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Interestingly, there appeared to be no relationship between the effective size and the total population size when the number of individuals exceeds the minimum number required to reach an N e of approximately 50.
To more directly test the connection between the effective size of the amino-acid alphabet and the LBA problem, we performed a phylogenetic estimation under two overly simple models.
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For simulating higher levels of LD between SNPs, the effective size, mutation rate or/and recombination rate were reduced.
The multispecies coalescent explicitly relates the probability of an incongruent gene tree to the time between species divergences and the effective size of the ancestral population.
The relationship between census size and the effective size of a population is complex (Wright 1938; Hill 1972; Nunney 1991), but the two major factors affecting Ne are fluctuations in population size and variance in reproductive success among individuals (see Leberg 2005; Wang 2005 for reviews).
What matters is a balance between generation time, effective and sample size (the rate of common ancestry: probability to reach a common ancestor per time unit) and time spacing: the greater the time spacing and the sample size, and the smaller the generation time and the effective size, the greater the heterochrony effect.
We consider effective population sizes between 100 and 1600 to be realistic for most breeding populations, where the high level of inbreeding reduces the effective size.
The ratio between the effective population size to the number of sexually mature adults in a population (census size), the Ne /N ratio, is of great potential interest.
We found that the ratio between the effective population size (Ne) and actual number of parents (N) varied between 0.60 and 0.76 in the orchards' seedlots.
Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation.
Indeed, a weakly significant positive correlation was found between the effective genome size and the potential for carrying novel genes [ 86].
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