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Finally, evidence of a recent bottleneck for each population was tested using BOTTLENECK 1.1 [ 47].
For instance, we decreased the lower bound on T for the BG model with a recent bottleneck, for sample sizes of 50 individuals.
At the microsatellite level, we found evidences of a recent bottleneck for P. panini from Negros, but also for P. m. subniger (Polillo Islands).
All analyses detected a recent bottleneck for inland populations 3 and 5 in harbouring significant heterozygosity excess, while no significant bottleneck was detected in inland populations 2 and 4 in any test.
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Nevertheless, no sign for a recent bottleneck was found for A. waldeni.
The Asiatic wild ass population in Mongolia shows no evidence of a recent bottleneck as reported for other wide-ranging animal species suffering from habitat fragmentation or range constriction (e.g. cougar Puma concolor; McRae et al., 2005).
We detected a strong, recent bottleneck for both primates, which we inferred to have resulted from the anthropogenic exploitation of forest resources in the last centuries.
Although this approach does not constitute a formal statistical test, detection of these pattern types can also provide heuristic evidence for a recent bottleneck [ 51].
Additionally, none of the Tajima's D values, either for single populations or lineages, were significantly positive, which would be indicative of a bottleneck [ 53], whereas seven out of the 10 populations analyzed showed a significant signature for a recent bottleneck, with at least one of the three microsatellite mutational models (Additional file 5).
The LD method provides information primarily about Ne in the parental generation, but residual disequilibrium from a recent bottleneck can affect the estimate for a few generations (Waples 2005, 2006).
Low genetic variation resulting from historically small population sizes, in contrast to that resulting from a recent bottleneck, may have different outcomes for the species (Spencer et al. 2000; England et al. 2003).
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