Figure S1. Illustration of Wahlund effect. Consider a population made up of two subpopulations of size N= 51 that are almost fixed for alternative alleles of a diallelic locus: each
of the two populations groups 50 identical homozygous individuals and a single heterozygote.
Such sub-populations do not deviate from HWE as the frequency of the almost fixed allele is
given by p = 101/102 ≈ 0.99, that of the rare allele is given by q = 1/102 ≈ 0.01, and thus the
number of expected heterozygous individuals under HWE would be given by 2pqN ≈ 1.
Things are very different for the total population. If we ignored the presence of two
genetically differentiated sub-populations, we would observe a population of size N= 102
with identical frequencies of both alleles (p=q= ½). However, in this case, we only observe
two heterozygous individuals rather than the 2pqN = 51 expected under HWE.
Figure S2. Comparisons of locus-specific estimates of F-statistics. For each F-statistic
estimate, population genetics software may compute confidence intervals. Here, we present a
putative analysis based on the polymorphism of nine independent genetic markers (i.e., in
linkage equilibrium). The means and standard errors of the per locus estimates of the
parameters FST (on left, estimator θ) and FIS (on right, estimator f) are displayed for the same
set of populations for the nine independent loci. Seven loci provide congruent estimates for
both parameters: they are thus likely to provide the information we are looking for, that is the
population structure that results from the balance among genetic drift, migration, mutation and
reproduction. Loci L8 and L9 provide different parameter estimates compared to the other
seven and should thus be considered with caution; the estimates driven for these loci are likely
to be biased by either the presence of null alleles and/or the action of selection pressures.
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Supplementary file- Glossary:
Bottleneck: Population bottleneck refers to drastic reduction in population sizes. This
induces, at all loci, a decrease in genetic diversity and an even more pronounced drop in the
allele numbers observed relative to a demographically stable population with the same census
size. In other words the bottlenecked population will remain away from mutation/drift
equilibrium for a number of generations following the reduction in census size. The more
generations the bottleneck lasts, the stronger the demographic reduction, and the more intense
and durable the genetic signature of such an event will be.
Epistatic effects: This occurs whenever expression of a given gene A modifies expression of
a gene B and vice versa.
Fixation: An allele has reached fixation in a population when it remains the only allele
present within a population. The immigration of different alleles into the population and
mutation into a different allelic state are the only ways of re-creating local polymorphism in a
fixed population.
Hardy-Weinberg expectations: By definition, allelic and genotypic frequencies are expected
to remain constant across generations within a population being at Hardy-Weinberg
equilibrium (HWE). Complementary, under HWE, allelic frequencies are fully determined by
the genotypic frequencies and vice versa. Consider one population of a diploid species and a
molecular marker with two alleles A1 and A2 present at frequencies p and q = 1 - p,
respectively. The frequency of A1A1 homozygous individuals will be given by the probability
of sampling the A1 allele twice within the population, thus p². The frequency of A2A2
homozygous individuals will be determined by the probability of sampling the A2 allele twice,
thus q². The frequency of A1A2 heterozygous individuals will be given by the probability of
first sampling allele A1, then sampling the A2 allele, or of sampling them in the reverse order,
thus pq + qp = 2pq= 1 - p² -q².
If the population is not panmictic (everything else equal), the genotypic frequencies A1A1,
A2A2 and A1A2 are given by [p²+pqFIS], [q²+pqFIS] and [2pq(1-FIS)], respectively.
Genetic drift: A finite population size implies that, among all possible offspring that could be
produced by a parental generation, only a sub-sample will occur and survive. This sampling
effect, referred to as genetic drift, induces random fluctuations in allelic frequencies across
generations until a point in time when, by chance (and in the absence of mutation or
migration), one allele will be fixed in the population. As genetic drift is a random effect, it
reduces the probability that nearby populations display the same distribution of allelic
frequencies (i.e., it increases the genetic differentiation among populations). Its effect is
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proportional to the effective size of the population; the smaller the population, the greater the
effect of drift on allele frequencies.
Linkage (dis)equilibrium: Linkage equilibrium refers to the independence between the
polymorphisms observed at two loci. This implies that knowledge of an individual’s genotype
at one locus provides no information on its genotype at the other locus. For the sake of
simplicity, let us consider two bi-allelic loci A (with alleles A1 and A2) and B (with alleles B1
and B2) so that the genotypic frequencies recorded within a population are given, at locus A,
by pA1A1, pA1A2 and pA2A2, and at locus B, by pB1B1, pB1B2, and pB2B2. These two loci are in
linkage equilibrium whenever the frequencies of the nine bi-locus genotypes are determined
by the product of the two mono-locus genotypic frequencies: pA1A1B1B1 = pA1A1 x pB1B1,
pA1A2B1B1 = pA1A2 x pB1B1, pA2A2B1B1 = pA2A2 x pB1B1, pA1A1B1B2 = pA1A1 x pB1B2, pA1A2B1B2 = pA1A2 x
pB1B2, pA2A2B1B2 = pA2A2 x pB1B2, pA1AB2B2 = pA1A1 x pB2B2, pA1A2B2B2 = pA1A2 x pB2B2, and pA2A2B2B2 =
pA2A2 x pB2B2.
The converse – linkage disequilibrium – refers to the case where there is some correlation
between the polymorphism recorded at locus A and that recorded at locus B. There are several
possible causes for linkage disequilibrium. Physical linkage among the considered loci is one
reason: in this case, recombination among the two loci is not frequent enough to make the two
mono-locus genotypes evolve independently from one another. Clonality and selfing generate
linkage disequilibrium throughout the genome of the considered species. Selection may create
linkage disequilibrium through epistatic effects, i.e., when the intensities of selection
pressures acting on the polymorphism at a given locus A vary among the various genotypes
observed at another locus B and vice versa. Finally, as an extension of the Wahlund effect
when considering more than one locus, population structure creates linkage disequilibrium
among loci, although not within subpopulations but at the level of the total (subdivided)
population.
Mutation/drift equilibrium: Consider an isolated population of constant finite size, and a
neutral locus at which panmixia is realized so that it tends to be at HWE. At this locus along
time, mutation will regularly introduce new alleles, whereas genetic drift will regularly drive
some alleles to extinction. The combined action of mutation and genetic drift will lead the
population to a dynamical equilibrium where the number of distinct alleles (hence the genetic
diversity) remains constant.
Panmixia: Zygote production follows random meeting of gametes produced in a population;
theoretically achieved only for species where individuals are self-compatible hermaphrodites.
Wahlund effect: Sampling errors so that individuals from distinct sub-populations are
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merged within samples are described as Wahlund effects. Such effects result in distorting the
relationships between the allelic and genotypic frequencies. An illustration is given in the
supplementary material (Figure S1).
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