Abstract
The genetic variance–covariance matrix (Gmatrix) summarizes the genetic architecture of multiple traits. It has a central role in the understanding of phenotypic divergence and the quantification of the evolutionary potential of populations. Laboratory experiments have shown that Gmatrices can vary rapidly under divergent selective pressures. However, because of the demanding nature of Gmatrix estimation and comparison in wild populations, the extent of its spatial variability remains largely unknown. In this study, we investigate spatial variation in Gmatrices for morphological and lifehistory traits using longterm data sets from one continental and three island populations of blue tit (Cyanistes caeruleus) that have experienced contrasting population history and selective environment. We found no evidence for differences in Gmatrices among populations. Interestingly, the phenotypic variance–covariance matrices (P) were divergent across populations, suggesting that using P as a substitute for G may be inadequate. These analyses also provide the first evidence in wild populations for additive genetic variation in the incubation period (that is, the period between last egg laid and hatching) in all four populations. Altogether, our results suggest that Gmatrices may be stable across populations inhabiting contrasted environments, therefore challenging the results of previous simulation studies and laboratory experiments.
Introduction
A central goal in evolutionary biology is to predict if and how natural populations will adapt to changing environmental conditions. This has become increasingly important in the context of global changes imposing strong selection on wild populations (Palumbi, 2001). The ability of a population to respond to selection will not only depend on the quantity of genetic variation for each adaptive phenotypic trait but also on the strength and direction of genetic correlations among traits (Lande, 1979; Arnold et al., 2001). The genetic architecture of traits linked by various genetic processes is summarized by the genetic variance–covariance matrix, also known as the Gmatrix (or G), that corresponds to a symmetric matrix with additive genetic variance for the different traits contained in the diagonal of the matrix and the genetic covariances between traits in its offdiagonal elements (Lande, 1979; Lynch and Walsh, 1998). Depending on the direction of selection, genetic covariances may facilitate, constrain or even prevent evolution (Arnold, 1992; Agrawal and Stinchcombe, 2009; Morrissey et al., 2012; Teplitsky et al., 2014b). As such, G plays a central role in modern quantitative genetic theory dedicated to the evolution of phenotypic traits, as it is one of the main elements of the multivariate breeder’s equation widely used for predicting phenotypic evolution (Lande, 1979). However, so far, attempts to understand adaptive responses in wild populations based on such quantitative genetics estimates have yielded equivocal results (Merilä et al., 2001; Kruuk et al., 2008; Walsh and Blows, 2009). Among the potential limitations to this approach is the general assumption that G remains constant over time and/or space (Turelli, 1988), yet we still have too few temporal and spatial replicates to properly understand the extent of variation of G in nature (Arnold et al., 2008; Aguirre et al., 2014).
Using simulationbased approaches, previous studies have shown that several processes influence the constancy of G. First, genetic drift is expected to affect all aspects of the structure of G, such as the quantity of genetic variance for each trait and the genetic correlations between traits defining the geometry of G (that is, its size, shape and orientation), especially in small and/or isolated populations (Turelli, 1988; Jones et al., 2003; Griswold et al., 2007). Second, directional and/or stabilizing selection is expected to trigger nonproportional changes in the structure of G (Roff, 2000), whereas correlational selection should progressively modify the orientation of Gmatrices until they are aligned with the adaptive landscape (Jones et al., 2007; Revell, 2007). Third, high migration rates are expected to homogenize all aspects of G (Guillaume and Whitlock, 2007).
Using controlled laboratory experiments, the effects of these processes have been confirmed to modify the structure of G (see, for example, Phillips et al., 2001 for genetic drift and Careau et al., 2015 for selection). Therefore, wild populations experiencing different environments, and thus different selective pressures, or having undergone different demographic history, can be expected to differ in terms of Gmatrices. At the univariate level, several studies have indeed shown that additive genetic variance is sometimes variable across populations (see, for example, Husby et al., 2010; reviewed in Charmantier and Garant, 2005). However, the rare empirical studies investigating the spatial stability of the Gmatrix in natural populations have yielded equivocal results: whereas some studies have found relatively stable Gmatrices among populations (see, for example, Arnold and Phillips, 1999; Ashman, 2003; Puentes et al., 2016; reviewed in Arnold et al., 2008; see Garant et al., 2008 for a temporal stability example in a wild population), others have found that Gmatrices could vary among populations (see, for example, Roff et al., 2004; Johansson et al., 2011; reviewed in Wood and Brodie, 2015; see Björklund et al., 2013 for a temporal variation example in a wild population).
Most of these studies used individuals from different populations subsequently bred under artificial laboratory conditions to estimate quantitative genetic parameters and thus very few have been conducted directly in wild populations. To our knowledge, Roff et al. (2004) is the only study that has investigated the variability of G among populations and where the phenotypes have been measured on individuals in their natural environments. This scarcity may be problematic given that there is growing evidence that laboratory experiments may not be generalizable to wild populations that are experiencing true natural conditions (Kruuk et al., 2008; Charmantier et al., 2014; Sniegula et al., 2016). Compared with laboratory experiments, the drawback of working with wild populations is that genotype by environment (G × E) interactions can confound tests of differences in Gmatrices when estimated in the wild (Wood and Brodie, 2015). However, in the wild, the estimated evolutionary potential is expressed in the environment where the individuals are selected so that comparing Gmatrices in populations differing in their adaptive optimum offers the opportunity to test whether different selection pressures trigger differentiation in Gmatrices (McGuigan, 2006; Johansson et al., 2011).
