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A Mathematical Study of the Founder Principle of Evolutionary Genetics

Author(s): P. Holgate
Source: Journal of Applied Probability, Vol. 3, No. 1, (Jun., 1966), pp. 115-128
Published by: Applied Probability Trust
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J. Appl.Prob. 3, 115-128(1966)
Printedin Israel



P. HOLGATE, The Nature Conservancy,London

Some comparisons are made between various characteristicsof the genetic
structures of populations of the same size and age, which have (i) evolved
from a small founder population, and (ii) evolved from a population which
has been of constant size throughout the period considered.

1. Introduction
Consider a gene having two alleles A and a. In the absence of selection, and if
there is no mutation, it is possible that one of these will become fixed in a popula-
tion as a result of the random fluctuations in its frequency from generation to
generation. This is generally known as the Sewall Wright effect, and its possible
contribution to evolution has been the subject of considerable discussion. A sum-
mary of Wright's own views and a survey of his mathematical work on the subject
are given in Wright (1964).
Mathematical work on the tendency to homozygosity of a finite population
has been surveyed by Moran (1962), and Kimura (1964). Roughly speaking, for
given initial gene frequencies, the probability that the populations will become
homozygous within a given number of generations may be appreciable for small
populations, but becomes negligible as the population size increases.
Suppose however that a small founder population colonises an area, and in
the course of several generations multiplies to a much greater size. Fixation may
occur at a given locus when the population is small, and the effect of population
growth will then lead to a homozygous population of such a size that fixation
as a result of random fluctuation would be inconceivable in a population which
had always had that same, large size. This phenomenon is known as the founder
principle, associated with Mayr (1942, 1963). Experimental work in relation to it
is reported by Dobzhansky and Pavlovsky (1957), and it has recently been invoked
in the controversy about the origins of geographical variations between snail
colonies in Southern England, (Goodhart 1962, 1963; Cain and Currey 1963a, b).
Despite its interest, little mathematical work has appeared on genetic fluctuations

Received in revised form 6 May 1965.


in populationswhose size does not remainconstant. Bartlett(1937) considered

selfing populations,in particularthose where the number of offspringof each
individualwas (a) a constant,and (b) a Poissonvariable, and derivedrecurrence
relationsfor the momentgeneratingfunctions,and hencethe meansand variances,
of the numberof heterozygotesin succesivegenerations.He also showed how
the theory could be developedto deal with other systems of inbreeding.Feller
(1951) approachedthe problemfrom the point of view of diffusiontheory and
discussedsome of the difficultiesin formulatingand solving the mathematical
problems.Mode (1964)has consideredanotheraspect.
In the present paper I consider a population which reproducesin discrete,
non-overlappinggenerations.However, instead of keeping the generationsot
constantsize, I have assumedthroughoutmost of the paperthat the population
exactlydoublesin size at each generation,startingwith a singleindividualor pair.
The fact that the overallgrowth is made deterministicin this way bringsabout
two relatedsimplifications.It reducesthe numberof randomlyvariablequantities
and eliminatesthe possibilityof the populationdying out completely.In models
for which this possibilitydoes exist, the interestingresultsare often those con-
ditional on it not occuring,which considerablyincreasesthe mathematicaldif-
ficulty of the problem.In a practicalbiologicalsituation,it would be impossible
for a populationto continuedoublingat each generationindefinitely,but as will
be shown, the effect of the first few generationsof breedingare overwhelming,
and sincein a largepopulationgeneticstructureis not affectedby randomsampling
variancein any case, the resultsobtainedshould have a certainrobustness.
Section 2 is devoted to selfingpopulationsinitiated by a single heterozygote,
and Section 3 to randommating populationsinitiatedby a single pair, each of
whose genes is A or a with probability1/2. From time to time I have compared
characteristics of the structureof the increasingpopulationwiththoseof a station-
ary population on the following basis. Suppose that after t generations,the
growing population has attained a size N. Then for comparisonI consider a
populationwhichhas evolvedthrought generationsof reproduction,maintaining
a constantsize N throughout,havingbeeninitiatedby a highlygeneticallyhetero-
geneous population.Thesecomparisonscan be computednumericallyfor small
values of t, and are given for t = 3, and asymptotic formulae are given for
large t. In Section4, somenumericalresultsaregivenfor thepopulationsresulting
from threegenerationsof breedingwith a fully stochasticmodel.
2. Selfingpopulations
Let us considera populationinitiatedby an Fo consistingof a single hetero-
zygote,Aa.Let each individualof Ft1 contributetwo offspringto Ft, the breeding
systembeing self-fertilisation.Ft will thereforeconsist of 2' individuals.
Oneof the featuresof selfingpopulationsof constantsizeis the rapidelimination
of heterozygotes.(See e.g. Li (1955,p. 103)),and it is thereforeof interestto study
A mathematicalstudy of thefounderprincipleof evolutionarygenetics 117

this question for the growing population. If Zt is the number of heterozygotes

in Ft then {Zo = 1, Z1, Z2, "*-} is a branching stochastic process of Galton-
Watson type. (For the theory of these processes see Bartlett (1960), Harris (1963)).
The probability generating function of the number of heterozygous offspring
of a heterozygote is

(1) f(s)=
(2+f s).

