Rapid and unpredictable changes of the G‐matrix in a natural bird population over 25 years

Knowledge of the genetic variances and covariances of traits (the G ‐matrix) is fundamental for the understanding of evolutionary dynamics of populations. Despite its essential importance in evolutionary studies, empirical tests of the temporal stability of the G ‐matrix in natural populations are few. We used a 25‐year‐long individual‐based field study on almost 7000 breeding attempts of the collared flycatcher (Ficedula albicollis) to estimate the stability of the G‐matrix over time. Using animal models to estimate G for several time periods, we show that the structure of the time‐specific G‐matrices changed significantly over time. The temporal changes in the G‐matrix were unpredictable, and the structure at one time period was not indicative of the structure at the next time period. Moreover, we show that the changes in the time‐specific G‐matrices were not related to changes in mean trait values or due to genetic drift. Selection, differences in acquisition/allocation patterns or environment‐dependent allelic effects are therefore likely explanations for the patterns observed, probably in combination. Our result cautions against assuming constancy of the G ‐matrix and indicates that even short‐term evolutionary predictions in natural populations can be very challenging.     

A TEST OF THE CONJECTURE THAT G‐MATRICES ARE MORE STABLE THAN B‐MATRICES

The G‐matrix occupies an important position in evolutionary biology both as a summary of the inheritance of quantitative traits and as an ingredient in predicting how those traits will respond to selection and drift. Consequently, the stability of G has an important bearing on the accuracy of predicted evolutionary trajectories. Furthermore, G should evolve in response to stable features of the adaptive landscape and their trajectories through time. Although the stability and evolution of G might be predicted from knowledge of selection in natural populations, most empirical comparisons of G‐matrices have been made in the absence of such a priori predictions. We present a theoretical argument that within‐sex G‐matrices should be more stable than between‐sex B‐matrices because they are more powerfully exposed to multivariate stabilizing selection. We tested this conjecture by comparing estimates of B‐ and within‐sex G‐matrices among three populations of the garter snake Thamnophis elegans. Matrix comparisons using Flury's hierarchical approach revealed that within‐sex G‐matrices had four principal components in common (full CPC), whereas B‐matrices had only a single principal component in common and eigenvalues that were more variable among populations. These results suggest that within‐sex G is more stable than B , as predicted by our theoretical argument.     

Experimental evolution of competing bean beetle species reveals long‐term reversals of short‐term evolution,but no consistent character displacement

Interspecific competition for shared resources should select for evolutionary divergence in resource use between competing species, termed character displacement. Many purported examples of character displacement exist, but few completely rule out alternative explanations. We reared genetically diverse populations of two species of bean beetles, Callosobruchus maculatus and Callosobruchus chinensis, in allopatry and sympatry on a mixture of adzuki beans and lentils, and assayed oviposition preference and other phenotypic traits after four, eight, and twelve generations of (co)evolution. C. maculatus specializes on adzuki beans; the generalist C. chinensis uses both beans. C. chinensis growing in allopatry emerged equally from both bean species. In sympatry, the two species competing strongly and coexisted via strong realized resource partitioning, with C. chinensis emerging almost exclusively from lentils and C. maculatus emerging almost exclusively from adzuki beans. However, oviposition preferences, larval survival traits, and larval development rates in both beetle species did not vary consistently between allopatric versus sympatric treatments. Rather, traits evolved in treatment‐independent fashion, with several traits exhibiting reversals in their evolutionary trajectories. For example, C. chinensis initially evolved a slower egg‐to‐adult development rate on adzuki beans in both allopatry and sympatry, then subsequently evolved back toward the faster ancestral development rate. Lack of character displacement is consistent with a previous similar experiment in bean beetles and may reflect lack of evolutionary trade‐offs in resource use. However, evolutionary reversals were unexpected and remain unexplained. Together with other empirical and theoretical work, our results illustrate the stringency of the conditions for character displacement.     