Overall, information about the spatial variability of evolutionary potential in wild populations is still very scarce. Therefore, there is now a crucial need for empirical studies aiming at understanding whether the genetic architecture of traits is actually variable in the wild and at which spatial scale (Steppan et al., 2002; Arnold et al., 2008; Aguirre et al., 2014). Because of the very demanding nature of estimating Gmatrices in the wild, substituting G by phenotypic variance–covariance matrices (P), which are much easier to estimate, is a common practice (see, for example, Berner et al., 2008). However, this substitution is useful only if P correctly reflects the underlying genetic architecture, and this may not always be the case (Willis et al., 1991; Hadfield et al., 2007). Furthermore, although comparison tools exist, until recently there was no statistical framework available to compare more than two matrices at the same time and to integrate the uncertainties around Gmatrix estimates that are often large (Aguirre et al., 2014). This stresses the need for more empirical studies in the wild aiming at reporting G variability for different kinds of traits and its consequences on the evolutionary potential of populations.
Here, we assess the extent and the nature of spatial variation in the Gmatrix for a set of morphological and reproductive traits in four wild populations displaying strong phenotypic differentiation. We use longterm data collected from four Mediterranean blue tit (Cyanistes caeruleus) populations ideally suited for quantitative genetic studies because of the availability of extensive pedigree information and phenotypic data. More specifically, we estimate Gmatrices for four morphological traits representing body size and shape (tarsus, wing and beak length as well as body mass) and for three reproductive traits (laying date, clutch size and incubation period). We focus particularly on incubation period, as, to our knowledge, the present study is only the second one to test for genetic variance associated with this trait in natural populations (Husby et al., 2012).
Our study populations are located in a typical Mediterranean landscape, in southern France mainland and on the island of Corsica, composed of patchy mosaics of heterogeneous habitats, with forest covers either dominated by deciduous oaks (Quercus pubescens) or evergeen oaks (Quercus ilex). This habitat variation translates into marked phenotypic differences in morphological and lifehistory traits (Blondel et al., 2006; Charmantier et al., 2016). For instance, in the evergreen habitat, birds lay fewer eggs and up to 1 month later in spring compared with birds in deciduous forests. Moreover, birds from the mainland are smaller (ca. 15%) than birds from Corsica (Charmantier et al., 2016). These differences are likely because of differences in selective pressures between the different habitats. In this respect, Porlier et al. (2012a) showed that selection is significantly different among populations for clutch size and laying date (mainly in the strength of the linear selection gradients). Charmantier et al. (2004b) also showed that selection on chick morphology differs between sites (also see Charmantier et al., 2016 for a thorough review of evidence for local adaptation). Based on mitochondrial genetic data and morphological data, Corsican populations have been attributed to a different subspecies Cyanistes caeruleus ogliastrae, occurring as well in the Iberian Peninsula, whereas the mainland population belongs to the subspecies C. caeruleus caeruleus (Kvist et al., 2004). Population genetic analyses have recently confirmed the limited gene flow between mainland and Corsica (Porlier et al., 2012b; Szulkin et al., 2016).
Taking advantage of this welldefined ecospatial context, this system provides an excellent setting to evaluate the effects of contrasted habitats and population history on the Gmatrix and their consequences on population evolutionary potential. First, we seek to estimate G in each population for the two sets of traits (morphology and reproduction) using Bayesian multivariate animal models and to describe precisely the differences observed between populations. To do so, we use a fourthorder genetic covariance tensor analysis (Hine et al., 2009), a method that can detect subtle differences in variance–covariance structure among a set of matrices. Second, we aim to explore whether the potential differences are explained by the contrast in habitat and/or by geographic distance (mainland vs island). We predict that Gmatrices may have diverged between mainland and island because of limited gene flow and different population histories (that is, neutral processes). We also predict that Gmatrices may differ between evergreen and deciduous habitats because of divergent selection pressures in these two environments. However, the existing theoretical framework does not provide any quantitative predictions regarding the direction and magnitude of these differences. We also aim to assess whether these differences are dependent on the suite of traits studied (life history vs morphology). Following Arnold et al. (2001), we predict stronger divergences between lifehistory Gmatrices than morphological Gmatrices as the former traits may experience stronger and more variable selective pressures. Finally, we compare Pmatrices among populations for the two sets of characters to assess what would have been inferred if the data prevented us from estimating Gmatrices.
Materials and methods
Study system
Data were collected in four blue tit populations, with landscapes dominated either by the deciduous downy oak Q. pubescens (site names starting with D) or by the evergreen holm oak Q. ilex (site names starting with E). One study site was located in southern France (DRouviere), and the other three sites were located in northwestern Corsica (EPirio, DMuro and EMuro) with 6 to 30 km separating them and distant to the mainland site by 440 km (Figure 1). All populations were monitored as part of a longterm research programme for 17 to 27 years (see Table 1 for sampling years). Capture and handling of the birds was conducted under permits provided by the Centre de Recherches sur la Biologie des Populations d'Oiseaux (CRBPO) and by the Direction Départementale des Services Vétérinaires (DDSV).
