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Finally, the influence of linkage on the degree of local adaptation, the migration load, and the effective migration rate at a neutral locus is explored.
The second method relies on the notion that variance- and homozygosity-based estimates of the population mutation rate θ are expected to be equal in a neutral locus in a population at mutation-drift equilibrium [63], [64].
The first method, implemented in the program Bottleneck [62], compares the expected heterozygosity estimated from allele frequencies with that estimated from the number of alleles and the sample size, which are expected to be identical in a neutral locus in a population at mutation-drift equilibrium.
The expectation for a neutral locus in a population is a Tajima's D of zero.
These statistics are expected to be equal in a neutral locus at mutation-drift equilibrium (MDE).
For this purpose, we included a neutral locus C with alleles C1 and C2.
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We modelled the fixation of an advantageous mutation and its effect on a linked neutral locus in large populations with a deterministic approach [ 3, 21].
Here we use Möhle's technique to derive the ancestral genetic process at a single neutral locus without recombination in an autotetraploid species.
In fact they assumed that the beneficial alleles are fixed in the population, thus focusing on a linked neutral locus.
However, in simulations of RHH, we are primarily interested in examining the diversity at a short, neutral locus.
One such model is known as recurrent hitchhiking, in which patterns of diversity at a selectively neutral locus are altered due to repeated positive selection at linked loci.
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