Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

We have observed extensive interindividual differences in DNA methylation of 8590 CpG sites of 6229 genes in 153 human adult cerebellum samples, enriched in CpG island “shores” and at further distances from CpG islands. To search for genetic factors that regulate this variation, we performed a genome-wide association study (GWAS) mapping of methylation quantitative trait loci (mQTLs) for the 8590 testable CpG sites. cis association refers to correlation of methylation with SNPs within 1 Mb of a CpG site. 736 CpG sites showed phenotype-wide significant cis association with 2878 SNPs (after permutation correction for all tested markers and methylation phenotypes). In trans analysis of methylation, which tests for distant regulation effects, associations of 12 CpG sites and 38 SNPs remained significant after phenotype-wide correction. To examine the functional effects of mQTLs, we analyzed 85 genes that were with genetically regulated methylation we observed and for which we had quality gene expression data. Ten genes showed SNP-methylation-expression three-way associations—the same SNP simultaneously showed significant association with both DNA methylation and gene expression, while DNA methylation was significantly correlated with gene expression. Thus, we demonstrated that DNA methylation is frequently a heritable continuous quantitatively variable trait in human brain. Unlike allele-specific methylation, genetic polymorphisms mark both cis- and trans-regulatory genetic sites at measurable distances from their CpG sites. Some of the genetically regulated DNA methylation is directly connected with genetically regulated gene expression variation.     

SEXUAL SELECTION,MULTIPLE MALE ORNAMENTS,AND AGE‐ AND CONDITION‐DEPENDENT SIGNALING IN THE COMMON YELLOWTHROAT

In many animals, sexual selection has resulted in complex signaling systems in which males advertise aspects of their phenotypic or genetic quality through elaborate ornamentation and display behaviors. Different ornaments might convey different information or be directed at different receivers, but they might also be redundant signals of quality that function reliably at different times (ages) or in different contexts. We explored sexual selection and age‐ and condition‐dependent signaling in the common yellowthroat (Geothlypis trichas), a sexually dichromatic warbler with two prominent plumage ornaments—a melanin‐based, black facial “mask” and carotenoid‐based, UV‐yellow “bib.” In a three‐year study, variance among males in the number of social (M_w) and extra‐pair (M_e) mates generated strong sexual selection on mask and bib attributes. Some traits (mask size, bib yellow brightness) were correlated with male age and did not experience selection beyond age‐related increases in M_w and M_e. Other traits showed age‐specific (bib size) or age‐reversed (ultraviolet brightness) patterns of selection that paralleled changes in the information‐content of each ornament. The components of male fitness generating selection in young versus old males were distinct, reflecting different sources of variation in male fertilization success. Age‐ and context‐dependent changes in the strength, direction, and target of selection may help explain the maintenance of multiple ornaments in this and other species.     

Multiple sexual ornaments signal heterozygosity in male blue tits

Higher individual genetic quality has been hypothesized to be associated with the expression of conspicuous ornaments. However, the relationship between multicomponent sexual signals and heterozygosity is poorly understood. In this study, we examined whether different ornaments, including song (repertoire size and bout length) and plumage coloration (yellow breast and blue crown), reflect individual genetic diversity in male blue tits (Aves: Cyanistes caeruleus). We estimated genetic diversity using 26 microsatellite markers that were classified as putatively functional (12 loci) and neutral (14 loci). We found that yellow breast carotenoid chroma, blue crown brightness, bout length and body condition were positively associated with heterozygosity at functional loci, but not with genetic diversity estimated at all typed loci or the subset of neutral markers. The lack of strong single‐locus effects and the presence of identity disequilibrium in our population suggest that the observed heterozygosity‐phenotype associations are driven by loci widely distributed across the genome. The predominant role of putatively functional loci evidences that the expression of secondary sexual characters is more tightly reflected by heterozygosity at genomic regions containing coding genes that are being actively expressed, a fact that may make ornamental traits more reliable indicators of the genetic quality of individuals. Overall, this study shows that multiple secondary sexual characters reflect male genetic diversity and lends support to the good‐genes‐as‐heterozygosity hypothesis. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 362–375.     

Population genetics of Wolbachia‐infected,parthenogenetic and uninfected,sexual populations of Tetrastichus coeruleus (Hymenoptera: Eulophidae)

