Abstract
1. Widely used methods to assess population genetic structure and
differentiation rely on independence of marker loci. Following the
assumption, the common metrics, for example FST, evaluate genetic
structure by averaging across loci. Common metrics do not use
information in the associations among loci at the individual level and
are often criticized for failing to measure true differentiation even
when loci segregate independently. 2. We introduce a new concept to
measure β-variation (Effective Number of Different Populations, ENDP).
It requires the following steps: (a) calculation of a proper
dissimilarity between genetic profiles of all individuals; (b)
calculation of suitable pairwise distances between the samples based on
the dissimilarities between individuals; (c) calculation of diversity
(in terms of Hill numbers) and dispersion of samples based on the
pairwise distances between samples; (d) ENDP is then estimated as a
combination of the diversity and dispersion. ENDP estimates β-variation
independently of within-sample α-variation. This new concept differs
from the existing standard where β-diversity is estimated based on the
‘partition of variation’ scheme (beta=gamma-alpha or beta=gamma/alpha).
3. Estimates of ENDP are obtained by evaluating information in the
available genetic profiles of individuals including association of loci.
Therefore, ENDP can be used even in an absence of panmixia. 4. We
illustrate the use of this concept by analyzing the population genetic
structure of a sexual species (a trematode parasite) occupying connected
populations across a broad geographic area. Analysis is complicated by
two coexisting cryptic sister clades and the potentially mixed-mating
system of this hermaphroditic parasite.