Transcriptomics of colour patterning and coloration shifts in crows.

Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating regional pigment production in two genetically near-identical crow taxa with striking differences in a eumelanin-based phenotype: black carrion and grey-coated hooded crows. We produced a high-quality genome annotation and analysed transcriptome data from a 2 × 2 design of active melanogenic feather follicles from head (black in both taxa) and torso (black in carrion and grey in hooded crow). Extensive, parallel expression differences between body regions in both taxa, enriched for melanogenesis genes (e.g. ASIP, CORIN, and ALDH6), indicated the presence of cryptic prepatterning also in all-black carrion crows. Meanwhile, colour-specific expression (grey vs. black) was limited to a small number of melanogenesis genes in close association with the central transcription factor MITF (most notably HPGDS, NDP and RASGRF1). We conclude that colour pattern differences between the taxa likely result from an interaction between divergence in upstream elements of the melanogenesis pathway and genes that provide an underlying prepattern across the body through positional information. A model of evolutionary stable prepatterns that can be exposed and masked through simple regulatory changes may explain the phylogenetically independent recurrence of colour patterns that is observed across corvids and many other vertebrate groups.

Transcontinental migratory connectivity predicts parasite prevalence in breeding populations of the European barn swallow.

Parasites exert a major impact on the eco-evolutionary dynamics of their hosts and the associated biotic environment. Migration constitutes an effective means for long-distance invasions of vector-borne parasites and promotes their rapid spread. Yet, ecological and spatial information on population-specific host-parasite connectivity is essentially lacking. Here, we address this question in a system consisting of a transcontinental migrant species, the European barn swallow (Hirundo rustica) which serves as a vector for avian endoparasites in the genera Plasmodium, Haemoproteus and Leucocytozoon. Using feather stable isotope ratios as geographically informative markers, we first assessed migratory connectivity in the host: Northern European breeding populations predominantly overwintered in dry, savannah-like habitats in Southern Africa, whereas Southern European populations were associated with wetland habitats in Western Central Africa. Wintering areas of swallows breeding in Central Europe indicated a migratory divide with both migratory programmes occurring within the same breeding population. Subsequent genetic screens of parasites in the breeding populations revealed a link between the host's migratory programme and its parasitic repertoire: controlling for effects of local breeding location, prevalence of Africa-transmitted Plasmodium lineages was significantly higher in individuals overwintering in the moist habitats of Western Central Africa, even among sympatrically breeding individuals with different overwintering locations. For the rarer Haemoproteus parasites, prevalence was best explained by breeding location alone, whereas no clear pattern emerged for the least abundant parasite Leucocytozoon. These results have implications for our understanding of spatio-temporal host-parasite dynamics in migratory species and the spread of avian borne diseases.

Gene interactions in the evolution of genomic imprinting.

Numerous evolutionary theories have been developed to explain the epigenetic phenomenon of genomic imprinting. Here, we explore a subset of theories wherein non-additive genetic interactions can favour imprinting. In the simplest genic interaction--the case of underdominance--imprinting can be favoured to hide effectively low-fitness heterozygous genotypes; however, as there is no asymmetry between maternally and paternally inherited alleles in this model, other means of enforcing monoallelic expression may be more plausible evolutionary outcomes than genomic imprinting. By contrast, more successful interaction models of imprinting rely on an asymmetry between the maternally and paternally inherited alleles at a locus that favours the silencing of one allele as a means of coordinating the expression of high-fitness allelic combinations. For example, with interactions between autosomal loci, imprinting functionally preserves high-fitness genotypes that were favoured by selection in the previous generation. In this scenario, once a focal locus becomes imprinted, selection at interacting loci favours a matching imprint. Uniparental transmission generates similar asymmetries for sex chromosomes and cytoplasmic factors interacting with autosomal loci, with selection favouring the expression of either maternal or paternally derived autosomal alleles depending on the pattern of transmission of the uniparentally inherited factor. In a final class of models, asymmetries arise when genes expressed in offspring interact with genes expressed in one of its parents. Under such a scenario, a locus evolves to have imprinted expression in offspring to coordinate the interaction with its parent's genome. We illustrate these models and explore key links and differences using a unified framework.

Imprinted gene expression in hybrids: perturbed mechanisms and evolutionary implications.