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. These manipulations are expected to have consequences on the population genetics of the host, such as heterozygosity levels, genetic diversity and gene flow. The parasitoid wasp Tetrastichus coeruleus has populations that are infected with parthenogenesis‐inducing Wolbachia and populations that are not infected. We studied the population genetics of T. coeruleus between and within Wolbachia‐infected and uninfected populations, using nuclear microsatellites and mitochondrial DNA. We expected reduced genetic diversity in both DNA types in infected populations. However, migration and gene flow could introduce new DNA variants into populations. We therefore paid special attention to individuals with unexpected (genetic) characteristics. Based on nuclear and mitochondrial DNA, two genetic clusters were evident: a thelytokous cluster containing all Wolbachia‐infected, parthenogenetic populations and an arrhenotokous cluster containing all uninfected, sexual populations. Nuclear and mitochondrial DNA did not exhibit concordant patterns of variation, although there was reduced genetic diversity in infected populations for both DNA types. Within the thelytokous cluster, there was nuclear DNA variation, but no mitochondrial DNA variation. This nuclear DNA variation may be explained by occasional sex between infected females and males, by horizontal transmission of Wolbachia, and/or by novel mutations. Several females from thelytokous populations were uninfected and/or heterozygous for microsatellite loci. These unexpected characteristics may be explained by migration, by inefficient transmission of Wolbachia, by horizontal transmission of Wolbachia, and/or by novel mutations. However, migration has not prevented the build‐up of considerable genetic differentiation between thelytokous and arrhenotokous populations.     

Genotype‐by‐environment interactions for cuticular hydrocarbon expression in Drosophila simulans

Genotype‐by‐environment interactions (G × Es) describe genetic variation for phenotypic plasticity. Recent interest in the role of these interactions in sexual selection has identified G × Es across a diverse range of species and sexual traits. Additionally, theoretical work predicts that G × Es in sexual traits could help to maintain genetic variation, but could also disrupt the reliability of these traits as signals of mate quality. However, empirical tests of these theoretical predictions are scarce. We reared iso‐female lines of Drosophila simulans across two axes of environmental variation (diet and temperature) in a fully factorial design and tested for G × Es in the expression of cuticular hydrocarbons (CHCs), a multivariate sexual trait in this species. We find sex‐specific environmental, genetic and G × E effects on CHC expression, with G × Es for diet in both male and female CHC profile and a G × E for temperature in females. We also find some evidence for ecological crossover in these G × Es, and by quantifying variance components, genetic correlations and heritabilities, we show the potential for these G × Es to help maintain genetic variation and cause sexual signal unreliability in D. simulans CHC profiles.     

Evolutionary trade‐off between naturally‐ and sexually‐selected melanin‐based colour traits in worldwide barn owls and allies

Natural selection typically constrains the evolution of sexually‐selected characters. The evolution of naturally‐ and sexually‐selected traits can be intertwined if they share part of their genetic machinery or if sex traits impair foraging success or increase the risk of depredation. The present study investigated phenotypic correlations between naturally‐ and sexually‐selected plumage traits in the Tytonidae (barn owls, grass owls, and masked owls). Phenotypic correlations indicate the extent to which selection on one trait will indirectly influence the evolution of another trait. In this group of birds, the ventral body side varies from white to dark reddish, a naturally‐selected pheomelanin‐based colour trait with important roles in predator–prey interactions. Owls also exhibit eumelanin‐based black spots, for which number and size signal different aspects of individual quality and are used in mate choice. These three plumage traits are strongly heritable and sexually dimorphic, with females being on average darker reddish and more spotted than males. Phenotypic correlations were measured between these three plumage traits in 3958 free‐living barn owls in Switzerland and 10 670 skin specimens from 34 Tyto taxa preserved in museums. Across Tyto taxa, the sexually‐selected plumage spottiness was positively correlated with the naturally‐selected reddish coloration, with redder birds being more heavily spotted. This suggests that they are genetically constrained or that natural and sexual selection are not antagonistically exerted on plumage traits. In a large sample of Swiss nestlings and within 34 Tyto taxa, the three plumage traits were positively correlated. The production of melanin pigments for one plumage trait is therefore not traded off against the production of melanin pigments for another plumage trait. Only in the most heavily‐spotted Tyto taxa do larger‐spotted individuals display fewer spots. This indicates that, at some threshold value, the evolution of many spots constrains the evolution of large spots. These analyses raise the possibility that different combinations of melanin‐based plumage traits may not be selectively equivalent.     

Development and validation of a novel 15‐CpG‐based signature for predicting prognosis in triple‐negative breast cancer

DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple‐negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15‐CpG‐based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15‐CpG‐based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG‐based signature and TNM stage was generated to predict the 1‐, 3‐ and 5‐year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.     

Sex‐specific heritability of cell‐mediated immune response in the blue tit nestlings (Cyanistes caeruleus)

Here, we aimed at estimating sex‐specific heritabilities of cell‐mediated immune response (CMI) in the blue tit nestlings (Cyanistes caeruleus). To separate genetic and environmental components of the phenotypic variance in CMI (measured using phytohaemagglutinin assay), we performed a cross‐fostering experiment. Additionally, controlled environmental variation was introduced by enlarging some broods. Our analyses revealed a significant genetic component (as approximated by the nest‐of‐origin term) of the phenotypic variance in immune response. More importantly, these genetic effects differed between sexes and experimentally manipulated brood sizes, as indicated by significant genotype‐by‐sex and genotype‐by‐environment interactions. We discuss possible causes of such sexual dimorphism in gene expression and suggest that sex‐ and environment‐specific genetic interactions may contribute to the maintenance of genetic variability in traits related to immune functions.     

