Marie A. Pointer

The influence of ontogeny and light environment on the expression of visual pigment opsins in the retina of the black bream, Acanthopagrus butcheri

SUMMARY The correlation between ontogenetic changes in the spectral absorption characteristics of retinal photoreceptors and expression of visual pigment opsins was investigated in the black bream, Acanthopagrus butcheri. To establish whether the spectral qualities of environmental light affected the complement of visual pigments during ontogeny, comparisons were made between fishes reared in: (1) broad spectrum aquarium conditions; (2) short wavelength-reduced conditions similar to the natural environment; or (3) the natural environment (wild-caught). Microspectrophotometry was used to determine the wavelengths of spectral sensitivity of the photoreceptors at four developmental stages: larval, post-settlement, juvenile and adult. The molecular sequences of the rod (Rh1) and six cone (SWS1, SWS2A and B, Rh2Aα and β, and LWS) opsins were obtained and their expression levels in larval and adult stages examined using quantitative RT-PCR. The changes in spectral sensitivity of the cones were related to the differing levels of opsin expression during ontogeny. During the larval stage the predominantly expressed opsin classes were SWS1, SWS2B and Rh2Aα, contrasting with SWS2A, Rh2Aβ and LWS in the adult. An increased proportion of long wavelength-sensitive double cones was found in fishes reared in the short wavelength-reduced conditions and in wild-caught animals, indicating that the expression of cone opsin genes is also regulated by environmental light.

Sexual selection drives evolution and rapid turnover of male gene expression

Significance Genes with different expression between males and females (sex-biased genes) show rapid rates of sequence and expression divergence in a range of taxa. These characteristics have led many to assume that sex-biased genes are the product of sexual selection and sexual conflict, but this assumption remains to be rigorously tested. Using a phylogenetically controlled analysis of birds that exhibit diverse levels of sexual selection, we show a rapid turnover in sex-biased gene expression primarily through evolution of male expression levels and that the degree of sexual selection predicts the proportion of male-biased genes but does not account for rates of coding sequence evolution. We also discuss the impact of allometry on gene expression studies, an issue rarely discussed in the literature. The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

W chromosome expression responds to female-specific selection

The W chromosome is predicted to be subject to strong female-specific selection stemming from its female-limited inheritance and therefore should play an important role in female fitness traits. However, the overall importance of directional selection in shaping the W chromosome is unknown because of the powerful degradative forces that act to decay the nonrecombining sections of the genome. Here we greatly expand the number of known W-linked genes and assess the expression of the W chromosome after >100 generations of different female-specific selection regimens in different breeds of chicken and in the wild ancestor, the Red Jungle Fowl. Our results indicate that female-specific selection has a significant effect on W chromosome gene-expression patterns, with a strong convergent pattern of up-regulation associated with increased female-specific selection. Many of the transcriptional changes in the female-selected breeds are the product of positive selection, suggesting that selection is an important force in shaping the evolution of gene expression on the W chromosome, a finding consistent with both the importance of the W chromosome in female fertility and the haploid nature of the W. Taken together, these data provide evidence for the importance of the sex-limited chromosome in a female heterogametic species and show that sex-specific selection can act to preserve sex-limited chromosomes from degrading forces.

Masculinization of gene expression is associated with exaggeration of male sexual dimorphism.

Gene expression differences between the sexes account for the majority of sexually dimorphic phenotypes, and the study of sex-biased gene expression is important for understanding the genetic basis of complex sexual dimorphisms. However, it has been difficult to test the nature of this relationship due to the fact that sexual dimorphism has traditionally been conceptualized as a dichotomy between males and females, rather than an axis with individuals distributed at intermediate points. The wild turkey (Meleagris gallopavo) exhibits just this sort of continuum, with dominant and subordinate males forming a gradient in male secondary sexual characteristics. This makes it possible for the first time to test the correlation between sex-biased gene expression and sexually dimorphic phenotypes, a relationship crucial to molecular studies of sexual selection and sexual conflict. Here, we show that subordinate male transcriptomes show striking multiple concordances with their relative phenotypic sexual dimorphism. Subordinate males were clearly male rather than intersex, and when compared to dominant males, their transcriptomes were simultaneously demasculinized for male-biased genes and feminized for female-biased genes across the majority of the transcriptome. These results provide the first evidence linking sexually dimorphic transcription and sexually dimorphic phenotypes. More importantly, they indicate that evolutionary changes in sexual dimorphism can be achieved by varying the magnitude of sex-bias in expression across a large proportion of the coding content of a genome.

Candidate genes for carotenoid coloration in vertebrates and their expression profiles in the carotenoid-containing plumage and bill of a wild bird

Carotenoid-based coloration has attracted much attention in evolutionary biology owing to its role in honest, condition-dependent signalling. Knowledge of the genetic pathways that regulate carotenoid coloration is crucial for an understanding of any trade-offs involved. We identified genes with potential roles in carotenoid coloration in vertebrates via (i) carotenoid uptake (SR-BI, CD36), (ii) binding and deposition (StAR1, MLN64, StAR4, StAR5, APOD, PLIN, GSTA2), and (iii) breakdown (BCO2, BCMO1). We examined the expression of these candidate loci in carotenoid-coloured tissues and several control tissues of the red-billed quelea (Quelea quelea), a species that exhibits a male breeding plumage colour polymorphism and sexually dimorphic variation in bill colour. All of the candidate genes except StAR1 were expressed in both the plumage and bill of queleas, indicating a potential role in carotenoid coloration in the quelea. However, no differences in the relative expression of any of the genes were found among the quelea carotenoid phenotypes, suggesting that other genes control the polymorphic and sexually dimorphic variation in carotenoid coloration observed in this species. Our identification of a number of potential carotenoid genes in different functional categories provides a critical starting point for future work on carotenoid colour regulation in vertebrate taxa.

