<p> </p><p> </p><p> </p><p>The extinction risk of threatened species has traditionally been assessed by the use of tools of Population Viability Analysis (PVA). Species interactions, however, have seldom been accounted for in PVA:s. The omission of species interactions in risk assessments may further lead to serious mistakes when setting target sizes of populations. Even a slight abundance decrease of a target species may result in changes of the community structure; in the worst case leading to a highly impoverished community. Of critical importance to conservation is therefore the question of how many individuals of a certain population that is needed in order to avoid this kind of consequences. In the current study, a stochastic multispecies model is used to estimate minimum ecological viable populations (MEVP); earlier defined as “the minimum size of a population that can survive before itself or some other species in the community becomes extinct”. The MEVP:s are compared to population sizes given by a single species model where interactions with other species are treated as a constant source incorporated in the species specific growth rate. MEVP:s are found to be larger than the population sizes given by the single species model. The results are trophic level dependent and multispecies approaches are suggested to be of major importance when setting target levels for species at the basal level. Species at higher trophic levels, however, are altogether more prone to extinction than species at the basal level, irrespective of food web size and food web complexity.</p><p> </p>

<p>Sex chromosomes are useful for the study of how factors such as mutation, selection, recombination and effective population size affect diversity and divergence.</p><p>A comparison of gametologous introns in seven different bird species revealed a complete lack of diversity on the female-specific W chromosome. In contrast, Z had at least one segregating site in all examined species. This can be explained by the lower mutation rate and lower effective population size of W but also suggests that selection affects diversity levels on the non-recombining W chromosome.</p><p>In a diverse set of chicken breeds, the Z chromosome showed reduced diversity compared to autosomes and significant heterogeneity in levels of variation. High variance in male reproductive success, leading to a reduced Z chromosome effective population size, can partly explain this observation. In addition, we suggest that selective sweeps frequently act on the Z chromosome and are responsible for a significant part of the observed Z reduction. </p><p>Differences in the mutation rate of Z and W chromosome sequences indicate that the time spent in male germ line is important for the mutation rate, but does not exclude a specifically reduced mutation rate on the Z chromosome. Estimates of mutation rate in autosomal, Z- and W-linked chicken and turkey sequences indicate a slight reduction in the rate on Z. However, due to rate heterogeneity among introns this reduction is not significant and we cannot exclude male biased mutation as the single cause of rate variation between the chromosomal classes.</p><p>Analysis of indel mutation rates in avian and mammalian gametologous introns show frequent occurrence of indels on both W and Y, excluding meiotic recombination as the only source of this type of mutation. The different indel rate patterns in birds (Z>W) and mammals (X=Y) suggest that indels are caused by both replication and recombination.</p>

<p>To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis.</p><p>Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication.</p><p>Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides.</p><p>Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition. </p><p>The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low<i> d</i><i>N</i><i>/d</i><i>S</i><i> </i>– ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the<i> d</i><i>N</i><i>/d</i><i>S</i> is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category.</p><p>Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.</p>

Sex chromosomes are useful for the study of how factors such as mutation, selection, recombination and effective population size affect diversity and divergence. A comparison of gametologous introns in seven different bird species revealed a complete lack of diversity on the female-specific W chromosome. In contrast, Z had at least one segregating site in all examined species. This can be explained by the lower mutation rate and lower effective population size of W but also suggests that selection affects diversity levels on the non-recombining W chromosome. In a diverse set of chicken breeds, the Z chromosome showed reduced diversity compared to autosomes and significant heterogeneity in levels of variation. High variance in male reproductive success, leading to a reduced Z chromosome effective population size, can partly explain this observation. In addition, we suggest that selective sweeps frequently act on the Z chromosome and are responsible for a significant part of the observed Z reduction. Differences in the mutation rate of Z and W chromosome sequences indicate that the time spent in male germ line is important for the mutation rate, but does not exclude a specifically reduced mutation rate on the Z chromosome. Estimates of mutation rate in autosomal, Z- and W-linked chicken and turkey sequences indicate a slight reduction in the rate on Z. However, due to rate heterogeneity among introns this reduction is not significant and we cannot exclude male biased mutation as the single cause of rate variation between the chromosomal classes. Analysis of indel mutation rates in avian and mammalian gametologous introns show frequent occurrence of indels on both W and Y, excluding meiotic recombination as the only source of this type of mutation. The different indel rate patterns in birds (Z&gt;W) and mammals (X=Y) suggest that indels are caused by both replication and recombination.

To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis. Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication. Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides. Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition. The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low dN/dS – ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the dN/dS is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category. Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.

