Veronika N. Laine

Evolutionary signals of selection on cognition from the great tit genome and methylome

For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

Next generation sequencing of fecal DNA reveals the dietary diversity of the widespread insectivorous predator Daubenton's Bat (Myotis daubentonii) in Southwestern Finland.

Understanding predator-prey dynamics is a fundamental task in the evaluation of the adaptive capacities of species. However, direct observations or morphological identification of fecal remains do not offer an effective way to study the dietary ecology of elusive species, such as nocturnal insectivorous bats. However, recent advances in molecular techniques have opened a new method for identifying prey species from fecal samples. In this study, we amplified species-specific mitochondrial COI fragments from fecal DNA extractions from 34 individual Daubenton’s bats (Myotis daubentonii) collected between 2008 and 2010 from southwestern Finland. Altogether, 128 different species of prey were identified based on a comprehensive local DNA reference library. In our study area, Daubenton’s bats feed most frequently on insects of the orders Diptera (found in the diet of 94% individuals), Trichoptera (69%) and Lepidoptera (63%). The most frequent dipteran family in the diet was Chironomidae, which was found in 31 of 34 individuals. Most common prey species were chironomids Microtendipes pedellus (found in 50% of bats), Glyptotendipes cauliginellus (44%), and Procladius ferrugineus (41%). For the first time, an accurate species level list of the diet of the insectivorous Daubenton’s bat (Myotis daubentonii) in Finland is presented. We report a generally applicable method for describing the arthropod diet of vertebrate predators. We compare public databases to a national database to highlight the importance of a local reference database.

Quantitative trait loci for growth and body size in the nine-spined stickleback Pungitius pungitius L.

Body size is an ecologically important trait shown to be genetically variable both within and among different animal populations as revealed by quantitative genetic studies. However, few studies have looked into underlying genetic architecture of body size variability in the wild using genetic mapping methods. With the aid of quantitative trait loci (QTL) analyses based on 226 microsatellite markers, we mapped body size and growth rate traits in the nine‐spined stickleback (Pungitius pungitius) using an F2‐intercross (n = 283 offspring) between size‐divergent populations. In total, 17 QTL locations were detected. The proportion of phenotypic variation explained by individual body size‐related QTL ranged from 3% to 12% and those related to growth parameters and increments from 3% to 10%. Several of the detected QTL affected either early or late growth. These results provide a solid starting point for more in depth investigations of structure and function of genomic regions involved in determination of body size in this popular model of ecological and evolutionary research.

What you need is what you eat? Prey selection by the bat Myotis daubentonii.

Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behaviour – yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual‐level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators.

Genetic Architecture of Parallel Pelvic Reduction in Ninespine Sticklebacks

Teleost fish genomes are known to be evolving faster than those of other vertebrate taxa. Thus, fish are suited to address the extent to which the same vs. different genes are responsible for similar phenotypic changes in rapidly evolving genomes of evolutionary independent lineages. To gain insights into the genetic basis and evolutionary processes behind parallel phenotypic changes within and between species, we identified the genomic regions involved in pelvic reduction in Northern European ninespine sticklebacks (Pungitius pungitius) and compared them to those of North American ninespine and threespine sticklebacks (Gasterosteus aculeatus). To this end, we conducted quantitative trait locus (QTL) mapping using 283 F2 progeny from an interpopulation cross. Phenotypic analyses indicated that pelvic reduction is a recessive trait and is inherited in a simple Mendelian fashion. Significant QTL for pelvic spine and girdle lengths were identified in the region of the Pituitary homeobox transcription factor 1 (Pitx1) gene, also responsible for pelvic reduction in threespine sticklebacks. The fact that no QTL was observed in the region identified in the mapping study of North American ninespine sticklebacks suggests that an alternative QTL for pelvic reduction has emerged in this species within the past 1.6 million years after the split between Northern European and North American populations. In general, our study provides empirical support for the view that alternative genetic mechanisms that lead to similar phenotypes can evolve over short evolutionary time scales.

Impact of tributyltin on immune response and life history traits of Chironomus riparius: single and multigeneration effects and recovery from pollution.

Chironomids play an important role in the detritus cycle and as a component in brackish- and freshwater benthic and terrestrial food webs. If TBT is present in their environment, then they may accumulate tributyltin (TBT) during their juvenile period, which negatively affects many of their life history characteristics. The aim of this experiment is to test the effects of three TBT sediment concentrations (nominal 30, 90, and 180 μg/kg) on life history traits (development time, survival, fecundity, and weight) and immune response (number of hemocytes and phenoloxidase activity) of the nonbiting midge, Chironomus riparius. These responses were recorded immediately after one generation of TBT exposure, and in the long run during five consecutive generations. We also assessed recovery from pollution after four generations of TBT exposure. In a single generation, TBT affected all measured parameters, except phenoloxidase activity, when compared to the control. Long-term-effects of TBT lead to extinction of all treatments after the fifth generation. Again, all measured variables significantly differ from the control, although TBT had varying effects on the measured variables. Most of the effects of TBT on population viability were not evident during recovery, once TBT was removed from the sediment. The effect of previous TBT contamination was observed only in delayed larval development, suggesting that TBT has only limited maternal/epigenetic effects on individual condition. However, altered schedules in the life-cycle can have unexpected ecological impacts. TBT decreases the viability of Chironomus riparius and the effect will become stronger if exposure to TBT continues for many generations. Yet, the harmful effect of TBT disappears quickly as the TBT is removed from the environment.