Since the mean of the distribution given by (1) is 1, the ultimate elimination of
heterozygotes is certain. The p.g.f. of Zt is obtained by functional iteration which
may be carried out explicitly for small t. For instance, the probability that F3
will contain j heterozygotes is the coefficient of sJ in

(2) f3(s)= 2( 2(s+2 + 2 +2 '

This distribution is tabulated in the first column of Table I.
The elimination of heterozygotes in a population where each individual con-
tributed a single offspring to the next generation was discussed by Bartlett (1937).
Suppose, for comparison with the above case, that a population had been initiated
by 8 heterozygotes, and had undergone 3 generations of selfing, with each individ-
ual contributing a single offspring to the next generation. The probability that a
given line would remain heterozygous is 1/8, and the p.g.f of the number of
heterozygotes in F3 is therefore

(3) g3(s) = ( 1 + 7)8

This binomial distribution is tabulated in the second column of Table I.

Distribution of number of heterozygotes
after three generations of selfing
Growing Stationary
Population Population
0 .483459 .343609J
1 .217285 .392696
2 .176514 .196348
3 .077637 .056099
4 .032593 .010018
5 .009277 .001145
6 .002686 .000082
7 .000488 .000003
8 .000061 .000000

Despite the smallnumberof generations,Table I illustratesthe fact that both the

probabilityof complete eliminationof heterozygotes,and the probabilitythat
theirnumberwill be large,are greaterfor the growingpopulation. The variances
are 1.5 for the growingpopulationand 0.875 for the stationaryone.
The varianceof Z, for generalt may be obtainedby lettingf -2 in Formula(7a)
in Bartlett(1937), or by substitutingfor a2 in Formula(5.3)in Harris(1963,p. 6),
eitherof whichlead to:

(4) Zt= 1, varZ,= t.

The probabilitythat there would be no heterozygotesafter t generationsis given

by the asymptoticformulaof Kolmogorov(1938)as

2 4-
(5) Pr(Z, =0) 1- tf(1)

In fact, the p.g.f. (1) and result(5) are mentionedby Kolmogorovas an example
at the end of Section4 of his paper,wherethey arisein the solutionof a different
problemin populationgenetics.It may be noted that t has to be quitelargefor (5)
to give good numericalresults. For t = 40 when (5) gives 0.9, the correctvalue
obtainedby iterationis 0.9142.Howeverthe derivationgivenby Harris(1963,p. 20
ff.) suggestst/(4 + t) as a betterapproximation,and for t = 40 it gives0.9091.For
comparisonconsider an Ft which had arisen from an Fo of 2t heterozygotes,
evolving throught t generationsof selfing at constant population size, and let
Zt be the numberof heterozygotesin Ft in this population.(It should be borne
in mind that the sequence{Z'}, althougha stochasticprocessin the mathematical
sense, does not representthe evolution of a definitepopulation.) By reasoning
similarto that given in the case t = 3, the distributionof Zt is binomial with
n = 2t, p = (1/2)t, and hence

(6) Z;=l1, varZt'=(1- ())

(7) Pr(Zf =0)== (1-( - ) e- =0.367879.

Comparisonof the variancesgivenin (4) and (6), and the probabilitiesthat hetero-
zygotes will be absent, given in (5) and (7), togetherwith the numericalresults
of Table I, illustratethe fact that selfingpopulationswhichhave reacheda large
size by repeateddoubling will be more variable in respect to proportions of
heterozygotes,and in particularwill be more likely to contain none, than those
studyof thefounderprincipleof evolutionary
A mathematical genetics 119

of the same size and age that have always been that size. The stochastic process
describing the number of individuals in Ft which are homozygous for a given
allele, say A, is not a branching process, nor even a Markov process. However,
the probability P, that Ft will consist entirely of AA's, has a simple recurrence
relation. The probabilities that the offspring of a heterozygote are (AA,AA),
(AA,Aa) or (Aa,Aa) are 1/16,1/4,1/4 respectively. It is then required that the
offspring should consist entirely of AA's after (t- 1) generations, which leads to
11 1 2
Pt =- + Pt-1 + Pt2-1

