Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation - PubMed (original) (raw)

Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

Darren J Parker et al. Genome Biol Evol. 2018.

Abstract

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

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Figures

<sc>Fig</sc>. 1.

Fig. 1.

—Tree used for multi-species PAML analyses. Cold-tolerant species (species that have a knockdown temperature of <3 °C) are shown in blue (data from Kellermann et al. [2012] and MacMillan et al. [2015]).

<sc>Fig</sc>. 2.

Fig. 2.

—Distributions of dN and dS estimates for each of the 250 genes from 13 Drosophila species with significant differences in ω between cold-tolerant and non-cold-tolerant species.

<sc>Fig</sc>. 3.

Fig. 3.

—The relationship between values of ω estimated for 5,619 genes in cold-tolerant and non-cold-tolerant species of Drosophila. 250 genes with significantly different estimates of ω are shown in black with red outline. Diagonal line indicates the 1–1 diagonal, points below the diagonal line show elevated levels of ω in cold-tolerant species compared with non-cold-tolerant species, whereas points above the diagonal show elevated levels of ω in non-cold-tolerant species.

<sc>Fig</sc>. 4.

Fig. 4.

—Semantic clustering of significantly (FDR < 0.1) enriched GO-terms for genes showing significantly elevated dN/dS in cold-tolerant or non-cold-tolerant species. Circle size corresponds to the number of genes annotated to the term in the reference database. Circle colour indicates log10 FDR of the GO term.

<sc>Fig</sc>. 5.

Fig. 5.

—Average values of ω between D. montana and D. virilis for candidate gene sets. FRTP = female reproductive tract SFP = seminal fluid proteins SRR = sex and reproduction related genes CA = cold acclimation genes. The red and dashed lines indicate the median and mean ω of the genomic background, respectively.

<sc>Fig</sc>. 6.

Fig. 6.

—Semantic clustering of significantly (FDR < 0.1) enriched GO-terms for genes showing high dN/dS between D. montana and D. virilis. Circle size corresponds to the number of genes annotated to the term in the reference database. Circle colour indicates log10 FDR of the GO term.

<sc>Fig</sc>. 7.

Fig. 7.

—Semantic clustering of significantly (FDR < 0.1) enriched GO-terms for genes showing significant divergence between populations of D. montana. Circle size corresponds to the number of genes annotated to the term in the reference database. Circle colour indicates log10 FDR of the GO term.

<sc>Fig</sc>. 8.

Fig. 8.

—Manhattan plot of _q_-values from the three pairwise BayeScan analyses for the SNPs on the mapped chromosomes. Red points denote SNPs which passed the 0.05 _q_-value FDR threshold. Alternating grey and black points denote different scaffolds that have been anchored to the chromosomes. The order of the mapped scaffolds is established but not their orientation.

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