Phenotypic data
Each year, nest boxes were visited at least once a week during the reproductive period, where data on laying date (date of first egg laid with 1=1st March) and clutch size (number of eggs) were collected. Incubation period was calculated as the number of days between the laying of the last egg and the hatching date of the first chick. Thus, what we call incubation period does not correspond to the physiological incubation time sensu stricto. This period can be longer than the physiological incubation time (14 days, Vedder, 2012) if the female adds a waiting time after her last egg is laid (typically in a relatively cold spring); it can also be shorter if the female begins to incubate before the last egg is laid (typically in warm springs). In these populations, most females lay only one clutch per year (0 to 1.5% of females lay second clutches in our populations), and upon breeding failure replacement clutches are sometimes laid. Second and replacement clutches were excluded from the data set. Breeding blue tits were captured in nest boxes during the feeding of their young, banded with a unique metal ring provided by the CRBPO. Nestlings were also uniquely banded before fledging. Four different morphological traits were measured on male and female breeders: body mass, tarsus length (from the intertarsal joint to the most distal undivided scute on the tarsometarsus), flattened wing length and bill length (from the anterior end of the nares to the tip of the upper mandible). Phenotypic differences among the different populations as well as their locations are presented in Figure 1 and Table 1 (see Charmantier et al., 2016 for a thorough review of phenotypic divergence in this system).
Pedigree construction
Pedigrees were constructed in a similar way for each population. We first included all ringed individuals and assigned their mother and father based on observational data (caught in the nest box while feeding the brood). For a subset of individuals (N=161), molecular assignation of the biological father using microsatellite data was performed (Charmantier et al., 2004a), and observational pedigree data were corrected accordingly. In populations of this study system, 14 to 25% of nestlings are sired by an extrapair mate (Charmantier and Blondel, 2003; Charmantier et al., 2004a), a proportion that could slightly underestimate but is unlikely to greatly bias our genetic variance estimates considering the sample sizes involved (Charmantier and Réale, 2005; Firth et al., 2015). Unknown parents of a given nest were coded using a dummy identity in the pedigree to preserve sibship information. Pedigrees were pruned for each data set studied to retain only phenotyped individuals and their ancestors using the pedantics Rpackage (Morrissey and Wilson, 2010). Pruned pedigree information for each population and trait type is presented in Table 1.
Quantitative genetic analyses
G and Pmatrix estimation
Gmatrices were estimated in each population by using multivariate animal models (Lynch and Walsh, 1998; Kruuk, 2004). Two different Gmatrices were constructed for each population: one for each type of traits (morphological and lifehistory traits). Random effects included additive genetic effects (V_{A}) estimated through the inclusion of multigenerational pedigree data, permanent environmental effects (V_{PE}) accounting for repeated measurements of the same individual (see Table 1 for details), year effect (V_{Y}) and residual variance (V_{R}). In addition, for morphological traits, we added a random effect for measurer identity in order to control for any potential confounding measurer effect (V_{OBS}, the number of measurer varying between 15 and 18 depending on the locality). For morphological models, all parents caught during the breeding period were included in the analyses, whereas models for lifehistory traits were female specific. Several fixed effects (age, sex and ordinal date) were added to account for potentially confounding effects (see Supplementary Appendix 1 and Supplementary Table S1 for more details). Ordinal date was included in order to remove the effect of potential trait changes within year (for example, seasonal variation of body mass or variation of wing length due to feather abrasion; Supplementary Appendix 1).
As the main purpose of our study was matrix comparison for several traits, we attached particular attention to trait standardization as scale differences between variables may potentially affect our conclusions (Hansen et al., 2011). Trait standardization is essentially done to remove any effects of differential measurement scale among traits and to compare traits with different orders of magnitude. All but one trait analysed were on a ratio scale (such as measurements and counts, that is, positive real numbers that are multipliable by real numbers without affecting the relationships among the measurements and possess a unique and nonarbitrary 0); laying date was on an interval scale (that is, a variable for which there is no natural 0). Transformations that preserve relationships among the measurements for variables on a ratio scale are multiplications by a constant. For variables on an interval scale, addition of a constant and multiplication by a constant are both permissible transformations (Houle et al., 2011). We chose to apply mean standardization within each population for all the phenotypic variables we used (that is, dividing raw trait values by the population mean) as variance scaling is not suitable when one is interested in evolutionary potential (Houle, 1992; Hansen and Houle, 2008; Houle et al., 2011; Hansen et al., 2011). Thus, mean scaling removes the disproportionate effect of traits with larger means, thereby avoiding multiple problems of interpretation (Houle et al., 2011; Hansen et al., 2011). Laying date was the only variable for which mean standardization was not relevant, and hence we accounted for differences in mean laying date between populations by subtracting the median laying date of each population from the raw values and then added 30 days in order to avoid negative values. This removed differences in variance only due to mean differences between populations while still allowing comparison with other phenotypic traits having a true natural zero.
The models we used can be described as follow:
Equation (1a) describes the animal models run on morphological traits with Y_{morpho} the vector of mean standardized morphological observations for all individuals and μ the vector of mean phenotypes. X is the design matrix relating to fixed effects, and b is the vector of fixed effects to be fitted. Z_{a}, Z_{pe}, Z_{yr} and Z_{obs} are the incidence matrices relating to additive genetic (a), permanent environment (pe), year (yr) and measurer (obs) random effects, respectively, and e is the vector of residual error. Equation (1b) describes the lifehistory animal models with Y_{LHT} the vector of mean standardized lifehistory traits observations for all individuals and μ the vector of mean phenotypes. X is the design matrix relating to fixed effects, and b is the vector of fixed effects to be fitted. Z_{a}, Z_{pe} and Z_{y} are the incidence matrices relating to additive genetic (a), permanent environment (pe) and year (y) random effects, respectively, and e is the vector of residual error.
