Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.     

Density effect on great tit (Parus major) clutch size intensifies in a polluted environment

Long-term data on a great tit (Parus major) population breeding in a metal-polluted zone around a copper–nickel smelter indicate that, against expectations, the clutch size of this species is decreasing even though metal emissions in the area have decreased considerably over the past two decades. Here, we document long-term population-level changes in the clutch size of P. major and explore if changes in population density, population numbers of competing species, timing of breeding, breeding habitat, or female age distribution can explain decreasing clutch sizes. Clutch size of P. major decreased by one egg in the polluted zone during the past 21 years, while there was no significant change in clutch size in the unpolluted reference zone over this time period. Density of P. major nests was similar in both environments but increased threefold during the study period in both areas (from 0.8 to 2.4 nest/ha). In the polluted zone, clutch size has decreased as a response to a considerable increase in population density, while a corresponding density change in the unpolluted zone did not have such an effect. The other factors studied did not explain the clutch size trend. Fledgling numbers in the polluted environment have been relatively low since the beginning of the study period, and they do not show a corresponding decrease to that noted for the clutch size over the same time period. Our study shows that responses of commonly measured life-history parameters to anthropogenic pollution depend on the structure of the breeding population. Interactions between pollution and intrinsic population characters should therefore be taken into account in environmental studies.     

Is there a trade-off between egg weight and clutch size in wild Lesser Snow Geese (Anser c. caerulescens)?

Previous studies of arctic nesting geese suggest that laying is limited by the size of a female's body reserves and that larger eggs contain more nutrients. These observations imply a life-history trade-off between egg size and clutch size which may give rise to a negative genetic correlation between the two characters. We estimated the genetic correlation between egg weight and clutch size using measurements from mothers and their daughters in a wild population of Lesser Snow Geese Anser caerulescens caerulescens. Between 65 and 80 % of the variance in egg weight is attributable to differences between individuals, and heritability of egg weight is about 60 %. In contrast, 10–20 % of the variance in clutch size is attributable to differences between individuals, and heritability of clutch size is about 15 %. The genetic correlation coefficient between egg weight and clutch size ranges from 0.09 to 0.32 and does not differ significantly from zero. We discuss the possible reasons for the lack of the expected negative genetic correlation.     

Testing hypotheses regarding the genetics of adaptation

Many of the hypotheses regarding the genetics of adaptation require that one know specific details about the genetic basis of complex traits, such as the number and effects of the loci involved. Developments in molecular biology have made it possible to create relatively dense maps of markers that can potentially be used to map genes underlying specific traits. However, there are a number of reasons to doubt that such mapping will provide the level of resolution necessary to specifically address many evolutionary questions. Moreover, evolutionary change is built upon the substitution of individual mutations, many of which may now be cosegregating in the same allele. In order for this developing area not to become a mirage that traps the efforts of an entire field, the genetic dissection of adaptive traits should be conducted within a strict hypothesis-testing framework and within systems that promise a reasonable chance of identifying the specific genetic changes of interest. Continuing advances in molecular technology may lead the way here, but some form of genetic testing is likely to be forever required.     

Genetic variability in mitochondrial DNA in a regional population of the great tit (Parus major)

Genetic variation of mitochondrial DNA (mtDNA) in 18 great tits (Parus major) from three neighboring localities in Sweden was investigated with eight tetranucleotide restriction endonucleases. The 18 individuals could be separated into 13 different maternal lineages. The high number of female lineages present in this regional population contrasts with a low level of sequence divergence between the different mtDNA clones, with a mean of 0.19% sequence divergence between all individuals. There was no obvious spatial structuring of mtDNA clones among the three localities. The presence of a high number of different clones with a low degree of sequence divergence could be explained by the effects of a large long-term effective population size, with the mtDNA clones having diverged about 25,000–200,000 years ago.This study was supported by the Swedish Natural Science Research Council, the Erik Philip-Sörensen Foundation, and the Nilsson-Ehle Foundation.     

