Developmental quantitative genetic models of evolutionary change

Discussions about evolutionary change in developmental processes or morphological structures are predicated on specific quantitative genetic models whose parameters predict whether evolutionary change can occur, its relative rate and direction, and if correlated change will occur in other related and unrelated structures. The appropriate genetic model should reflect the relevant genetical and developmental biology of the organisms, yet be simple enough in its parameters so that deductions can be made and hypotheses tested. As a consequence, the choice of the most appropriate genetic model for polygenically controlled traits is a complex tissue and the eventual choice of model is often a compromise between completeness of the model and computational expediency. Herein, we discuss several developmental quantitative genetic models for the evolution of development and morphology. The models range from the classical direct effects model to complex epigenetic models. Further, we demonstrate the algebraic equivalency of the Cowley and Atchley epigenetic model and Wagner's developmental mapping model. Finally, we propose a new multivariate model for continuous growth trajectories. The relative efficacy of these various models for understanding evolutionary change in developmental and morphological traits is discussed. © 1994 Wiley-Liss, Inc.     

The change in quantitative genetic variation with inbreeding

Inbreeding is known to reduce heterozygosity of neutral genetic markers, but its impact on quantitative genetic variation is debated. Theory predicts a linear decline in additive genetic variance (V(A)) with increasing inbreeding coefficient (F) when loci underlying the trait act additively, but a nonlinear hump-shaped relationship when dominance and epistasis are important. Predictions for heritability (h2) are similar, although the exact shape depends on the value of h2 in the absence of inbreeding. We located 22 published studies in which the level of genetic variation in experimentally inbred populations (measured by V(A) or h2) was compared with that in outbred control populations. For life-history traits, the data strongly supported a nonlinear change in genetic variation with increasing F. V(A) and h2 were, respectively, 244% and 50% higher at F = 0.4 than in outbred populations, and dominance plus epistatic variance together exceeded additive variance by a factor of four. For nonfitness traits the decline was linear and estimates of nonadditive variance were small. These results confirm that population bottlenecks frequently increase V(A) in some traits, and imply that life-history traits are underlain by substantial dominance or epistasis. However, the importance of drift-induced genetic variation in conservation or evolutionary biology is questionable, in part because inbreeding depression usually accompanies inbreeding.     

Patterns of genetic variation in US federal bison herds

Like many wide‐ranging mammals, American bison (Bison bison) have experienced significant range contraction over the past two centuries and are maintained in artificially isolated populations. A basic understanding of the distribution of genetic variation among populations is necessary to facilitate long‐term germplasm preservation and species conservation. The 11 herds maintained within the US federal system are a critically important source of germplasm for bison conservation, as they include many of the oldest herds in the USA and have served as a primary resource for the establishment of private and public herds worldwide. In this study, we used a panel of 51 nuclear markers to investigate patterns of neutral genetic variation among these herds. Most of these herds have maintained remarkably high levels of variation despite the severe bottleneck suffered in the late 1800s. However, differences were noted in the patterns of variation and levels of differentiation among herds, which were compared with historical records of establishment, supplementation, herd size, and culling practices. Although some lineages have been replicated across multiple herds within the US federal system, other lineages with high levels of genetic variation exist in isolated herds and should be considered targets for the establishment of satellite herds. From this and other studies, it is clear that the genetic variation represented in the US federal system is unevenly distributed among National Park Service and Fish and Wildlife Service herds, and that these resources must be carefully managed to ensure long‐term species conservation.     

Spatial variation in the evolutionary potential and constraints of basal metabolic rate and body mass in a wild bird

An organism's energy budget is strongly related to resource consumption, performance, and fitness. Hence, understanding the evolution of key energetic traits, such as basal metabolic rate (BMR), in natural populations is central for understanding life-history evolution and ecological processes. Here we used quantitative genetic analyses to study evolutionary potential of BMR in two insular populations of the house sparrow (Passer domesticus). We obtained measurements of BMR and body mass (M_b) from 911 house sparrows on the islands of Leka and Vega along the coast of Norway. These two populations were the source populations for translocations to create an additional third, admixed ‘common garden’ population in 2012. With the use of a novel genetic group animal model concomitant with a genetically determined pedigree, we differentiate genetic and environmental sources of variation, thereby providing insight into the effects of spatial population structure on evolutionary potential. We found that the evolutionary potential of BMR was similar in the two source populations, whereas the Vega population had a somewhat higher evolutionary potential of M_b than the Leka population. BMR was genetically correlated with M_b in both populations, and the conditional evolutionary potential of BMR (independent of body mass) was 41% (Leka) and 53% (Vega) lower than unconditional estimates. Overall, our results show that there is potential for BMR to evolve independently of M_b, but that selection on BMR and/or M_b may have different evolutionary consequences in different populations of the same species.     

