Clade and monophyletic group on one hand and grade and paraphyletic group on the other hand are commonly used as pairs of interchangeable terms. I question this apparent synonymy and propose that "monophyly" and "paraphyly" should refer to a property of a set, whereas "clade" and "grade" should apply to individuals resulting from evolutionary process.

Studies on genetic connectivity are important for the management of fisheries. In this study we used AFLP to investigate population structure of the endemic Spinefoot shoemaker, Siganus sutor, from 6 countries, Kenya, Tanzania, Comoros, Seychelles and Mauritius in the Western Indian Ocean. We collected 506 samples from 20 fish landing sites, 171 variable loci were used in the statistical analysis. Global F_ST was significant and showed a pattern of isolation by distance, mostly influenced by remote oceanic islands. In a previous study we have described the temporal variation of Siganus sutor to be about 1/5 of the global variation, and by applying a 1/5 of the global variation cut of value for the pair-wise comparisons we were able to account some of the pair- wise genetic variation as temporal fluctuations. A STRUCTURE analysis was also preformed that corroborates the pair-wise F_ST comparisons. Overall these results show that S. sutor is genetically diverse and subdivided throughout the region, but also that the current management regime might not be optimal. 

This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of similar to 2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4-26 degrees S and 33-48 degrees E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D-EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale-across national borders.

The processes underlying divergent selection and genetic adaptation have been on the evolutionary biologists agenda for a long time. In this study we used the three-spined stickleback (Gasterosteus aculeatus) study system, a perfect system to study the evolution of similar traits in different lineages exposed to similar environmental conditions. Lind and Grahn (2011) have found directional selection caused by pulp mill effluent on populations of three-spined stickleback along the Swedish coast. In their study, they identified 21 AFLP- outlier loci indicated to be under selection. Here we converted some of these anonymous AFLP loci into sequenced markers and aligned them to the stickleback genome. Four out of five loci, aligned within or close to coding regions, on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the locus, located on chromosome VIII, have been identified to be under selection for fresh water adaption in other studies, including Baltic Sea stickleback populations (Mäkinen et al. 2008a,b). We believe that this is feasibly method that can be used as a starting point for identification of genes and genomic regions possible involved in adaptation, both for model and non-model organisms. 

The last century, humans have been altering almost all natural environments at an accelerating rate, including the Baltic Sea that has highly eutrophicated areas and many coastal industries such as Pulp-mills. For animals living in a habitat that changes there are basically two alternatives, either to cope with the change or become locally extinct. This thesis aims to investigate if recent anthropogenic disturbance in the Baltic Sea can affect natural populations on a genetic level through natural selection.

First, we found a fine-scale genetic structure in three-spine sticklebacks (Gasterosteus aculeatus) populations along the Swedish coast (paper I), indicating limited gene-flow between populations in geographic proximity. Different genetic markers, specifically Amplified Fragment Lenght Polymorpism (AFLP, and microsatellites,  gave different results, highlighting the heterogeneous character of genomes which demonstrates that it is important to choose a genetic marker that is relevant for the question at hand. With a population genomic approach, and a multilocus genetic marker (AFLP), we detected convergent evolution in genotype composition in stickleback populations living in environments affected by pulp-mill effluent (paper II) and in highly eutrophicated environments (paper III), compared to adjacent reference populations. We found loci, in both studies (paper II, III), that were different from a neutral distribution and thus probably under divergent selection for the habitat differences investigated. The selective effect from pulp-mill effluents were more pronounced, but the two different habitats had mutual characters (AFLP loci). In paper IV, we converted five anonymous AFLP loci to sequenced markers and aligned them to the stickleback genome. Four out of five loci aligned within, or close to, coding regions on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the loci, located on chromosome VIII and identified as under divergent selection in both paper II and III, has been identified in other studies as to be under selection for fresh water adaptation, including Baltic Sea stickleback populations.

In conclusion, anthropogenic alterations of natural environments can have evolutionary consequences, probably adaptive, for the animals living there and the evolutionary response exhibited by natural populations can be very fast.

Anthropogenic activities are causing change in natural habitats at an accelerating rate and affecting populations by altered selection pressures. One example is human-induced eutrophication in the Baltic Sea, were behaviour alterations are well documented in three-spined sticklebacks (Gasterosteus aculeatus). Here we have used 204 variable Amplified Fragment Length Polymorphism (AFLP) markers to investigate genetic differences between a set of ten hierarchal sampled populations of sticklebacks, five populations inhabiting eutrophicated habitats and five from control populations, in total 292 individuals. We found significant genetic variation that could be attributed to habitat (4.3% AMOVA). A combination of F_ST outlier analysis and classification analysis revealed seven AFLP-loci likely to be affected by divergent selection by eutrophication. Four of these seven loci have earlier been identified as under selection in stickleback populations living in pulp-mill effluents suggesting some similar selective factors between eutrophication and pulp-mill effluent effected habitats. 