Resistance to oxidative damage but not immunosuppression by organic tin compounds in natural populations of Daubenton's bats (Myotis daubentonii).

The acute toxicity of organic tin compounds (OTCs) has been studied in detail. However, due to their complex nature, very little is known about species-specific methods of accumulation and consequences for food-webs. Chironomids, on which e.g. Daubentons bats feed, may act as vectors for the transport of organic tin compounds from aquatic to terrestrial ecosystems. Bats are prone to environmental toxins because of their longevity and their ecological role as top predators. Organic tin compounds are associated with increased formation of reactive oxygen species and associated oxidative damage as well as suppression of immune function. The present paper investigates whether the OTC, tributyltin (TBT) and its metabolite, dibutyltin (DBT), accumulate in natural populations of Daubentons bats and whether TBT-associated effects are seen in general body condition, redox balance, redox enzyme activities, associated oxidative damage of red blood cells and complement function. We discovered the concentration of bat fur DBT correlated with local marine sediment TBT concentrations. However, we did not find a correlation between the explanatory factors, bat fur DBT and marine sediment TBT concentrations, and several physiological and physical response variables apart from complement activity. Higher DBT concentrations resulted in weaker complement activity and thus a weaker immune response. Although the observed physiological effects in the present study were not strongly correlated to butyltin concentrations in fur or sediment, the result is unique for natural populations so far and raises interesting questions for future ecotoxicological studies.

Recent natural selection causes adaptive evolution of an avian polygenic trait

Recent natural selection in a wild bird Many studies have found evidence of rapid evolution in response to environmental change. In most cases, there has been some suggestion of which traits might be most responsive ahead of time. Bosse et al. turn this approach on its head by using genomic regions with a signature of selection to identify traits that are changing. In great tits (Parus major) in the United Kingdom, genomic regions showing selection invariably contained genes associated with bill growth. Indeed, U.K. birds not only have longer bills, but these longer bills are associated with increased fitness. These changes likely reflect an increase in domestic garden bird feeders over the past several decades. Science, this issue p. 365 Genomic regions under selection reveal that bills have lengthened in great tits in the UK. We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.

Heterozygosity-behaviour correlations in nine-spined stickleback (Pungitius pungitius) populations: contrasting effects at random and functional loci.

The study of heterozygosity‐fitness correlations (HFCs) has a long history in the fields of ecology and evolutionary biology but remains controversial. Recently, it has been shown that the genetic distance of markers from functional loci can be an important factor to be considered in addition to marker numbers and variability. In this study, we investigated the correlation between individual heterozygosity and behaviour (aggression, boldness and feeding activity) in nine‐spined stickleback (Pungitius pungitius) individuals originating from four populations in two contrasting environments. Offspring of full‐sib families raised in a common garden setting were assessed for behaviour and genotyped using 84 microsatellite markers that were either located within or near behaviourally or physiologically important genes (termed ‘functional’) or were randomly selected. No associations were detected with any behavioural trait in any population or over all populations when genetic variability was measured using all 84 markers combined. However, when the markers were separated into three functional categories (behavioural, physiological and random), several significant associations were observed both with functional markers and random markers in one of the four populations assessed. Interestingly, contrasting correlations with behaviour were observed when using physiological gene (negative) and random (positive) markers. Upon dividing the physiological gene markers into further subcategories based on their specific physiological functions, a strong relationship between the heterozygosity of markers linked to osmoregulation‐related genes, and behaviour was revealed in the brackish water population. Our results indicate that both local (physiological) and general (neutral) effects are important in shaping behaviour and that heterozygosity–behaviour correlations are population dependent.

Isolation and Characterization of 13 New Nine-Spined Stickleback, Pungitius pungitius, Microsatellites Located Nearby Candidate Genes for Behavioural Variation

Nine-spined stickleback (Pungitius pungitius) is a good model species for studying personality traits such as boldness and aggression as large variation in these behaviours has been observed in populations from different habitats. Here we used genomic information from three-spined sticklebacks to identify and characterise 13 new nine-spined stickleback microsatellite loci which are located close to candidate genes for behaviour. All loci were polymorphic with 3–31 alleles per locus and expected heterozygosity varied from 0 to 0.97 and observed heterozygosity from 0 to 1. These markers should provide a useful resource for better understanding the genetic basis of behaviour in stickleback fishes.