Federico C. F. Calboli

Seminal fluid protein allocation and male reproductive success.

Postcopulatory sexual selection can select for sperm allocation strategies in males [1, 2], but males should also strategically allocate nonsperm components of the ejaculate [3, 4], such as seminal fluid proteins (Sfps). Sfps can influence the extent of postcopulatory sexual selection [5-7], but little is known of the causes or consequences of quantitative variation in Sfp production and transfer. Using Drosophila melanogaster, we demonstrate that Sfps are strategically allocated to females in response to the potential level of sperm competition. We also show that males who can produce and transfer larger quantities of specific Sfps have a significant competitive advantage. When males were exposed to a competitor male, matings were longer and more of two key Sfps, sex peptide [8] and ovulin [9], were transferred, indicating strategic allocation of Sfps. Males selected for large accessory glands (a major site of Sfp synthesis) produced and transferred significantly more sex peptide, but not more ovulin. Males with large accessory glands also had significantly increased competitive reproductive success. Our results show that quantitative variation in specific Sfps is likely to play an important role in postcopulatory sexual selection and that investment in Sfp production is essential for male fitness in a competitive environment.

MultiPhen: joint model of multiple phenotypes can increase discovery in GWAS.

The genome-wide association study (GWAS) approach has discovered hundreds of genetic variants associated with diseases and quantitative traits. However, despite clinical overlap and statistical correlation between many phenotypes, GWAS are generally performed one-phenotype-at-a-time. Here we compare the performance of modelling multiple phenotypes jointly with that of the standard univariate approach. We introduce a new method and software, MultiPhen, that models multiple phenotypes simultaneously in a fast and interpretable way. By performing ordinal regression, MultiPhen tests the linear combination of phenotypes most associated with the genotypes at each SNP, and thus potentially captures effects hidden to single phenotype GWAS. We demonstrate via simulation that this approach provides a dramatic increase in power in many scenarios. There is a boost in power for variants that affect multiple phenotypes and for those that affect only one phenotype. While other multivariate methods have similar power gains, we describe several benefits of MultiPhen over these. In particular, we demonstrate that other multivariate methods that assume the genotypes are normally distributed, such as canonical correlation analysis (CCA) and MANOVA, can have highly inflated type-1 error rates when testing case-control or non-normal continuous phenotypes, while MultiPhen produces no such inflation. To test the performance of MultiPhen on real data we applied it to lipid traits in the Northern Finland Birth Cohort 1966 (NFBC1966). In these data MultiPhen discovers 21% more independent SNPs with known associations than the standard univariate GWAS approach, while applying MultiPhen in addition to the standard approach provides 37% increased discovery. The most associated linear combinations of the lipids estimated by MultiPhen at the leading SNPs accurately reflect the Friedewald Formula, suggesting that MultiPhen could be used to refine the definition of existing phenotypes or uncover novel heritable phenotypes.

Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the worlds most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.

Thermal plasticity in Drosophila melanogaster: A comparison of geographic populations

BackgroundPopulations of Drosophila melanogaster show differences in many morphometrical traits according to their geographic origin. Despite the widespread occurrence of these differences in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of such variation are not fully understood. Thermal selection is considered to be the most likely cause explaining these differences.ResultsIn our work, we investigated several life history traits (body size, duration of development, preadult survival, longevity and productivity) in two tropical and two temperate natural populations of D. melanogaster recently collected, and in a temperate population maintained for twelve years at the constant temperature of 18°C in the laboratory. In order to characterise the plasticity of these life history traits, the populations were grown at 12, 18, 28 and 31.2°C. Productivity was the fitness trait that showed clearly adaptive differences between latitudinal populations: tropical flies did better in the heat but worse in the cold environments with respect to temperate flies. Differences for the plasticity of other life history traits investigated between tropical and temperate populations were also found. The differences were particularly evident at stressful temperatures (12 and 31.2°C).ConclusionOur results evidence a better cold tolerance in temperate populations that seems to have been evolved during the colonisation of temperate countries by D. melanogaster Afrotropical ancestors, and support the hypothesis of an adaptive response of plasticity to the experienced environment.

QTL MAPPING REVEALS A STRIKING COINCIDENCE IN THE POSITIONS OF GENOMIC REGIONS ASSOCIATED WITH ADAPTIVE VARIATION IN BODY SIZE IN PARALLEL CLINES OF DROSOPHILA MELANOGASTER ON DIFFERENT CONTINENTS

Abstract Latitudinal genetic clines in body size are common in many ectotherm species and are attributed to climatic adaptation. Here, we use Quantitative Trait Loci (QTL) mapping to identify genomic regions associated with adaptive variation in body size in natural populations of Drosophila melanogaster from extreme ends of a cline in South America. Our results show that there is a significant association between the positions of QTL with strong effects on wing area in South America and those previously reported in a QTL mapping study of Australian cline end populations (P < 0.05). In both continents, the right arm of the third chromosome is associated with QTL with the strongest effect on wing area. We also show that QTL peaks for wing area and thorax length are associated with the same genomic regions, indicating that the clinal variation in the body size traits may have a similar genetic basis. The consistency of the results found for the South American and Australian cline end populations indicate that the genetic basis of the two clines may be similar and future efforts to identify the genes producing the response to selection should be focused on the genomic regions highlighted by the present work.

