Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.

Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.

Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea.

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40-60 degrees) and elevational (350-3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.

Lead exposure and biological effects in pied flycatchers (Ficedula hypoleuca) before and after the closure of a lead mine in northern Sweden.

Mining activities affect the surrounding environment by increasing exposure to metals. In this study, metal accumulation and its effects on reproduction and health of pied flycatcher (Ficedula hypoleuca) nestlings were monitored before and up to five years after a lead mine and enrichment plant closed down. The lead concentration in moss, nestling blood, liver and feces all indicated decreased lead exposure by at least 31% after closure, although only blood lead decreased significantly. Although the birds responded fairly well to the changed atmospheric deposition (based on moss samples), concentrations were still higher compared with birds in a reference area, and breeding was affected at the mine (smaller clutches and higher mortality). Surviving nestlings suffered from lower hemoglobin levels, mean cell hemoglobin concentrations and inhibited delta-aminolevulinic acid dehydratase activity. Lead poisoning contributed to poor health and adverse reproductive effects, but other factors (e.g. increased parasitic load) probably also affected the birds.

An excess of nonsynonymous polymorphism and extensive haplotype structure at the PtABI1B locus in European aspen (Populus tremula): a case of balancing selection in an obligately outcrossing plant?

Here, we describe an unusually pronounced haplotype structure at the PtABI1B locus in the obligately outcrossing tree Populus tremula. Both nucleotide diversity and divergence at PtABI1B was low compared to other P. tremula genes suggesting that the gene is located in a region with a low mutation rate. Despite this, PtABI1B shows a very marked excess of nonsynonymous polymorphisms across the entire coding region and linkage disequilibrium (LD) extending across the entire PtABI1B region of approximately 2.6 kb. Such extensive LD is normally not seen in P. tremula. The extensive LD at PtABI1B is caused by the presence of two distinct haplotypes. The haplotype structure is not caused by a lack of recombination in the region, because evidence of recombination can be detected. In addition, several statistical tests strongly reject neutrality for the PtABI1B region, suggesting that the unusual haplotype structure could be actively maintained by balancing selection.

Restoration of genetic variation lost - the genetic rescue hypothesis.

It has been long known that immigrants from surrounding populations might prevent the extinction of small populations, a process known as the 'rescue effect'. This focuses on the demographic effects of migration through the direct positive influence that immigrants have on abundance of the recipient population. Now, two recent papers have indicated another potentially important way that migration might rescue populations from extinction - replenishing genetic variation and reducing inbreeding depression, or what has been termed 'genetic rescue'.

Heterosis increases the effective migration rate.

Individuals coming from the same subpopulation are more likely to share deleterious mutations at any given locus than hybrids formed between parents from different populations. Offspring of migrants therefore may experience heterosis and have higher fitness than resident individuals. This will, in turn, result in the immigrant alleles being present in higher frequencies than predicted from neutral expectations and thus a higher effective migration rate. In this paper we derive a formula to calculate the effective migration rate in the presence of heterosis. It is shown that the effect of heterosis on the migration rate can be substantial when fitness reduction within local populations is severe. The effect will be more pronounced in species with relatively short map lengths. Furthermore the heterosis effect will be highly variable throughout the genome, with the largest effect seen near selected genes and in regions of high gene density.

Differential migration from high fitness demes in the shining fungus beetle, Phalacrus substriatus.

Using data from three years (1994-1996), I tested whether differential migration occurs from demes of high mean fitness in the shining fungus beetle, Phalacrus substriatus. The results show evidence for differential migration, thus providing evidence from a natural population for a critical demographic assumption of many interdemic selection models. To predict the evolutionary response to interdemic selection through differential migration, the genetic basis of the variation among demes in mean fitness must be known because the observed patterns could also be explained by some demes having an intrinsically favorable habitat. Thus, the importance of differential migration through interdemic selection in natural populations cannot be unequivocally answered without experiments specifically addressing the question of what causes differences in mean fitness among demes.

Local drift load and the heterosis of interconnected populations.

We use Wright's distribution of equilibrium allele frequency to demonstrate that hybrids between populations interconnected by low to moderate levels of migration can have large positive heterosis, especially if the populations are small in size. Beneficial alleles neither fix in all populations nor equilibrate at the same frequency. Instead, populations reach a mutation-selection-drift-migration balance with sufficient among-population variance that some partially recessive, deleterious mutations can be masked upon crossbreeding. This heterosis is greatest with intermediate mutation rates, intermediate selection coefficients, low migration rates and recessive alleles. Hybrid vigour should not be taken as evidence for the complete isolation of populations. Moreover, we show that heterosis in crosses between populations has a different genetic basis than inbreeding depression within populations and is much more likely to result from alleles of intermediate effect.

Population dynamics of resource limited plants and their pollinators.

In this paper we build upon and generalize an earlier model of the interactions between a plant and its pollinator (Ingvarsson and Lundberg, 1995). In this model we assume that the performance of the pollinator population is directly linked to the size of the plant population. To avoid the problem of both populations growing exponentially we have, without loss of generality, assumed the plant population to be resource limited. Analysis of the system shows that there exists either two or no internal equilibrium points. The case with no equilibrium points corresponds to the trivial case where the system cannot persist, resulting in the extinction of both the plant and pollinator population. When the two internal equilibrium points do exist, one of them will always be unstable. This unstable equilibrium can be viewed as an equivalent of the threshold criteria derived in Ingvarsson and Lundberg (1995) in the sense that whenever the system is initiated above the unstable equilibrium point, persistence of the system is assured, while both species will go extinct whenever the system is initiated below the unstable equilibrium point. The analytical results were verified by numerical simulations of the system. We conclude that the existence of a threshold criteria, below which the system cannot persist is a general feature of plant-pollinator systems. We discuss how the existence of the threshold criteria will affect the persistence of plant-pollinator systems in light of, for instance, habitat fragmentation or stochastic reductions in the densities of either the plant or pollinator population. We further highlight some recent empirical studies that indicate the existence of a threshold in natural populations below which extinction is inevitable.