from which P3 = 0.083840. Since the Pt are obviously increasing, lim0 Pt = P,

the probability that the population ultimately consists entirely of AA's satisfies
11 1 1 2
P=- +-p +P2
16 4 4
of which the relevant root is P = 1 1/2 - V2 = 0.085786. For the comparable
stationary population the chance that all its members are AA is given by
(1/4 + 1/2 * 1/4 + 1/2 * 1/2 * 1/4)8 = 0.001342.
In the doubling population the elimination of heterozygotes occurs with
probability one. When it has occurred the population which will then consist
entirely of AA's and aa's will continue to increase, but with the numbers of these
types, and hence of the two alleles, in a constant proportion. The remainder
of this section is devoted to obtaining some properties of Y,the random proportion
of AA's when the heterozygotes have been eliminated. Clearly, Y can take only
those values whose expression as a binary fraction can be written in terminating
form, and every such value in the interval [0,1] is taken with positive probability.
It is therefore an example of a random variable whose distribution function has
jumps at a set of points everywhere dense (in [0,1]), although this peculiarity is a
mathematical consequence of insisting on the population doubling exactly at each
generation. If Yt is the proportion of the limiting population belonging to lines
which became AA at exactly the tth generation, then Y = t 1 Yt.It is interesting
to note that the stochastic process

2fYt, j=1,2,-.,
t= I

is such that almost every realisation is monotonically increasing, the form of the
'remainder' term in the submartingale decomposition theorem (Loeve, 1963,
p. 389). Some properties of Y may be obtained by enumerating the possible
structures of F1, and equating the unconditional expectations of certain variables,
to the appropriate expectations obtained after conditioning by the outcome of F1.
The possible F1 's are listed in column 2 of Table II, preceded by their probabilities.
Column 3 gives the conditionalexpectationof Y, columns 4 and 5 give thecon-
ditional varianceof Y and the probabilitythat Y = 0, wherev and P denotethe
unconditionalvalues of these quantities.Column 6 gives the conditionalexpec-
tation of ez, wherem(z) is the unconditionalvalue.
Probabilitiesof possibleF1's, and values of variouscharacteristicsof population
structureconditional on these, for the growing,selfingpopulation

Pr. F,1 S{Y\F1} var{Yr|FI Pr{Y=OIF,} ?{ez\F,}

AA,AA 1 0 0 ez

- AA,Aa 4 ^ 0 e '2m( z)

AA,aa 0 0 ezI

Aa,Aa 2 \ (z

aa,aa 0 0 1 1

For instanceto obtain v we have on writingdown the two expressionsfor the

secondmomentabout zero:

6 +4v+8(1+
which v = For the
gives of the eliminationof
1/12. probability A,
1 1 1 2
P=- +-P +p-p2

whichwas derivedabove by a more or less equivalentmethod.An identityfor the

moment generatingfunction written down from the last column simplifiesto

4m(z)= {(l+ez/2)+m( z)}2

Clearly,Y is distributedsymmetricallyabout 1/2. If (z)is the momentgenerating

A mathematicalstudy of thefounderprincipleof evolutionarygenetics 121

function of Y - 1/2, then on writing m(z) = e'Z2l/(z), and then replacing z by

2z for convenience, +(z) is found to satisfy the functional relation

(9) 4+(z)= cosh z + (z) .

Since Y is bounded, all its moments exist, and expansion of the m.g.f. in (9)
provides a recurrencerelation for the even order central moments. The first few are
1 11 121 61663
#2 2= , P4 =
720 6 = 36288' P8 79315200'

of which the first value confirms the solution of (8). Since the probabilities of
the end points are known exactly, the moments of the distribution conditional
on fixation not occurring can be calculated from the formula

(10) 12k -2P 2k-2P )

from which we obtain

12 = 0.048816, /14= 0.005498, 16 = 0.000789, % = 0.000129.

The coefficient of kurtosis of the conditional distribution is f2 = 2.3071.

