Components of phenotypic variation in the morphometrics of shearwater (Puffinus) species

Coefficients of variation were used to examine the variability of bill, wing and foot measurements of 11 sexually size dimorphic and seven monomorphic shearwater ( Puffinus ) species, and to investigate the selective regimes that may be acting on these traits. The effects of phylogeny can lead to a lack of statistical independence among interspecies data, so randomization tests were performed in addition to standard statistical approaches, which assume independence. However, the results obtained from the two approaches always agreed. Among the 18 species, bill measurements were significantly more variable than those of the wing or foot; furthermore, bill depth dimensions exhibited the greatest amount of phenotypic variation. Both sexually monomorphic and sexually dimorphic species exhibited the same patterns of phenotypic variation. In the sexually dimorphic species, patterns of trait variation did not differ significantly between sexes. The findings suggest that variation in the bill of dimorphic Puffinus species is not due to sexual selection. More probably, variability among the traits is due to differences in the strength of natural selection, with those traits under strong stabilizing selection (e.g. wing, tarsus and mid-toe) exhibiting reduced variability, as optimum physical dimensions are being selected for.     

Sexual dimorphism and dental variability in platyrrhine primates

Leutenegger and Cheverud (1982, 1985) propose a hypothesis to explain why larger primates are more sexually dimorphic in body weight and canine size. Their hypothesis states that any factor selecting for an evolutionary increase in body size will produce an increase in sexual dimorphism in any character if either heritability or phenotypic variability is greater in males than in females for that character. They cite no evidence for heritability but give some data to suggest that males are, in fact, more variable than females. We test the latter proposition more fully using measurements on the dentitions of platyrrhine primates. Male and female phenotypic variances are not significantly different in most cases. Cases of greater male phenotypic variance are not limited to sexually dimorphic species. We conclude that the hypothesis of Leutenegger and Cheverud does not explain the observed patterns of dental sexual dimorphism, at least in platyrrhines.     

Bat genitalia: allometry, variation and good genes

Male genitalia are typically highly variable across species, for which sexual selection is thought to be responsible. Sexually selected traits characteristically show positive allometry and high phenotypic variation, although genitalia seem to be typified by negative allometry due to stabilizing selection. Additionally, while sexual selection appears to be the primary force responsible for genital evolution, the precise mechanism is unclear, but good-genes selection could be involved. If so, male genital variation should correlate with some male quality measure(s). We investigated the allometry of male Nyctalus noctula genitalia and investigated associations between genital size and three phenotypic measures of male quality (body size, relative body mass, and fluctuating asymmetry (FA)). We found that the penis exhibited positive allometry and high phenotypic variation, and was positively associated with male body size and relative body mass, but not with FA. This pattern is more typical of sexually selected display traits, contrasting with general patterns of genital allometry. The baculum was negatively allometric and was not associated with any quality measure. Our results suggest that the N. noctula penis is under directional sexual selection and is a reliable indicator of male phenotypic quality.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 497–507.     

Convergence in pigmentation at multiple levels: mutations,genes and function

Convergence—the independent evolution of the same trait by two or more taxa—has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida''s Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.     

The evolution of sexually dimorphic tail feathers is not associated with tail skeleton dimorphism

Sexual selection can influence the evolution of sexually dimorphic exaggerated display structures. Herein, we explore whether such costly ornamental integumentary structures evolve independently or if they are correlated with phenotypic change in the associated skeletal system. In birds, elongate tail feathers have frequently evolved in males and are beneficial as intraspecific display structures but impart a locomotor/energetic cost. Using the sexually dimorphic tail feathers of several passeriform species as a model system, we test the hypothesis that taxa with sexually dimorphic tail feathers also exhibit sexual dimorphism in the caudal skeleton that supports the muscles and integument of the tail apparatus. Caudal skeletal morphology is quantified using both geometric morphometrics and linear morphometrics across four sexually dimorphic passeriform species and four closely related monomorphic species. Sexual dimorphism is assessed using permutational MANOVA. Sexual dimorphism in caudal skeletal morphology is found only in those taxa that exhibit active functional differences in tail use between males and females. Thus, dimorphism in tail feather length is not necessarily correlated with the evolution of caudal skeletal dimorphism. Sexual selection is sufficient to generate phenotypic divergence in integumentary display structures between the sexes, but these change are not reflected in the underlying caudal skeleton. This suggests that caudal feathers and bones evolve semi‐independently from one another and evolve at different rates in response to different types of selective pressures.     

Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome

The X chromosome constitutes a unique genomic environment because it is present in one copy in males, but two copies in females. This simple fact has motivated several theoretical predictions with respect to how standing genetic variation on the X chromosome should differ from the autosomes. Unmasked expression of deleterious mutations in males and a lower census size are expected to reduce variation, while allelic variants with sexually antagonistic effects, and potentially those with a sex-specific effect, could accumulate on the X chromosome and contribute to increased genetic variation. In addition, incomplete dosage compensation of the X chromosome could potentially dampen the male-specific effects of random mutations, and promote the accumulation of X-linked alleles with sexually dimorphic phenotypic effects. Here we test both the amount and the type of genetic variation on the X chromosome within a population of Drosophila melanogaster, by comparing the proportion of X linked and autosomal trans-regulatory SNPs with a sexually concordant and discordant effect on gene expression. We find that the X chromosome is depleted for SNPs with a sexually concordant effect, but hosts comparatively more SNPs with a sexually discordant effect. Interestingly, the contrasting results for SNPs with sexually concordant and discordant effects are driven by SNPs with a larger influence on expression in females than expression in males. Furthermore, the distribution of these SNPs is shifted towards regions where dosage compensation is predicted to be less complete. These results suggest that intrinsic properties of dosage compensation influence either the accumulation of different types of trans-factors and/or their propensity to accumulate mutations. Our findings document a potential mechanistic basis for sex-specific genetic variation, and identify the X as a reservoir for sexually dimorphic phenotypic variation. These results have general implications for X chromosome evolution, as well as the genetic basis of sex-specific evolutionary change.     

Species: the concept, category and taxon

The term species by itself is vague because it refers to the species concept, the species category and the species taxon, all of which are distinct although related to one another. The species concept is not primarily a part of systematics, but has always been an integral part of basic biological theory, It is based on evolutionary theory and applies only to sexually reproducing organisms. The species concept and the phyletic lineage concept are quite distinct although they are related to one another. The important aspect of the species concept is lack of gene flow between different species, and hence the defining criterion of the species is genetic isolation. The species concept is often considered as non‐dimensional, both in time and space. Species possess three different major properties, namely genetic isolation, reproductive isolation and ecological isolation; these properties evolve at different times and under the effect of different causes during the speciation process. Speciation requires an external isolating barrier during the initial allopatric phase in which genetic isolation evolves and must reach 100% efficiency. The subsequent sympatric phase of speciation occurs after the disappearance of the external isolating barrier when members of the two newly evolved species can interact with one another and exert mutual selective demands on one another. Much of the reproductive and ecological isolation evolves during this secondary sympatric phase. The species category is a rank in the taxonomic hierarchy and serves as the basis on which the diversity of organisms is described; it is not the same as the species concept. The species category applied to all organisms, sexually and asexually reproducing. The species taxon is the practical application of the species category in systematics with the recognition of species taxa requiring many arbitrary decisions. No single set of rules exist by which the species category can be applied to all organisms. Recognition of species taxa in asexually reproducing organisms is based on amount of variation and gaps in the variation of phenotypic features associated with ecological attributes of these organisms as compared with similar attributes in sympatric species taxa of sexually reproducing organisms. Species taxa are multidimensional in that they exist over space–time and often have fuzzy borders. Because recognition of species taxa, including those in sexually reproducing organisms, depends on many arbitrary decisions especially when dealing with broad geographical and temporal ranges, species taxa cannot be used as the foundation for developing and testing theoretical concepts in evolutionary theory which can only be done with the non‐dimensional species concept.     

