Estimates of mean 1-kb <i>F</i>_<i>ST</i> for Maine vs. Panama population samples.

<p>Estimates of mean 1-kb <i>F</i>_<i>ST</i> for Maine vs. Panama population samples.</p

Overview of the assembled Muller elements of <i>D</i>. <i>hydei</i>.

<p>Overview of the assembled Muller elements of <i>D</i>. <i>hydei</i>.</p

Overview of the system.

<p><i>D</i>. <i>hydei</i> and <i>D</i>. <i>mojavensis</i> are members of <i>repleta</i> species group, and <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i> are members of <i>melanogaster</i> subgroup. For each species pair we performed MK tests to identify the targets of parallel recurrent protein adaptation. Maine and Panama population genomes and transcriptomes of <i>D</i>. <i>hydei</i> and <i>D</i>. <i>melanogaster</i> were used to study parallel population differentiation between species.</p

Nucleotide diversity (π) and sequence coverage of each chromosome.

<p>Nucleotide diversity (π) and sequence coverage of each chromosome.</p

Number of genes harboring non-synonymous SNP <i>F</i>_<i>ST</i> outliers.

<p>Number of genes harboring non-synonymous SNP <i>F</i>_<i>ST</i> outliers.</p

Density of <i>F</i>_<i>ST</i> estimates from 1-kb windows between Panama and Maine populations.

<p>The 1%, 2.5%, and 5% tail cutoffs are indicated with hash marks.</p

McDonald-Kreitman tests of <i>Relish</i> variation for four species pairs.

a<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000442#pone.0000442-Begun1" target="_blank">[16]</a></p

Parallel Gene Expression Differences between Low and High Latitude Populations of <i>Drosophila melanogaster</i> and <i>D</i>. <i>simulans</i>

<div><p>Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of <i>Drosophila melanogaster</i> and its sister species, <i>D</i>. <i>simulans</i>, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i> sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in <i>D</i>. <i>melanogaster</i>. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.</p></div

Panama vs. Maine parallel gene expression differences in <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i>.

<p>10,085 one-to-one orthologs satisfied our minimum expression criteria in all samples. <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i> genes refer to geographically differentially expressed genes that have one-to-one orthologs. “Shared genes” correspond to one-to-one orthologs differentially expressed in both species. P-values were generated by hypergeometric test.</p><p>Panama vs. Maine parallel gene expression differences in <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i>.</p

Chromosomal distribution of geographically differentially expressed genes.

<p>P-values were calculated by <i>χ</i>^<i>2</i> test.</p><p>** P<0.01</p><p>*** P <0.001</p><p>Chromosomal distribution of geographically differentially expressed genes.</p