Population genomics of eusocial insects: the costs of a vertebrate‐like effective population size

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life‐history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome‐wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA‐seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes – a marker of the effective population size – in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.     

Low variability and absence of phenotypic correlates of Clock gene variation in a great tit Parus major population

Studies of a range of taxa, including birds, have revealed latitudinal clines in allele length at the conserved Clock locus, a gene with known influences on behaviour and physiology. Such clines might reflect adaptation to seasonal variation, a suggestion supported by a recent within‐population analysis of blue tits Cyanistes caeruleus, which found associations between Clock genotype and timing of breeding in females. To test the generality of this pattern, we sequenced the polymorphic poly‐Q locus of the Clock gene in 521 female great tits Parus major, which were selected based on possession of extreme breeding phenotypes. In total, we identified five alleles with one allele accounting for 96% of allelic diversity in the sample set. Overall variability at the poly‐Q locus was very low, and the spatial distribution of Clock alleles across Wytham was highly homogenous. Our data further provide no evidence for a connection between Clock genotype and reproductive timing phenotype in female great tits; further, we found no effect of Clock genotype on reproductive success. Hence, these results are in contrast to the pattern found for the sympatric blue tit population inhabiting the same woodlands, suggesting that phenotypic effects of Clock are not general in passerine birds.     

Fitness cost of incubation in great tits (Parus major) is related to clutch size

Life-history theory predicts that parents produce the number of offspring that maximizes their fitness. In birds, natural selection on parental decisions regarding clutch size may act during egg laying, incubation or nestling phase. To study the fitness consequences of clutch size during the incubation phase, we manipulated the clutch sizes during this phase only in three breeding seasons and measured the fitness consequences on the short and the long term. Clutch enlargement did not affect the offspring fitness of the manipulated first clutches, but fledging probability of the subsequent clutch in the same season was reduced. Parents incubating enlarged first clutches provided adequate care for the offspring of their first clutches during the nestling phase, but paid the price when caring for the offspring of their second clutch. Parents that incubated enlarged first clutches had lower local survival in the 2 years when the population had a relatively high production of second clutches, but not in the third year when there was a very low production of second clutches. During these 2 years, the costs of incubation were strong enough to change positive selection, as established by brood size manipulations in this study population, into stabilizing selection through the negative effect of incubation on parental fitness.     

Sexual size dimorphism in the great tit (Parus major) in relation to history and current selection

We investigated the possible causes of the evolution of sexual size and shape dimorphism in the great tit (Parus major) by using two different approaches. First, we used the equilibrium approach, i.e. analysing current selection to see whether it was possible to find directional selection in the direction of the dimorphism, or stabilising selection maintaining dimorphism at its current level. Second, we used the historical approach, i.e. putting the degree of dimorphism in a phylogenetic perspective to analyse what kind of changes (if any) have occurred. This was carried out in the following way: (i) we described the level of sexual dimorphism in a population of Swedish great tits by means of path model. (ii) We used the path model design to analyse survival and reproductive selection in this population. (iii) We compared the level of dimorphism in relation to size in the great tit with that of the closest congener, the blue tit P. caeruleus. (iv) We compared the amount of interspecific morphological variation with that which would be expected under a drift model. We found no evidence of either stabilising or directional survival or reproductive selection. Size and shape variation in the great tit seemed unrelated to fitness in adults. Dimorphism was somewhat greater in the great tit compared to the blue tit, but only with an amount predictable by its larger size. In terms of phenotypic standard deviations, the great tit was not more dimorphic than the blue tit, although it was larger. The amount of interspecific variance with regard to size was lower or equal to that expected by the drift model, showing that long-term directional selection for an increase in size and dimorphism is improbable. These results agree with recent theoretical findings that size and dimorphism should be related and that strong conservatism with regard to dimorphism is to be expected. They also agree with the view that in equilibrium populations, fitness components (if there are many of them) should appear neutral with regard to total fitness.     

