Logo: to the web site of Uppsala University

Background: Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. Results: The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. Conclusion: The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.

A large number of bird species live in stable groups, and this sets the scene for complex social behaviours, such as cooperative breeding. The vast majority of groups consist of families which arise when young postpone dispersal and remain with their parents beyond independence. However, the factors selecting for the evolution of families and thus also cooperative breeding among birds, are still a challenging puzzle. The currently accepted key explanation for the evolution of families and cooperative breeding focuses on dispersal constraints. While constraints successfully explain within‐population dispersal decisions, they fail as an ultimate explanation because offspring in the majority of species face some sort of dispersal constraint, yet still disperse promptly. Recent alternative explanations focus on the role of philopatry and nepotism, and emphasise a key role of life‐history for the evolution of families. Phylogenetic analyses and field studies have indicated that living in family groups is far more widespread among long‐lived species than short‐lived ones. A long lifespan gives parents the opportunity to invest in their offspring for a prolonged period, while this option is less viable for short‐lived species. Thus, living with nepotistic parents provides offspring with direct fitness benefits that can select for the evolution of family living beyond independence. Nevertheless this generalisation is brought into question since many long‐lived bird species do not live in family groups. An alternative approach attempts to explain family living through the variation in territory quality. Here the incentive to remain with the parents is created by the availability of resources on the natal territory independent of parental nepotism. However, there is not only cooperation, conflicts are also common place in families. Living with independent, sexually mature offspring can lead to conflicts through a change in resource availability or the death of aparent. Therefore families can be expected to be dynamic societies where both parent and offspring decisions depend on each other, and family maintenance depends upon the current ecological conditions. Based on  this background, here we review recent studies that have investigated the processes that facilitate family formation, and which highlight both cooperation and conflict that arises from living in family groups. We examine the strengths of current models and explore ideas for a more coherent framework in which to understand prolonged family association in birds. We argue that two paths lead to family living, depending on the life-history. In medium-short lived species where the postponement of independent reproduction comes at a high cost, offspring can benefit from an association with their parents until the next breeding season. In longer-lived species, offspring actually benefit from postponing the onset of independent reproduction, making family living beyond the first year of life an adaptive strategy, and giving the option for cooperative breeding. These processes are illustrated by 5 species-specific case studies. We then finally suggest a number of key questions to developing a deeper understanding of the evolution of family living in birds.

Background: There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (similar to 10(-3)) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance.

Results: We sequenced 18 autosomal protein coding loci from approximately 15-18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (pi(t)) was between 1.30 x 10(-4) and 7.66 x 10(-3) (average pi(t) = 2.72 x 10(-3) +/- 2.06 x 10(-3)) and silent nucleotide diversity varied between 4.20 x 10(-4) and 2.76 x 10(-2) (average pi(S) = 9.22 x 10(-3) +/- 7.43 x 10(-4)). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 x 10(-3) (average pi(a) = 5.08 x 10(-4) +/- 7.43 x 10(3)), which suggest that purifying selection is strong in these genes. F-ST values based on synonymous SNP's varied between -5.60 x 10(-4) and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of F-ST = 0.03 (95% CI: 0.006 -0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r(2) = 0.084 +/- 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (rho) was comparably high (0.028 +/- 0.018), indicating high recombination rates in these genes.

Conclusion: We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.

We found all developmental stages of the midge Telmatogeton japonicus (Chironomidae) on offshore windmills near the major Swedish seaport Kalmar in the southern Baltic Sea. This might be the first record of an insect species really inhabiting the offshore areas of the Baltic Sea. A thorough analysis of previous findings of the species, its history in Europe and its ecology indicates that T. japonicus quite likely is an alien species in Europe introduced from the Pacific Ocean. Shipping is probably the vector, as all records in the Baltic Sea and several from the Eastern Atlantic Sea are near major seaports. Our analysis further suggests that T. japonicus might be both advantageous and disadvantageous to native species in the Baltic Sea. T. japonicus should be kept under observation within monitoring programmes as it might expand its distribution as a result of the construction of new windmills in the Baltic Sea and elsewhere in European marine and brackish water habitats.

A new species of the chironomid genus Tavastia was frequently collected in wetlands of the River Dalalven lowlands in central Sweden from 2002 to 2007. Unpublished data revealed that the species has been known from Finland since 1974. The new species T. yggdrasilia can be separated from other Tavastia species by the combination of a gonostylus with strong crista dorsalis in proximal half, AR 0.93-1.16, and wing veins M3+4 and Cu1 without setae. A description of the male and the female is included, as is also a key to the males of the four known species of Tavastia. All records of T. yggdrasilia are from sites with mesotrophic or eutrophic conditions.

The scarce heath (Coenonympha hero) is an internationally threatened butterfly in Western Europe, where it occurs primarily on hay fields and abandoned arable land in a small-scale agricultural landscape of south-central Scandinavia. Due to afforestation, this habitat is becoming increasingly fragmented in Sweden, and it can be expected that the scarce heath will decline abruptly when threshold conditions for metapopulation persistence are no longer met. We used stepwise polychotomous logistic regression to compare habitat characteristics and isolation measures for patches that harbour large, small or no populations, respectively, in an area of south-western Sweden. We found that patch area, distance to the nearest large population and amount of Galium spp. explained a significant part of the variation in relative abundance among patches. Distance to nearest large population resulted in a better model to predict occupancy than both distance to the nearest inhabited patch and connectivity, which suggests that primarily large populations act as sources for small satellite populations. Today, sites of three of the eight larger populations in the study area have been planted with spruce or pine and will disappear within 20 years. We argue that the disappearance of these patches may very well lead to rapid extinction of the whole metapopulation system.