Diverse mechanisms contribute to the evolution of reproductive barriers, a process that is critical in speciation. Amongst these are alterations in gene products and in gene dosage that affect development and reproductive success in hybrid offspring. Because of its strict parent-of-origin dependence, genomic imprinting is thought to contribute to the aberrant phenotypes observed in interspecies hybrids in mammals and flowering plants, when the abnormalities depend on the directionality of the cross. In different groups of mammals, hybrid incompatibility has indeed been linked to loss of imprinting. Aberrant expression levels have been reported as well, including imprinted genes involved in development and growth. Recent studies in humans emphasize that genetic diversity within a species can readily perturb imprinted gene expression and phenotype as well. Despite novel insights into the underlying mechanisms, the full extent of imprinted gene perturbation still remains to be determined in the different hybrid systems. Here we review imprinted gene expression in intra- and interspecies hybrids and examine the evolutionary scenarios under which imprinting could contribute to hybrid incompatibilities. We discuss effects on development and reproduction and possible evolutionary implications.

The evolution of genomic imprinting: theories, predictions and empirical tests.

The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternal-offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal-offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted.

Hybridization and speciation.

Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone.

Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (∼3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima's D, Fu's FS, DHEW and HKA (Hudson-Kreitman-Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner∼0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.

Genotype-dependent responses to levels of sibling competition over maternal resources in mice.

Research on phenotypic plasticity has often focused on how a given genotype responds to the changing physical environments such as temperature or diet. However, for many species the social environment has an equally important role because of competition for resources. During early development, the level of competition for limited (maternally provided) resources will often depend critically on the number of siblings. Therefore, competition among siblings should drive the evolution of genes that allow flexible responses to realized levels of competition and maternal resource availability. However, it is unknown whether genetically based differences between individuals exist in their response to the social environment that affect their future development. Using a quantitative trait locus approach in an experimental population of mice we demonstrate that effects of sibling number on body weight depend on individual genotype at seven loci, over and above the general negative litter size effect. Overall, these litter size-by-genotype interactions considerably modified the degree to which increasing litter size caused reduced weight. For example at one locus this effect leads to a 7% difference in body weight at week 7 between individuals experiencing the extremes of the normal range of litter sizes in our population (five to nine litter mates). The observed interaction between genotype and the competitive environment can produce differences in body weight that are similar in magnitude to the main effect of litter size on weight. Our results show that different genotypes respond to the social environment differentially and that interaction effects of genotype with litter size can be as important as genotype-independent effects of litter size.

Complex genotype interactions influence social fitness during the developmental phase of the social amoeba Dictyostelium discoideum.

When individuals interact, phenotypic variation can be partitioned into direct genetic effects (DGEs) of the individuals' own genotypes, indirect genetic effects (IGEs) of their social partners' genotypes and epistatic interactions between the genotypes of interacting individuals ('genotype-by-genotype (GxG) epistasis'). These components can all play important roles in evolutionary processes, but few empirical studies have examined their importance. The social amoeba Dictyostelium discoideum provides an ideal system to measure these effects during social interactions and development. When starved, free-living amoebae aggregate and differentiate into a multicellular fruiting body with a dead stalk that holds aloft viable spores. By measuring interactions among a set of natural strains, we quantify DGEs, IGEs and GxG epistasis affecting spore formation. We find that DGEs explain most of the phenotypic variance (57.6%) whereas IGEs explain a smaller (13.3%) but highly significant component. Interestingly, GxG epistasis explains nearly a quarter of the variance (23.0%), highlighting the complex nature of genotype interactions. These results demonstrate the large impact that social interactions can have on development and suggest that social effects should play an important role in developmental evolution in this system.

The molecular genetics and evolution of colour and polarization vision in stomatopod crustaceans.