Comparison of genetic (co)variance matrices within and between Scabiosa canescens and S. columbaria

In the current study, we used bootstrap analyses and the common principal component (CPC) method of Flury (1988) to estimate and compare the G ‐matrix of Scabiosa columbaria and S. canescens populations. We found three major patterns in the G ‐matrices: (i) the magnitude of the (co)variances was more variable among characters than among populations, (ii) different populations showed high (co)variance for different characters, and (iii) there was a tendency for S. canescens to have higher genetic (co)variances than S. columbaria. The hypothesis of equal G ‐matrices was rejected in all comparisons and there was no evidence that the matrices differed by a proportional constant in any of the analyses. The two ‘species matrices’ were found to be unrelated, both for raw data and data standardized over populations, and there was significant between‐population variation in the G ‐matrix in both species. Populations of S. canescens showed conservation of structure (principal components) in their G ‐matrices, contrasting with the lack of common structure among the S. columbaria matrices. Given these observations and the results from previous studies, we propose that selection may be responsible for some of the variation between the G ‐matrices, at least in S. columbaria and at the between‐species level.     

Genetic basis of between‐individual and within‐individual variance of docility

Between‐individual variation in phenotypes within a population is the basis of evolution. However, evolutionary and behavioural ecologists have mainly focused on estimating between‐individual variance in mean trait and neglected variation in within‐individual variance, or predictability of a trait. In fact, an important assumption of mixed‐effects models used to estimate between‐individual variance in mean traits is that within‐individual residual variance (predictability) is identical across individuals. Individual heterogeneity in the predictability of behaviours is a potentially important effect but rarely estimated and accounted for. We used 11 389 measures of docility behaviour from 1576 yellow‐bellied marmots (Marmota flaviventris) to estimate between‐individual variation in both mean docility and its predictability. We then implemented a double hierarchical animal model to decompose the variances of both mean trait and predictability into their environmental and genetic components. We found that individuals differed both in their docility and in their predictability of docility with a negative phenotypic covariance. We also found significant genetic variance for both mean docility and its predictability but no genetic covariance between the two. This analysis is one of the first to estimate the genetic basis of both mean trait and within‐individual variance in a wild population. Our results indicate that equal within‐individual variance should not be assumed. We demonstrate the evolutionary importance of the variation in the predictability of docility and illustrate potential bias in models ignoring variation in predictability. We conclude that the variability in the predictability of a trait should not be ignored, and present a coherent approach for its quantification.     

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large‐scale genomic and phylogenetic data with gene co‐expression networks to extensively study the evolutionary make‐up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co‐expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de .     

Evolutionary transition between bee pollination and hummingbird pollination in Salvia: Comparing means,variances and covariances of corolla traits

Covariation among traits can modify the evolutionary trajectory of complex structures. This process is thought to operate at a microevolutionary scale, but its long‐term effects remain controversial because trait covariation can itself evolve. Flower morphology, and particularly floral trait (co)variation, has been envisioned as the product of pollinator‐mediated selection. Available evidence suggests that major changes in pollinator assemblages may affect the joint expression of floral traits and their phenotypic integration. We expect species within a monophyletic lineage sharing the same pollinator type will show not only similarity in trait means but also similar phenotypic variance‐covariance structures. Here, we tested this expectation using eighteen Salvia species pollinated either by bees or by hummingbirds. Our findings indicated a nonsignificant multivariate phylogenetic signal and a decoupling between means and variance‐covariance phenotypic matrices of floral traits during the evolution to hummingbird pollination. Mean trait value analyses revealed significant differences between bee‐ and hummingbird‐pollinated Salvia species although fewer differences were detected in the covariance structure between groups. Variance‐covariance matrices were much more similar among bee‐ than hummingbird‐pollinated species. This pattern is consistent with the expectation that, unlike hummingbirds, bees physically manipulate the flower, presumably exerting stronger selection pressures favouring morphological convergence among species. Overall, we conclude that the evolution of hummingbird pollination proceeded through different independent transitions. Thus, although the evolution of hummingbird pollination led to a new phenotypic optimum, the process involved the diversification of the covariance structure.     

Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp.

Corallimorpharia are the closest noncalcifying relatives of reef‐building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef‐building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp. The draft genomes encompass 370 and 445 Mbp, respectively, and encode for 21,372 and 23,199 genes. To facilitate future studies using these resources, we provide annotations for the predicted gene models—not only at gene level, by annotating gene models with the function of the best‐matching homologue, and GO terms when available; but also at protein domain level, where gene function can be better verified through the conservation of the sequence and order of protein domains. Further, we provide an online platform ( http://corallimorpharia.reefgenomics.org ), which includes a blast interface and a genome browser to facilitate the use of these resources. We believe that these two genomes are important resources for future studies on hexacorallian systematics and the evolutionary basis of their specific traits such as the symbiotic relationship with dinoflagellates of the genus Symbiodinium or the evolution of calcification in reef‐building corals.     

The effects of stochastic and episodic movement of the optimum on the evolution of the G‐matrix and the response of the trait mean to selection

Theoretical and empirical results demonstrate that the G ‐matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G ‐matrix could potentially have wide‐ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G ‐matrix stability and evolution when movement of an intermediate optimum includes large, episodic jumps or stochasticity. Here, we investigate such scenarios by using simulation‐based models of G ‐matrix evolution. These analyses yield four important insights regarding the evolution and stability of the G ‐matrix. (i) Regardless of the model of peak movement, a moving optimum causes the G ‐matrix to orient towards the direction of net peak movement, so that genetic variance is enhanced in that direction (the variance enhancement effect). (ii) Peak movement skews the distribution of breeding values in the direction of movement, which impedes the response to selection. (iii) The stability of the G ‐matrix is affected by the overall magnitude and direction of peak movement, but modes and rates of peak movement have surprisingly small effects (the invariance principle). (iv) Both episodic and stochastic peak movement increase the probability that a population will fall below its carrying capacity and go extinct. We also present novel equations for the response of the trait mean to multivariate selection, which take into account the higher moments of the distribution of breeding values.     

TYPE I ERROR RATES FOR TESTING GENETIC DRIFT WITH PHENOTYPIC COVARIANCE MATRICES: A SIMULATION STUDY

Studies of evolutionary divergence using quantitative genetic methods are centered on the additive genetic variance–covariance matrix ( G ) of correlated traits. However, estimating G properly requires large samples and complicated experimental designs. Multivariate tests for neutral evolution commonly replace average G by the pooled phenotypic within‐group variance–covariance matrix ( W ) for evolutionary inferences, but this approach has been criticized due to the lack of exact proportionality between genetic and phenotypic matrices. In this study, we examined the consequence, in terms of type I error rates, of replacing average G by W in a test of neutral evolution that measures the regression slope between among‐population variances and within‐population eigenvalues (the Ackermann and Cheverud [AC] test) using a simulation approach to generate random observations under genetic drift. Our results indicate that the type I error rates for the genetic drift test are acceptable when using W instead of average G when the matrix correlation between the ancestral G and P is higher than 0.6, the average character heritability is above 0.7, and the matrices share principal components. For less‐similar G and P matrices, the type I error rates would still be acceptable if the ratio between the number of generations since divergence and the effective population size (t/N_e) is smaller than 0.01 (large populations that diverged recently). When G is not known in real data, a simulation approach to estimate expected slopes for the AC test under genetic drift is discussed.     