All these analyses were performed in a Bayesian framework using the MCMCglmm Rpackage (Hadfield, 2010). As the use of posterior distributions propagates the errors in all estimates derived from animal models, Bayesian inference has a clear advantage over the other existing methods (Morrissey et al., 2014). Posterior distributions were composed of 1000 values for each parameter. We used 1 200 000 iterations per animal model with sampling every 1000 steps. The 200 000 first iterations were discarded as burnin. To facilitate convergence, we used slightly informative priors with and nu=n with Vp being the phenotypic variance, r the number of random factors and n the number of traits. We assessed convergence of the models by graphically checking the posterior estimates and ensuring that autocorrelation of all the parameter estimates was lower than 0.05.
Gmatrices thus correspond to the variance–covariance matrix associated with the additive genetic random effect. Pmatrices were calculated as the sum of all the variance–covariance matrices associated with the different random effects but the observer effect, that is, summing a, pe, yr and e in equations (1a and 1b). Heritabilities and the proportion of phenotypic covariances explained by genetic covariances were estimated by standardizing the Gmatrix by the Pmatrix, that is, result of the product P^{−1/2}·G·P^{−1/2}.
Matrix description: size and shape
The additive genetic variance associated with each trait was characterized with I_{A} evolvabilities. I_{A} estimates can be interpreted as the expected percentage of trait change per generation if it were submitted to selection as strong as on fitness itself (Hansen and Houle, 2008). In order to describe accurately every estimated G and Pmatrices, we also computed a series of descriptors of their size and shape. Total volume (V_{tot}, V_{tot_G and} V_{tot_P} for G and P, respectively), a measure of the variance contained in each matrix, was calculated as the sum of the eigenvalues (Equation (2)). Eccentricity (Ω, Ω_{G} and Ω_{P} for G and P, respectively), a measure of the shape of the matrix, was calculated as the ratio of the first eigenvalue over the sum of all eigenvalues (Equation (3), Jones et al., 2003).
with λ_{i} the ith eigenvalues of a given G or Pmatrix, and n the number of traits. To assess the credible interval of the shape and size metrics, we estimated these descriptors for each of the 1000 estimates that compose the distribution of G and P. We then computed the mode of their distribution and the 95% credible interval calculated as the 95% highest posterior density interval with the Rpackage (MCMCglmm; Hadfield, 2010).
Comparing G matrices among populations
Comparison of Gmatrices has long been a statistical challenge and numerous methods have been applied (Steppan et al., 2002; Roff et al., 2012; Aguirre et al., 2014). However, most of these methods were not directly related to evolutionary theory (Hansen and Houle, 2008; Aguirre et al., 2014). Methods were usually designed to compare matrices element by element or based on criteria that were hardly interpretable in terms of change of genetic variance or response to selection (Aguirre et al., 2014). Here we used the fourthorder genetic covariance tensor method (Hine et al., 2009), recently highlighted by Aguirre et al. (2014) as it is directly related to the evolutionary consequences of divergence in G for populations, can detect subtle differences between variance–covariance matrices and allows to compare more than two matrices at the same time and to integrate uncertainty in estimates.
Tensors are geometric objects that describe linear relationships between scalars, vectors, matrices and other tensors. The order of a tensor reflects the number of indices required to define its elements (De Lathauwer et al., 2004). For example, a linear map is represented by a matrix (a twodimensional array), and therefore is a secondorder tensor. Here, in order to describe the variation among several additive genetic variances, two indices are required (for example, the genetic covariance between trait x and y is denoted G_{xy}). The Gmatrix is thus a secondorder tensor. Multilinear algebra extends tensors to higher order structures that can be used to describe variation in lower order structures such as matrices. The complete description of the variation among Gmatrices requires to estimate the relationships between the (co)variances among populations, that is, the (co)variances between genetic (co)variances, for example, the variances among populations of the covariances between traits x and y (G_{xy}) or the covariance of G_{xy} and G_{zw} (the covariance between traits z and w). Such elements are denoted ∑_{G:xy,zw} and require the use of four indices. Therefore, the variation among Gmatrices (that is, secondorder tensors) can be described using a fourthorder genetic covariance tensor (∑) (Hine et al., 2009).
To simplify ∑, it can be represented as a secondorder tensor that corresponds to a covariance matrix (S) of dimension n(n+1)/2 with n the number of traits (Basser and Pajevic, 2007). The eigenanalysis of the Smatrix mirrors the spectral decomposition of ∑ and describes accurately variation among the different Gmatrices using eigenvalues and secondorder eigentensors (E). These eigentensors are higher level equivalent of eigenvectors for matrices and describe independent aspects of variation between the different Gmatrices and their eigenvalues reflect the amount by which an eigentensor contributes to variation among Gmatrices. These independent eigentensors may be interpreted as biologically relevant axes of differentiation representing different sources of selective pressures for example (Hine et al., 2009). Large values in the diagonal elements but small values in the offdiagonal elements of E would indicate differences among G mainly in the quantity of variance for individual traits, the relative magnitude of these values indicating the relative contribution of each trait to these differences. On the other hand, the magnitude of the offdiagonal elements of E indicates differences in trait covariances between Gmatrices. Practically, each secondorder eigentensor can be decomposed into its eigenvalues and eigenvectors (e) that describe genetically independent linear combinations of traits that show differences in genetic variance and covariance. The distribution of the eigenvalues of an eigentensor indicates the number of independent genetic directions in which the Gmatrices differ (within the space of independent change represented by the eigentensor). For example, if the first eigenvector of an eigentensor accounts for most of the variance (its eigenvalue is large compared with the others), the Gmatrices differ likely only in a single combination of traits that corresponds to the trait loadings on this eigenvector. We strongly encourage the reader to refer to Hine et al. (2009) for more details on theoretical aspects of the genetic covariance tensor method.