Quantitative genetic analysis of cranial morphology in the cotton-top (Saguinus oedipus) and saddle-back (S. fuscicollis) tamarins

Patterns of morphological variation play an important role in evolutionary diversification and are critical to an informed interpretation of interspecific differences. When patterns of genetic variation have not diverged substantially, it is possible to reconstruct the differences in selection which gave rise to morphological differences among extant species. Morphological variation patterns are compared between two tamarin species, the cotton-top tamarin (Saguinus oedipus) and the saddle-back tamarin (S. fuscicollis illigeri). Genetic, phenotypic, and environmental variance/covariance and correlation matrices were obtained for a series of 39 cranial characters in each species (cotton-top tamarin, N = 328; saddle-back tamarin, N = 209) and for the species combined using crania from individuals of known genealogical relationship. After accounting for the effects of estimation error on measures of matrix similarity, patterns of phenotypic, genetic, and environmental variation and correlation were found to be very similar across species and among the types of variance within species. Taking the saddle-back tamarins as the standard, cotton-top tamarins have been selected for an enlarged anterior temporalis attachment area and increased facial prognathism. In primates, an enlarged anterior temporalis muscle is associated with incisive food preparation, especially at wide gape.     

Comparing evolvabilities: common errors surrounding the calculation and use of coefficients of additive genetic variation

In 1992, David Houle showed that measures of additive genetic variation standardized by the trait mean, CV(A) (the coefficient of additive genetic variation) and its square (I(A) ), are suitable measures of evolvability. CV(A) has been used widely to compare patterns of genetic variation. However, the use of CV(A) s for comparative purposes relies critically on the correct calculation of this parameter. We reviewed a sample of quantitative genetic studies, focusing on sire models, and found that 45% of studies use incorrect methods for calculating CV(A) and that practices that render these coefficients meaningless are frequent. This may have important consequences for conclusions drawn from comparative studies. Our results are suggestive of a broader problem because miscalculation of the additive genetic variance from a sire model is prevalent among the studies sampled, implying that other important quantitative genetic parameters might also often be estimated incorrectly. We discuss the most prominent issues affecting the use of CV(A) and I(A) , including scale effects, data transformation, and the comparison of traits with different dimensions. Our aim is to increase awareness of the potential mistakes surrounding the calculation and use of evolvabilities, and to compile general guidelines for calculating, reporting, and interpreting these useful measures in future studies.     

Genetic variation and asexual reproduction in the facultatively parthenogenetic cockroach Nauphoeta cinerea: implications for the evolution of sex

Asexual reproduction could offer up to a two‐fold fitness advantage over sexual reproduction, yet higher organisms usually reproduce sexually. Even in facultatively parthenogenetic species, where both sexual and asexual reproduction is sometimes possible, asexual reproduction is rare. Thus, the debate over the evolution of sex has focused on ecological and mutation‐elimination advantages of sex. An alternative explanation for the predominance of sex is that it is difficult for an organism to accomplish asexual reproduction once sexual reproduction has evolved. Difficulty in returning to asexuality could reflect developmental or genetic constraints. Here, we investigate the role of genetic factors in limiting asexual reproduction in Nauphoeta cinerea, an African cockroach with facultative parthenogenesis that nearly always reproduces sexually. We show that when N. cinerea females do reproduce asexually, offspring are genetically identical to their mothers. However, asexual reproduction is limited to a nonrandom subset of the genotypes in the population. Only females that have a high level of heterozygosity are capable of parthenogenetic reproduction and there is a strong familial influence on the ability to reproduce parthenogenetically. Although the mechanism by which genetic variation facilitates asexual reproduction is unknown, we suggest that heterosis may facilitate the switch from producing haploid meiotic eggs to diploid, essentially mitotic, eggs.     

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch

The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.     

