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Genome-wide linkage disequilibrium in nine-spined stickleback populations.

Yang J, Shikano T, Li MH, Merilä J - G3 (Bethesda) (2014)

Bottom Line: In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations.The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations.In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.

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Linkage disequilibrium (LD, measured by D’) decay between all syntenic markers in five different habitat types (blue = marine populations, red = lake populations, green = pond populations, gray = river population, black = coastal freshwater [CF] populations). Combined population data of 109 microsatellite loci within the same habitat type were employed to estimate habitat-specific D’ values.
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fig4: Linkage disequilibrium (LD, measured by D’) decay between all syntenic markers in five different habitat types (blue = marine populations, red = lake populations, green = pond populations, gray = river population, black = coastal freshwater [CF] populations). Combined population data of 109 microsatellite loci within the same habitat type were employed to estimate habitat-specific D’ values.

Mentions: Comparison of the patterns of LD decay as a function of genomic distance revealed very weak and statistically nonsignificant (R2 < 0.01, P > 0.05; Table S6 and Figure 3) correlations between D’ and genomic distance. With regard to LD decay in different habitats, the dataset of all marine populations combined or all freshwater populations combined showed higher correlations and shorter LD half-length compared with the combined lake or pond datasets (Figure 4 and Table S6). Interestingly, we found that the three coastal freshwater populations (Mat, Kro, Rbol; Figure 3B), which were geographically close to the marine populations (Hel, Sbol, Lev; Figure 3A), exhibited similar LD patterns as their marine neighbors, but deviated from the typical LD pattern in the inland freshwater populations (Figure 3C and Table 3). In addition, LD values increased slightly with genomic distance in three inland freshwater populations (Ska, Byn, Pyo; Figure 3D and Table S6), and the level of LD in Por was independent of genomic distance (Figure 3D and Table S6). This finding could be ascribable to stochasticity caused by the small number of marker pairs used to measure LD in each distance bin in these highly homozygous populations (Table S7).


Genome-wide linkage disequilibrium in nine-spined stickleback populations.

Yang J, Shikano T, Li MH, Merilä J - G3 (Bethesda) (2014)

Linkage disequilibrium (LD, measured by D’) decay between all syntenic markers in five different habitat types (blue = marine populations, red = lake populations, green = pond populations, gray = river population, black = coastal freshwater [CF] populations). Combined population data of 109 microsatellite loci within the same habitat type were employed to estimate habitat-specific D’ values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199698&req=5

fig4: Linkage disequilibrium (LD, measured by D’) decay between all syntenic markers in five different habitat types (blue = marine populations, red = lake populations, green = pond populations, gray = river population, black = coastal freshwater [CF] populations). Combined population data of 109 microsatellite loci within the same habitat type were employed to estimate habitat-specific D’ values.
Mentions: Comparison of the patterns of LD decay as a function of genomic distance revealed very weak and statistically nonsignificant (R2 < 0.01, P > 0.05; Table S6 and Figure 3) correlations between D’ and genomic distance. With regard to LD decay in different habitats, the dataset of all marine populations combined or all freshwater populations combined showed higher correlations and shorter LD half-length compared with the combined lake or pond datasets (Figure 4 and Table S6). Interestingly, we found that the three coastal freshwater populations (Mat, Kro, Rbol; Figure 3B), which were geographically close to the marine populations (Hel, Sbol, Lev; Figure 3A), exhibited similar LD patterns as their marine neighbors, but deviated from the typical LD pattern in the inland freshwater populations (Figure 3C and Table 3). In addition, LD values increased slightly with genomic distance in three inland freshwater populations (Ska, Byn, Pyo; Figure 3D and Table S6), and the level of LD in Por was independent of genomic distance (Figure 3D and Table S6). This finding could be ascribable to stochasticity caused by the small number of marker pairs used to measure LD in each distance bin in these highly homozygous populations (Table S7).

Bottom Line: In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations.The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations.In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.

Show MeSH
Related in: MedlinePlus