Consequences of Asexuality in Natural Populations: Insights from Stick Insects.

Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.

Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack.

BACKGROUND: Parasitoid resistance in Drosophila varies considerably, among and within species. An immune response, lamellocyte-mediated encapsulation, evolved in a subclade of Drosophila and was subsequently lost in at least one species within this subclade. While the mechanisms of resistance are fairly well documented in D. melanogaster, much less is known for closely related species. Here, we studied the inter- and intra-species variation in gene expression after parasitoid attack in Drosophila. We used RNA-seq after parasitization of four closely related Drosophila species of the melanogaster subgroup and replicated lines of D. melanogaster experimentally selected for increased resistance to gain insights into short- and long-term evolutionary changes. RESULTS: We found a core set of genes that are consistently up-regulated after parasitoid attack in the species and lines tested, regardless of their level of resistance. Another set of genes showed no up-regulation or expression in D. sechellia, the species unable to raise an immune response against parasitoids. This set consists largely of genes that are lineage-restricted to the melanogaster subgroup. Artificially selected lines did not show significant differences in gene expression with respect to non-selected lines in their responses to parasitoid attack, but several genes showed differential exon usage. CONCLUSIONS: We showed substantial similarities, but also notable differences, in the transcriptional responses to parasitoid attack among four closely related Drosophila species. In contrast, within D. melanogaster, the responses were remarkably similar. We confirmed that in the short-term, selection does not act on a pre-activation of the immune response. Instead it may target alternative mechanisms such as differential exon usage. In the long-term, we found support for the hypothesis that the ability to immunologically resist parasitoid attack is contingent on new genes that are restricted to the melanogaster subgroup.

Genomic changes under rapid evolution: selection for parasitoid resistance.

In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow 'selected regions'. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.

Social environment affects juvenile dispersal in great tits (Parus major).

1. Habitat selection can affect individual fitness, and therefore, individuals are expected to assess habitat quality of potential breeding sites before settlement. 2. We investigated the role of social environment on juvenile dispersal behaviour in the great tit (Parus major). Two main contradictory hypotheses can be formulated regarding social effects on juvenile dispersal as follows: (i) High fledgling density and sex ratio may enhance the intensity of local (kin) competition and, therefore, reduce individual survival chance, enhance emigration and reduce settlement ('repulsion' hypothesis) (ii) Alternatively, high fledgling density and sex ratio may signal high-quality habitat or lead to aggregation and thus increase individual survival chance, reduce emigration and enhance settlement ('attraction' hypothesis). 3. To disentangle positive from negative effects of high density and male-biased sex ratio on dispersal, we manipulated the social composition of the fledgling population in 12 semi-isolated nest-box areas (plots) via a change of fledgling density (low/high) as well as fledgling sex ratio (female-biased/balanced/male-biased) across 3 years. We then tested whether experimental variation in male and female fledgling densities affected variation in local survival, emigration and settlement of juveniles, and whether social effects on survival and dispersal support the 'repulsion' or 'attraction' hypothesis. 4. We found no experimental effects on local survival and emigration probabilities. However, consistent with the 'attraction' hypothesis, settlement was significantly and positively affected by local experimental sex ratio in each of the study years: both male and female juveniles avoided female-biased plots and settled more in plots that were balanced and male-biased the previous year. 5. Our study provides unprecedented experimental evidence that local sex ratio plays a causal role in habitat selection. We suggest that settlers avoid female-biased plots because a high proportion of females may reflect the absence or the low quality of local resources in the habitat. Alternatively, male territory acquisition may be facilitated by a high local density of 'candidate' males, and therefore, juveniles were less successful in settling in female-biased plots.

Natural and Artificial Selection for Parasitoid Resistance in Drosophila melanogaster Leave Different Genetic Signatures.

Adaptation of complex traits depends on standing genetic variation at multiple loci. The allelic variants that have positive fitness effects, however, can differ depending on the genetic background and the selective pressure. Previously, we interrogated the Drosophila melanogaster genome at the population level for polymorphic positions and identified 215 single nucleotide polymorphisms (SNPs) that had significantly changed in frequency after experimental evolution for increased parasitoid resistance. In the current study, we follow up on 11 of these SNPs as putative targets of the experimental selection process (Jalvingh et al., 2014). We study the patterns of genetic variation for these SNPs in several European field populations. Furthermore, we associate the genetic variation of these SNPs to variation in resistance against the parasitoid Asobara tabida, by determining the individual phenotype and SNP genotype for 144 individuals from four Selection lines and four non-selected Control lines and for 400 individuals from 12 Field lines that differ in parasitoid resistance. For the Selection lines we additionally monitored the changes in allele frequencies throughout the five generations of experimental selection. For three genes, mbl (Zn-finger protein), mthl4 (G-protein coupled receptor) and CG17287 (protein-cysteine S-palmitoyltransferase) individual SNP genotypes were significantly associated with resistance level in the Selection and Control lines. Additionally, the minor allele in mbl and mthl4 were consistently and gradually favored throughout the five generations of experimental evolution. However, none of these alleles did appear to be associated to high resistance in the Field lines. We suggest that, within field populations, selection for parasitoid resistance is a gradual process that involves co-adapted gene complexes. Fast artificial selection, however, enforces the sudden cumulating of particular alleles that confer high resistance (genetic sweep). We discuss our findings in the context of local adaptation.