We applied the fourthorder genetic covariance tensor in a Bayesian framework following Aguirre et al. (2014). To do so, we simply estimated the S_{i} matrix for every ith sample (i varied from 1 to 1000) of the set of posterior distributions for the different Gmatrices. We then calculated the posterior modes (S̄) of the elements of S_{i} and their associated eigentensors. We then projected every ith sample of G on the different eigentensors to obtain the distribution of the position of the different Gmatrices on each eigentensor. We encourage the reader to refer to Aguirre et al. (2014) and Careau et al. (2015) for concrete examples and R scripts to use these methods. In order to test for differences between Gmatrices, we tested whether the credible interval of their positions along the eigentensors accounting for most of the total variance overlapped. In order to explore the robustness of these results we used several confidence intervals (0.95, 0.925 and 0.9). As complementary approaches, to assess the robustness of our results to different statistical methods, we also tested these differences using a method based on the generation of null matrices developed by Aguirre et al. (2014) (see Supplementary Appendix 2) and a method developed by Ovaskainen et al. (2008) (see Supplementary Appendix 3).
In order to compare the evolutionary potential of each population, we also calculated the multivariate average unconditional and conditional evolvabilities for the different estimated Gmatrices following the approach of Hansen and Houle (2008). Univariate unconditional evolvability is the ability of a trait to respond to selection. It thus mainly depends on the standing variation available in the population and corresponds to the expected evolutionary response per generation in the direction of a linear selection gradient of unit strength (Hansen and Houle, 2008). The multivariate version of unconditional evolvability corresponds to the amount of predicted evolutionary response occurring in the direction of selection. To obtain an overall estimation of the evolutionary potential associated with the Gmatrix, average unconditional evolvability over random selection gradients can be calculated following Hansen and Houle (2008):
where E[λ] denotes the expectation of λ (corresponding to the eigenvalues of G).
As the average unconditional evolvability ē is unaffected by covariances between traits, we also calculated the average conditional evolvability c̄. The conditional evolvability of a trait corresponds to the response of this trait to a unit directional selection when a set of constraining (that is, covarying) traits is not allowed to change. When averaged over all directions in the phenotype space, it provides a global measure of genetic constraints (low constraint for high value of c̄). It can be calculated following Hansen and Houle (2008):
where H[λ] is the harmonic mean of λ and I[x]≡var[x]/E[x]^{2} denotes the meanstandardized variance.
These different quantities and their associated credible intervals were compared among populations for each type of traits.
Are P matrices different among populations? In order to know what would have been inferred if the pedigree data to estimate Gmatrices was not available, we used the covariance tensor analysis on Pmatrices (for the two set of characters) to test whether they differed between populations. The rationale of this analysis is that finding homogeneous Pmatrices across populations is often interpreted as an indication that Gmatrices are probably homogeneous as well (Arnold et al., 2001). Besides, we also estimated the eigenvalues of P^{−1/2}GP^{−1/2} for lifehistory and morphological traits for each population. A flat distribution of the eigenvalues of P^{−1/2}GP^{−1/2} indicates that all regions of the phenotypic space are equally heritable and the G and P matrices are proportional, whereas a skew in the distribution of the eigenvalues indicates that there are regions of phenotypic space that are more heritable than others, so that P and G are not proportional.
Results
Gmatrices among trait types and populations
We found substantial levels of additive genetic variation (posterior distributions disjunct from 0, see Supplementary Figure S1 for details on distributions) in all of the 28 trait/population combinations (Tables 2a and 3). All morphological traits displayed lower levels of I_{A} evolvabilities (ranging from 0.012 to 0.095; Table 2a) than lifehistory traits (ranging from 0.109 to 1.533; Table 3). As a result, Gmatrices for lifehistory traits displayed substantially higher V_{tot} (ranging from 1.457 to 3.242; details in Supplementary Table S2) than Gmatrices for morphological traits (ranging from 0.177 to 0.232; details in Supplementary Table S2). However, when converted into heritabilities (that is, divided by phenotypic variance estimates), values for morphological traits were on average higher than for lifehistory ones (Tables 2a and 3). In terms of trait associations, the posterior modes of genetic covariances between morphological traits were all positive and presented similar values in each population (Table 2b, see Supplementary Table S3a for genetic correlation estimates). All genetic covariances were significant for DRouvière and EMuro, except for genetic covariances between bill length and the other morphological traits in EMuro. For EPirio and DMuro, all genetic covariances between bill length and the other morphological traits were positive but only significant with body mass. For lifehistory traits, the genetic covariance between laying date and clutch size was negative in all populations but significant only for DMuro (Table 3; see Supplementary Table S3b for genetic correlation estimates). All other genetic covariances for lifehistory traits were nonsignificant. In addition, estimates of the other variance components are provided in Supplementary Table S4.
All morphological traits loaded in the same direction on the first eigenvector of G, with body mass having the strongest statistical weight (Supplementary Table S5). For morphological Gmatrices, eccentricity (that is, the proportion of variance accounted for by the first eigenvector of a matrix) ranged from 55.6 to 66.4% (Supplementary Table S2). For lifehistory traits, laying date and clutch size had opposed loadings on the first eigenvector (Supplementary Table S5). Incubation period had little influence on the first eigenvector. Lifehistory Gmatrices showed similar eccentricity values to those obtained for morphological traits (ranging from 55 to 81.1% for lifehistory G; Supplementary Table S2). As eccentricity corresponds to the quantity of variance contained in the main axis of variation over the total variance contained in the matrix, it provides an indication on the shape of the Gmatrix and is bounded between V_{tot}/n (sphere shape) and 1 (line). Our values of eccentricity thus indicated ellipsoid Gmatrices.
