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Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG - G3 (Bethesda) (2015)

Bottom Line: Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe.We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample.We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.

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Related in: MedlinePlus

Summary of the Number of Potentially Functional Population-specific single-nucleotide polymorphisms. High-frequency derived allele counts for genic (A and B) and UTR regions (C) at frequencies between 20% and 100% are plotted for five populations. All sites in the plot are based on the IBD and callability-masked SNP dataset, have <20% missing data, and carry ≥70% posterior probability for their ancestral state. Panels (D) and (E) attempt to normalize the nonsynonymous and untranslated region (UTR) counts by showing the ratio to the putatively more neutral synonymous counts. IBD, identity by descent.
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fig7: Summary of the Number of Potentially Functional Population-specific single-nucleotide polymorphisms. High-frequency derived allele counts for genic (A and B) and UTR regions (C) at frequencies between 20% and 100% are plotted for five populations. All sites in the plot are based on the IBD and callability-masked SNP dataset, have <20% missing data, and carry ≥70% posterior probability for their ancestral state. Panels (D) and (E) attempt to normalize the nonsynonymous and untranslated region (UTR) counts by showing the ratio to the putatively more neutral synonymous counts. IBD, identity by descent.

Mentions: A major interest of the field is lineage-specific differentiation and the extent to which such differences might be driven by local adaptation. As a first look into this question we extracted all SNPs that were private to a single population and that also had a relatively high allele frequency (≥20%). Figure 7, A−C plots the counts for these alleles stratified by allele frequency bins. The finding of thousands of population-specific nonsynonymous, synonymous and UTR SNPs is highly unlikely, given a simple island model with the observed FST (these counts ranged from 1387 for Ithaca to 52,079 for Zimbabwe). These initial observations suggest a role for natural selection-driving patterns of differentiation and motivate a more thorough analysis of local adaptation detectable with these data.


Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG - G3 (Bethesda) (2015)

Summary of the Number of Potentially Functional Population-specific single-nucleotide polymorphisms. High-frequency derived allele counts for genic (A and B) and UTR regions (C) at frequencies between 20% and 100% are plotted for five populations. All sites in the plot are based on the IBD and callability-masked SNP dataset, have <20% missing data, and carry ≥70% posterior probability for their ancestral state. Panels (D) and (E) attempt to normalize the nonsynonymous and untranslated region (UTR) counts by showing the ratio to the putatively more neutral synonymous counts. IBD, identity by descent.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390575&req=5

fig7: Summary of the Number of Potentially Functional Population-specific single-nucleotide polymorphisms. High-frequency derived allele counts for genic (A and B) and UTR regions (C) at frequencies between 20% and 100% are plotted for five populations. All sites in the plot are based on the IBD and callability-masked SNP dataset, have <20% missing data, and carry ≥70% posterior probability for their ancestral state. Panels (D) and (E) attempt to normalize the nonsynonymous and untranslated region (UTR) counts by showing the ratio to the putatively more neutral synonymous counts. IBD, identity by descent.
Mentions: A major interest of the field is lineage-specific differentiation and the extent to which such differences might be driven by local adaptation. As a first look into this question we extracted all SNPs that were private to a single population and that also had a relatively high allele frequency (≥20%). Figure 7, A−C plots the counts for these alleles stratified by allele frequency bins. The finding of thousands of population-specific nonsynonymous, synonymous and UTR SNPs is highly unlikely, given a simple island model with the observed FST (these counts ranged from 1387 for Ithaca to 52,079 for Zimbabwe). These initial observations suggest a role for natural selection-driving patterns of differentiation and motivate a more thorough analysis of local adaptation detectable with these data.

Bottom Line: Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe.We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample.We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.

Show MeSH
Related in: MedlinePlus