A ROLE FOR LEARNING IN POPULATION DIVERGENCE OF MATE PREFERENCES

Learning and other forms of phenotypic plasticity have been suggested to enhance population divergence. Mate preferences can develop by learning, and species recognition might not be entirely genetic. We present data on female mate preferences of the banded demoiselle (Calopteryx splendens) that suggest a role for learning in population divergence and species recognition. Populations of this species are either allopatric or sympatric with a phenotypically similar congener (C. virgo). These two species differ mainly in the amount of wing melanization in males, and wing patches thus mediate sexual isolation. In sympatry, sexually experienced females discriminate against large melanin wing patches in heterospecific males. In contrast, in allopatric populations within the same geographic region, females show positive (“open‐ended”) preferences for such large wing patches. Virgin C. splendens females do not discriminate against heterospecific males. Moreover, physical exposure experiments of such virgin females to con‐ or hetero‐specific males significantly influences their subsequent mate preferences. Species recognition is thus not entirely genetic and it is partly influenced by interactions with mates. Learning causes pronounced population divergence in mate preferences between these weakly genetically differentiated populations, and results in a highly divergent pattern of species recognition at a small geographic scale.     

QUANTITATIVE VARIATION IN FINITE PARTHENOGENETIC POPULATIONS: WHAT STOPS MULLER'S RATCHET IN THE ABSENCE OF RECOMBINATION?

Finite parthenogenetic populations with high genomic mutation rates accumulate deleterious mutations if back mutations are rare. This mechanism, known as Muller's ratchet, can explain the rarity of parthenogenetic species among so called higher organisms. However, estimates of genomic mutation rates for deleterious alleles and their average effect in the diploid condition in Drosophila suggest that Muller's ratchet should eliminate parthenogenetic insect populations within several hundred generations, provided all mutations are unconditionally deleterious. This fact is inconsistent with the existence of obligatory parthenogenetic insect species. In this paper an analysis of the extent to which compensatory mutations can counter Muller's ratchet is presented. Compensatory mutations are defined as all mutations that compensate for the phenotypic effects of a deleterious mutation. In the case of quantitative traits under stabilizing selection, the rate of compensatory mutations is easily predicted. It is shown that there is a strong analogy between the Muller's ratchet model of Felsenstein (1974) and the quantitative genetic model considered here, except for the frequency of compensatory mutations. If the intensity of stabilizing selection is too small or the mutation rate too high, the optimal genotype becomes extinct and the population mean drifts from the optimum but still reaches a stationary distribution. This distance is essentially the same as predicted for sexually reproducing populations under the same circumstances. Hence, at least in the short run, compensatory mutations for quantitative characters are as effective as recombination in halting the decline of mean fitness otherwise caused by Muller's ratchet. However, it is questionable whether compensatory mutations can prevent Muller's ratchet in the long run because there might be a limit to the capacity of the genome to provide compensatory mutations without eliminating deleterious mutations at least during occasional episodes of sex.     

Male Genital Allometry in Scathophagidae (Diptera)

Male genital structures are extremely divergent across species and sexual selection is largely responsible. Many sexually selected traits show positive allometry and have high phenotypic coefficients of variation (CV). Sexually-selected genital traits that come into contact with females during copula may be an exception to this general pattern. We compared the within species size allometry of the genital claspers, mandibular palps, and testes in a comparative study across the Scathophagidae. We additionally compared the levels of phenotypic variation in these traits and in hind tibia length. Within species, claspers typically displayed negative allometry and had low CV, indicative of stabilizing selection. In contrast, testis size was more like sexually selected display traits, typically being positively allometric and having very large CV. Palps tended to be positively allometric or isometric, and intermediate in levels of phenotypic variation, much like leg length. In spite of intraspecific stabilizing selection on the genital claspers, there has been major divergence of these characters across species. Co-ordinating editor. F. Stuefer     

RNA repair for haemophilia A

The mainstay of gene transfer studies is the use of wild-type cDNAs to effect phenotypic correction of diseases. However, this strategy is not feasible for genetic diseases caused either by mutations of large genes or by dominant-negative mutations, or where the regulation of the gene is critical. In this review, we will discuss a novel RNA reprogramming strategy - spliceosome-mediated RNA trans-splicing - where the pre-messenger RNA is modified by the splicing of two independent RNA species. The use of trans-splicing to effect phenotypic change in the hereditary bleeding disorder haemophilia A will be discussed.     

