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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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Site frequency spectra for four single-nucleotide polymorphisms (SNP) classes. Unfolded (polarized for ancestral state) SFS are shown for the four SNP classes separated for the autosomes (left) and the X chromosome (right). Insets display the two extreme ends of the distributions where differences between the SNP classes are most pronounced.
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fig6: Site frequency spectra for four single-nucleotide polymorphisms (SNP) classes. Unfolded (polarized for ancestral state) SFS are shown for the four SNP classes separated for the autosomes (left) and the X chromosome (right). Insets display the two extreme ends of the distributions where differences between the SNP classes are most pronounced.

Mentions: Another data quality check examined the unfolded SFS for four SNP classes combined across the full dataset and partitioned into an X chromosome set and an autosomal set: (1) nonsynonymous, (2) synonymous, but not fourfold degenerate, (3) intergenic, and (4) a “neutral” class comprised of fourfold degenerate and small intronic SNPs (Figure 6). The number of SNPs (~167,000) was balanced to match the limiting counts from the ‘neutral’ set.


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)

Site frequency spectra for four single-nucleotide polymorphisms (SNP) classes. Unfolded (polarized for ancestral state) SFS are shown for the four SNP classes separated for the autosomes (left) and the X chromosome (right). Insets display the two extreme ends of the distributions where differences between the SNP classes are most pronounced.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: Site frequency spectra for four single-nucleotide polymorphisms (SNP) classes. Unfolded (polarized for ancestral state) SFS are shown for the four SNP classes separated for the autosomes (left) and the X chromosome (right). Insets display the two extreme ends of the distributions where differences between the SNP classes are most pronounced.
Mentions: Another data quality check examined the unfolded SFS for four SNP classes combined across the full dataset and partitioned into an X chromosome set and an autosomal set: (1) nonsynonymous, (2) synonymous, but not fourfold degenerate, (3) intergenic, and (4) a “neutral” class comprised of fourfold degenerate and small intronic SNPs (Figure 6). The number of SNPs (~167,000) was balanced to match the limiting counts from the ‘neutral’ set.

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