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601.
Robert J. Dugand J. David Aguirre Emma Hine Mark W. Blows Katrina McGuigan 《Proceedings of the National Academy of Sciences of the United States of America》2021,118(31)
Genetic variance is not equal for all multivariate combinations of traits. This inequality, in which some combinations of traits have abundant genetic variation while others have very little, biases the rate and direction of multivariate phenotypic evolution. However, we still understand little about what causes genetic variance to differ among trait combinations. Here, we investigate the relative roles of mutation and selection in determining the genetic variance of multivariate phenotypes. We accumulated mutations in an outbred population of Drosophila serrata and analyzed wing shape and size traits for over 35,000 flies to simultaneously estimate the additive genetic and additive mutational (co)variances. This experimental design allowed us to gain insight into the phenotypic effects of mutation as they arise and come under selection in naturally outbred populations. Multivariate phenotypes associated with more (less) genetic variance were also associated with more (less) mutational variance, suggesting that differences in mutational input contribute to differences in genetic variance. However, mutational correlations between traits were stronger than genetic correlations, and most mutational variance was associated with only one multivariate trait combination, while genetic variance was relatively more equal across multivariate traits. Therefore, selection is implicated in breaking down trait covariance and resulting in a different pattern of genetic variance among multivariate combinations of traits than that predicted by mutation and drift. Overall, while low mutational input might slow evolution of some multivariate phenotypes, stabilizing selection appears to reduce the strength of evolutionary bias introduced by pleiotropic mutation.The presence of genetic variation in natural populations is a basic tenet of biology, and yet we still understand very little about how evolutionary processes interact to maintain genetic variance (1). One reason this presents such a difficult challenge is the ubiquitous, but poorly understood, nature of pleiotropy (2). The presence of pleiotropy substantially changes two fundamental aspects of genetic variation: the relative magnitude of genetic variance associated with multivariate trait combinations (3), and the efficacy of processes such as mutation–selection balance in maintaining genetic variation (4–9).While genetic variation in individual traits is ubiquitous (6, 10), the genetic variance of multivariate trait combinations gives a very different picture (3, 11). For sets of morphological, behavioral, or life-history traits, genetic variation tends to be concentrated in a few multivariate trait combinations, leaving other trait combinations with very little genetic variation (11, 12). This inequality in the magnitude of multivariate genetic variances plays a crucial role in determining short-term evolutionary responses (13–15). However, the genetic (co)variance matrix, G, itself can evolve (e.g., ref. 16), and understanding whether G is a good predictor of divergence over longer evolutionary timescales (17) ultimately depends on understanding how evolutionary processes shape G.Empirically, the contributions of mutation and selection to shaping G can be inferred by comparing G to M, the mutational (co)variance matrix, or comparing G to γ, the matrix describing multivariate nonlinear selection. If G is shaped by mutation and drift, then G should be proportional to M, and multivariate traits with relatively large mutational variances will have relatively large genetic variances, although individual populations are likely to deviate from this null expectation due to the sampling variance of the evolutionary process itself (18, 19). If new mutations have similar pleiotropic effects to standing genetic variants, then mutation might act to stabilize G (20, 21) and constrain evolution over the long-term (17). Conversely, if G is primarily shaped by selection, then G should be proportional to γ, and the long-term stability of G depends on the stability of the adaptive landscape (22). Under some genetic architectures, long-term consistency of γ might lead to the evolution of M and result in the proportionality of γ and M and the long-term stasis of G (23, 24).The magnitude of mutational correlation among pairs of life-history traits (e.g., refs. 25 to 26), as well as multivariate analyses of larger trait sets (e.g., refs. 27 and 28), suggest that mutational variance, like genetic variance, may typically vary markedly in magnitude among different trait combinations. However, few studies have directly compared G to M to infer the roles of mutation and selection in shaping G. Standing genetic correlations among life-history traits tend to be less positive than mutational correlations (e.g., refs. 29 and 30). Similarly, some multivariate analyses suggest differences between G and M. For example, Latimer et al. (31, 32) showed that there was little additive genetic variance along the major axis of mutational variance in Drosophila serrata thermal activity curves, implicating selection in shaping G. Similarly, Camara et al. (33) demonstrated that, as mutation rate (higher mutagen dose) increased in Arabidopsis thaliana, the phenotypic covariance matrices became increasingly dissimilar between the ancestral and mutated populations. In contrast, Houle et al. (17) found G and M to be markedly similar for wing traits in Drosophila melanogaster. Moreover, M predicted patterns of wing divergence across drosophilids (17), suggesting a major role for mutation in determining long-term adaptation, as well as G.Inference of selection via comparison of standing genetic to mutational variance is difficult for several reasons. Classical inbred-line experimental designs for estimating mutational parameters cannot provide estimates of standing genetic variance, and, while outbred populations provide estimates of standing genetic variance, it has proven difficult to estimate mutational variance in these populations (34). Thus, differences between G and M might arise due to the varying experimental conditions under which each is measured. Furthermore, the majority of studies estimating M have utilized inbred mutation accumulation (MA) lines or mutagens. Whether these studies are representative of the contribution of naturally occurring mutations to standing genetic variance in outbred populations is unknown. Wray (35) proposed a modification of the animal (mixed) model to account for the effect of mutations, allowing for the simultaneous estimation of standing genetic and mutational variance in an outbred population. This approach provides a way of estimating both G and M from the same sample of outbred individuals, allowing for a direct comparison of G and M without differences in experimental conditions, populations, or levels of inbreeding, that have, to date, confounded most comparisons of genetic and mutational variances (36). The substantial potential of Wray’s (35) mixed model has not yet been widely appreciated, with only three studies applying the method, each reporting estimates for individual traits only (36–38).Here, we implement Wray’s (35) approach in a multivariate model to simultaneously estimate G and M for a set of wing traits in an outbred population of D. serrata. We maintained the population under a middle-class neighborhood (MCN) breeding design, where the population size is fixed and family sizes are equalized, thereby minimizing between-family selection and allowing nonlethal mutations to accumulate in the population via random genetic drift (39). McGuigan et al. (36) demonstrated the utility of combining an MCN breeding design with Wray’s (35) approach, but their study presented estimates for individual traits only. In this paper, we report results from a large MCN population, comprising nearly 48,000 individuals from ∼7,900 families (Relatedness Examples of relationship/s Count 0.1 to 0.2 Great grandparent–great-grand offspring; first cousins 1,439,093 0.2 to 0.3 Grandparent–grand offspring; uncle–nephew 618,618 0.5 to 0.6 Full siblings; parent–offspring 216,705 (7,899 families) ≥1 Individuals (diagonals of A) 47,996 (37,076 with phenotype data)