Stomatopod crustaceans have the most complex assemblage of visual receptor classes known; retinas of many species are thought to express up to 16 different visual pigments. Physiological studies indicate that stomatopods contain up to six distinct middle-wavelength-sensitive (MWS) photoreceptor classes, suggesting that no more than six different MWS opsin gene copies exist per species. However, we previously reported the unexpected expression of 6-15 different MWS genes in retinas of each of five stomatopod species (Visual Neurosci 26: 255-266, 2009). Here, we present a review of the results reported in this publication, plus new results that shed light on the origins of the diverse colour and polarization visual capabilities of stomatopod crustaceans. Using in situ hybridization of opsins in photoreceptor cells, we obtained new results that support the hypothesis of an ancient functional division separating spatial and polarizational vision from colour vision in the stomatopods. Since evolutionary trace analysis indicates that stomatopod MWS opsins have diverged both with respect to spectral tuning and to cytoplasmic interactions, we have now further analyzed these data in an attempt to uncover the origins, diversity and potential specializations among clades for specific visual functions. The presence of many clusters of highly similar transcripts suggests exuberant opsin gene duplication has occurred in the stomatopods, together with more conservative, ancient gene duplication events within the stem crustacean lineage. Phylogenetic analysis of opsin relatedness suggests that opsins specialized for colour vision have diverged from those devoted to polarization vision, and possibly motion and spatial vision.

Evolution of strategic cooperation.

Group-beneficial behaviors have presented a long-standing challenge for evolutionary theory because, although their benefits are available to all group members, their costs are borne by individuals. Consequently, an individual could benefit from "cheating" their group mates by not paying the costs while still reaping the benefits. There have been many proposed evolutionary mechanisms that could favor cooperation (and disfavor cheating) in particular circumstances. However, if cooperation is still favored in some circumstances, then we might expect evolution to favor strategic cooperation, where the level of contribution toward group-beneficial behavior is varied in response to the social context. To uncover how and why individuals should contribute toward group-beneficial behavior across social contexts, we model strategic cooperation as an evolutionary game where players can quantitatively adjust the amount they contribute toward group-beneficial behavior. We find that the evolutionarily stable strategy (ESS) predicts, unsurprisingly, that players should contribute in relation to their relatedness to the group. However, we surprisingly find that players often contribute to cooperation in such a way that their fitness is inverse to their relatedness to the group such that those that contribute to cooperation end up with the same return from group-beneficial behavior, essentially removing any potential advantage of higher relatedness. These results bring to light a paradox of group-beneficial cooperation: groups do best when they contain highly related individuals, but those with the highest relatedness to the group will often have the lowest fitness within the group.

Selective abortion and the evolution of genomic imprinting.

Mothers can determine which genotypes of offspring they will produce through selective abortion or selective implantation. This process can, at some loci, favour matching between maternal and offspring genotype whereas at other loci mismatching may be favoured (e.g. MHC, HLA). Genomic imprinting generally renders gene expression monoallelic and could thus be adaptive at loci where matching or mismatching is beneficial. This hypothesis, however, remains unexplored despite evidence that loci known to play a role in genetic compatibility may be imprinted. We develop a simple model demonstrating that, when matching is beneficial, imprinting with maternal expression is adaptive because the incompatible paternal allele is not detected, protecting offspring from selective abortion. Conversely, when mismatching is beneficial, imprinting with paternal expression is adaptive because the maternal genotype is more able to identify the presence of a foreign allele in offspring. Thus, imprinting may act as a genomic 'cloaking device' during critical periods in development when selective abortion is possible.

A search for quantitative trait loci exhibiting imprinting effects on mouse mandible size and shape.

Genomic imprinting refers to the pattern of monoallelic parent-of-origin-dependent gene expression where one of the two alleles at a locus is expressed and the other silenced. Although some genes in mice are known to be imprinted, the true scope of imprinting and its impact on the genetic architecture of a wide range of morphometric traits is mostly unknown. We therefore searched for quantitative trait loci (QTL) exhibiting imprinting effects on mandible size and shape traits in a large F(3) population of mice originating from an intercross of the LG/J (Large) and SM/J (Small) inbred strains. We discovered a total of 51 QTL affecting mandible size and shape, 6 of which exhibited differences between reciprocal heterozygotes, the usual signature of imprinting effects. However, our analysis showed that only one of these QTL (affecting mandible size) exhibited a pattern consistent with true imprinting effects, whereas reciprocal heterozygote differences in the other five all were due to maternal genetic effects. We concluded that genomic imprinting has a negligible effect on these specific morphometric traits, and that maternal genetic effects may account for many of the previously reported instances of apparent genomic imprinting.

Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity.

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal (Arctocephalus gazella) genome (assembly size: 2.41 Gb; scaffold/contig N50 : 3.1 Mb/27.5 kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe-to-genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron-exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, reanalysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modelling.

Nonideal statistics and positive correlation in phage recombination: studies with lambda tandem duplication phages.

The question of nonideality in phage recombination, that is, the extent to which recombinant frequencies differ from those expected from the proportions of the two parental types in the mass culture, was addressed by experiments with lambda tandem duplication phages. Isolation and genotypic analysis of triplication-phage progeny, all of which must be the result of intermolecular recombination, yielded a value of about 0.5 for the nonideality parameter h, i.e., the frequency of unlike-parent matings was only about 1/2 the "ideal" value. This value was independent of multiplicity and about the same for the Rec or Red recombination systems. Similar analysis of single-copy phage progeny yielded estimates of k, the ratio of intramolecular to intermolecular recombination of about 1/6 for the Rec system; no intramolecular events were detected in Red-mediated crosses. Consideration of known nonideality factors (finite input, limited number of intracellular sites for phage growth) suggests that the observed h values correspond to intracellular mixing efficiencies of 55 to 100%, depending on the number of intracellular phage growth sites assumed. Analysis of long-range positive correlation (negative interference) indicates that statistical effects caused unlike-parent double crossovers to be three to four times as frequent as an independent-event calculation would predict. In addition, Rec-mediated crosses showed a 1.3-fold positive correlation for unlike-parent crossovers (in a second interval) among the progeny of like-parent recombinations.

Gene interactions from maternal effects.

Theoretical analyses have demonstrated a potential role for epistasis in many of the most important processes in evolution. These analyses generally assume that an individual's genes map directly to its phenotype and epistasis results from interactions among loci that contribute to the same biochemical or developmental pathways (termed physiological, or within-genotype, epistasis). For many characters, particularly those expressed early in life, an individual's phenotype may also be affected by genes expressed by its parents. The presence of these parental effects allows for interactions between the genes present in the parental and offspring genomes. When the phenotypic effect of a locus in the offspring depends on the alleles possessed by its parents, genotype-by-genotype, or among-genotype, epistasis occurs. The among-genotype epistasis resulting from parental effects may contribute to ruggedness of adaptive landscapes because early mortality often accounts for much of the variance in fitness in populations. To demonstrate how parent-offspring interactions can result in among-genotype epistasis, I use a two-locus model, with one maternal effect locus and one direct effect locus, each with two alleles. Dynamical equations are presented for the two-locus model and are directly contrasted with the dynamical equations derived for a model for physiological epistasis. The relationship between the evolutionary dynamics resulting from these two forms of epistasis is discussed. Three scenarios are presented to illustrate systems in which maternal-offspring, genotype-by-genotype epistasis may occur. The implications of maternal-offspring epistasis for quantitative-trait-loci studies are also discussed.

Developmental interactions and the constituents of quantitative variation.

Development is the process by which genotypes are transformed into phenotypes. Consequently, development determines the relationship between allelic and phenotypic variation in a population and, therefore, the patterns of quantitative genetic variation and covariation of traits. Understanding the developmental basis of quantitative traits may lead to insights into the origin and evolution of quantitative genetic variation, the evolutionary fate of populations, and, more generally, the relationship between development and evolution. Herein, we assume a hierarchical, modular structure of trait development and consider how epigenetic interactions among modules during ontogeny affect patterns of phenotypic and genetic variation. We explore two developmental models, one in which the epigenetic interactions between modules result in additive effects on character expression and a second model in which these epigenetic interactions produce nonadditive effects. Using a phenotype landscape approach, we show how changes in the developmental processes underlying phenotypic expression can alter the magnitude and pattern of quantitative genetic variation. Additive epigenetic effects influence genetic variances and covariances, but allow trait means to evolve independently of the genetic variances and covariances, so that phenotypic evolution can proceed without changing the genetic covariance structure that determines future evolutionary response. Nonadditive epigenetic effects, however, can lead to evolution of genetic variances and covariances as the mean phenotype evolves. Our model suggests that an understanding of multivariate evolution can be considerably enriched by knowledge of the mechanistic basis of character development.