Comparisons of Gmatrices between populations
In the covariance tensor analyses, the first and second eigentensors explained 90% of the variance among matrices for lifehistory traits and 70% for morphological traits (Supplementary Table S6). Along the first eigentensors (E_{1} and E_{2}, respectively, the first and second eigentensors), the 95% confidence intervals of posterior distributions of the position of the Gmatrices overlapped (Figures 2a and b). As confidence intervals are usually large with Gmatrix estimates, we computed less stringent confidence intervals (0.925, 0.9) to test whether our results were robust to less stringent criteria. For morphological traits, we obtained the same results. For lifehistory traits, 90% confidence intervals did not overlap on E_{1} between EPirio and DMuro. However, note that their relative positions on the tensors were very close.
In line with this, evolutionary potential estimates indicated weak differentiation. The different measures of evolutionary potential from each Gmatrix also largely overlapped between the different populations apart from conditional evolvability of the morphological Gmatrix between EPirio and DRouvière (Figure 3a). This may indicate that the Gmatrices from DRouvière and EPirio were very weakly differentiated, a trend perceptible in Figure 2a (along E_{2}, see also Supplementary Appendix 3 and Supplementary Figure S2). Moreover, using the method developed by Aguirre et al. (2014) to test differences with the tensor analysis, we did not detect any difference between Gmatrices for both types of traits (Supplementary Appendix 2, Supplementary Table S7 and Supplementary Figure S3a). Therefore, the only slight differences we found were inconsistent across methods suggesting weak global pattern. Thus, we found little evidence for differences among Gmatrices whatever the type of trait, the type of habitat or the geographic position of the population considered (mainland vs island). Note however that a valid test of an insular effect on the Gmatrix would require at least replicate mainland populations. Apart from being nonsignificant with 95% confidence intervals, the differences in the posterior modes of the different metrics computed represent negligible differences in evolutionary potential. Indeed, although evolvability values showed that lifehistory traits harbour slightly more genetic variance in DMuro, conditional evolvability values, a measure that takes the genetic architecture into account, were similar for the four blue tit populations (Figure 3).
Pmatrix comparison
At the phenotypic level, covariances between morphological traits were similar in terms of magnitude to the genetic covariances. However, in contrast with the nonsignificant genetic correlations, tarsus length and bill length phenotypes covaried significantly at the phenotypic level in all populations (Table 2b; see Supplementary Table S3a for correlation estimates). In addition, phenotypic covariances for lifehistory traits tended to be significant, especially for covariance involving clutch size (Table 3 and Supplementary Figure S4; see Supplementary Table S3b for genetic correlation estimates). For both types of traits, the distributions of the eigenvalues of P^{−1/2}·G·P^{−1/2} were skewed indicating nonproportionality between G and P (Figure 4 and Supplementary Figure S5).
Using the covariance tensor analysis to compare the different Pmatrices among populations, we found that Pmatrices differed significantly among populations for morphological and lifehistory traits. For morphological traits, the first covariance tensor (E_{1}), which accounted for 55.4% of the variance among matrices, described significant variation between the Pmatrices for DMuro, EMuro and DRouvière (posterior distributions of their position on E_{2} did not overlap, Figure 2c; although confidence intervals slightly overlapped in additional analyses, see Supplementary Appendix 2, Supplementary Figure S3 and Supplementary Table S7). For lifehistory trait Pmatrices, we found that the second covariance tensor (E_{2}), which accounted for 29.4% of the variance among matrices, described significant variation between the Pmatrices for DRouvière and the three Corsican populations (that is, posterior distributions of their position on E_{2} did not overlap, Figure 2d, Supplementary Figure S3 and Supplementary Table S7). Laying date and clutch size had opposing loadings (respective loadings: 0.750, −0.604) on the first eigenvector of the second eigentensor (e_{21}; which explained 55.9 % of the variation captured by E_{2}, Supplementary Table S6) meaning that the differences between these matrices lie mainly in the quantity of variance contained in these two traits.
Discussion
Using detailed pedigrees and multivariate animal models on longterm phenotypic datasets of blue tits, we estimated Gmatrices for morphological and lifehistory traits in four wild populations. Although these populations belonged to two different subspecies, experienced contrasted environments imposing different selection pressures and exhibited strong phenotypic divergence on many traits (Porlier et al., 2012b; Charmantier et al., 2016), we found no evidence for differences among populations in Gmatrices for both set of traits. In contrast, although Pmatrices for morphological traits were quite conserved among populations, Pmatrices for lifehistory traits were different, thus highlighting that Pmatrices can be poor surrogates of Gmatrices.
Genetic architecture of lifehistory and morphological traits
All studied traits displayed substantial levels of additive genetic variance in all populations (Tables 2a and 3 and Supplementary Figure S1). In birds, numerous studies have previously found significant V_{A} for morphological traits (reviewed in Postma, 2014). For lifehistory traits, results from previous studies are more equivocal, yet clutch size and laying date usually display low but significant heritable variation (Postma, 2014). In terms of magnitude, morphological traits show substantially (10 times) lower I_{A} than lifehistory traits. Traits closely associated with fitness are predicted to harbour little genetic variance (Fisher, 1930; Falconer and Mackay, 1996), and in line with this, lifehistory traits have been shown to have low heritability (Kruuk et al., 2000; McCleery et al., 2004; Teplitsky et al., 2009). However, these results are likely explained by the general use of variance scaling that leads traits with large phenotypic variance, such as lifehistory traits, to present relatively small estimated heritabilities (Houle, 1992). For this reason, several authors have advocated the use of mean scaling that better reflects the potential of lifehistory traits for rapid evolution (Hansen and Houle, 2008; Hansen et al., 2011).
