Evolution and medicine share a dependence on the genotypephenotype map. Although genotypes exist and are inherited in a discrete space convenient for many sorts of analyses, the causation of key ...phenomena such as natural selection and disease takes place in a continuous phenotype space whose relationship to the genotype space is only dimly grasped. Direct study of genotypes with minimal reference to phenotypes is clearly insufficient to elucidate these phenomena. Phenomics, the comprehensive study of phenotypes, is therefore essential to understanding biology. For all of the advances in knowledge that a genomic approach to biology has brought awareness is growing that many phenotypes are highly polygenic and susceptible to genetic interactions. Prime examples are common human diseases. Phenomic thinking is starting to take hold and yield results that reveal why it is so critical. The dimensionality of phenotypic data are often extremely high, suggesting that attempts to characterize phenotypes with a few key measurements are unlikely to be completely successful. However, once phenotypic data are obtained, causation can turn out to be unexpectedly simple. Phenotypic data can be informative about the past history of selection and unexpectedly predictive of long-term evolution. Comprehensive efforts to increase the throughput and range of phenotyping are an urgent priority.
Populations unable to evolve to selectively favored states are constrained. Genetic constraints occur when additive genetic variance in selectively favored directions is absent (absolute constraints) ...or present but small (quantitative constraints). Quantitative—unlike absolute—constraints are presumed surmountable given time. This ignores that a population might become extinct before reaching the favored state, in which case demography effectively converts a quantitative into an absolute constraint. Here, we derive criteria for predicting when such conversions occur. We model the demography and evolution of populations subject to optimizing selection that experience either a single shift or a constant change in the optimum. In the single‐shift case, we consider whether a population can evolve significantly without declining or else declines temporarily while avoiding low sizes consistent with high extinction risk. We analyze when populations in constantly changing environments evolve sufficiently to ensure long‐term growth. From these, we derive formulas for critical levels of genetic variability that define demography‐caused absolute constraints. The formulas depend on estimable properties of fitness, population size, or environmental change rates. Each extends to selection on multivariate traits. Our criteria define the nearly null space of a population’sGmatrix, the set of multivariate directions effectively inaccessible to it via adaptive evolution.
Mutation enables evolution, but the idea that adaptation is also shaped by mutational variation is controversial. Simple evolutionary hypotheses predict such a relationship if the supply of mutations ...constrains evolution, but it is not clear that constraints exist, and, even if they do, they may be overcome by long-term natural selection. Quantification of the relationship between mutation and phenotypic divergence among species will help to resolve these issues. Here we use precise data on over 50,000 Drosophilid fly wings to demonstrate unexpectedly strong positive relationships between variation produced by mutation, standing genetic variation, and the rate of evolution over the last 40 million years. Our results are inconsistent with simple constraint hypotheses because the rate of evolution is very low relative to what both mutational and standing variation could allow. In principle, the constraint hypothesis could be rescued if the vast majority of mutations are so deleterious that they cannot contribute to evolution, but this also requires the implausible assumption that deleterious mutations have the same pattern of effects as potentially advantageous ones. Our evidence for a strong relationship between mutation and divergence in a slowly evolving structure challenges the existing models of mutation in evolution.
Evolution of morphological allometry Pélabon, Christophe; Firmat, Cyril; Bolstad, Geir H. ...
Annals of the New York Academy of Sciences,
July 2014, Letnik:
1320, Številka:
1
Journal Article
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Morphological allometry refers to patterns of covariance between body parts resulting from variation in body size. Whether measured during growth (ontogenetic allometry), among individuals at similar ...developmental stage (static allometry), or among populations or species (evolutionary allometry), allometric relationships are often tight and relatively invariant. Consequently, it has been suggested that allometries have low evolvability and could constrain phenotypic evolution by forcing evolving species along fixed trajectories. Alternatively, allometric relationships may result from natural selection for functional optimization. Despite nearly a century of active research, distinguishing between these alternatives remains difficult, partly due to wide differences in the meaning assigned to the term allometry. In particular, a broad use of the term, encompassing any monotonic relationship between body parts, has become common. This usage breaks the connection to the proportional growth regulation that motivated Huxley's original narrow‐sense use of allometry to refer to power–law relationships between traits. Focusing on the narrow‐sense definition of allometry, we review here evidence for and against the allometry‐as‐a‐constraint hypothesis. Although the low evolvability and the evolutionary invariance of the static allometric slope observed in some studies suggest a possible constraining effect of this parameter on phenotypic evolution, the lack of knowledge about selection on allometry prevents firm conclusions.
Precise exponential scaling with size is a fundamental aspect of phenotypic variation. These allometric power laws are often invariant across taxa and have long been hypothesized to reflect ...developmental constraints. Here we test this hypothesis by investigating the evolutionary potential of an allometric scaling relationship in drosophilid wing shape that is nearly invariant across 111 species separated by at least 50 million years of evolution. In only 26 generations of artificial selection in a population of Drosophila melanogaster, we were able to drive the allometric slope to the outer range of those found among the 111 sampled species. This response was rapidly lost when selection was suspended. Only a small proportion of this reversal could be explained by breakup of linkage disequilibrium, and direct selection on wing shape is also unlikely to explain the reversal, because the more divergent wing shapes produced by selection on the allometric intercept did not revert. We hypothesize that the reversal was instead caused by internal selection arising from pleiotropic links to unknown traits. Our results also suggest that the observed selection response in the allometric slope was due to a component expressed late in larval development and that variation in earlier development did not respond to selection. Together, these results are consistent with a role for pleiotropic constraints in explaining the remarkable evolutionary stability of allometric scaling.