Immune stress and facultative sex in a parasitic nematode

It has been suggested that sexual reproduction in parasites may be advantageous because it helps evade genotype‐specific host immune responses. Indirect support for this hypothesis has recently come from work on Strongyloides ratti, a parasitic nematode of rats that develops and reproduces sexually or asexually. In this species, host immune responses against S. ratti lead to a higher proportion of individuals reproducing sexually. However, an alternative explanation for these results is that sex is favoured by general environmental stress, including host responses against antigen sources other than S. ratti. Here we test this hypothesis, by determining how host immunity against two other parasitic nematode species (Nippostrongylus brasiliensis & Strongyloides venezuelensis) and commonly used mammalian antigens (sheep red blood cells) affects the likelihood of S. ratti larvae developing sexually. Our results show that increased levels of sex occur in response to immune responses generated against these other species, and not just host immunity elicited by S. ratti. This is consistent with the idea that sex is favoured under stressful conditions, and does not support the immune evasion hypothesis.     

Sexual dimorphism,phenotypic integration,and the evolution of head structure in casque‐headed lizards

Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque‐headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus) while in others, both sexes are monomorphic. To characterize these patterns, we define phenotypic integration at the interspecific level as a pattern or network of traits evidenced by phylogenetically adjusted correlations that persist among species. At this level, modularity is an increased connectedness (e.g., higher correlation) among sections of these networks that persist in a lineage during the evolution of complex phenotypes. To test both concepts, we used phylogenetic geomorphometrics to characterize the head structure of corytophanid lizards, based on a time‐calibrated phylogeny that includes candidate fossil ancestors. We found evidence of an older diversification of corytophanids than previously reported (~67 vs. ~23.5 MYA) and show that this clade includes two morphological head architectures: (1) Sexually dimorphic crests present in males that are evolving independently from the rest of the head structure, and (2) full integration of the head morphology in monomorphic species. We propose that both architectures are optimal evolutionary trajectories of the parietal crest bones in the head of these lizards. In sexually dimorphic species, these bones are elongated and thinner, and gave rise to the extended crest used in male courtship displays. In monomorphic species, the parietal crest grew thicker in both sexes to allow for a better insertion of muscles associated with a stronger bite.     

The genetics of adaptation: the roles of pleiotropy, stabilizing selection and drift in shaping the distribution of bidirectional fixed mutational effects

Pleiotropy allows for the deterministic fixation of bidirectional mutations: mutations with effects both in the direction of selection and opposite to selection for the same character. Mutations with deleterious effects on some characters can fix because of beneficial effects on other characters. This study analytically quantifies the expected frequency of mutations that fix with negative and positive effects on a character and the average size of a fixed effect on a character when a mutation pleiotropically affects from very few to many characters. The analysis allows for mutational distributions that vary in shape and provides a framework that would allow for varying the frequency at which mutations arise with deleterious and positive effects on characters. The results show that a large fraction of fixed mutations will have deleterious pleiotropic effects even when mutation affects as little as two characters and only directional selection is occurring, and, not surprisingly, as the degree of pleiotropy increases the frequency of fixed deleterious effects increases. As a point of comparison, we show how stabilizing selection and random genetic drift affect the bidirectional distribution of fixed mutational effects. The results are then applied to QTL studies that seek to find loci that contribute to phenotypic differences between populations or species. It is shown that QTL studies are biased against detecting chromosome regions that have deleterious pleiotropic effects on characters.     

Masculinization of the X Chromosome in the Pea Aphid

Evolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution.     

Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes

Meiotic recombination is a fundamental process needed for the correct segregation of chromosomes during meiosis in sexually reproducing organisms. In humans, 80% of crossovers are estimated to occur at specific areas of the genome called recombination hotspots. Recently, a protein called PRDM9 was identified as a major player in determining the location of genome-wide meiotic recombination hotspots in humans and mice. The origin of this protein seems to be ancient in evolutionary time, as reflected by its fairly conserved structure in lineages that diverged over 700 million years ago. Despite its important role, there are many animal groups in which Prdm9 is absent (e.g. birds, reptiles, amphibians, diptera) and it has been suggested to have disruptive mutations and thus to be a pseudogene in dogs. Because of the dog's history through domestication and artificial selection, we wanted to confirm the presence of a disrupted Prdm9 gene in dogs and determine whether this was exclusive of this species or whether it also occurred in its wild ancestor, the wolf, and in a close relative, the coyote. We sequenced the region in the dog genome that aligned to the last exon of the human Prdm9, containing the entire zinc finger domain, in 4 dogs, 17 wolves and 2 coyotes. Our results show that the three canid species possess mutations that likely make this gene non functional. Because these mutations are shared across the three species, they must have appeared prior to the split of the wolf and the coyote, millions of years ago, and are not related to domestication. In addition, our results suggest that in these three canid species recombination does not occur at hotspots or hotspot location is controlled through a mechanism yet to be determined.     

