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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

Genome-wide diversity summaries. (A) Sliding window plots display summary statistics for the single-nucleotide polymorphism data along all four chromosome arms. The window size for chromosomes other than the 4th are 10 kb, with stride length equal to 5 kb; Windows for the small 4th chromosome are 500 bp with stride length equal 250 bp. Population abbreviations are: B = Beijing, I = Ithaca, N = Netherlands, T = Tasmania, and Z = Zimbabwe. “Polymorphism” refers to the average pairwise nucleotide difference (π), “Poly/Div” refers to the polymorphism divided by divergence, and “TajD” refers to Tajimas D. (B) Boxplots summarize the diversity data shown in (A) for all chromosomes. Heterogeneity in genome-wide nucleotide diversity (π) is observed across all populations (one-way analysis of variance, F4, 146050 = 2583.8, P << 0.01; all pairwise comparisons contribute significantly to this result {all Tukey post-hoc comparisons P < < 0.01}) . The most notable difference is between the non-African populations’ and the Zimbabwe’s X chromosomes. Non-African X chromosomes display 37–46% less diversity within the X chromosome as compared with the normally recombining autosomes (Wilcoxon P << 0.01), whereas the Zimbabwe sample has a slight excess (2%). As a result, the autosomal-chromosome X comparison for Zimbabwe is nominally significant in the opposite direction (Wilcoxon P = 0.011). Within population comparisons of Tajima’s D values (D) on the X vs. autosomes are also significantly different (Wilcoxon P << 0.01 for all contrasts), as are most comparisons across populations (one-sample Wilcoxon P << 0.01). Tukey post-hoc comparisons indicate that only the Ithaca-Beijing X chromosome and the Tasmania-Ithaca autosome comparisons are nonsignificant (P > 0.05). Zimbabwe stands out as having a significantly negative mean autosomal D, whereas for the X chromosome it is not different from zero (Wilcoxon P > 0.05).
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fig8: Genome-wide diversity summaries. (A) Sliding window plots display summary statistics for the single-nucleotide polymorphism data along all four chromosome arms. The window size for chromosomes other than the 4th are 10 kb, with stride length equal to 5 kb; Windows for the small 4th chromosome are 500 bp with stride length equal 250 bp. Population abbreviations are: B = Beijing, I = Ithaca, N = Netherlands, T = Tasmania, and Z = Zimbabwe. “Polymorphism” refers to the average pairwise nucleotide difference (π), “Poly/Div” refers to the polymorphism divided by divergence, and “TajD” refers to Tajimas D. (B) Boxplots summarize the diversity data shown in (A) for all chromosomes. Heterogeneity in genome-wide nucleotide diversity (π) is observed across all populations (one-way analysis of variance, F4, 146050 = 2583.8, P << 0.01; all pairwise comparisons contribute significantly to this result {all Tukey post-hoc comparisons P < < 0.01}) . The most notable difference is between the non-African populations’ and the Zimbabwe’s X chromosomes. Non-African X chromosomes display 37–46% less diversity within the X chromosome as compared with the normally recombining autosomes (Wilcoxon P << 0.01), whereas the Zimbabwe sample has a slight excess (2%). As a result, the autosomal-chromosome X comparison for Zimbabwe is nominally significant in the opposite direction (Wilcoxon P = 0.011). Within population comparisons of Tajima’s D values (D) on the X vs. autosomes are also significantly different (Wilcoxon P << 0.01 for all contrasts), as are most comparisons across populations (one-sample Wilcoxon P << 0.01). Tukey post-hoc comparisons indicate that only the Ithaca-Beijing X chromosome and the Tasmania-Ithaca autosome comparisons are nonsignificant (P > 0.05). Zimbabwe stands out as having a significantly negative mean autosomal D, whereas for the X chromosome it is not different from zero (Wilcoxon P > 0.05).

Mentions: As indicated by the SFS previously, significant heterogeneity in genome-wide nucleotide diversity is observed across all populations (Figure 8). Median genome-wide diversity levels (π) range from ~0.3% (Beijing) to ~0.6% (Zimbabwe); Watterson’s θ ranges from ~0.03% to ~0.07%. Consistent with previous studies, broad-scale patterns of within-genome diversity covary with local recombination intensity and display reduced diversity near the telomeres and centromeres (Figure 8A). In addition, the X chromosomes of all populations—except for Zimbabwe —display a marked reduction in diversity levels as compared with the normally recombining autosomes (excluding chromosome 4).