An analysis of population genetic differentiation and genotype-phenotype association across the hybrid zone of carrion and hooded crows using microsatellites and MC1R.

The all black carrion crow (Corvus corone corone) and the grey and black hooded crow (Corvus corone cornix) meet in a narrow hybrid zone across Europe. To evaluate the degree of genetic differentiation over the hybrid zone, we genotyped crows from the centre and edges of the zone, and from allopatric populations in northern (Scotland–Denmark–Sweden) and southern Europe (western–central northern Italy), at 18 microsatellites and at a plumage candidate gene, the MC1R gene. Allopatric and edge populations were significantly differentiated on microsatellites, and populations were isolated by distance over the hybrid zone in Italy. Single‐locus analyses showed that one locus, CmeH9, differentiated populations on different sides of the zone at the same time as showing only weak separation of populations on the same side of the zone. Within the hybrid zone there was no differentiation of phenotypes at CmeH9 or at the set of microsatellites, no excess of heterozygotes among hybrids and low levels of linkage disequilibrium between markers. We did not detect any association between phenotypes and nucleotide variation at MC1R, and the two most common haplotypes occurred in very similar frequencies in carrion and hooded crows. That we found a similar degree of genetic differentiation between allopatric and edge populations irrespectively of their location in relation to the hybrid zone, no differentiation between phenotypes within the hybrid zone, and neither heterozygote excess nor consistent linkage disequilibrium in the hybrid zone, is striking considering that carrion and hooded crows are phenotypically distinct and sometimes recognised as separate species.

Variation in promiscuity and sexual selection drives avian rate of Faster‐Z evolution

Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster‐Z Effect. To assess the magnitude and drivers of Faster‐Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster‐Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster‐Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution.

INDEPENDENT STRATUM FORMATION ON THE AVIAN SEX CHROMOSOMES REVEALS INTER CHROMOSOMAL GENE CONVERSION AND PREDOMINANCE OF PURIFYING SELECTION ON THE W CHROMOSOME

We used a comparative approach spanning three species and 90 million years to study the evolutionary history of the avian sex chromosomes. Using whole transcriptomes, we assembled the largest cross‐species dataset of W‐linked coding content to date. Our results show that recombination suppression in large portions of the avian sex chromosomes has evolved independently, and that long‐term sex chromosome divergence is consistent with repeated and independent inversions spreading progressively to restrict recombination. In contrast, over short‐term periods we observe heterogeneous and locus‐specific divergence. We also uncover four instances of gene conversion between both highly diverged and recently evolved gametologs, suggesting a complex mosaic of recombination suppression across the sex chromosomes. Lastly, evidence from 16 gametologs reveal that the W chromosome is evolving with a significant contribution of purifying selection, consistent with previous findings that W‐linked genes play an important role in encoding sex‐specific fitness.

Testing whether macroevolution follows microevolution: Are colour differences among swans (Cygnus) attributable to variation at the MC1R locus?

BackgroundThe MC1R (melanocortin-1 receptor) locus underlies intraspecific variation in melanin-based dark plumage coloration in several unrelated birds with plumage polymorphisms. There is far less evidence for functional variants of MC1R being involved in interspecific variation, in which spurious genotype-phenotype associations arising through population history are a far greater problem than in intraspecific studies. We investigated the relationship between MC1R variation and plumage coloration in swans (Cygnus), which show extreme variation in melanic plumage phenotypes among species (white to black).ResultsThe two species with melanic plumage, C. atratus and C. melanocoryphus (black and black-necked swans respectively), both have amino acid changes at important functional sites in MC1R that are consistent with increased MC1R activity and melanism. Reconstruction of MC1R evolution over a newly generated independent molecular phylogeny of Cygnus and related genera shows that these putative melanizing mutations were independently derived in the two melanic lineages. However, interpretation is complicated by the fact that one of the outgroup genera, Coscoroba, also has a putative melanizing mutation at MC1R that has arisen independently but has nearly pure white plumage. Epistasis at other loci seems the most likely explanation for this discrepancy. Unexpectedly, the phylogeny shows that the genus Cygnus may not be monophyletic, with C. melanocoryphus placed as a sister group to true geese (Anser), but further data will be needed to confirm this.ConclusionOur study highlights the difficulty of extrapolating from intraspecific studies to understand the genetic basis of interspecific adaptive phenotypic evolution, even with a gene whose structure-function relationships are as well understood as MC1R as confounding variation make clear genotype/phenotype associations difficult at the macroevolutionary scale. However, the identification of substitutions in the black and black-necked swan that are known to be associated with melanic phenotypes, suggests Cygnus may be another example where there appears to be convergent evolution at MC1R. This study therefore provides a novel example where previously described intraspecific genotype/phenotype associations occur at the macroevolutionary level.

RUNX2 tandem repeats and the evolution of facial length in placental mammals

BackgroundWhen simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary ‘tuning knobs’, supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2), which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length.ResultsIn this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation between RUNX2 sequence and face length across placental mammals.ConclusionsResults of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a ‘tuning knob’ modifying face length in carnivorans, this relationship is not conserved across mammals in general.