Sexual Antagonism,Temporally Fluctuating Selection,and Variable Dominance Affect a Regulatory Polymorphism in Drosophila melanogaster

Understanding how genetic variation is maintained within species is a major goal of evolutionary genetics that can shed light on the preservation of biodiversity. Here, we examined the maintenance of a regulatory single-nucleotide polymorphism (SNP) of the X-linked Drosophila melanogaster gene fezzik. The derived variant at this site is at intermediate frequency in many worldwide populations but absent in populations from the ancestral species range in sub-Saharan Africa. We collected and genotyped wild-caught individuals from a single European population biannually over a period of 5 years, which revealed an overall difference in allele frequency between the sexes and a consistent change in allele frequency across seasons in females but not in males. Modeling based on the observed allele and genotype frequencies suggested that both sexually antagonistic and temporally fluctuating selection may help maintain variation at this site. The derived variant is predicted to be female-beneficial and mostly recessive; however, there was uncertainty surrounding our dominance estimates and long-term modeling projections suggest that it is more likely to be dominant. By examining gene expression phenotypes, we found that phenotypic dominance was variable and dependent upon developmental stage and genetic background, suggesting that dominance may be variable at this locus. We further determined that fezzik expression and genotype are associated with starvation resistance in a sex-dependent manner, suggesting a potential phenotypic target of selection. By characterizing the mechanisms of selection acting on this SNP, our results improve our understanding of how selection maintains genetic and phenotypic variation in natural populations.     

Resource-mediated condition dependence in sexually dichromatic butterfly wing coloration

Theory predicts that traits subject to strong sexual selection should evolve to be more exaggerated and developmentally integrated than nonsexual traits, thus leading to heightened condition dependence. Until recently, however, efforts to evaluate this prediction have suffered from either a purely correlational (nonmanipulative) approach, or from using manipulations of doubtful ecological relevance. Here I address these issues by integrating observation and manipulation to study condition- and sex-related color variation in a butterfly. The focal species, Eurema hecabe (Pieridae), possesses three sexually homologous and morphogenetically discrete dorsal wing color elements-coherently scattered ultraviolet (UV), pteridine yellow, and melaninic black. The UV is most strongly sexually selected, and is also the only color element with restricted distribution across female wings. Condition dependence and sexual dichromatism were pervasive, characterizing all color traits except the melanic black, and acting such that low condition males resembled high condition females. Although female coloration tended to exhibit greater phenotypic variation, size-scaled UV was more variable and condition dependent in males. Importantly, manipulation of larval resources was sufficient to closely reconstruct the extent and patterns of field-observed phenotypic variation in condition, and color trait expression, which implicates larval resource acquisition as a primary driver of condition dependence. These results support theories regarding phenotypic variation in sexually selected traits.     

GOOD GENES AND DIRECT SELECTION IN THE EVOLUTION OF MATING PREFERENCES

A model is used to study quantitatively the impact of a good genes process and direct natural selection on the evolution of a mating preference. The expression of a male display trait is proportional to genetic quality, which is determined by the number of deleterious mutations a male carries throughout his genome. Genetic variances and covariances, including the covariance between the preference and male trait that drives the good genes process, are allowed to evolve under an infinitesimal model. Results suggest that the good genes process generates only weak indirect selection on preferences, with an effective selection intensity of a few percent or less. If preferences are subject to direct natural selection of the intensity observed for other characters, the good genes process alone is not expected to exaggerate the male trait by more than a few phenotypic standard deviations, contrary to what is observed in highly sexually selected species. Good genes can, however, cause substantial exaggeration if preference genes are nearly selectively neutral. Alternatively, direct selection on preference genes, acting on mating behavior itself or on the genes' pleiotropic effects, can cause mating preferences and male display traits to be exaggerated by any degree. Direct selection of preference genes may therefore play an important role in species that show extreme sexual selection.     

Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.