In contrast to the large literature on clutch size and laying date, our study is, to our knowledge, only the second one to test for genetic variance in incubation period in natural populations (Husby et al., 2012) and the first one to show evidence for additive genetic variation in incubation period. Note that incubation period measured here is not the strict physiological duration of egg incubation by the female, but rather the time interval between the last egg laid and hatching. This interval is a crucial period for insectivorous birds in temperate forests that need to adjust their breeding phenology in order to synchronize the late nestling stage with the food peak period (Dunn, 2004; Visser et al., 2006). Although it is well known that females can adjust their laying date via individual phenotypic plasticity (see, for example, Both et al., 2004; Charmantier and Gienapp, 2014), the fine tuning of breeding phenology can also be modulated through variation in this incubation period, either by: (1) a delay of the start of incubation after clutch completion (Cresswell and Mccleery, 2003; Kluen et al., 2011, 2) a start of incubation before the last egg is laid leading to asynchronous hatching (Kontiainen et al., 2010; Vedder, 2012) or (3) an adjustment of the efficiency of incubation following the completion of the clutch (Haftorn, 1988; Hadfield et al., 2013). Both hatching delay and asynchrony have been shown to have substantial impact on fitness (Kontiainen et al., 2010; Kluen et al., 2011; Hadfield et al., 2013). Asynchronous hatching produces generally a size hierarchy in the brood staggering the food demand over time. In turn, this hierarchy may help sibling negotiation, reduce rivalry and increase offspring survival (see, for example, Kontiainen et al., 2010). Thereby, evidence for additive genetic variation in incubation period implies that this trait could not only be adjusted through phenotypic plasticity, but also that it could evolve in the long term if targeted by natural selection. This is particularly important in the actual context of global environmental changes, as it could further help avian populations to track the advancing phenology of their food resources because of warming spring temperatures (Both and Visser, 2005; Visser et al., 2006; Visser, 2008).
In our blue tit study, genetic covariances between morphological traits were all positive and significant as found in numerous other studies (see, for example, Roff, 1996; Kruuk et al., 2008) denoting classic positive allometric relationships between morphological traits linked to body size. For lifehistory traits, significant negative phenotypic correlations between laying date and clutch size were found in all populations, but the genetic covariance between these two traits was significant only in DMuro. Larger clutches for earlier laying dates are very common in birds (see, for example, Winkler and Allen, 1996; Husby et al., 2010), and this correlation corresponds to a classic tradeoff in lifehistory theory (Klomp, 1970). However, whether this correlation has a strong genetic basis remains unclear as significant genetic correlations were found in several previous studies on insectivorous passerines (Sheldon et al., 2003; Garant et al., 2008 and in this study for DMuro), but not in others (Gienapp et al., 2008; Husby et al., 2010, and here DRouvière, EPirio and EMuro). As genetic correlations often suffer from large sampling variances (Falconer and Mackay, 1996; Roff, 1996; Kruuk et al., 2008), it is difficult to understand the causes of such variability in estimates. In our case, we found contrasted results across the three populations with welldetailed pedigree (DMuro, EPirio and DRouvière). Hence, it is unlikely that the nonsignificance of genetic correlations is due to power limitations. Thus, the reason why early breeding birds are laying larger clutches could be because of a plastic response to environmental variation, whereby females may lay fewer eggs in late spring in order to adjust to the decreasing food availability (Perrins, 1970; Goodenough et al., 2009).
No difference in Gmatrix between populations
Simulation studies have shown that genetic drift or divergent selection can change G characteristics from one generation to another (see, for example, Roff, 2000; Jones et al., 2003). It is thus interesting that we found no significant Gmatrix differences between the four blue tits populations, as they differ in many respects (habitats, phenotypic distributions and selective pressures; Charmantier et al., 2004b, 2016; Porlier et al., 2012a). A lack of difference in G between populations also indicates a lack of evidence for any G × E interactions. Nevertheless, these results are in line with other studies investigating Gmatrix variation among populations highlighting strong similarity of Gmatrices (see, for example, Roff et al., 2004; review in Arnold et al., 2008). Compelling examples of divergent Gmatrices across populations exist but they generally used particular experimental designs with individuals collected in the field and subsequently bred in the laboratory in contrasting environmental conditions, thus complicating the interpretation for Gmatrix evolution (see, for example, Cano et al., 2004; Doroszuk et al., 2008). Moreover, for many of these studies, it is difficult to evaluate the robustness of the different tests because of (1) lack of inclusion or biased estimation of error estimates (Ovaskainen et al., 2008) and (2) inadequate pedigree structure (for example, few related individuals; problems already highlighted in the field; Charmantier and Garant, 2005). Therefore, interestingly, although it seems relatively easy to modify G by applying artificial selection (see, for example, Careau et al., 2015), in nature, Gmatrices seem stable, even between populations exposed to strong habitat differences (Arnold et al., 2008 but see Wood and Brodie, 2015). Several nonmutually exclusive hypotheses may explain this observation.
First, in nature, conspecific populations are generally not genetically isolated. Migration between populations can potentially counteract the diversifying effect of divergent selective pressures and thus tend to homogenize Gmatrices (Guillaume and Whitlock, 2007). In our system, although significant genetic structure has been revealed within Corsica (Porlier, et al., 2012b; Szulkin et al., 2016), dispersal between the three Corsican blue tit populations occurs and might be a powerful homogenizing force. However, dispersal has a limited role regarding island/mainland differentiation as these populations have probably evolved in allopatry and belong to two different mitochondrial lineages (Kvist et al., 2004).