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)

Genome-wide diversity summaries. (A) Sliding window plots display summary statistics for the single-nucleotide polymorphism data along all four chromosome arms. The window size for chromosomes other than the 4th are 10 kb, with stride length equal to 5 kb; Windows for the small 4th chromosome are 500 bp with stride length equal 250 bp. Population abbreviations are: B = Beijing, I = Ithaca, N = Netherlands, T = Tasmania, and Z = Zimbabwe. “Polymorphism” refers to the average pairwise nucleotide difference (π), “Poly/Div” refers to the polymorphism divided by divergence, and “TajD” refers to Tajimas D. (B) Boxplots summarize the diversity data shown in (A) for all chromosomes. Heterogeneity in genome-wide nucleotide diversity (π) is observed across all populations (one-way analysis of variance, F4, 146050 = 2583.8, P << 0.01; all pairwise comparisons contribute significantly to this result {all Tukey post-hoc comparisons P < < 0.01}) . The most notable difference is between the non-African populations’ and the Zimbabwe’s X chromosomes. Non-African X chromosomes display 37–46% less diversity within the X chromosome as compared with the normally recombining autosomes (Wilcoxon P << 0.01), whereas the Zimbabwe sample has a slight excess (2%). As a result, the autosomal-chromosome X comparison for Zimbabwe is nominally significant in the opposite direction (Wilcoxon P = 0.011). Within population comparisons of Tajima’s D values (D) on the X vs. autosomes are also significantly different (Wilcoxon P << 0.01 for all contrasts), as are most comparisons across populations (one-sample Wilcoxon P << 0.01). Tukey post-hoc comparisons indicate that only the Ithaca-Beijing X chromosome and the Tasmania-Ithaca autosome comparisons are nonsignificant (P > 0.05). Zimbabwe stands out as having a significantly negative mean autosomal D, whereas for the X chromosome it is not different from zero (Wilcoxon P > 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig8: Genome-wide diversity summaries. (A) Sliding window plots display summary statistics for the single-nucleotide polymorphism data along all four chromosome arms. The window size for chromosomes other than the 4th are 10 kb, with stride length equal to 5 kb; Windows for the small 4th chromosome are 500 bp with stride length equal 250 bp. Population abbreviations are: B = Beijing, I = Ithaca, N = Netherlands, T = Tasmania, and Z = Zimbabwe. “Polymorphism” refers to the average pairwise nucleotide difference (π), “Poly/Div” refers to the polymorphism divided by divergence, and “TajD” refers to Tajimas D. (B) Boxplots summarize the diversity data shown in (A) for all chromosomes. Heterogeneity in genome-wide nucleotide diversity (π) is observed across all populations (one-way analysis of variance, F4, 146050 = 2583.8, P << 0.01; all pairwise comparisons contribute significantly to this result {all Tukey post-hoc comparisons P < < 0.01}) . The most notable difference is between the non-African populations’ and the Zimbabwe’s X chromosomes. Non-African X chromosomes display 37–46% less diversity within the X chromosome as compared with the normally recombining autosomes (Wilcoxon P << 0.01), whereas the Zimbabwe sample has a slight excess (2%). As a result, the autosomal-chromosome X comparison for Zimbabwe is nominally significant in the opposite direction (Wilcoxon P = 0.011). Within population comparisons of Tajima’s D values (D) on the X vs. autosomes are also significantly different (Wilcoxon P << 0.01 for all contrasts), as are most comparisons across populations (one-sample Wilcoxon P << 0.01). Tukey post-hoc comparisons indicate that only the Ithaca-Beijing X chromosome and the Tasmania-Ithaca autosome comparisons are nonsignificant (P > 0.05). Zimbabwe stands out as having a significantly negative mean autosomal D, whereas for the X chromosome it is not different from zero (Wilcoxon P > 0.05).
Mentions: As indicated by the SFS previously, significant heterogeneity in genome-wide nucleotide diversity is observed across all populations (Figure 8). Median genome-wide diversity levels (π) range from ~0.3% (Beijing) to ~0.6% (Zimbabwe); Watterson’s θ ranges from ~0.03% to ~0.07%. Consistent with previous studies, broad-scale patterns of within-genome diversity covary with local recombination intensity and display reduced diversity near the telomeres and centromeres (Figure 8A). In addition, the X chromosomes of all populations—except for Zimbabwe —display a marked reduction in diversity levels as compared with the normally recombining autosomes (excluding chromosome 4).

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