Paternal leakage of mitochondrial DNA in the great tit (Parus major)

Animal mitochondrial DNA is normally inherited clonally from a mother to all her offspring. Mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype within an individual, can be generated by relatively common somatic mutations within an individual, by heteroplasmy of the oocytes, or by paternal leakage of mitochondria during fertilization of an egg. This biparental inheritance has so far been reported only in mice, mussels, Drosophila, and humans. Here we present evidence that paternal leakage occurs in a bird, the great tit Parus major. The major and minor subspecies groups of the great tit mix in the middle Amur Valley in far-eastern Siberia, where we found a bird that possessed the very distinct haplotypes of the two groups. To our knowledge this is the first report of paternal leakage in birds.     

Sea buckthorn berries Hippophae rhamnoides L. predict size and composition of a great tit population Parus major L

In seasonal environments variation in food abundance in the non‐breeding season is thought to affect songbird population dynamics. In a unique tit‐sea buckthorn berry system we can estimate the berry abundance and both the tit consumption and population dynamics. Six hundred nest boxes were available to great and blue tits Cyanistes caeruleus for breeding in spring and roosting in winter. We followed the dynamics including the recapture histories of individually marked great tits from 2008 to 2014. In each year we estimated 1) the winter sea buckthorn berry availability, 2) an index of berry consumption in December based on the colour of the faeces of roosting birds, 3) the number of breeding great and blue tits, 4) both recapture probability and the return rate of the great tits and 5) immigration rates. December berry abundance positively predicted the number of breeding pairs of both species in the subsequent season and great tit return rates in the second half of the winter. There was support for a sex specific berry effect on the adult return rate in the great tit: female return rate was associated less strongly to berry abundance than male return rate. This skewed the sex ratio of the local breeders in the following breeding season. Intriguingly, annual berry consumption in December was not related to berry abundance, and individuals consuming more berries tended to have slightly lower return rates. Reproductive rate was not related to berry abundance. There was hardly support for a relation between immigration rates of first year breeders and berry abundance. Taken together these results imply that berry stock not only affected population size but also the population composition through sex specific exchange with the surroundings. Since population density covaried with berry abundance, density dependent effects provide an alternative explanation for the patterns observed.     

The design and cross-population application of a genome-wide SNP chip for the great tit Parus major

The vast amount of phenotypic information collected in some wild animal populations makes them extremely valuable for unravelling the genetics of ecologically important traits and understanding how populations adapt to changes in their environment. Next generation sequencing has revolutionized the development of large marker panels in species previously lacking genomic resources. In this study, a unique genomics toolkit was developed for the great tit (Parus major), a model species in ecology and behavioural biology. This toolkit consists of nearly 100,000 SNPs, over 250 million nucleotides of assembled genomic DNA and more than 80 million nucleotides of assembled expressed sequences. A SNP chip with 9193 SNP markers expected to be spaced evenly along the great tit genome was used to genotype 4702 birds from two of the most intensively studied natural vertebrate populations [Wytham Woods/Bagley Woods (United Kingdom) and de Hoge Veluwe/Westerheide (The Netherlands)]. We show that (i) SNPs identified in either of the two populations have a high genotyping success in the other population, (ii) the minor allele frequencies of the SNPs are highly correlated between the two populations and (iii) despite this high correlation, a large number of SNPs display significant differentiation (F(ST) ) between the populations, with an overrepresentation of genes involved in cardiovascular development close to these SNPs. The developed resources provide the basis for unravelling the genetics of important traits in many long-term studies of great tits. More generally, the protocols and pitfalls encountered will be of use for those developing similar resources.     

