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When repeating the sister pairs analysis without comparisons where the wild relative has experienced bottlenecks (camel, pigs, horse, donkey, and the water buffalo), we found that domesticates have a significantly higher dN/ dS than their wild relatives (Wilcoxon signed-ranks P = 0.02).
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We have shown that most of the demes studied have low genetic variability and have experienced bottlenecks and founder effects [ 34, 35].
The Bottleneck analysis suggested both the Manhole Sacramento and Zoo populations have experienced bottlenecks, but also detected the signature of a bottleneck in several other populations that would not be expected to have them.
These LD patterns depend on the ancestral background, as populations that have experienced bottlenecks (e.g., Caucasians) tend to show longer LD blocks and less evidence of recombination events when compared to Hispanics or African American.
For example, if both types of populations have experienced bottlenecks, a >50% reduction in molecular genetic variation in selfing compared with outcrossing populations might be more difficult to detect.
Soybean is a self-pollinating species that has experienced genetic bottlenecks during domestication and modern improvement (Hyten et al. 2006; Li et al. 2013).
We suggest that such a sex determination meltdown may not be unlikely in an introduced population that has been founded by few individuals or has experienced population bottlenecks during establishment.
The population on the island of Vis has been well characterized in terms of demographic and population genetic events [ 23], and these have suggested that the population has experienced several bottleneck events in the relatively recent past, within the last 25 years.
Considering that tomato has experienced severe genetic bottlenecks it is difficult to distinguish selective sweeps from the effects of genetic drift due to the bottlenecks themselves.
This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.
Comparing the ΦST value of 0.86 found in populations of Stipa capillata (Poaceae) with the estimated mean value for autogamous species, Hensen et al. (2010) suggest that the species has experienced strong genetic bottlenecks, reproductive isolation and self-fertilization.
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