith, A. Onyekwere, J. Boissier" "Blood flukes within the genus Schistosoma (schistosomes) are responsible for the major disease, schistosomiasis, in tropical and sub-tropical areas. This disease is predominantly present on the African continent with more than 85% of the human cases. Schistosomes are also parasites of veterinary importance infecting livestock and wildlife. Schistosoma population genetic structure and diversity are important characteristics that may reflect variations in selection pressures such as those induced by host (mammalian and snail) environments, habitat change, migration and also treatment/control interventions, all of which also shape speciation and evolution of the whole Schistosoma genus. Investigations into schistosome population genetic structure, diversity and evolution has been an area of important debate and research. Supported by advances in molecular techniques with capabilities for multi-locus genetic analyses for single larvae schistosome genetic investigations have greatly progressed in the last decade. This paper aims to review the genetic studies of both animal and human infecting schistosome. Population genetic structures are reviewed at different spatial scales: local, regional or continental (i.e. phylogeography). Within species genetic diversities are discussed compared and the compounding factors discussed, including the effect of mass drug administration. Finally, the ability for intra-species hybridisation questions species integrities and poses many questions in relation to the natural epidemiology of co-endemic species. Here we review molecularly confirmed hybridisation events (in relation to human disease) and discuss the possible impact for ongoing and future control and elimination." "Population genetics of the East African White-eye species complex" "Jan Christian Habel, Siobhan Cox, Franz Gassert, Ronald K Mulwa, Jobst Meyer, Luc Lens" "Population and landscape genetics in the water flea Daphnia" "Summary The population genetic structure of natural populations in landscapes is the result of a complex interaction between ecological and evolutionary processes such as gene flow, genetic drift and selection, which in turn are shaped by landscape characteristics (environmental gradients and geography), historical processes, or their combined effects. Understanding the relative role of these processes is fundamental to improve our ecological insight and to design strategies for biodiversity conservation. Landscape genetics is a young discipline that enables us to understand the processes behind patterns of genetic structure as observed in nature by relating spatial genetic variation to local environmental conditions and geographic location. The main goal of this dissertation was to analyse the relative role of environmental variables and spatial variables in structuring genetic variation in Daphnia populations. I used multivariate approaches that are commonly applied in community ecology to quantify genetic diversity within and genetic differentiation among populations and disentangle the relative contribution of local environmental conditions and spatial drivers to explain variation in genetic composition in natural landscapes. I applied this approach to four different settings: clonal composition in obligately asexual species of the Daphnia pulex species complex in Greenland, coexistence and genetic variation in an obligately asexual and a cyclically parthenogenetic D. pulex species in northern Finland, genetic variation in the cyclic parthenogen D. magna in coastal rock pools along the Baltic, and genetic variation in the cyclic parthenogen D. sinensis in young artificial reservoirs in Ethiopia. In all these settings, ecological and geographic distances among populations were related to genetic distances in multivariate redundancy analyses (RDA) to explore whether genetic variation in the landscape was more structured along environmental gradients or along spatial gradients. In Chapter I, I show that the newly created habitats created by recent deglaciation in Greenland get colonized by multiple genotypes within decades of their formation. Furthermore, an increase in clonal richness with age of habitat resulted in a clear gradient of clonal richness in the direction of retreat of the Greenland ice sheet. In Chapter II, I build further on these results and disentangle the processes that structured the asexual clonal assemblages in two age clusters using multivariate partitioning analysis techniques. The results show that a significant proportion of variation in clonal composition was attributed to environmental variation among habitats, whereas pure spatial models did not account for a significant portion of the variation in clonal composition among habitats. From this, I concluded that the cause of the increase in clonal richness with age as observed in Chapter I is due to an increase in habitat environmental heterogeneity with age, leading to an increase in niche diversity in older habitats. The results of my analyses show that local environmental variables act as an important filter determining colonization of newly created habitats and reveal that dispersal is high enough to sustain a pattern of clonal sorting so that clonal composition reflects local environmental conditions. In Chapter III, I have estimated the number of founders of Daphnia sinensis populations inhabiting recently created reservoirs in Ethiopia based on nuclear and mitochondrial markers. The results showed that the genetic structure of the recently established D. sinesis populations are strongly influenced by founder effects and reflect a small number of founders (typically lower than five). I did not detect any evidence for the importance of environmental and spatial variables in determining landscape genetic structure. In Chapter IV, I quantified the degree to which two regionally coexisting and ecologically very similar species coexist in single pond or pond clusters in the tundra of Northern Finland. I quantified the importance of environmental variation and space in determining landscape genetic structure of two species: the cyclically parthenogenetic species Daphnia pulicaria and the obligately asexual species I refer to as panarctic Daphnia pulex. I relate both community structure and the population genetic structure of the two species (clonal composition in the asexual species and allele frequencies in the cyclically parthenogenetic species) to environmental and spatial drivers. I observe a significant effect of environmental variation but no effect of space in determining both species composition as well as clonal composition in the asexual taxon, whereas there is no environmental nor a spatial signal in the landscape genetic structure of the cyclically parthenogenetic species. The niche overlap between the cyclically and obligately parthenogenetic species is high. My results indicate that there is no dispersal limitation in this system, and that the lack of coexistence of the two species at the level of single ponds or pond clusters likely reflects strong priority effects. In Chapter V, I have report strong genetic differentiation among local populations (FST = 0.382) and low genetic diversity within populations in Daphnia magna inhabiting rock pools along the Swedish Baltic coast. There was a significant correlation between genetic and geographic distances at regional level, which largely reflects differences among populations located on different isolated islands, but no correlation between salinity levels and genetic differentiation. Overall the different analyses done on different species and settings amongst others revealed that 1) there is a significant correlation between genetic distance and environmental distance but not geographic distance in the obligate parthenogens from Greenland and Finland, 2) a significant correlation between genetic distance and geographic distance but not with ecological distance in the populations of the cyclically parthenogenetic species D. magna populations from Sweden, and 3) no correlation between genetic distance and both environmental and geographic distance in the cyclically parthenogenetic species D. sinensis population from Ethiopia. My results strongly suggest that isolation-by-environment is a key process structuring genetic variation at the landscape level in obligately parthenogens, whereas the sexual populations in the Baltic coast rock pools show a weak sign of isolation-by-dispersal limitation. I also obtained strong indications for founder effects, suggesting that the landscape genetic structure of Daphnia populations is also influenced by patterns of colonization. The results I obtained for the Daphnia populations in the Ethiopian reservoirs suggest that the regional population structure is strongly impacted by founder effects that are the result of a low number of colonists and the absence of strong subsequent gene flow. More in general, the results of the landscape genetic analyses in this thesis reveal highly repeatable patterns of genetic structure of Daphnia populations even though our analyses involved strongly diverging habitat types, landscapes and geographical settings. One recurrent pattern was that there is little evidence for strong dispersal limitation but also little evidence for strong gene flow. The observed patterns of landscape genetic structure were strongly influenced by the reproductive mode of the water flea species studied." "Sex ratio variation and population genetics of gynodioecious plant species" "Sascha van der Meer" "Plants display remarkable sexual diversity. Regardless of this variation, most flowering plants are hermaphrodites and contain flowers with both male and female sex organs. However, various sexual systems have evolved in which male and female organs have been separated between flowers and between individuals. In gynodioecious species, hermaphrodites co-exist with females, plants that lack pollen production (male-sterile individuals). Since females have lost their ability to produce pollen, they are dependent on hermaphrodites for fertilization. One necessary condition for the maintenance of this sexual polymorphism is the occurrence of a reproductive ‘female advantage’. The female advantage implies that females should produce more seeds or higher quality seedlings in comparison to hermaphrodites and the magnitude of the female advantage is dependent on the sex determination system. In the most common form of gynodioecy, nuclear-cytoplasmic gynodioecy, mutations that lead to male-sterility are located in the cytoplasm and the effect of these male-sterility mutations can be counteracted by nuclear alleles (male- fertility restorers). In species with nuclear-cytoplasmic gynodioecy, females require only a slight reproductive advantage over hermaphrodites to be maintained within a population (female advantage > 1). The female advantage is generally attributed to resource reallocation from pollen to seed production and avoidance of inbreeding depression since females are obligate outcrossers. In most gynodioecious species that have been studied over the years, females had a clear reproductive advantage over hermaphrodites, although the magnitude of the female advantage generally differed among populations. Variation in the magnitude of the female advantage is not surprising since seed production of females is strongly dependent on pollen availability. In populations or patches with a low number of hermaphrodites, females may experience low seed set due to pollen limitation, while in populations or patches with a high number of hermaphrodites, females may have a reproductive advantage. When females produce more seeds than hermaphrodites the frequency of females may locally increase, which in turn may contribute to variation in sex ratios among populations. Population female frequencies are highly variable and generally range from a low percentage to more than 50% females. Many gynodioecious species also have populations that consist purely of hermaphrodites. When the frequency of females within a population is low, floral sex ratios can still be highly variable, since sex expression can also vary within individuals. Hermaphrodites of many gynodioecious species are dichogamous, indicating that they separate the maturation of male and female organs in time. Differences in timing of male and female function of a flower, typically lead to a shift in floral sex ratio during a population’s flowering season. To gain insights into the various aspects that may affect seed production and genetic variation in gynodioecious plant species, I quantified seed production and offspring fitness across a wide range of populations