Genomic Response to Selection for Predatory Behavior in a Mammalian Model of Adaptive Radiation

Evolutionary trade-offs constraining the MHC gene expansion: beyond simple TCR depletion model

The immune system is as much shaped by the pressure of pathogens as it is by evolutionary trade-offs that constrain its structure and function. A perfect example comes from the major histocompatibility complex (MHC), molecules that initiate adaptive immune response by presentation of foreign antigens to T cells. The remarkable, population-level polymorphism of MHC genes is assumed to result mainly from a co-evolutionary arms race between hosts and pathogens, while the limited, within-individual number of functional MHC loci is thought to be the consequence of an evolutionary trade-off between enhanced pathogen recognition and excessive T cell depletion during negative selection in the thymus. Certain mathematical models and infection studies suggest that an intermediate individual MHC diversity would thus be optimal. A recent, more direct test of this hypothesis has shown that the effects of MHC diversity on T-cell receptor (TCR) repertoires may differ between MHC classes, supporting the depletion model only for MHC class I. Here, we used the bank vole (Myodes=Cletronomys glareolus), a rodent species with variable numbers of expressed MHC genes, to test how an individual MHC diversity influences the proportions and TCR repertoires of responding T cell subsets. We found a non-linear relationship between MHC diversity and T cell proportions (with intermediate MHC numbers coinciding with the largest T cell proportions), perhaps reflecting an optimality effect of balanced positive and negative thymic selection. The association was strongest for the relationship between MHC class I and splenic CD8+ T cells. The CD8+ TCR richness alone was unaffected by MHC class I diversity, suggesting that MHC class I expansion may be limited by decreasing T cell counts, rather than by direct depletion of TCR richness. In contrast, CD4+ TCR richness was positively correlated with MHC class II diversity, arguing against a universal TCR depletion. It also suggests that different evolutionary forces or trade-offs may limit the within-individual expansion of the MHC class II loci.

Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails

(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.

Artificial selection for predatory behaviour results in dietary niche differentiation in an omnivorous mammal

The diet of an individual is a result of the availability of dietary items and the individual's foraging skills and preferences. Behavioural differences may thus influence diet variation, but the evolvability of diet choice through behavioural evolution has not been studied. We used experimental evolution combined with a field enclosure experiment to test whether behavioural selection leads to dietary divergence. We analysed the individual dietary niche via stable isotope ratios of nitrogen (δ¹⁵N) and carbon (δ¹³C) in the hair of an omnivorous mammal, the bank vole, from four lines selected for predatory behaviour and four unselected control lines. Predatory voles had higher hair δ¹⁵N values than control voles, supporting our hypothesis that predatory voles would consume a higher trophic level diet (more animal versus plant foods). This difference was significant in the early but not the late summer season. The δ¹³C values also indicated a seasonal change in the consumed plant matter and a difference in food sources among selection lines in the early summer. These results imply that environmental factors interact with evolved behavioural tendencies to determine dietary niche heterogeneity. Behavioural selection thus has potential to contribute to the evolution of diet choice and ultimately the species' ecological niche breadth.

Flexibility and rigidity in hunting behaviour in rodents: is there room for cognition?

Predatory hunting is a complex species-typical behaviour involving different skills, some of which may include learning. This research aims to distinguish between rigid and flexible parts in live-insect hunting behaviour in nine herbivorous and granivorous rodent species, and to find out whether there is room for cognition in this activity. In laboratory experiments, all species studied manifest skilful attacks towards insects in a manner that is typical for specialised predators chasing a fleeing prey. Voles demonstrate a "core" and somewhat primitive scheme of a hunting pattern: approaching a potential victim, biting it, and then seizing and handling. Hamsters display the tendency to start their attacks by actions with paws, but they can achieve success only using teeth as well. Gerbils can successfully use both paws and teeth to start the attack, which brings their hunting behaviour closer to that of specialised rodent predators. We revealed variability in the display of hunting in different species, methods of seizing the prey, and the number of attempts to attack an insect before catching it. We found specific flexible fragments within the "bite-grasp-handle" bouts that can be precursors for adaptive phenotypic variations and include some cognitive attributes. We hypothesise that the divergence and specialisation of predatory behaviour in rodents can be based on the natural fragmentation of the original hunting patterns, that is, on the loss or recombination of particular behavioural elements. We consider a possible link between the fragmentation of hunting behaviour and social learning in different classes of animals and conjecture an intriguing correlation between predatory activity, cognitive skills and personal traits in rodents.

On the evolution of trophic position

The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.

Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice

The biological basis of exercise behavior is increasingly relevant for maintaining healthy lifestyles. Various quantitative genetic studies and selection experiments have conclusively demonstrated substantial heritability for exercise behavior in both humans and laboratory rodents. In the "High Runner" selection experiment, four replicate lines of Mus domesticus were bred for high voluntary wheel running (HR), along with four nonselected control (C) lines. After 61 generations, the genomes of 79 mice (9-10 from each line) were fully sequenced and single nucleotide polymorphisms (SNPs) were identified. We used nested ANOVA with MIVQUE estimation and other approaches to compare allele frequencies between the HR and C lines for both SNPs and haplotypes. Approximately 61 genomic regions, across all somatic chromosomes, showed evidence of differentiation; 12 of these regions were differentiated by all methods of analysis. Gene function was inferred largely using Panther gene ontology terms and KO phenotypes associated with genes of interest. Some of the differentiated genes are known to be associated with behavior/motivational systems and/or athletic ability, including Sorl1, Dach1, and Cdh10 Sorl1 is a sorting protein associated with cholinergic neuron morphology, vascular wound healing, and metabolism. Dach1 is associated with limb bud development and neural differentiation. Cdh10 is a calcium ion binding protein associated with phrenic neurons. Overall, these results indicate that selective breeding for high voluntary exercise has resulted in changes in allele frequencies for multiple genes associated with both motivation and ability for endurance exercise, providing candidate genes that may explain phenotypic changes observed in previous studies.

Does selection for behavioral and physiological performance traits alter glucocorticoid responsiveness in bank voles?

One of the key elements of an animal's Darwinian fitness is its ability to adequately respond to and cope with challenging situations. Glucocorticoid hormones, such as corticosterone, affect an organism's ability to overcome such challenges. We hypothesized that changes in the glucocorticoid response curve contribute to the evolution of increased performance during challenging conditions, and tested it on bank voles (Myodes glareolus) from a multidirectional artificial selection experiment, which involves lines selected for high aerobic exercise metabolism achieved during swimming (A - Aerobic), predatory behavior towards a cricket (P - Predatory) and ability to maintain body mass on a low-quality herbivorous diet (H - Herbivorous), as well as unselected control lines (C - Control). We elicited a glucocorticoid response either by restraining the animal or by maximum pharmacological stimulation, and measured plasma corticosterone levels at baseline, during the response and during the recovery phase. Response-level corticosterone was higher in females, and recovery from maximal level was faster than that of males. Selection did not affect baseline or stress-induced corticosterone levels, but it decreased the maximum corticosterone level in Aerobic and Predatory lines, reducing the difference between stress-induced and maximum levels. Recovery from restraint-induced corticosterone level tended to be slower in the Herbivorous than in the other lines, an effect that was stronger in females than in males. In conclusion, successful selection for increased performance in challenging conditions was not associated with changes in absolute values of the glucocorticoid response to stress, but can affect other characteristics of the glucocorticoid response curve.

Stress coping and evolution of aerobic exercise performance: corticosterone levels in voles from a selection experiment

The locomotor performance achieved in a challenging situation depends not only on physiological limitations, such as the aerobic exercise capacity, but also on behavioral characteristics, such as adequate coping with stress. The stress response is mediated largely by the hypothalamic-pituitary-adrenal (HPA) axis, through modulated release of glucocorticoids. We used a unique experimental evolution model system to test the hypothesis that the evolution of an increased aerobic exercise performance can be facilitated by modification of the glucocorticoid-related stress-coping mechanisms. Bank voles (Myodes glareolus) from 'aerobic' (A) lines, selected for 22 generations for high maximum swim-induced rate of oxygen consumption (V̇ _O2,swim), achieved a 64% higher V̇ _O2,swim than those from unselected, control lines. The temporal pattern of exercise during the swimming trial also evolved, and the A-line voles achieved V̇ _O2,swim later in the course of the trial, which indicates a modification of the stress response characteristics. Both V̇ _O2,swim and the average metabolic rate measured during the trial tended to increase with baseline corticosterone level, and decreased with the post-exercise corticosterone level. Thus, increased baseline corticosterone level promotes high metabolic performance, but a high corticosterone response to swimming acts as an inhibitor rather than stimulator of intense activity. However, neither of the corticosterone traits differed between the A-selected and control lines. Thus, the experiment did not provide evidence that evolution of increased aerobic performance is facilitated by the modification of glucocorticoid levels. The results, however, do not exclude the possibility that other aspects of the HPA axis function evolved in response to the selection.