Second, artificial selection pressures applied in experimental studies among populations are often strong and designed to be contrasted (see, for example, Doroszuk et al., 2008). In nature, although spatial variation of selection seems common, strength variability appears as the main component of variation in selection across populations, whereas direction is relatively conserved (Siepielski et al., 2013). This pattern seems to hold in our study system for laying date and clutch size (Porlier et al., 2012a). In laboratory experiments, the selection pressures applied to different treatments might also differ in direction rather than in strength alone. In this respect, an interesting study by Bolstad et al. (2015) showed that an extremely conserved allometric relationship in Drosophila can be modified by applying specific selective pressures. However, once the selective pressures were released, the population rapidly recovered the original allometric slope. They concluded that the allometric slope change generated deleterious pleiotropic responses because of links with unknown traits. Thus, it is possible that the reason why we rarely observe changes is because of strong pleiotropic links with unmeasured traits that prevent structural changes of Gmatrices unless particularly new selective gradients are applied such as in laboratory experiments (Bolstad et al., 2015). In nature, if the components of selection influencing the most Gmatrices are not variable across populations, spatial stability may actually not be surprising. In this respect, Roff and Fairbairn (2012) showed that correlational selection seems to be responsible for the eigenstructure of Gmatrices. It is possible that this type of selection is remarkably stable across populations and environments. Unfortunately, very little is known about spatial variation of some components of selection such as nonlinear (quadratic and correlational) selection (Siepielski et al., 2013, but see Garant et al., 2007), and hence further investigations in this sense will be of interest.
Using Pmatrices as substitutes for Gmatrices
P may differ substantially from G for various reasons (Willis et al., 1991). However, data sets allowing the estimation of Gmatrices in the wild are still scarce. Therefore, in numerous studies, P is used as a surrogate of G either for comparative or for predictive purposes (see, for example, Berner et al., 2008). In this study, we showed that morphological Pmatrices displayed similar patterns compared with Gmatrices. In this respect, they may appear as an adequate measure of the underlying Gmatrices, but this conclusion is antagonized by the fact that P and G were not proportional for morphological traits (Figure 4). For lifehistory traits, the patterns observed for Pmatrices were different from those observed for Gmatrices, indicating that basing our population comparisons on Pmatrices could have led to erroneous conclusions in this case. The more heritable a trait is, the more similar phenotypic correlations are to genetic ones (Cheverud, 1988; Hadfield et al., 2007). Therefore, using P instead of Gmatrices is likely to give more reliable results for traits having substantial heritabilities, such as morphological traits, but not for traits showing low heritabilities, such as lifehistory traits (Roff, 1996). However, based on the general nonproportionality of P and Gmatrices, great caution should be taken.
An issue that may affect our conclusions is the difference in statistical power generally observed between G and P estimates. Phenotypic (co)variances are easier to estimate with small sample sizes than genetic (co)variances (Cheverud, 1988). This leads genetic estimates to be often more imprecise and have wider confidence intervals. Therefore, one reason why we observe differences between P but not Gmatrices could be because of lower statistical power to estimate G. We are nevertheless confident that our results are robust as the Gmatrices were estimated using a large number of individuals and good pedigree characteristics that seem sufficient to detect significant differences (see simulations by Teplitsky et al., 2014a). Moreover, even if the Gmatrices were weakly differentiated in our study system, these differences are unlikely to result in strong differences in evolutionary potential as evolvability values were similar among the four populations (Figure 3). We also used three different statistical methods commonly used in the literature to compare our results with other studies. Combining the analysis of P, G and E (that is, the environmental variance–covariance matrix) matrices with selection and divergence estimates will definitely help us to better depict the origin of phenotypic divergence in this system.
Conclusions
Although the populations studied here differ in many respects, they have similar evolutionary potential based on estimated Gmatrices for morphological and lifehistory traits. Future comparative genomic data analyses performed in these populations will help us understand the genetic basis of these different characters and whether the same genes underlie traits in different populations (Santure et al., 2015). As most estimations of G obtained from wild populations are limited to a few model species and populations, further studies exploring spatial variation of G across the whole range of the species will be necessary to test whether our results can be extrapolated to other populations. If Gmatrices are conserved across the entire species range, it will open interesting perspectives regarding the predictive power of such estimations. Our findings finally highlight the value of longterm data sets in several wild populations of the same species in heterogeneous environments to better understand the complexity of evolutionary dynamics across space and time.
Data archiving
Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.03mn0.
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Acknowledgements
We thank all the people who helped to maintain the study sites and conduct the blue tit monitoring since 1988, in particular Jacques Blondel, Philippe Perret, Marcel Lambrechts, Arnaud Grégoire, Claire Doutrelant and Christophe de Franceschi. We thank Loeske Kruuk, LuisMiguel Chevin, Charles Perrier and four anonymous reviewers for useful advice and comments on earlier drafts. This project was funded by the Agence Nationale de la Recherche (BioAdapt Grant ANR12ADAP000602PEPS to CT and AC), the European Research Council (Starting grant ERC2013StG337365SHE to AC), the Natural Sciences and Engineering Research Council of Canada (NSERC discovery grant to DG) and the OSUOREME.
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Delahaie, B., Charmantier, A., Chantepie, S. et al. Conserved Gmatrices of morphological and lifehistory traits among continental and island blue tit populations. Heredity 119, 76–87 (2017). https://doi.org/10.1038/hdy.2017.15
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