The aims of this thesis were to evaluate the effects of agriculture on amphibians in terms of (i) population genetic consequences of agriculture-induced spatial changes of the landscape and (ii) local adaptation and tolerance to frequently used agrochemicals. The study was performed using the common frog Rana temporaria as a model. Abundance, occurrence, genetic diversity and gene flow were negatively affected by agriculture in southern Sweden, but unaffected or even positively affected by agriculture in the central and northern regions, respectively. These test parameters correlated positively with landscape diversity both in the south and in the north. Moreover, the size and occurrence of R. temporaria populations decreased towards the north i.e. the margin of the species’ distribution range. In accordance with theoretical expectations, genetic variability decreased and population substructuring increased as a negative function of (effective) population size. Southern Swedish common frogs are naturally exposed to higher levels of nitrates, and thus have a higher tolerance to high nitrate levels than their northern conspecifics. This suggests local adaptation to naturally varying nitrate levels. Consequently, increased anthropogenic supplementation of nitrate could impact more the northern than the southern Swedish common frog populations. Exposure to the pesticides azoxystrobin, cyanazine and permethrin at ecologically relevant concentrations had small or no effects on R. temporaria tadpoles. The populations with lowest microsatellite variation (fragmented populations) in southern Sweden had considerably lower fitness in terms of survival and growth as compared to those with the highest genetic variability (non-fragmented populations). The results indicate that populations with low levels of neutral genetic variability were phenotypically less differentiated than populations with higher levels of variability. One possible explanation for this is that the degree of population differentiation in low variability populations has been constrained due to lack of suitable genetic variation or inefficiency of selection relative to genetic drift.

In this thesis, molecular genetic methods were used to study a threatened species, the Eurasian otter. Estimates of population size and population dynamics parameters were obtained, the genetic effects of a restocking program was evaluated, and a population viability analysis was conducted to assess which demographic parameters are most important for the future viability of an otter population. Many of the studies were based on noninvasive genetic sampling of faeces. In the genetic evaluation of the restocking program, it was found that the released otters had contributed to subsequent generations. However, the effects were to a large degree limited to the near surroundings of the release areas. Comparison of two census methods, snow-tracking and noninvasive genetic census based on faeces, showed that approximately only half of the otters detected with the genetic census were found with the snow-tracking census. It is recommended to combine these two methods to obtain the most reliable estimates of population size. A short-term study on population dynamics in otters showed that apparent survival was higher in females than in males and that the rate of addition was also high and likely influenced by migration. The population viability analysis incorporated both genetics and demography and revealed that survival to first reproduction was the most crucial demographic parameter affecting the viability of the study population. This result suggests that conservation efforts should be focused on protocols that enhance the survival prospects of young females. Environmental stochasticity was also found to have large effects on the probability of extinction of this population.

The extinction risk of threatened species has traditionally been assessed by the use of tools of Population Viability Analysis (PVA). Species interactions, however, have seldom been accounted for in PVA:s. The omission of species interactions in risk assessments may further lead to serious mistakes when setting target sizes of populations. Even a slight abundance decrease of a target species may result in changes of the community structure; in the worst case leading to a highly impoverished community. Of critical importance to conservation is therefore the question of how many individuals of a certain population that is needed in order to avoid this kind of consequences. In the current study, a stochastic multispecies model is used to estimate minimum ecological viable populations (MEVP); earlier defined as “the minimum size of a population that can survive before itself or some other species in the community becomes extinct”. The MEVP:s are compared to population sizes given by a single species model where interactions with other species are treated as a constant source incorporated in the species specific growth rate. MEVP:s are found to be larger than the population sizes given by the single species model. The results are trophic level dependent and multispecies approaches are suggested to be of major importance when setting target levels for species at the basal level. Species at higher trophic levels, however, are altogether more prone to extinction than species at the basal level, irrespective of food web size and food web complexity.