The influence of variation and of developmental constraints on the rate of multivariate phenotypic evolution

A model of multivariate phenotypic evolution is analysed under the assumption that all characters have the same variance or at least constant ratios of variance. The rate of evolution is examined as a function of the amount of phenotypic variance in a variety of adaptive landscapes (fitness functions). It is demonstrated that the effect of variation depends on the type of adaptive landscape. In “well behaved” adaptive landscapes the rate of evolution can theoretically increase without limits, depending on the amount of heritable phenotypic variation. However, in other adaptive landscapes there are upper limits to the rate of evolution which cannot be exceeded if phenotypic variation is developmentally unconstrained, i. e. if it is the same for all characters. Further it is shown that the maximal rate of evolution becomes small if the number of characters becomes large. Fitness functions of this type are called malignant. It is argued that malignant fitness functions are more adequate models for the evolution of typical organismic systems, because they are models of functionally interdependent characters. It is concluded that there are upper limits to the rate of phenotypic evolution if the variation of functionally interdependent characters is developmentally unconstrained. The possible role of developmental constraints in adaptive phenotypic evolution is discussed.     

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.     

What can genetic variation tell us about the evolution of senescence?

Quantitative genetic approaches have been developed that allow researchers to determine which of two mechanisms, mutation accumulation (MA) or antagonistic pleiotropy (AP), best explain observed variation in patterns of senescence using classical quantitative genetic techniques. These include the creation of mutation accumulation lines, artificial selection experiments and the partitioning of genetic variances across age classes. This last strategy has received the lion''s share of empirical attention. Models predict that inbreeding depression (ID), dominance variance and the variance among inbred line means will all increase with age under MA but not under those forms of AP that generate marginal overdominance. Here, we show that these measures are not, in fact, diagnostic of MA versus AP. In particular, the assumptions about the value of genetic parameters in existing AP models may be rather narrow, and often violated in reality. We argue that whenever ageing-related AP loci contribute to segregating genetic variation, polymorphism at these loci will be enhanced by genetic effects that will also cause ID and dominance variance to increase with age, effects also expected under the MA model of senescence. We suggest that the tests that seek to identify the relative contributions of AP and MA to the evolution of ageing by partitioning genetic variance components are likely to be too conservative to be of general value.     

Discerning evolutionary processes in patterns of tamarin (genus Saguinus) craniofacial variation

Quantitative genetic theory specifies evolutionary expectations for morphological diversification by genetic drift in a monophyletic clade. If genetic drift is responsible for the evolutionary morphological diversification of a clade, patterns of within- and between-taxon morphological variance/covariance should be proportional. We tested for proportionality of within- and between-species craniofacial morphological variation in 12 species of tamarins (genus Saguinus). We found that within- and between-taxon morphological variations across the entire genus were not proportional, and hence not likely to be due to genetic drift alone. The primary deviation from proportionality is that size and size-related shape in the cranium is more variable relative to other aspects of cranial morphology than expected under genetic drift, suggesting differential size selection between the two major clades, the small-bodied and large-bodied tamarins. Within each of these major clades, most of the interspecific variation is consistent with the pattern expected under genetic drift, although specific contrasts may indicate the involvement of differential selection. Morphological distances among taxa do not correspond very closely to the phylogeny derived from mtDNA. In particular, S. oedipus and S. geoffroyi are very distinct morphologically from the rest of the tamarins, although they are phylogenetically the sister clade to a clade containing S. midas and S. bicolor. Morphological similarity is not a good guide to phylogenetic affinity in the tamarins, especially with regard to deeper nodes in the phylogenetic tree.     

Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)

The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species’ divergence.     

Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis

Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G-protein ODR-3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr-3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr-3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr-3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr-3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans.     

Contrasting variation within and covariation between gender-related traits in autogamous versus outcrossing species: Alternative evolutionary predictions

