Thomas L. Turner

Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster

Drosophila melanogaster shows clinal variation along latitudinal transects on multiple continents for several phenotypes, allozyme variants, sequence variants, and chromosome inversions. Previous investigation suggests that many such clines are due to spatially varying selection rather than demographic history, but the genomic extent of such selection is unknown. To map differentiation throughout the genome, we hybridized DNA from temperate and subtropical populations to Affymetrix tiling arrays. The dense genomic sampling of variants and low level of linkage disequilibrium in D. melanogaster enabled identification of many small, differentiated regions. Many regions are differentiated in parallel in the United States and Australia, strongly supporting the idea that they are influenced by spatially varying selection. Genomic differentiation is distributed nonrandomly with respect to gene function, even in regions differentiated on only one continent, providing further evidence for the role of selection. These data provide candidate genes for phenotypes known to vary clinally and implicate interesting new processes in genotype-by-environment interactions, including chorion proteins, proteins regulating meiotic recombination and segregation, gustatory and olfactory receptors, and proteins affecting synaptic function and behavior. This portrait of differentiation provides a genomic perspective on adaptation and the maintenance of variation through spatially varying selection.

Genomic islands of speciation or genomic islands and speciation

Populations of the malaria mosquito, Anopheles gambiae, are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high‐density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in near‐perfect disequilibrium with each other. This is in stark contrast to the remaining 97% of the assembled genome, where fixed differences between populations have not been found, and many polymorphisms are shared. This pattern, coupled with direct evidence of hybridization in nature, supports models of “mosaic” speciation, where ongoing hybridization homogenizes variation in most of the genome while loci under strong selection remain in disequilibrium with each other. However, unambiguously demonstrating that selection maintains the association of these pericentric “speciation islands” in the face of gene flow is difficult. Low recombination at all three loci complicates the issue, and increases the probability that selection unrelated to the speciation process alters patterns of variation in these loci. Here, we discuss these different scenarios in light of this new data.

siRNA–Mediated Methylation of Arabidopsis Telomeres

Chromosome termini form a specialized type of heterochromatin that is important for chromosome stability. The recent discovery of telomeric RNA transcripts in yeast and vertebrates raised the question of whether RNA–based mechanisms are involved in the formation of telomeric heterochromatin. In this study, we performed detailed analysis of chromatin structure and RNA transcription at chromosome termini in Arabidopsis. Arabidopsis telomeres display features of intermediate heterochromatin that does not extensively spread to subtelomeric regions which encode transcriptionally active genes. We also found telomeric repeat–containing transcripts arising from telomeres and centromeric loci, a portion of which are processed into small interfering RNAs. These telomeric siRNAs contribute to the maintenance of telomeric chromatin through promoting methylation of asymmetric cytosines in telomeric (CCCTAAA)n repeats. The formation of telomeric siRNAs and methylation of telomeres relies on the RNA–dependent DNA methylation pathway. The loss of telomeric DNA methylation in rdr2 mutants is accompanied by only a modest effect on histone heterochromatic marks, indicating that maintenance of telomeric heterochromatin in Arabidopsis is reinforced by several independent mechanisms. In conclusion, this study provides evidence for an siRNA–directed mechanism of chromatin maintenance at telomeres in Arabidopsis.

Evolutionary Biology for the 21st Century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.

Investigating Natural Variation in Drosophila Courtship Song by the Evolve and Resequence Approach

A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development.

Natural Variation in Decision-Making Behavior in Drosophila melanogaster

There has been considerable recent interest in using Drosophila melanogaster to investigate the molecular basis of decision-making behavior. Deciding where to place eggs is likely one of the most important decisions for a female fly, as eggs are vulnerable and larvae have limited motility. Here, we show that many natural genotypes of D. melanogaster prefer to lay eggs near nutritious substrate, rather than in nutritious substrate. These preferences are highly polymorphic in both degree and direction, with considerable heritability (0.488) and evolvability. Relative preferences are modulated by the distance between options and the overall concentration of ethanol, suggesting Drosophila integrate many environmental factors when making oviposition decisions. As oviposition-related decisions can be efficiently assessed by simply counting eggs, oviposition behavior is an excellent model for understanding information processing in insects. Associating natural genetic polymorphisms with decision-making variation will shed light on the molecular basis of host choice behavior, the evolutionary maintenance of genetic variation, and the mechanistic nature of preference variation in general.

Combining Genome-Wide Methods to Investigate the Genetic Complexity of Courtship Song Variation in Drosophila melanogaster

Little is currently known about the genetic complexity of quantitative behavioral variation, the types of genes involved, or their effects on intermediate phenotypes. Here, we conduct a genome-wide association study of Drosophila melanogaster courtship song variation using 168 sequenced inbred lines, and fail to find highly significant associations. However, by combining these data with results from a well-powered Evolve and Resequence (E&R) study on the same trait, we provide statistical evidence that some power to associate genotype and phenotype is available. Genes that are significant in both analyses are enriched for expression in the nervous system, and affect neural development and synaptic growth when perturbed. Quantitative complementation at one of these loci, Syntrophin-like 1, supports a hypothesis that variation at this locus affects variation in the inter-pulse interval of courtship song. These results suggest that experimental evolution may provide an approach for genome-scale replication in Drosophila.

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

DNA samples are often pooled, either by experimental design or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of sequencing. Alternatively, the sample itself may be a mixture of multiple species or strains (e.g., bacterial species comprising a microbiome or pathogen strains in a blood sample). We present an expectation–maximization algorithm for estimating haplotype frequencies in a pooled sample directly from mapped sequence reads, in the case where the possible haplotypes are known. This method is relevant to the analysis of pooled sequencing data from selection experiments, as well as the calculation of proportions of different species within a metagenomics sample. Our method outperforms existing methods based on single-site allele frequencies, as well as simple approaches using sequence read data. We have implemented the method in a freely available open-source software tool.

Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster

Assortative mating has been a focus of considerable research because of its potential to influence biodiversity at many scales. Sharon et al. (2010) discovered that an inbred strain of Drosophila melanogaster mated assortatively based on the diet of previous generations, leading to initial reproductive isolation without genetic evolution. This behavior was reproduced by manipulating the microbiome independently of the diet, pointing to extracellular bacterial symbionts as the assortative mating cue. To further investigate the biological significance of this result, we attempted to reproduce this phenomenon in an independent laboratory using different genotypes and additional mating assays. Supporting the previous result, we found that a different inbred strain also mated assortatively based on the diets of previous generations. However, we were unable to generate assortative mating in an outbred strain from North Carolina. Our results support the potential for non-genetic mechanisms to influence reproductive isolation, but additional work is needed to investigate the importance of this mechanism in natural populations of Drosophila.