that differed in population size and sex ratio to understand how these variables affected the female advantage and sex ratio evolution. I assessed genetic diversity in a number of spatially separated populations to understand how genetic variation is partitioned among populations and between sex morphs. Moreover, I studied temporal variation in female reproductive success within and among individuals across an entire flowering season to get a better understanding of the impact of within-population sex ratio variation on seed set. To address these research objectives, two gynodioecious species, Saxifraga granulata (meadow saxifrage) and Plantago coronopus (buck’s- horn plantain), were studied. In this thesis, I show that variation in sex expression within inflorescences, among individuals and among populations highly affected seed production of my study species. In populations of P . coronopus, seed production was highly dependent on population sex ratio, in populations with a low frequency of females both females and hermaphrodites produced more seeds than in populations with a high female frequency. Females produced fewer seeds than hermaphrodites on average, however, offspring fitness of females was higher than offspring fitness of hermaphrodites. Furthermore, genetic analyses showed that both females and hermaphrodites were highly genetically diverse, but adult hermaphrodites showed increased levels of homozygosity as well as severe inbreeding depression after selfing. In S. granulata, the occurrence of female individuals was low, but flowers of hermaphrodites differentially invested in male and female function; the first-opening central flower generally had a long female phase and produced significantly more seeds than early and late lateral flowers. Furthermore, early flowering plants produced more seeds than late flowering plants. Populations of S. granulata were highly genetically diverse, which was most likely related to its high ploidy level (octoploid) and the ability to reproduce clonally. Despite the differences between Saxifraga granulata and Plantago coronopus in terms of reproduction, floral biology, pollination mode, and ploidy level, I have shown that the large variation in sex expression within inflorescences, among individuals and among populations highly affected seed production. My results further showed that plant mating system and the extent of inbreeding depression affect the distribution of genetic variation among populations and sex morphs. Although not explicitly investigated, they also point to the importance of local spatial structure of gynodioecious populations for regulating the evolutionary maintenance of gynodioecy." "Contribution of genetics for implementing population translocation of the threatened Arnica montana." "Fabienne Van Rossum, Olivier Raspé" "Ecological restoration programmes aiming at population recovery of imperilled plant species increasingly involve plant translocations. Evaluating the genetic status of seed source and target populations is essential for designing plant translocation protocols and optimizing recovery success. We developed nine polymorphic microsatellite markers and used three plastid markers to investigate genetic variation and structure of the two last large and six small remaining populations of the selfincompatible, clonally-propagating Arnica montana in southern Belgium and bordering France. The aim of the study was to determine the genetic status of these remaining populations and whether the large populations can be used as seed source for translocations. Most small populations maintained high genetic diversity and showed no inbreeding or a heterozygote excess, which may be explained by high genet longevity thanks to clonal propagation, heterosis, inbreeding depression at early development stages and/or no recruitment. Genotypic diversity was low in small populations, with clonal propagation mainly contributing to rosette production. The number of genets, and therefore effective population size, was often very small, restricting compatible mate availability. The situation is therefore more critical than it seems on the field, and bringing new genetic variation is necessary. Although no polymorphism was found in plastid DNA markers, between-population differentiation based on microsatellite markers was moderate, except for very small populations, where it was greater (FST > 0.200). These patterns of differentiation were likely due to genetic drift effects and demographic stochasticity. We recommend using mixed seed material from the two large populations for translocations, and before conducting reinforcements, to first implement crossing experiments and reintroductions of mixed and crossed material in ecologically restored sites to understand the long-term effects of combining genotypes from different locations." "The impact of urbanization on population genetics and microorganisms associated with floral nectar of Linaria vulgaris ,," "Jacek Bartlewicz" "Entering the XXIst century, humanity will face enormous challenges to its continued prosperity. This is because the ecosystem in which mankind participates is undergoing planetary scale alterations, giving birth to new unprecedented problems. The growth and changing distribution of human population is a constituent part of this so-called global change, and must be carefully studied in order to give the coming generations a chance for a better future. One of the processes that strongly affects the global distribution of human populace is urbanization. A strong, stable and longterm trend of migration from rural zones to the cities exists worldwide, and it is predicted that by 2050, 66% of all Earth’s inhabitants will call one city or another their home. Because the well-being and in many instances survival of humans is dependent on a variety of services the ecosystem provides, understanding what impact urbanization has on ecosystems is crucial. That is also the goal of the emerging discipline of urban ecology, and the present dissertation attempts to help developing this novel field. Specifically, this thesis tackles issues concerning plant reproduction in cities. Two aspects linked to the pollination process of a plant species were looked into: their population genetic structure and its nectar microbial communities. A wild plant called yellow toadflax (Linaria vulagaris) was investigated here because, among other reasons, it is common in urban areas (facilitating study), it features a closed flower architecture (so microbes are unlikely to enter its nectar via air) and it is self-incompatible (this type of mating system is expected to react strongly to urban habitat fragmentation). First, microsatellite genetic markers were developed for L. vulgaris. These were then used to study population genetic structure of yellow toadflax and factors shaping it in city landscapes. In urban environments, the increased amount of sealed surfaces means that plant individuals may suffer from loss of suitable habitat and fragmentation of its remaining patches. Because smaller patches can only sustain smaller plant populations, rare gene alleles are more likely to be lost due to random events. Such alleles may disappear with time, rendering urban populations less genetically diverse. Moreover, because of the fragmentation between the remnant habitat patches, the exchanges of genes between populations is more difficult. The results of the experiments presented here indicated that L. vulgaris populations were highly differentiated, and that there was no correlation between genetic and geographic distances. This, as hypothesized, suggested low gene flow. A further paternity analysis on the subset of the populations revealed that current pollen flow patterns are probably higher than those estimated from standing genetic variation. This suggested that although pollen does travel between populations, many of the resulting seedlings do not reach sexual maturity. In all likelihood, the seedlings cannot establish themselves in such small patches due to competition with already mature individuals. In other words, it is habitat loss rather than habitat fragmentation that contributes to population differentiation. Nevertheless, in the study system researched in this dissertation genetic diversity was not lower in urban regions than in agricultural zones. This was contrary to expectations. One possible reason for such indifference may be relative similarity, in terms of environmental impact, of landscapes undergoing intensive agricultural regime, and mildly urbanized zones as exemplified by the city of Leuven (in the vicinity of which the experiments presented in this dissertation were conducted), which according to United Nations classifications is a small city. Second, nectar microbial communities of L. vulgaris were investigated. Floral nectar yeasts and bacteria are thought to be mainly distributed by insects, the same ones that provide pollination services. Thus, changes in incidence, abundance and structure of pollinator communities might not only impact plant population structure, but also the composition of their nectar microbial communities, too. In the study system investigated here, the microbial incidence in L. vulgaris was high and did not change along the investigated urbanization gradient. The communities were species poor, and no particular species, except for singletons, was present only in urbanizaed or rural zones. The sampling of bacteria may also have been incomplete, as indicated by rarefaction curves. Thus, although the microbial communities showed a nested substructure, indicating that species-poor communities were a subset of species-rich communities, it is difficult to speculate on the relevance of this result. In search for potential factors responsible different conditions experienced by nectar microbial communities in urban and rural landscapes, the impact of an agricultural fungicide mixture was assessed on nectar yeasts both in vitro and in planta. The results indicated that pesticides hamper the growth of Metschnikowia reukaufii and Metschnikowia gruessii, leading to a decrease of their number in treated plants. However, nectar bacteria, which are presumably competitors of nectar yeasts, do not reach higher abundances as a result of hampered yeast growth." "Population genetics of Plasmodium vivax in four rural communities in central Vietnam" "Van Hong Nguyen, Christopher Delgado-Ratto, Pham Vinh Thanh, P. Van den Eede, Pieter Guetens, Nguyen Thi Huong Binh, Bui Quang Phuc, Tran Thanh Duong, Jean-Pierre Van Geertruyden, D'Alessandro, Annette Erhart, Anna Rosanas-Urgell" "BACKGROUND: The burden of malaria in Vietnam has drastically reduced, prompting the National Malaria Control Program to officially engage in elimination efforts. Plasmodium vivax is becoming increasingly prevalent, remaining a major problem in the country's central and southern provinces. A better understanding of P. vivax genetic diversity and structure of local parasite populations will provide baseline data for the evaluation and improvement of current efforts for control and elimination. The aim of this study was to examine the population genetics and structure of P. vivax isolates from four communities in Tra Leng commune, Nam Tra My district in Quang Nam, Central Vietnam.METHODOLOGY/PRINCIPAL FINDINGS: P. vivax mono infections collected from 234 individuals between April 2009 and December 2010 were successfully analyzed using a panel of 14 microsatellite markers. Isolates displayed moderate genetic diversity (He = 0.68), with no significant differences between study communities. Polyclonal infections were frequent (71.4%) with a mean multiplicity of infection of 1.91 isolates/person. Low but significant genetic differentiation (FST value from -0.05 to 0.18) was observed between the community across the river and the other communities. Strong linkage disequilibrium ([Formula: see text] = 0.113, p < 0.001) was detected across all communities, suggesting gene flow within and among them. Using multiple approaches, 101 haplotypes were grouped into two genetic clusters, while 60.4% of haplotypes were admixed.CONCLUSIONS/SIGNIFICANCE: In this area of Central Vietnam, where malaria transmission has decreased significantly over the past decade, there was moderate genetic diversity and high occurrence of polyclonal infections. Local human populations have frequent social and economic interactions that facilitate gene flow and inbreeding among parasite populations, while decreasing population structure. Findings provide important information on parasites populations circulating in the study area and are relevant to current malaria elimination efforts."