Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions

Estimated regions of linkage disequilibrium and associations between SNPs and expression level in regions flanking CPRs for which sequence variation could explain gene expression variation and was subject to purifying selection or selective sweep. Flanking regions (±5000 bp) of CPRs for CG15743 (A), CG9044 (B), brat (C), Cyp4d1 (D), CG14253 (E), Nmda1 (F), CG6950 (G), CG10463 (H), and CG33506 (I) are shown. Gray shades indicate haplotype blocks within which linkage disequilibrium could be found. Orange bars indicate coding region. Green bar indicates CPR. Each dot indicates a false discovery rate value (FDR) using the Wald test for the association between expression levels and SNPs. Horizontal line indicates FDR threshold (α = 0.01). (PDF 626 kb

Evolution for the Next Generation

Do you want to know about evolution? Brian and Deborah Charlesworth provide an excellent and concise account of the core issues for a broad range of reader

A genetically explicit model of speciation by sensory drive within a continuous population in aquatic environments

<p>Abstract</p> <p>Background</p> <p>The sensory drive hypothesis predicts that divergent sensory adaptation in different habitats may lead to premating isolation upon secondary contact of populations. Speciation by sensory drive has traditionally been treated as a special case of speciation as a byproduct of adaptation to divergent environments in geographically isolated populations. However, if habitats are heterogeneous, local adaptation in the sensory systems may cause the emergence of reproductively isolated species from a single unstructured population. In polychromatic fishes, visual sensitivity might become adapted to local ambient light regimes and the sensitivity might influence female preferences for male nuptial color. In this paper, we investigate the possibility of speciation by sensory drive as a byproduct of divergent visual adaptation within a single initially unstructured population. We use models based on explicit genetic mechanisms for color vision and nuptial coloration.</p> <p>Results</p> <p>We show that in simulations in which the adaptive evolution of visual pigments and color perception are explicitly modeled, sensory drive can promote speciation along a short selection gradient within a continuous habitat and population. We assumed that color perception evolves to adapt to the modal light environment that individuals experience and that females prefer to mate with males whose nuptial color they are most sensitive to. In our simulations color perception depends on the absorption spectra of an individual's visual pigments. Speciation occurred most frequently when the steepness of the environmental light gradient was intermediate and dispersal distance of offspring was relatively small. In addition, our results predict that mutations that cause large shifts in the wavelength of peak absorption promote speciation, whereas we did not observe speciation when peak absorption evolved by stepwise mutations with small effect.</p> <p>Conclusion</p> <p>The results suggest that speciation can occur where environmental gradients create divergent selection on sensory modalities that are used in mate choice. Evidence for such gradients exists from several animal groups, and from freshwater and marine fishes in particular. The probability of speciation in a continuous population under such conditions may then critically depend on the genetic architecture of perceptual adaptation and female mate choice.</p

Size-dependent foraging gene expression and behavioral caste differentiation in Bombus ignitus

<p>Abstract</p> <p>Background</p> <p>In eusocial hymenopteran insects, <it>foraging </it>genes, members of the cGMP-dependent protein kinase family, are considered to contribute to division of labor through behavioral caste differentiation. However, the relationship between <it>foraging </it>gene expression and behavioral caste in honeybees is opposite to that observed in ants and wasps. In the previously examined eusocial Hymenoptera, workers behave as foragers or nurses depending on age. We reasoned that examination of a different system of behavioral caste determination might provide new insights into the relationship between <it>foraging </it>genes and division of labor, and accordingly focused on bumblebees, which exhibit size-dependent behavioral caste differentiation. We characterized a <it>foraging </it>gene (<it>Bifor</it>) in bumblebees (<it>Bombus ignitus</it>) and examined the relationship between <it>Bifor </it>expression and size-dependent behavioral caste differentiation.</p> <p>Findings</p> <p>A putative open reading frame of the <it>Bifor </it>gene was 2004 bp in length. It encoded 668 aa residues and showed high identity to orthologous genes in other hymenopterans (85.3-99.0%). As in ants and wasps, <it>Bifor </it>expression levels were higher in nurses than in foragers. <it>Bifor </it>expression was negatively correlated with individual body size even within the same behavioral castes (regression coefficient = -0.376, P < 0.001, all individuals; -0.379, <it>P </it>= 0.018, within foragers).</p> <p>Conclusion</p> <p>These findings indicate that <it>Bifor </it>expression is size dependent and support the idea that <it>Bifor </it>expression levels are related to behavioral caste differentiation in <it>B. ignitus</it>. Thus, the relationship between <it>foraging </it>gene expression and behavioral caste differentiation found in ants and wasps was identified in a different system of labor determination.</p