Temperature-related genetic changes in laboratory populations of Drosophila subobscura: Evidence against simple climatic-based explanations for latitudinal clines

Parallel latitudinal clines to the long‐standing ones in the original Palearctic populations have independently evolved at different rates for chromosomal polymorphism and body size in South and North American populations of Drosophila subobscura since colonization around 25 years ago. This strongly suggests that (micro) evolutionary changes are largely predictable, but the underlying mechanisms are unknown. The putative role of temperature per se was investigated by using three sets of populations at each of three temperatures (13°, 18°, and 22°C) spanning much of the tolerable range for this species. We found a lower chromosomal diversity at the warmest temperature; a quick and consistent shift in gene arrangement frequencies in response to temperature; an evolutionary decrease in wing size, mediated by both cell area and cell number, at 18°C; no relationship between wing size and those inversions involved in latitudinal clines; and a shortening of the basal length of longitudinal vein IV relative to its total length with increasing standard dose. The trends for chromosomal polymorphism and body size were generally inconsistent from simple climatic‐based explanations of worldwide latitudinal patterns. The findings are discussed in the light of available information on D. subobscura and results from earlier thermal selection experiments with various Drosophila species.

A Genome-Wide Association Study of Neuroticism in a Population-Based Sample

Neuroticism is a moderately heritable personality trait considered to be a risk factor for developing major depression, anxiety disorders and dementia. We performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism, making this the largest association study for neuroticism to date. Neuroticism was measured by the Eysenck Personality Questionnaire. After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. We found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect (p<10−6) and GPC6 showed suggestive evidence for interaction with age (p≈10−7). We found support for one previously-reported association (PDE4D), but failed to replicate other recent reports. These results suggest common SNP variation does not strongly influence neuroticism. Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism.

DIFFERENT CELL SIZE AND CELL NUMBER CONTRIBUTION IN TWO NEWLY ESTABLISHED AND ONE ANCIENT BODY SIZE CLINE OF DROSOPHILA SUBOBSCURA

Abstract Latitudinal genetic clines in body size occur in many ectotherms including Drosophila species. In the wing of D. melanogaster, these clines are generally based on latitudinal variation in cell number. In contrast, differences in wing area that evolve by thermal selection in the laboratory are in general based on cell size. To investigate possible reasons for the different cellular bases of these two types of evolutionary response, we compared the newly established North and South American wing size clines of Drosophila subobscura. The new clines are based on latitudinal variation in cell area in North America and cell number in South America. The ancestral European cline is also based on latitudinal variation in cell number. The difference in the cellular basis of wing size variation in the American clines, which are roughly the same age, together with the similar cellular basis of the new South American cline and the ancient European one, suggest that the antiquity of a cline does not explain its cellular basis. Furthermore, the results indicate that wing size as a whole, rather than its cellular basis, is under selection. The different cellular bases of different size clines are most likely explained either entirely by chance or by different patterns of genetic variance—or its expression—in founding populations.

Prediagnostic plasma IgE levels and risk of adult glioma in four prospective cohort studies.

BACKGROUND Increased levels of serum immunoglobulin E (IgE) because of allergies have been inversely associated with risk of glioma in observational studies. Despite consistency across studies examining history of allergies and glioma, questions remain as to whether those are causal associations. An inverse association between serum IgE and risk of glioma was reported in a large case-control study, but reverse causality and treatment effects remain potential explanations for those findings. METHODS We combined data from four prospective cohort studies and used a nested case-control design to examine the association between allergy and glioma. We included glioma case subjects who were confirmed from medical or pathology records or from death certificates, and with prediagnostic blood available. We matched three control subjects per case subject, and the final numbers for analyses were 169 case subjects and 520 control subjects. Total IgE, food allergen-specific IgE, and respiratory allergen-specific IgE levels were measured using a highly sensitive fluorescent assay. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using conditional logistic regression analysis. Stratified analyses were conducted by age and birth cohorts. RESULTS Borderline elevated total IgE levels (25-100 kU/L) showed a statistically significant inverse association with glioma (OR = 0.63, 95% CI = 0.42 to 0.93), but no association was noted between elevated IgE (>100 kU/L) and glioma (OR = 0.98, 95% CI = 0.61 to 1.56) compared with clinically normal IgE levels (<25 kU/L). The association between glioma and total IgE was consistent for both men and women. Non-statistically significant inverse associations were noted for elevated IgE levels among individuals born before year 1930 (OR = 0.67, 95% CI = 0.34 to 1.34) and when restricting analyses to highly fatal (deceased within 2 years of diagnosis) glioma case subjects (OR = 0.64, 95% CI = 0.34 to 1.19) compared with individuals with clinically normal IgE levels. No associations were observed for either food allergen-specific or respiratory allergen-specific IgE levels. CONCLUSIONS Overall, our prospective findings are consistent with recent retrospective studies and support an association between total IgE levels and glioma. However, this association requires further elucidation.

Insulin signalling regulates remating in female Drosophila

Mating rate is a major determinant of female lifespan and fitness, and is predicted to optimize at an intermediate level, beyond which superfluous matings are costly. In female Drosophila melanogaster, nutrition is a key regulator of mating rate but the underlying mechanism is unknown. The evolutionarily conserved insulin/insulin-like growth factor-like signalling (IIS) pathway is responsive to nutrition, and regulates development, metabolism, stress resistance, fecundity and lifespan. Here we show that inhibition of IIS, by ablation of Drosophila insulin-like peptide (DILP)-producing median neurosecretory cells, knockout of dilp2, dilp3 or dilp5 genes, expression of a dominant-negative DILP-receptor (InR) transgene or knockout of Lnk, results in reduced female remating rates. IIS-mediated regulation of female remating can occur independent of virgin receptivity, developmental defects, reduced body size or fecundity, and the receipt of the female receptivity-inhibiting male sex peptide. Our results provide a likely mechanism by which females match remating rates to the perceived nutritional environment. The findings suggest that longevity-mediating genes could often have pleiotropic effects on remating rate. However, overexpression of the IIS-regulated transcription factor dFOXO in the fat body—which extends lifespan—does not affect remating rate. Thus, long life and reduced remating are not obligatorily coupled.