We present several predictions concerning the expression of genetic variation in, and covariation among, gender-related traits in perfect-flowered plant taxa with different breeding systems. We start with the inference that the pollen:ovule (P/O) ratio in obligately autogamous species (in which the ovules in a flower are fertilized only by the pollen it produces) should be under much stronger stabilizing selection than in outcrossing taxa. Consequently, we predict that obligately autogamous taxa should exhibit lower genetic coefficients of variation in the P/O ratio. Nevertheless, genetic variation in both pollen and ovule production per flower might persist within autogamous as well as outcrossing populations. In autogamous taxa, genotypes with relatively few pollen grains and ovules per flower (but producing relatively high numbers of flowers) and genotypes with comparatively high numbers of gametes per flower (but producing relatively few flowers) could co-exist if lifetime flower production is selectively neutral. In contrast, in outcrossers, the maintenance of genetic variation in ovule and pollen production per flower might result predominantly from their ability to maintain variation in phenotypic and functional gender. Given genetic variation in primary sexual traits, we predict that the genetic correlation between investment in male and female gametes per flower should qualitatively differ between selfers and outcrossers. We predict a positive genetic correlation between pollen and ovule production per flower in obligately autogamous taxa, primarily because strong stabilizing selection on the P/O ratio should select against the gender specialists that would be necessary to effect a negative genetic correlation between mean pollen and ovule production per flower. Moreover, the fact that autogamous individuals are 50% female and 50% male means that gender-biased phenotypes cannot be functionally gender-biased, preventing selection from favouring phenotypic extremes. In contrast, in outcrossing taxa, in which functionally male- and female-biased genotypes may co-exist, the maintenance of contrasting genders could contribute to the expression of negative genetic correlations between pollen and ovule production per flower. We discuss these and a number of corollary predictions, and we provide a preliminary empirical test of the first prediction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Predicting evolutionary responses to climate change in the sea

An increasing number of short‐term experimental studies show significant effects of projected ocean warming and ocean acidification on the performance on marine organisms. Yet, it remains unclear if we can reliably predict the impact of climate change on marine populations and ecosystems, because we lack sufficient understanding of the capacity for marine organisms to adapt to rapid climate change. In this review, we emphasise why an evolutionary perspective is crucial to understanding climate change impacts in the sea and examine the approaches that may be useful for addressing this challenge. We first consider what the geological record and present‐day analogues of future climate conditions can tell us about the potential for adaptation to climate change. We also examine evidence that phenotypic plasticity may assist marine species to persist in a rapidly changing climate. We then outline the various experimental approaches that can be used to estimate evolutionary potential, focusing on molecular tools, quantitative genetics, and experimental evolution, and we describe the benefits of combining different approaches to gain a deeper understanding of evolutionary potential. Our goal is to provide a platform for future research addressing the evolutionary potential for marine organisms to cope with climate change.     

Maxillary sinus variation in hybrid macaques: implications for the genetic basis of craniofacial pneumatization

There has been a long‐standing debate regarding the diversification of paranasal sinuses, namely pneumatized spaces in the face. Functional adaptation and structural constraints have generally been suggested to explain sinus diversification in vertebrates. Here we investigated variation in the maxillary sinus and the external facial cranium in hybrid Taiwanese–Japanese macaques to estimate the genetic basis of phenotypic differences. The Taiwanese macaques have a large sinus, whereas the Japanese macaques have a small sinus; they are also significantly different in their external craniofacial morphology. Variations in the hybrids' external craniofacial morphology can be mostly explained by a simple additive model. In contrast, their sinus morphology significantly deviates from the value expected under this additive model, wherein most hybrids have a large sinus, similar to that in Taiwanese macaques, regardless of the degree of hybridization. When the whole structure is considered, a novel phenotype can be seen in the hybrids. Our results suggest that the sinus and face are independent of each other, both genetically and developmentally, and that the small sinus is mainly caused by intrinsic genetic factors, rather than being structurally constrained by the craniofacial architecture. Such genetic factors may have contributed to the enigmatic diversity of craniofacial pneumatization. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 333–347.     

A test of genetic models for the evolutionary maintenance of same-sex sexual behaviour

The evolutionary maintenance of same-sex sexual behaviour (SSB) has received increasing attention because it is perceived to be an evolutionary paradox. The genetic basis of SSB is almost wholly unknown in non-human animals, though this is key to understanding its persistence. Recent theoretical work has yielded broadly applicable predictions centred on two genetic models for SSB: overdominance and sexual antagonism. Using Drosophila melanogaster, we assayed natural genetic variation for male SSB and empirically tested predictions about the mode of inheritance and fitness consequences of alleles influencing its expression. We screened 50 inbred lines derived from a wild population for male–male courtship and copulation behaviour, and examined crosses between the lines for evidence of overdominance and antagonistic fecundity selection. Consistent variation among lines revealed heritable genetic variation for SSB, but the nature of the genetic variation was complex. Phenotypic and fitness variation was consistent with expectations under overdominance, although predictions of the sexual antagonism model were also supported. We found an unexpected and strong paternal effect on the expression of SSB, suggesting possible Y-linkage of the trait. Our results inform evolutionary genetic mechanisms that might maintain low but persistently observed levels of male SSB in D. melanogaster, but highlight a need for broader taxonomic representation in studies of its evolutionary causes.