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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

Population structure revealed by principal on autosomal “neutral” sites. Principal component clustering plots demonstrate the genetic structure present among the five populations. Left panel displays the strong separation of the Zimbabwe and Beijing populations from the remaining three populations based on the first two principal components. The right panel displays further separation of the Netherland, Tasmania, and Ithaca populations based on principal components two and three. Although less structured, clear separation is still observed for these latter three populations.
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fig5: Population structure revealed by principal on autosomal “neutral” sites. Principal component clustering plots demonstrate the genetic structure present among the five populations. Left panel displays the strong separation of the Zimbabwe and Beijing populations from the remaining three populations based on the first two principal components. The right panel displays further separation of the Netherland, Tasmania, and Ithaca populations based on principal components two and three. Although less structured, clear separation is still observed for these latter three populations.

Mentions: Principal component analysis performed on the genome-wide “neutral” sites, which should best reflect demographic processes, reveals notable population structure among all populations (Figure 5). Plotting the first two principal components cleanly separates not only Zimbabwe but also Beijing. However one line annotated as having an African origin (ZW184) does not group with the other Zimbabwe lines; we have excluded this line from subsequent population genetic analyses because its Zimbabwe origin is suspect, although it remains included in the global set of lines for modeling and mapping applications. Plotting the additional principal components (or removing the Zimbabwe lines, data not shown) reveals that even the Ithaca, Tasmania, and Netherlands population samples can be clearly separated.


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)

Population structure revealed by principal on autosomal “neutral” sites. Principal component clustering plots demonstrate the genetic structure present among the five populations. Left panel displays the strong separation of the Zimbabwe and Beijing populations from the remaining three populations based on the first two principal components. The right panel displays further separation of the Netherland, Tasmania, and Ithaca populations based on principal components two and three. Although less structured, clear separation is still observed for these latter three populations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: Population structure revealed by principal on autosomal “neutral” sites. Principal component clustering plots demonstrate the genetic structure present among the five populations. Left panel displays the strong separation of the Zimbabwe and Beijing populations from the remaining three populations based on the first two principal components. The right panel displays further separation of the Netherland, Tasmania, and Ithaca populations based on principal components two and three. Although less structured, clear separation is still observed for these latter three populations.
Mentions: Principal component analysis performed on the genome-wide “neutral” sites, which should best reflect demographic processes, reveals notable population structure among all populations (Figure 5). Plotting the first two principal components cleanly separates not only Zimbabwe but also Beijing. However one line annotated as having an African origin (ZW184) does not group with the other Zimbabwe lines; we have excluded this line from subsequent population genetic analyses because its Zimbabwe origin is suspect, although it remains included in the global set of lines for modeling and mapping applications. Plotting the additional principal components (or removing the Zimbabwe lines, data not shown) reveals that even the Ithaca, Tasmania, and Netherlands population samples can be clearly separated.

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