How tissues acquire their characteristic shape is a fundamental unresolved question in biology. While genes have been characterized that control local mechanical forces to elongate epithelial ...tissues, genes controlling global forces in epithelia have yet to be identified. Here, we describe a genetic pathway that shapes appendages in Drosophila by defining the pattern of global tensile forces in the tissue. In the appendages, shape arises from tension generated by cell constriction and localized anchorage of the epithelium to the cuticle via the apical extracellular-matrix protein Dumpy (Dp). Altering Dp expression in the developing wing results in predictable changes in wing shape that can be simulated by a computational model that incorporates only tissue contraction and localized anchorage. Three other wing shape genes, narrow, tapered, and lanceolate, encode components of a pathway that modulates Dp distribution in the wing to refine the global force pattern and thus wing shape.
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•The apical extracellular matrix protein Dumpy (Dp) is required for appendage shape•Dp anchors the epidermis to the cuticle, generating tension during tissue contraction•Alteration of the pattern of Dp gives rise to predictable changes in appendage shape•Narrow (Nw), Tapered (Ta), and Lanceolate (Ll) affect shape by modulating Dp
Regulation of global tensile forces in epithelia is one mechanism of determining tissue shape. Ray and Matamoro-Vidal et al. show that tissue contraction, in combination with localized anchorage to the cuticle by the apical extracellular matrix protein Dumpy, gives rise to anisotropic tensions that shape the appendages in the Drosophila pupa.
Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally ...based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome of Drosophila melanogaster lines that had undergone approximately 200 generations of spontaneous mutation accumulation (MA). We detected a total of 28 point mutations and eight insertion-deletion (indel) mutations, yielding an estimate for the single-nucleotide mutation rate of 6.2 x 10(-8) per site per fly generation. Most mutations were heteroplasmic within a line, and their frequency distribution suggests that the effective number of mitochondrial genomes transmitted per female per generation is about 30. We observed repeated occurrences of some indel mutations, suggesting that indel mutational hotspots are common. Among the point mutations, there is a large excess of G-->A mutations on the major strand (the sense strand for the majority of mitochondrial genes). These mutations tend to occur at nonsynonymous sites of protein-coding genes, and they are expected to be deleterious, so do not become fixed between species. The overall mtDNA mutation rate per base pair per fly generation in Drosophila is estimated to be about 10x higher than the nuclear mutation rate, but the mitochondrial major strand G-->A mutation rate is about 70x higher than the nuclear rate. Silent sites are substantially more strongly biased towards A and T than nonsynonymous sites, consistent with the extreme mutation bias towards A+T. Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent evidence suggests that sexually selected traits have unexpectedly high genetic variance. In this paper, we offer a simple and general mechanism to explain this observation. Our explanation ...offers a resolution to the lek paradox and rests on only two assumptions; condition dependence of sexually selected traits and high genetic variance in condition. The former assumption is well supported by empirical evidence. We discuss the evidence for the latter assumption. These two assumptions lead inevitably to the capture of genetic variance into sexually selected traits concomitantly with the evolution of condition dependence. We present a simple genetic model to illustrate this view. We then explore some implications of genic capture for the coevolution of female preference and male traits. Our exposition of this problem incidentally leads to new insights into the similarities between sexually selected traits and life history traits, and therefore into the maintenance of high genetic variance in the latter. Finally, we discuss some shortcomings of a recently proposed alternative solution to the lek paradox; selection on variance.
Quantitative genetics provides one of the most promising frameworks with which to unify the fields of macroevolution and microevolution. The genetic variance–covariance matrix (
G) is crucial to ...quantitative genetic predictions about macroevolution. In spite of years of study, we still know little about how
G evolves. Recent studies have been applying an increasingly phylogenetic perspective and more sophisticated statistical techniques to address
G matrix evolution. We propose that a new field, comparative quantitative genetics, has emerged. Here we summarize what is known about several key questions in the field and compare the strengths and weaknesses of the many statistical and conceptual approaches now being employed. Past studies have made it clear that the key question is no longer whether
G evolves but rather how fast and in what manner. We highlight the most promising future directions for this emerging field.
Comparative methods that use phylogenetic information are providing a more powerful tool to explore quantitative genetic questions. New statistical methods can help determine how genetic correlations and other parameters evolve.
The sensory bias model of sexual selection posits that female mating preferences are by‐products of natural selection on sensory systems. Although sensory bias was proposed 20 years ago, its critical ...assumptions remain untested. This paradox arises because sensory bias has been used to explain two different phenomena. First, it has been used as a hypothesis about signal design, that is, that males evolve traits that stimulate female sensory systems. Second, sensory bias has been used as a hypothesis for the evolution of female preference itself, that is, to explain why females exhibit particular preferences. We focus on this second facet. First, we clarify the unique features of sensory bias relative to the alternative models by considering each in the same quantitative genetic framework. The key assumptions of sensory bias are that natural selection is the predominant evolutionary mechanism that affects preference and that sexual selection on preferences is quantitatively negligible. We describe four studies that would test these assumptions and review what we can and cannot infer about sensory bias from existing studies. We suggest that the importance of sensory bias as an explanation for the evolution of female preferences remains to be determined.
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