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

<p>Abstract</p> <p>Background</p> <p>The <it>MC1R </it>(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 <it>MC1R </it>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 <it>MC1R </it>variation and plumage coloration in swans (<it>Cygnus</it>), which show extreme variation in melanic plumage phenotypes among species (white to black).</p> <p>Results</p> <p>The two species with melanic plumage, <it>C. atratus </it>and <it>C. melanocoryphus </it>(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 <it>Cygnus </it>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, <it>Coscoroba</it>, 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 <it>Cygnus </it>may not be monophyletic, with <it>C. melanocoryphus </it>placed as a sister group to true geese (<it>Anser</it>), but further data will be needed to confirm this.</p> <p>Conclusion</p> <p>Our 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 <it>Cygnus </it>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.</p

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

Background When 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. Results In 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. Conclusions Results 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

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

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

Abstract 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

Data from: 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

Genes shared between morphs.

<p>Venn diagrams for the number of autosomal (panel A) and Z-linked (panel B) genes expressed in females (red), subordinate males (light blue) and dominant males (dark blue).</p

Expression similarity across sexual forms.

<p>Spearman rank order (ρ) correlations for average expression for females, subordinate males and dominant males for autosomal unbiased (panel A), autosomal male-biased (panel B), autosomal female-biased (panel C), and Z-linked (panel D) genes. Correlation values are colour coded with lighter colours indicating greater correlation.</p

Average log₂ expression for all sex-biased genes.

<p>Panel A, autosomal male-biased and female-biased genes in females (red), subordinate males (light blue) and dominant males (dark blue). Panel B, autosomal male-biased genes ranked by male-bias. Panel C, autosomal female-biased genes ranked by female bias, and Panel D, Z-linked male-biased genes ranked by male-bias. Whiskers extend to the most extreme data point, excluding outliers that exceeded 1.5× the interquartile range. Significant <i>p</i>-values as calculated by Wilcoxon tests are indicated by asterisks above each comparison between dominant and subordinate males (* <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001, **** <i>p</i><0.0001).</p

Heat maps and hierarchical clustering of gene expression for females, subordinate males and dominant males.

<p>Shown is the relative expression for autosomal male-biased (n = 2,217, panel A), female-biased (n = 2,908, panel B) and Z-linked (n = 364, panel C) genes. Hierarchical gene clustering is based on Euclidean distance for average log₂ expression for each gene for the three sexual morphs. The number at each node is the percentage bootstrap result from 1000 replicates.</p

Sex-bias in the spleen of females (red), subordinate males (light blue) and dominant males (dark blue).

<p>Sex-bias was defined in panel A based on a 1.5-fold change threshold between females and dominant males, with a p-value<0.05. Sex-bias in panel B is defined solely on statistical difference (<i>p</i><0.05) between females and dominant males. Significant difference between dominant and subordinate males is indicated (Wilcoxon test, * <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001, **** <i>p</i><0.0001).</p