The effect of monoamines reuptake inhibitors on aerobic exercise performance in bank voles from a selection experiment

Exercise performance depends on both physiological abilities (e.g., muscle strength) and behavioral characteristics (e.g., motivation). We tested the hypothesis that evolution of increased aerobic exercise performance can be facilitated by evolution of neuropsychological mechanisms responsible for motivation to undertake physical activity. We used a unique model system: lines of bank voles Myodes glareolus selected for high swim-induced aerobic metabolism ("aerobic" A lines). In generation 21, voles from the 4 A lines achieved a 57% higher "voluntary maximum" swim-induced aerobic metabolism (VO2swim) than voles from 4 unselected, "control" C lines. In C lines, VO2swim was 9% lower than the maximum forced-exercise aerobic metabolism (VO2run; P = 0.007), while in A lines it was even higher than VO2run, although not significantly (4%, P = 0.15). Thus, we hypothesized that selection changed both the aerobic capacity and the neuronal mechanisms behind motivation to undertake activity. We investigated the influence of reuptake inhibitors of dopamine (DARI), serotonin (SSRI), and norepinephrine (NERI) on VO2swim. The drugs decreased VO2swim both in C and A lines (% decrease compared with saline: DARI 8%, P < 0.001; SSRI 6%, P < 0.001; NERI 8%, P < 0.001), but the proportional response differed between selection directions only for NERI (stronger effect in C lines: P = 0.008) and the difference was marginally non-significant for SSRI (P = 0.07) and DARI (P = 0.06). Thus, the results suggest that all the 3 monoamines are involved in signaling pathways controlling the motivation to be active and that norepinephrine could have played a role in the evolution of increased aerobic exercise performance in our animal model.

Using the Data-Compression Method for Studying Hunting Behavior in Small Mammals

Using the data-compression method we revealed a similarity between hunting behaviors of the common shrew, which is insectivorous, and several rodent species with different types of diet. Seven rodent species studied displayed succinct, highly predictable hunting stereotypes, in which it was easy for the data compressor to find regularities. The generalist Norway rat, with its changeable manipulation of prey and less predictable transitions between stereotype elements, significantly differs from other species. The levels of complexities of hunting stereotypes in young and adult rats are similar, and both groups had no prior experience with the prey, so one can assume that it is not learning, but rather the specificity of the organization of the stereotype that is responsible for the nature of the hunting behavior in rats. We speculate that rodents possess different types of hunting behaviors, one of which is based on a succinct insectivorous standard, and another type, perhaps characteristic of generalists, which is less ordered and is characterized by poorly predictable transitions between elements. We suggest that the data-compression method may well be more broadly applicable to behavioral analysis.

Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra

Backgroud

Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra.

Results

We have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset.

Conclusions

We demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5239-z) contains supplementary material, which is available to authorized users.

Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden

Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High-throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. In particular, population genomics may provide preliminary insights into the genes shaping tolerance and potentially influencing epidemiological dynamics. Here, we addressed these questions in the bank vole Myodes glareolus, the specific asymptomatic reservoir host of Puumala hantavirus (PUUV), which causes nephropathia epidemica (NE) in humans. Despite the continuous spatial distribution of M. glareolus in Sweden, NE is endemic to the northern part of the country. Northern bank vole populations in Sweden might exhibit tolerance strategies as a result of coadaptation with PUUV. This may favor the circulation and maintenance of PUUV and lead to high spatial risk of NE in northern Sweden. We performed a genome-scan study to detect signatures of selection potentially correlated with spatial variations in tolerance to PUUV. We analyzed six bank vole populations from Sweden, sampled from northern NE-endemic to southern NE-free areas. We combined candidate gene analyses (Tlr4, Tlr7, and Mx2 genes) and high-throughput sequencing of restriction site-associated DNA (RAD) markers. Outlier loci showed high levels of genetic differentiation and significant associations with environmental data including variations in the regional number of NE human cases. Among the 108 outliers that matched to mouse protein-coding genes, 14 corresponded to immune-related genes. The main biological pathways found to be significantly enriched corresponded to immune processes and responses to hantavirus, including the regulation of cytokine productions, TLR cascades, and IL-7, VEGF, and JAK-STAT signaling. In the future, genome-scan replicates and functional experimentations should enable to assess the role of these biological pathways in M. glareolus tolerance to PUUV.