Evolution,plasticity and evolving plasticity of phenology in the tree species Alnus glutinosa

Both traits and the plasticity of these traits are subject to evolutionary change and therefore affect the long‐term persistence of populations and their role in local communities. We subjected clones from 12 different populations of Alnus glutinosa, located along a latitudinal gradient, to two different temperature treatments, to disentangle the distribution of genetic variation in timing of bud burst and bud burst plasticity within and among genotypes, populations, and regions. We calculated heritability and evolvability estimates for bud burst and bud burst plasticity and assessed the influence of divergent selection relative to neutral drift. We observed higher levels of heritability and evolvability for bud burst than for its plasticity, whereas the total phenological heritability and evolvability (i.e. combining timing of bud burst and bud burst plasticity) suggest substantial evolutionary potential with respect to phenology. Earlier bud burst was observed for the low‐latitudinal populations than for the populations from higher latitudes, whereas the high‐latitudinal populations did not show the expected delayed bud burst. This countergradient variation can be due to evolution towards increased phenological plasticity at higher latitudes. However, because we found little evidence for adaptive differences in phenological plasticity across the latitudinal gradient, we suggest differential frost tolerance as the most likely explanation for the observed phenological patterns in A. glutinosa.     

A genome scan of diversifying selection in Ophiocordyceps zombie‐ant fungi suggests a role for enterotoxins in co‐evolution and host specificity

Identification of the genes underlying adaptation sheds light on the biological functions targeted by natural selection. Searches for footprints of positive selection, in the form of rapid amino acid substitutions, and the identification of species‐specific genes have proved to be powerful approaches to identifying the genes involved in host specialization in plant‐pathogenic fungi. We used an evolutionary comparative genomic approach to identify genes underlying host adaptation in the ant‐infecting genus Ophiocordyceps, which manipulates ant behaviour. A comparison of the predicted genes in the genomes of species from three species complexes—O. unilateralis, O. australis and O. subramanianii—revealed an enrichment in pathogenesis‐associated functions, including heat‐labile enterotoxins, among species‐specific genes. Furthermore, these genes were overrepresented among those displaying significant footprints of positive selection. Other categories of genes suspected to be important for virulence and pathogenicity in entomopathogenic fungi (e.g., chitinases, lipases, proteases, core secondary metabolism genes) were much less represented, although a few candidate genes were found to evolve under positive selection. An analysis including orthologs from other entomopathogenic fungi in a broader context showed that positive selection on enterotoxins was specific to the ant‐infecting genus Ophiocordyceps. Together with previous studies reporting the overexpression of an enterotoxin during behavioural manipulation in diseased ants, our findings suggest that heat‐labile enterotoxins are important effectors in host adaptation and co‐evolution in the Ophiocordyceps entomopathogenic fungi.     

Chromosome‐level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high‐quality chromosome‐level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single‐molecule real‐time sequencing, Illumina paired‐end sequencing, 10X Genomics linked‐reads and Hi‐C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single‐Copy Orthologs were determined in this genome assembly. And Hi‐C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein‐coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.     

EVOLUTION OF RESISTANCE TO A MULTIPLE‐HERBIVORE COMMUNITY: GENETIC CORRELATIONS,DIFFUSE COEVOLUTION,AND CONSTRAINTS ON THE PLANT'S RESPONSE TO SELECTION

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple‐herbivore communities—particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic‐selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one‐third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance.     

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long‐lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common‐garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change‐induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short‐term population survival in a changing climate.     

A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts

When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow‐down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the “early burst” prediction on species diversification and also on traits of putative ecological relevance (cell‐size and fermentation versatility). We found that speciation rates are constant during the time‐range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell‐size), suggesting that lineages resemble each other in trait‐values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell‐size. We also found a significant phylogenetic regression between cell‐size and fermentation versatility (R² = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common‐garden conditions combined with comparative analyses are warranted.     

Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid‐based plumage colouration

Many colour ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of colour elaboration are condition dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid‐based plumage colouration, one of the best‐known condition‐dependent ornaments, colour elaboration stems from both condition‐dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here, we tested whether multiple colour components may be condition dependent, by using a comprehensive 3 × 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of colouration. Plumage colouration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition‐dependent pathways, affected by different sources of variation, determine colour elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.     

Testing for a genetic response to sexual selection in a wild Drosophila population

In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)‐5,9‐C_27 : 2. Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response.