The reason why some bird species live in family groups is an important question of evolutionary biology that remains unanswered. Families arise when young delay the onset of independent reproduction and remain with their parents beyond independence. Explanations for why individuals forgo independent reproduction have hitherto focused on dispersal constraints, such as the absence of high-quality breeding openings. However, while constraints successfully explain within-population dispersal decisions, they fail as an ultimate explanation for variation in family formation across species. Most family-living species are long-lived and recent life-history studies demonstrated that a delayed onset of reproduction can be adaptive in long-lived species. Hence, delayed dispersal and reproduction might be an adaptive life-history decision rather than ‘the best of a bad job’. Here, we attempt to provide a predictive framework for the evolution of families by integrating life-history theory into family formation theory. We suggest that longevity favours a delayed onset of reproduction and gives parents the opportunity of a prolonged investment in offspring, an option which is not available for short-lived species. Yet, parents should only prolong their investment in offspring if this increases offspring survival and outweighs the fitness cost that parents incur, which is only possible under ecological conditions, such as a predictable access to resources. We therefore propose that both life-history and ecological factors play a role in determining the evolution of family living across species, yet we suggest different mechanisms than those proposed by previous models.

The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

An analysis of reproductive success in the green woodhoopoe Phoeniculus purpures challenges the view that delayed dispersal is costly. Females delaying dispersal for longer had more reproductive events in life and higher lifetime production of offspring.

We found low, albeit significant, genetic differentiation among turbot (Psetta maxima) in the Baltic Sea but in contrast to earlier findings we found no evidence of isolation by distance. In fact temporal variation among years in one locality exceeded spatial variation among localities. This is an unexpected result since adult turbot are sedentary and eggs are demersal at the salinities occurring in the Baltic. Our findings are most likely explained by the fact that we sampled fish that were born after/during a large influx of water to the Baltic Sea, which may have had the consequence that previously locally and relatively sedentary populations became admixed. These results suggest that populations that colonize relatively variable habitats, like the Baltic, face problems. Any adaptations to local conditions that may build up during stable periods may quickly become eroded when conditions change and/or when populations become admixed. Our results indicate that the ability of turbot to survive and reproduce at the low salinity in the Baltic is more likely due to phenotypic plasticity than a strict genetic adaptation to low salinity.

An increasing number of studies have demonstrated phenotypic plasticity in brain size and architecture in response to environmental variation. However, our knowledge on how brain architecture is affected by commonplace ecological interactions is rudimentary. For example, while intraspecific competition and risk of predation are known to induce adaptive plastic modifications in morphology and behaviour in a wide variety of organisms, their effects on brain development have not been studied. We studied experimentally the influence of density and predation risk on brain development in common frog (Rana temporaria) tadpoles. Tadpoles grown at low density and under predation risk developed smaller brains than tadpoles at the other treatment combinations. Further, at high densities, tadpoles developed larger optic tecta and smaller medulla oblongata than those grown at low densities. These results demonstrate that ecological interactions - like intraspecific competition and predation risk - can have strong effects on brain development in lower vertebrates.

Predation is a powerful agent of natural selection, driving the evolution of antipredator calls [1]. These calls have been shown to communicate predator category [2-4] and/or predator distance to conspecifics [5-7]. However, the risk posed by predators depends also on predator behavior [8], and the ability of prey to communicate predator behavior to conspecifics would be a selective advantage reducing their predation risk. I tested this idea in Siberian jays (Perisoreus infaustus), a group-living bird species. Predation by hawks, and to a lesser extent by owls, is substantial and the sole cause of mortality in adult jays [9]. By using field data and predator-exposure experiments, I show here that jays used antipredator calls for hawks depending on predator behavior. A playback experiment demonstrated that these prey-to-prey calls were specific to hawk behavior (perch, prey search, attack) and elicited distinct, situation-specific escape responses. This is the first study to demonstrate that prey signals convey information about predator behavior to conspecifics. Given that antipredator calls in jays aim at protecting kin group members [10, 11], consequently lowering their mortality [9], kin-selected benefits could be an important factor for the evolution of predator-behavior-specific antipredator calls in such systems.

Prey often use visual cues to detect predators, and consequently, many studies have assessed the effect of small-scale habitat structure on prey antipredator vigilance. This scale may be inappropriate to assess the link between habitat structure and vigilance, however, because visually hunting predators often detect prey from several hundred meters away. As a result, large-scale habitat structure could affect both the hunting decisions of predators and antipredator behaviors of prey. Here we investigated the effect of small- and large-scale habitat structure, as well as group composition (kinship) on vigilance allocation of breeders in the Siberian jay Perisoreus infaustus. Vigilance had an antipredator function and was increased after exposure to a predator model. Small-scale habitat structure did not affect vigilance rates, however, habitat structure of the whole territory, measured as the proportion of visual cover, affected vigilance depending on group composition. Breeders with retained offspring (kin) in their group were more vigilant in managed open territories than on pristine dense territories, whereas breeders without kin in their groups did not adjust vigilance rates in relation to large-scaled habitat structure. Earlier studies have revealed that hawks, the main predators of jays, primarily kill non-kin group members living in groups inhabiting open territories. Therefore, we suggest that breeders adjusted their vigilance depending on the habitat-specific predation risk to protect their retained offspring. This demonstrates that large-scale habitat structure affects predator-prey interactions and is crucial to understanding spatial variation in antipredator allocation and mortality.