There are three basic types of population structures in marine environments; populations that are distinct, with a continuous change and without any differentiation. In each type the population units are characterized by groups of individuals with panmixia within groups and site fidelity to a limited geographic area. Earlier studies of the population genetic structure on sticklebacks in the Baltic Sea have shown none or only little structure. We have sampled 8 sites (253 individuals) along Sweden’s coast to estimate the genetic structure, using five microsatellites and 173 Amplified Fragment Length Polymorphism (AFLP) markers and detected a fine scale genetic structure (AFLP F_ST= 25%, microsatellites F_ST = 2.7%). With AFLPs the observed variation followed isolation by distance model (but not with microsatellites). Even sites separated by only 2 km of water are significantly separated. Both Bayesian clustering analysis and Capscale separated populations and identified populations from Gulf of Bothnia (4 psu) and from the west coast (20 psu) as genetically distinctly different from Baltic populations (about 7-8 psu).  In conclusion, gene flow is limited between sampled sites, and since no geographic barriers can be distinguished the population structure is likely caused by the sticklebacks’ behavior. Hence, we have probably sampled either stationary populations of marine sticklebacks, or homing sticklebacks. In this study AFLP and microsatellites did not give congruent results; with AFLPs we got high separation, and genetic variation followed isolation by distance model and supported the continuous change type of population structure.

It is well established that differences in migratory behavior between populations of songbirds have a genetic basis but the actual genes underlying these traits remains largely unknown. In an attempt to identify such candidate genes we de novo assembled the genome of the willow warbler Phylloscopus trochilus, and used whole-genome resequencing and a SNP array to associate genomic variation with migratory phenotypes across two migratory divides around the Baltic Sea that separate SW migrating P. t. trochilus wintering in western Africa and SSE migrating P. t. acredula wintering in eastern and southern Africa. We found that the genomes of the two migratory phenotypes lack clear differences except for three highly differentiated regions located on chromosomes 1, 3, and 5 (containing 146, 135, and 53 genes, respectively). Within each migratory phenotype we found virtually no differences in allele frequencies for thousands of SNPs, even when comparing geographically distant populations breeding in Scandinavia and Far East Russia (>6000 km). In each of the three differentiated regions, multidimensional scaling-based clustering of SNP genotypes from more than 1100 individuals demonstrates the presence of distinct haplotype clusters that are associated with each migratory phenotype. In turn, this suggests that recombination is absent or rare between haplotypes, which could be explained by inversion polymorphisms. Whereas SNP alleles on chromosome 3 correlate with breeding altitude and latitude, the allele distribution within the regions on chromosomes 1 and 5 perfectly matches the geographical distribution of the migratory phenotypes. The most differentiated 10 kb windows and missense mutations within these differentiated regions are associated with genes involved in fatty acid synthesis, possibly representing physiological adaptations to the different migratory strategies. The ∼200 genes in these regions, of which several lack described function, will direct future experimental and comparative studies in the search for genes that underlie important migratory traits.

The objective was to investigate at what the age specimen of Cliostomum corrugatum become fertile in order to estimate the time span between the meiosis events. The species has its main distribution in Europe but has also been found on the west coast of British Columbia and is red listed, e.g., in Sweden (nearly threatened), Denmark, Germany and England. In the province of Östergötland, southern Sweden it is most frequent on old Quercus robur trees in open oak forest or meadows. I may also be found on other deciduous trees as Ulmus and Fraxinus species. It is mainly groving on the flat terminal parts of the rough bark of the tree trunks and not on the sides of the cracks. Cliostomum corrugatum does not grow on young oak trees. The smallest tree trunk diameter with Cliostomum corrugatum was is 0.65 m, a tree of at least 100 years of age. On two localities in Östergötland all oaks were studied and the size of the trees and the size of the largest thallus of Cliostomum corrugatum were recorded. Out of this data the size of how small a tree can possibly be for hosting Cliostomum corrugatum. This estimate was compared with the size of the smallest thalli with apothecia and the size of trees on which these appeared. With knowledge of the peripheral secondary growth of oaks it was possible to estimate the age of the youngest fertile Cliostomum corrugatum to about 30 years. Thus, equal to the time span between two meiosis events.

Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.