Experimental evolution of personality traits: open-field exploration in bank voles from a multidirectional selection experiment

Evolution of complex physiological adaptations could be driven by natural selection acting on behavioral traits. Consequently, animal personality traits and their correlation with physiological traits have become an engaging research area. Here, we applied a unique experimental evolution model-lines of bank voles selected for (A) high exercise-induced aerobic metabolism, (H) ability to cope with low-quality herbivorous diet, and (P) intensity of predatory behavior, that is, traits shaping evolutionary path and diversity of mammals-and asked how the selection affected the voles' personality traits, assessed in an open field test. The A- and P-line voles were more active, whereas the H-line voles were less active, compared those from unselected control lines (C). H-line voles moved slower but on more meandering trajectories, which indicated a more thorough exploration, whereas the A- and P-line voles moved faster and on straighter trajectories. A-line voles showed also an increased escape propensity, whereas P-line voles tended to be bolder. The remarkable correlated responses to the selection indicate a common genetic underlying mechanism of behavioral and physiological traits, and support the paradigm of evolutionary physiology built around the concept of correlated evolution of behavior and physiology.

Profiling of the TCRβ repertoire in non-model species using high-throughput sequencing

In recent years, immune repertoire profiling with high-throughput sequencing (HTS) has advanced our understanding of adaptive immunity. However, fast progress in the field applied mostly to human and mouse research, with only few studies devoted to other model vertebrates. We present the first in-depth characterization of the T-cell receptor (TCR) repertoire in a non-model mammal (bank vole, Myodes glareolus), widely used in ecological and evolutionary research. We used RNA from spleens, 5′RACE and HTS to describe V and J segments of TCRβ, qualitatively characterize preferential V–J segment usage and CDR3 length distribution. Overall orthology to murine genes was preserved, with 11 J and 37 V genes found in voles (although 3 V genes lacked a close orthologue). Further, we implemented unique molecular identifiers for quantitative analysis of CDR3 repertoire with stringent error correction. A conservative, lower bound estimation of the TCRβ repertoire was similar to that found for mice (1.7–2.3 × 10⁵ clonotypes). We hope that by providing an easy-to-follow molecular protocol and on-line bioinformatics tools that do not require reference sequences (AmpliTCR and AmpliCDR3), we will encourage HTS immune repertoire profiling in other non-model vertebrates, thus opening new research avenues in e.g. comparative immunology, ecology and evolutionary biology.

A Mixed Model Approach to Genome-Wide Association Studies for Selection Signatures, with Application to Mice Bred for Voluntary Exercise Behavior

Selection experiments and experimental evolution provide unique opportunities to study the genetics of adaptation because the target and intensity of selection are known relatively precisely. In contrast to natural selection, where populations are never strictly "replicated," experimental evolution routinely includes replicate lines so that selection signatures-genomic regions showing excessive differentiation between treatments-can be separated from possible founder effects, genetic drift, and multiple adaptive solutions. We developed a mouse model with four lines within a high running (HR) selection treatment and four nonselected controls (C). At generation 61, we sampled 10 mice of each line and used the Mega Mouse Universal Genotyping Array to obtain single nucleotide polymorphism (SNP) data for 25,318 SNPs for each individual. Using an advanced mixed model procedure developed in this study, we identified 152 markers that were significantly different in frequency between the two selection treatments. They occurred on all chromosomes except 1, 2, 8, 13, and 19, and showed a variety of patterns in terms of fixation (or the lack thereof) in the four HR and four C lines. Importantly, none were fixed for alternative alleles between the two selection treatments. The current state-of-the-art regularized F test applied after pooling DNA samples for each line failed to detect any markers. We conclude that when SNP or sequence data are available from individuals, the mixed model methodology is recommended for selection signature detection. As sequencing at the individual level becomes increasingly feasible, the new methodology may be routinely applied for detection of selection.

De novo transcriptome assembly facilitates characterisation of fast-evolving gene families, MHC class I in the bank vole (Myodes glareolus)

The major histocompatibility complex (MHC) plays a central role in the adaptive immune response and is the most polymorphic gene family in vertebrates. Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying MHC genes, its potential to facilitate early steps in the characterisation of MHC variation in nonmodel organism has not been fully explored. In this study we evaluated the usefulness of de novo transcriptome assembly in characterisation of MHC sequence diversity. We found that although de novo transcriptome assembly of MHC I genes does not reconstruct sequences of individual alleles, it does allow the identification of conserved regions for PCR primer design. Using the newly designed primers, we characterised MHC I sequences in the bank vole. Phylogenetic analysis of the partial MHC I coding sequence (2-4 exons) of the bank vole revealed a lack of orthology to MHC I of other Cricetidae, consistent with the high gene turnover of this region. The diversity of expressed alleles was characterised using ultra-deep sequencing of the third exon that codes for the peptide-binding region of the MHC molecule. High allelic diversity was demonstrated, with 72 alleles found in 29 individuals. Interindividual variation in the number of expressed loci was found, with the number of alleles per individual ranging from 5 to 14. Strong signatures of positive selection were found for 8 amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.