Offspring sex ratio is related to male body size in the great tit (Parus major)

Sex allocation theory predicts that the allocation of resourcesto male and female function should depend on potential fitnessgain realized through investment in either sex. In the greattit (Parus major), a monogamous passerine bird, male resourceholdingpotential (RHP) and fertilization success both depend on malebody size (e.g., tarsus length) and plumage traits (e.g., breaststripe size). It is predicted that the proportion of sons ina brood should increase both with male body size and plumage traits,assuming that these traits show a father—offspring correlation. Thiswas confirmed in our study: the proportion of sons in the brood increasedsignificantly with male tarsus length and also, though not significantly,with the size of the breast stripe. A sex ratio bias in relationto male tarsus length was already present in the eggs because(1) the bias was similar among broods with and without mortalitybefore the nestlings' sex was determined, and (2) the bias remainedsignificant when the proportion of sons in the clutch was conservativelyestimated, assuming that differential mortality before sex determinationcaused the bias. The bias was still present among recruits.The assumption of a father—offspring correlation was confirmedfor tarsus length. Given that both RHP and fertilization successof male great tits depend on body size, and size of father andoffspring is correlated, the sex ratio bias may be adaptive.     

Sources of (co)variation in alternative siring routes available to male great tits (Parus major)

Males of socially monogamous species can increase their siring success via within‐pair and extra‐pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five‐year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as “interactive phenotypes” arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra‐pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra‐pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multilevel structure of male fertilization routes when studying the evolution of male mating strategies.     

Genetic basis of natural variation in body pigmentation in Drosophila melanogaster

Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects.     

Isolation of polymorphic microsatellite markers in the great tit (Parus major minor)

Six microsatellite loci were developed for a passerine bird, the great tit (Parus major), using two methods. These loci were polymorphic (3–8 alleles per locus) and exhibited expected heterozygosities from 0.45 to 0.77. At one locus the genotypic frequencies deviated significantly from Hardy–Weinberg expectations.     

Egg shell quality,clutch size and hatching success of the great tit (Parus major) and the pied flycatcher (Ficedula hypoleuca) in an air pollution gradient

Egg shell thickness, egg volume, clutch size and hatching success of Parus major and Ficedula hypoleuca were studied at 14 study sites around a copper smelter complex in Harjavalta, south-west Finland, in 1991–1993. In 1991–1992 unhatched eggs were collected to measure shell quality. F. hypoleuca was more susceptible to pollutants than P. major, the response of which was weaker in all aspects studied. Egg shells of F. hypoleuca were about 17% thinner and eggs were about 8% smaller in volume near the factory than at a distance of 10 km. The clutch size of F. hypoleuca was significantly smaller and hatching success markedly lower at a study site next to the factory complex than at all other sites. In P. major, variation in shell thickness and egg volume was not significantly related to the distance from the pollution source. Clutch size and hatching success of P. major did not significantly differ among study sites, although the trend in hatching success was in the same direction as in F. hypoleuca. Clutches of both species contained less shell material and both species had more nests without eggs near the factory than further away. The surface structure of the eggshells was studied by scanning electron microscope. Especially in F. hypoleuca, the egg shell surface was more rough and porous near the factory. The roles of Ca and heavy metals in shell thinning are discussed.     

Brood defense and brood size in the great tit (Parus major): a test of a model of unshared parental investment

To understand the interaction of the many contextual variablesthat affect parental behavior a number of static optimalitymodels have been developed. Among these the one by Lazarus andInglis (1986) is the only one to specifically predict the magnitudeof unshared parental investment (PI), i.e., of parental carethat carries a cost to the parent and that benefits all currentoffspring equally because it cannot be divided among them. Weinvestigated specifically how parent great tits (Parus major)gear their brood defense, a form of unshared PI, to the sizeof the brood at stake and to the risk incurred as a functionof the type of predator. The predators used were dummies ofthe great spotted woodpecker (Picoides major) and of the tawnyowl (Strix aluco). Normally, adults can approach the woodpeckerwith impunity; it had inflicted heavy losses to nestlings ofthe study populations of great tits near Wolfsburg, Lower Saxony.Parent great tits whose brood had been artificially reducedto two young responded to the dummy with less defense than dida control group with their pre-test brood size left intact.The nature of defense was qualitatively the same as that elicitedby a live woodpecker. Parents confronting the owl near theirbrood decreased their response with an artificial reductionin brood size much less. Because the owl used poses a seriousrisk to the defenders, as compared to the woodpecker, the resultlends powerful support to the "total loss" version of the modelof unshared PI; it predicts brood size to affect unshared PImore strongly when there is less risk to the parent. This interpretationis correct to the extent that one premise of the model, namelythat of uncompromised parentage, can be relaxed; great tit broodscontain a sizeable number of extrapair young. Males defendedtheir brood more strongly than did females. Sex and brood manipulationadded up linearly when affecting defense level, i.e., therewas no interaction.     