Evidence of introgressive hybridization between the morphologically divergent land snails Ainohelix and Ezohelix

Hybridization between different taxa is likely to take place when adaptive morphological differences evolve more rapidly than reproductive isolation. When studying the phylogenetic relationship between two land snails of different nominal genera, Ainohelix editha and Ezohelix gainesi, from Hokkaido, Japan, using nuclear internal transcribed spacer and mitochondrial 16S ribosomal DNA, we found a marked incongruence in the topology between nuclear and mitochondrial phylogenies. Furthermore, no clear association was found between shell morphology (which defines the taxonomy) and nuclear or mitochondrial trees and morphology of reproductive system. These patterns are most likely explained by historical introgressive hybridization between A. editha and E. gainesi. Because the shell morphologies of the two species are quite distinct, even when they coexist, the implication is that natural selection is able to maintain (or has recreated) distinct morphologies in the face of gene flow. Future studies may be able to reveal the regions of the genome that maintain the morphological differences between these species

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system– and sperm motility–related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.Swedish Research Council Formas (grant 2010-1295).http://www.nature.comhb201

The MC1R gene in the guppy (Poecilia reticulata): Genotypic and phenotypic polymorphisms

<p>Abstract</p> <p>Background</p> <p>The guppy (<it>Poecilia reticulata</it>) is an important model organism for studying sexual selection; male guppies have complex and conspicuous pigmentation, and female guppies exhibit preferences for males with specific color spots. Understanding the genetic basis underlying pigmentation variation in the guppy is important for exploring the factors causing the maintenance of color polymorphism in wild populations.</p> <p>Findings</p> <p>We focused on the melanic black pigmentation of guppies, and examined genetic variations in the <it>melanocortin 1 receptor </it>(<it>MC1R</it>) gene because variation in this gene is known to contribute to polymorphism of melanin pigmentation in several animal species. The complete coding sequence of the guppy <it>MC1R </it>gene was determined, and two different <it>MC1R </it>alleles (963 and 969 bp) were found in wild populations. Ornamental strain guppies with a 963-bp <it>MC1R </it>tended to show less black pigmentation than those with a 969-bp <it>MC1R</it>, although the association between <it>MC1R </it>genotype and black pigmentation disappeared in the F₂offspring.</p> <p>Conclusions</p> <p>The guppy <it>MC1R </it>gene showed variation in the five wild Trinidadian populations we examined, and these populations also differed in terms of allele frequencies. We identified a significant association between black pigmentation and <it>MC1R </it>genotype in fish obtained from aquarium shops. However, the results from F₂families suggest that there are other genes that modify the effects of the <it>MC1R </it>gene.</p

Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms

Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation

Evidence of introgressive hybridization between the morphologically divergent land snails Ainohelix and Ezohelix

Hybridization between different taxa is likely to take place when adaptive morphological differences evolve more rapidly than reproductive isolation. When studying the phylogenetic relationship between two land snails of different nominal genera, Ainohelix editha and Ezohelix gainesi, from Hokkaido, Japan, using nuclear internal transcribed spacer and mitochondrial 16S ribosomal DNA, we found a marked incongruence in the topology between nuclear and mitochondrial phylogenies. Furthermore, no clear association was found between shell morphology (which defines the taxonomy) and nuclear or mitochondrial trees and morphology of reproductive system. These patterns are most likely explained by historical introgressive hybridization between A. editha and E. gainesi. Because the shell morphologies of the two species are quite distinct, even when they coexist, the implication is that natural selection is able to maintain (or has recreated) distinct morphologies in the face of gene flow. Future studies may be able to reveal the regions of the genome that maintain the morphological differences between these species