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Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

Asgharian H, Chang PL, Lysenkov S, Scobeyeva VA, Reisen WK, Nuzhdin SV - Proc. Biol. Sci. (2015)

Bottom Line: We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection.The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes.We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation.

View Article: PubMed Central - PubMed

Affiliation: Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

ABSTRACT
We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

No MeSH data available.


The first three PCs of Pool-hmm scores of genes from C. pipiens samples (a,b) or C. pipiens and C. torrentium together (c,d).
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RSPB20150728F1: The first three PCs of Pool-hmm scores of genes from C. pipiens samples (a,b) or C. pipiens and C. torrentium together (c,d).

Mentions: For both Pool-hmm and Tajima's D, we performed PCA once with the six C. pipiens samples only, and a second time with all of eight Culex samples included. The first principal component (PC) was always highly correlated with all of the sample labels and did not separate the samples from each other decisively (figure 1a,c). In the case of the six C. pipiens samples, the second and third PCs demonstrated the local nature of adaptation in the most conspicuous way, producing three distinct clusters containing the samples from Moscow, Aleksin and Sacramento (figure 1b). Including all eight samples, the combination of the second and the third components produced four clusters: one for the C. torrentium samples and three for each of the C. pipiens locations (figure 1d). The results of PCA on Tajima's D values were very similar (not shown).FigureĀ 1.


Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

Asgharian H, Chang PL, Lysenkov S, Scobeyeva VA, Reisen WK, Nuzhdin SV - Proc. Biol. Sci. (2015)

The first three PCs of Pool-hmm scores of genes from C. pipiens samples (a,b) or C. pipiens and C. torrentium together (c,d).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4590483&req=5

RSPB20150728F1: The first three PCs of Pool-hmm scores of genes from C. pipiens samples (a,b) or C. pipiens and C. torrentium together (c,d).
Mentions: For both Pool-hmm and Tajima's D, we performed PCA once with the six C. pipiens samples only, and a second time with all of eight Culex samples included. The first principal component (PC) was always highly correlated with all of the sample labels and did not separate the samples from each other decisively (figure 1a,c). In the case of the six C. pipiens samples, the second and third PCs demonstrated the local nature of adaptation in the most conspicuous way, producing three distinct clusters containing the samples from Moscow, Aleksin and Sacramento (figure 1b). Including all eight samples, the combination of the second and the third components produced four clusters: one for the C. torrentium samples and three for each of the C. pipiens locations (figure 1d). The results of PCA on Tajima's D values were very similar (not shown).FigureĀ 1.

Bottom Line: We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection.The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes.We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation.

View Article: PubMed Central - PubMed

Affiliation: Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

ABSTRACT
We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

No MeSH data available.