Ultraviolet reflectance of plumage for parent-offspring communication in the great tit (Parus major)

Ultraviolet (UV) reflectance has been implicated in mate selection.Yet, in some bird species the plumage of young varies in UVreflectance already in the nest and long before mate choiceand sexual selection come into play. Most birds molt the juvenilebody plumage before reaching sexual maturity, and thus, someconspicuous traits of the juvenile body plumage may rather haveevolved by natural selection, possibly via predation or parentalpreference. This second hypothesis is largely untested and predictsa differential allocation of food between fledging and totalindependence, which is a time period of 2–3 weeks whereoffspring mortality is also highest. Here, we test the predictionthat parents use the individual variation in UV reflectanceamong fledglings for differential food allocation. We manipulatedUV reflectance of the plumage of fledgling great tits Parusmajor by treating chest and cheek feathers with a lotion thateither did or did not contain UV blockers and then recordedfood allocation by parents in an outdoor design simulating postfledgingconditions. The visible spectrum was minimally affected by thistreatment. Females were found to feed UV-reflecting offspringpreferentially, whereas males had no preference. It is the firstevidence showing that the UV reflectance of the feathers ofyoung birds has a signaling function in parent–offspringcommunication and suggests that the UV traits evolved via parentalpreference.     

Density effects on life-history traits in a wild population of the great tit Parus major: analyses of long-term data with GIS techniques

1. Population density often has strong effects on the population dynamics and reproductive processes of territorial animals. However, most estimates of density-dependent effects use the number of breeding pairs per unit area in a given season and look for correlations across seasons, a technique that assigns the same density score to each breeding pair, irrespective of local spatial variation. 2. In this study, we employed GIS techniques to estimate individual breeding densities for great tits breeding in Wytham Woods UK, between 1965 and 1996. We then used linear mixed modelling to analyse the effect of density on reproductive processes. 3. The areas of Thiessen polygons formed around occupied nestboxes were used to approximate territory size (necessarily inverse of breeding density). There were significant, independent and positive relationships between clutch size, fledging mass and the number of offspring recruited to the population, and territory size (all P < 0.001), but no effect of territory size on lay-date or egg mass. 4. Thiessen polygons are contiguous and cover all of the available area. Therefore, at low nest densities territory polygons were excessively oversized. Using a novel procedure to address this limitation, territory sizes were systematically capped through a range of maxima, with the greatest effect in the models when territories were capped at 0.9-2.3 ha. This figure approximates to the maximum effective territory size in our population and is in close agreement with several field-based studies. This capping refinement also revealed a significant negative relationship between lay-date and territory size capped at 0.9 ha (P < 0.001). 5. These density-dependent effects were also detected when analyses were restricted to changes within individual females, suggesting that density effects do not merely result from either increased proportions of low-quality individuals, or increased occupation of poor sites, when population density is high. 6. Overall, these results suggest that, in the current population, great tits with territories smaller than c. 2 ha independently lay smaller and later clutches, have lighter fledglings, and recruit fewer offspring to the breeding population. These analyses thus suggest a pervasive and causal role of local population density in explaining individual reproductive processes.