Vildbiet guldsandbi (Andrena marginata F.) har en central roll i jordbrukslandkapet som en viktig pollinatör av grödor och vilda växter. I Sverige hotas artens fortlevnad av biotopförlust, habitatfragmentering och födobrist. En av de viktigaste näringskällorna är växten ängsvädd (Succisa pratensis M.) som tidigare var vanligt förekommande men som nu minskar i sin utbredning. Syftet med denna studie var att utreda om populationsstorlekarna av guldsandbi och ängsvädd är relaterade. Guldsandbinas observationsbaserad populationsstorlek uppskattades samt att ängsväddens bestånd inventerades vid fyra lokaler i Övre Klarälvsdalen, i norra Värmland. Binas populationsstorlek uppskattades genom transektinventeringar mellan 30 juli och 11 augusti 2013. Under perioden observerades totalt 286 honor och per observationsdag noterades ett medelvärde på 40,86 (± 8,1 SE, 95% konfidensintervall; n=7) honor. Ängsväddpopulationen uppskattades till totalt 2328 växter från alla fyra områden. Det fanns inget statistiskt samband mellan populationsstorlekarna av ängsvädd och guldsandbin. En jämförelse mellan den för biet förväntade populationsstorleken, baserad på förekomst av näringsväxten, och den observerade populationsstorleken, korrigerad för inventeringsbias, visade bra överensstämmelse vid två av fyra områden (8,4% respektive 5,7% från det teoretiska värdet) och dålig överensstämmelse vid de andra två områdena. Det kan mycket väl vara så att det finns en relation mellan populationerna i Övre Klarälvsdalen, men man måste öka antalet lokaler och ta hänsyn till ytterligare miljöfaktorer som påverkar både bina och växterna för att kunna dra säkrare slutsatser om ett samband. / The wild-bee Andrena marginata has a key function as an important pollinator of crops and wild plants in agriculture landscapes. The species’ persistence is threatened in Sweden due to loss of habitat, fragmentation and food scarcity. One of the most important food sources is the plant Succisa pratensis, which previously was very common but now has declining populations. The purpose of this study was to analyse if there was a relation between the population sizes of A. marginata and S. pratensis. The population size of the bees was estimated and the plant population was surveyed at four sites in the upper valley of the River Klarälven, Värmland. Bee population size was estimated by visual transect surveys conducted between 30 July and 11 August 2013. In this period a total of 286 females was observed, with a mean of 40,86 (± 8,1 SE, 95% confidence interval; n=7) per day. The total population size of S. pratensis from the four sites was estimated to 2328 plants. There was no significant correlation between the population sizes of the bees and the host plant. A comparison between the bee’s predicted theoretical population size, based on the number of host plants, and the observed population size, corrected for observer bias, showed good agreement for two of the sites (within 8,4% and 5,7% of the theoretical value) and poor agreement at the other two sites. There may well be a relation between the bee and plant populations in the upper valley of Klarälven, but one needs to increase the number of sites and take into account additional environmental factors that affect both the bees and the plants to draw a firmer conclusion about such a relationship.

Resumo: O objetivo deste estudo foi estimar parâmetros genéticos para caracteres de crescimento e forma em um teste de progênies de Eucalyptus cloeziana, com 24 anos de idade, estabelecido em Luiz Antônio, SP. O teste foi instalado com sementes de polinização aberta provenientes de 35 árvores matrizes oriundas de Helenvale e Cardwell St. Forest, Austrália. O delineamento experimental utilizado foi o de blocos ao acaso, com parcela composta por apenas uma planta, com 100 repetições. O ensaio foi mensurado aos 24 anos de idade para diâmetro a altura do peito (DAP), altura total, volume e forma. Foram detectadas diferenças significativas entre progênies para todos os caracteres avaliados. Foram detectados altos coeficientes de variação genética e herdabilidade para todos os caracteres estudados, o que demonstra um forte controle genético na herança destes e a possibilidade de se obter altos ganhos com a seleção massal e individual entre e dentro de progênies. Os ganhos esperados para plantios com 24 anos de idade, realizados em locais com as mesmas características ambientais de Luiz Antônio e com sementes coletadas após a seleção no teste de progênies, foram estimados em 42,91% para DAP e 16,82% para altura / Abstract: The aim of this study was to estimate genetic parameter for growth and stem shape traits in a progeny test of Eucalyptus cloeziana, at 24 years old, established in Luiz Antônio, SP. The trial was established with open-pollinated seeds from 35 mother trees from provenances Helenvale and Cardwell St. Forest, Australia. The trial was established in a random block design, with single tree plots and 100 replications. The trial was measured at 24 years old of age for diameter at breast height (DBH), total height, volume and stem shape. All studied traits presented significant differences among progenies. All studied traits presented also high coefficient of variation and heritability, showing a strong genetic control in this traits and the possibility to obtain genetic gains by massal and among and within progenies selection. The expected genetic gains for stands with 24 years old, growing in sites with the same environmental characteristics of Luiz Antônio and with seeds collected after selection in the progeny test were estimated in 42.91% for DAP and 16.82% for height / Orientador: Miguel Luiz Menezes Freitas / Coorientador: Mario Luiz Teixeira de Moraes / Banca: Walter Veriano Valério Filho / Banca: Rinaldo César de Paula / Mestre