Hormonal correlates and thermoregulatory consequences of molting on metabolic rate in a northerly wintering shorebird.

Even though molt involves both endocrine and energetic changes in bird bodies, this study is among the first to combine assessments of energy costs together with thyroid hormone variations in molting birds. Individual shorebirds (red knots Calidris canutus islandica) were measured while in full summer and winter plumage as well as during peak of molt. Molt was associated with a 9.8% increase in average mass-independent basal metabolic rate (BMR) above nonmolting levels. Individual plasma levels of thyroxine (T(4)) were correlated with individual rate of body feather renewal, confirming that T(4) is related to body molt but also showing that it is potentially regulating its rate. Across seasons, mass-independent average heat loss measured as conductance gradually declined with conductance during molt falling between measured values for summer and winter. During the molting period, however, body molting rate was positively correlated with thermal conductance, indicating that for a given ambient temperature below thermoneutrality, the fastest molting birds were losing more body heat. Across seasons, triiodothyronine (T(3)), a hormone typically upregulated in response to a cold stimulus, was correlated with individual thermal conductance and BMR. We suggest that the increased heat loss of fast-molting birds leads to a cold-acclimatization response that may be partly responsible for the elevated BMR measured during molt. This could be mediated through a stimulatory effect of T(3) on BMR in response to increased heat loss. Our interpretation is supported by a positive relationship between the individual changes in conductance and the change in BMR from summer to the molting period.

Thermogenic side effects to migratory predisposition in shorebirds.

In the calidrine sandpiper red knot (Calidris canutus), the weeks preceding takeoff for long-distance migration are characterized by a rapid increase in body mass, largely made up of fat but also including a significant proportion of lean tissue. Before takeoff, the pectoral muscles are known to hypertrophy in preparation for endurance flight without any specific training. Because birds facing cold environments counterbalance heat loss through shivering thermogenesis, and since pectoral muscles represent a large proportion of avian body mass, we asked the question whether muscle hypertrophy in preparation for long-distance endurance flight would induce improvements in thermogenic capacity. We acclimated red knots to different controlled thermal environments: 26 degrees C, 5 degrees C, and variable conditions tracking outdoor temperatures. We then studied within-individual variations in body mass, pectoral muscle size (measured by ultrasound), and metabolic parameters [basal metabolic rate (BMR) and summit metabolic rate (M(sum))] throughout a 3-mo period enclosing the migratory gain and loss of mass. The gain in body mass during the fattening period was associated with increases in pectoral muscle thickness and thermogenic capacity independent of thermal acclimation. Regardless of their thermal treatment, birds showing the largest increases in body mass also exhibited the largest increases in M(sum). We conclude that migratory fattening is accompanied by thermoregulatory side effects. The gain of body mass and muscle hypertrophy improve thermogenic capacity independent of thermal acclimation in this species. Whether this represents an ecological advantage depends on the ambient temperature at the time of fattening.

Acclimation to different thermal conditions in a northerly wintering shorebird is driven by body mass-related changes in organ size.

Seasonal acclimatization and experimental acclimation to cold in birds typically results from increased shivering endurance and elevated thermogenic capacity leading to improved resistance to cold. A wide array of physiological adjustments, ranging from biochemical transformations to organ mass variations, are involved in this process. Several studies have shown that improved cold endurance is accompanied by increases in summit metabolic rate (M(sum)), a measure of maximal heat production and an indicator of the level of sustainable thermogenic capacity. However, improved endurance to cold can also be achieved without significant changes in M(sum). The same is true for basal metabolic rate (BMR), which is known to increase in association with cold acclimatization or acclimation in some species but not in others. We investigated cold acclimation in a migrant shorebird known for extreme physiological flexibility, the red knot (Calidris canutus, the northerly wintering subspecies islandica). We measured BMR and M(sum) over two months in birds caught in the wild and transferred to experimentally controlled conditions representative of aspects of their seasonal thermal environment (two groups at constant 25 degrees C, one group at constant 4 degrees C and two groups experiencing variable outdoor temperatures). Birds maintained in both cold and variable ambient temperatures showed a 14-15% higher body mass, 33-45% higher food intake, and 26% and 13% elevations in BMR and M(sum), respectively, compared with birds kept at thermoneutrality. These results, together with data on alimentary tract size and pectoral muscle thickness measured by ultrasonography, suggest that red knots acclimate to cold primarily through modulation of (lean) body mass components. Heavier individuals have larger muscles, which allow higher maximal heat production and better thermal compensation. Cold acclimation effects on BMR are most probably due to changes in the size of visceral organs, although not the alimentary tract in this specific case. The liver, known for its thermogenic capacity, is a probable candidate. Overall, our results indicate that relatively small changes in body mass and muscle size allow enough reserve capacity in terms of heat production to cope with typical wintering ambient temperature variations as measured on the red knot's wintering grounds.