Genome‐wide DNA methylation signatures of infection status in Trinidadian guppies (Poecilia reticulata)

Epigenetic modification, especially DNA methylation, can play an important role in mediating gene regulatory response to environmental stressors and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their hosts, yet it remains unclear how parasites influence host methylation patterns. Here, we used a well‐studied host–parasite system, the guppy Poecilia reticulata and its ectoparasitic monogenean Gyrodactylus turnbulli to gain mechanistic insight into the dynamics of DNA methylation in host–parasite interactions. To explore this, we quantitatively measured genome‐wide DNA methylation in guppy skin tissue using reduced representation bisulphite sequencing and characterized differential methylation patterns in guppies during distinct phases of infection. We identified 365, 313, and 741 differentially methylated regions (DMRs) between infected and control fish in early infection, peak infection and recovery phases, respectively. The magnitude of the methylation difference was moderate in DMRs, with an average of 29% (early infection), 27% (peak infection) and 30% (recovery) differential methylation per DMR. Approximately 50% of DMRs overlapped with CpG islands, and over half of the DMRs overlapped with gene bodies, several of which encode proteins relevant to immune response. These findings provide the first evidence of an epigenetic signature of infection by ectoparasites and demonstrate the changing relationship between epigenetic variation and immune response in distinct phases of infection.     

Condition‐dependent expression of pre‐ and postcopulatory sexual traits in guppies

Female choice can impose persistent directional selection on male sexually selected traits, yet such traits often exhibit high levels of phenotypic variation. One explanation for this paradox is that if sexually selected traits are costly, only the fittest males are able to acquire and allocate the resources required for their expression. Furthermore, because male condition is dependent on resource allocation, condition dependence in sexual traits is expected to underlie trade‐offs between reproduction and other life‐history functions. In this study we test these ideas by experimentally manipulating diet quality (carotenoid levels) and quantity in the guppy (Poecilia reticulata), a livebearing freshwater fish that is an important model for understanding relationships between pre‐ and post‐copulatory sexually selected traits. Specifically, we test for condition dependence in the expression of pre‐ and postcopulatory sexual traits (behavior, ornamentation, sperm traits) and determine whether diet manipulation mediates relationships among these traits. Consistent with prior work we found a significant effect of diet quantity on the expression of both pre‐ and postcopulatory male traits; diet‐restricted males performed fewer sexual behaviors and exhibited significant reductions in color ornamentation, sperm quality, sperm number, and sperm length than those fed ad libitum. However, contrary to our expectations, we found no significant effect of carotenoid manipulation on the expression of any of these traits, and no evidence for a trade‐off in resource allocation between pre‐ and postcopulatory episodes of sexual selection. Our results further underscore the sensitivity of behavioral, ornamental, and ejaculate traits to dietary stress, and highlight the important role of condition dependence in maintaining the high variability in male sexual traits.     

Age,sex and beauty: methodological dependence of age‐ and sex‐dichromatism in the great tit Parus major

Carotenoid‐based colour expression is frequently involved in sexual dichromatism, particularly in bird plumage, suggesting a role in sexual selection. Despite much work on expression of the carotenoid‐based ventral plumage coloration of the great tit (Parus major), which represents a popular model in evolution and ecology, a consensus on even the most basic demographic patterns of variation (e.g. age and sex differences) is lacking. This may reflect the use of variable methods for analysing colour variation, although what is not clear, either in this case or in general, is the extent to which these alternative methods are equally effective at describing age‐ and sex‐related dichromatism. Using data obtained over 4 years from a large sample of free‐ranging great tits, we examined how colour‐scoring methodology influences estimates of age‐ and sex‐related dichromatism. We compare: (1) principal components analysis‐derived scores; (2) tristimulus colour variables; (3) a visual model‐independent, carotenoid‐focussed colour score; and (4) two colour scoring methods based on avian visual models, examining how they assess colour variation with respect to age and sex to determine how methodology may influence results. We demonstrate clear age‐ and sex‐dependent expression of this colour trait, both in our own data and in meta‐analyses of results from great tit populations across Europe, and discuss the merits of the various colour scores, which yield very different estimates of the extent of age‐ and sex‐dependent dichromatism. We show variation is likely to be visible to conspecifics and propose a novel, visual model‐derived scoring system for describing variation in carotenoid‐based colour patches, where the perceived signal is divided into independent chromatic and achromatic components, in line with current understanding of visual perception. The present study highlights the impact of colour‐scoring methodology and shows that, as novel measures continue to be developed, researchers should consider carefully how they quantify colour expression. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 777–796.