3. Random mating
Notation used in this section is not everywherecomparable with that of the last.
Since a random mating population cannot be initiated by a single individual,
in order to make the situations in this section and the last as similar as possible,
I have assumed that the population begins with an F1 consisting of 2 animals,
each of whose 4 genes are A or a with probability 1/2. This means that if the
mathematical definition were extrapolated backwards, independently of its
interpretation, we could imagine an Fo consisting of a single heterozygote. As in
studies of random mating populations of constant size, only the number of genes
in each generation is considered, and they are supposed to be determined inde-
pendently, being A or a with probabilities equal to the proportions in the previous
generation. Moran (1962, pp. 12-20) has discussed the implications for the form
of the offspring distribution of the constant population model and analogous
considerations apply here. Let Zt be the number of A genes in F,. The distribution
of Zt conditional on Z- = z,_ is binomial with n =2'+ p = (1/2)tzti.
The distribution may be computed explicitly for small t, and for t = 3 it is given
in the first column of Table III. For a comparable population of constant size,
suppose that Fo had consisted of 8 heterozygotes, which had then evolved through
3 generations of random mating. The distribution of Z3, the number of A's in
F3 is given by post-multiplying the 1 x 17 row vector with 1 in its ninth column
and zeros elsewhere, three times by the matrix (ail) with elements
al= ( 16- ( i
{ HJ) (6) 16)
(Feller, 1951). The resulting distribution is given in the second column of Table III.
In this case the probability of elimination of A can be seen to be greater for the
growing population. The variances of the proportion of A genes are 0.0962 and
0.0440 for the growing and stationary populations respectively.
Distribution of number of A's after three generations of random mating
(The distribution is symmetric about 8.)
Growing Stationary
j Population Population
0 .0996 .0068
1 .0284 .0155
2 .0423 .0290
3 .0505 .0457
4 .0562 .0639
5 .0607 .0816
6 .0738 .0964
7 .0655 .1062
8 .0661 .1096

Now consider the sequence of random variables Y = Z/2t+1, the proportions

of A genes in successive generations.
It will be shown that Yttends to a limit Y as t -+ oo, and some of the properties
of Y obtained.
A recurrence relation can be derived for the second moments of the Zt about
the origin as follows: let P(z,t) = Pr(Zt = z),

He(t) = 2 x2P(x, t)
=O 0
t 2
=x y(2X

= ]
P(y,t - 1) X2y

2= P(yt - 1) 4(2
2y 1I1)
+ - --
2(H; -)+( 2-^l )82( -)

A mathematicalstudy of thefounderprincipleof evolutionarygenetics 123

The step from the third to the fourth line follows from the fact that the second
summationis the second moment about zero of a binomial distributionwith
n = 2+, p = y/2t. On writing 4 = u2 + ,u2 a recurrencerelationfor the var-
iancesof Z, is obtained
82(t) = - 1 2(t-1) + 2t-.

If v2(t) = #2(t)/4t+l denotesthe variancesof the Ytthey satisfytherecurrencerela-

(11) v2(t)= v2(t- 1) +
V-4T ~- v2(t 1) )

Since the variancesof all distributionson [0,1] are boundedabove by 1/4, (11
shows that the sequence tends monotonically, as t -> oo to a limit 1/4.
On writing(11) in the form
I I 1
( V2(t)) ()(--2(t-))
an explicit solution can be obtainedfor any t,

(--.(,): (1_4) (,-)..( __ ) -(4 0(0)).

More lengthy algebraleads to the following recurrencerelation for the fourth
{/IV 1 I 2t 3 1\t
V4(t) = )

d2) +
(,-,){~) )_ -() ) T ).
Withinitial values v2(0) = v4(0)=0, computationusing (11) and (12) leads to the
(13) v2 = 0.105606, V4= 0.020182.
For everyk,
V2k(t) = ( Yt - )

-tPr (Yt-1 = q) 2 Yt-=

>_ Pr(y,t = ) (?-

= V20(t-1),

on applyingJensen'stheoremto the convex function {(Yt- )2k Yt-1=t }, and

then using the symmetryof Yt-1 about ?. Hencethe sequencev2k(t) is increasing
and it is bounded above by (1/2)2k.Hencethe momentsequencesof the Yttend to
a limiting sequenceand since this must be the moment sequenceof a bounded
random variable,it defines it uniquely, and the convergenceof the sequence
{Yt} follows from the second limit theorem of the probabilitycalculus. (See
e.g. Rao and Kendall (1950)).Alternatively,{&Yt| Yt_-=I Yt-} = Yt-1 and so
{Yt} is a martingale,and the fact that its random variables are bounded is
easily enough seen to ensureconvergenceby the martingaleconvergencetheorem
(Doob, 1953,Chapter7).
In this paragraphand the next I obtain upperand lower boundsfor the proba-
bility of ultimatehomozygosity,showingin particularthat it is less than one. In
the presentproblem, actual computationfor the early generationsfollowed by
numerical extrapolation enables the exact value to be calculatedaccurately,
but the methods of obtainingthe bounds are of interest,and may be of value in
parallel studies, since it is clearly importantto know whetherthe probability
of absorption is bounded away from one. The coefficientof kurtosis of Y is
P2 = 1.809738.Hence using the generalisationof Tchebychef'sinequalityquoted
e.g. by Cram6r(1946,p. 256)

Pr Pry( | - 1.5385997)

(P2- 1)/{(1.5385992 - 1)2 + P2- 1}

= 0.3022.

The probabilitythat a given allele, say A, will be fixed is less than half this, i.e.
Let yt be the probabilitythat the populationbecomeshomozygousat exactly
the tth generationconditionalon it being heterozygousat the (t - 1)th, y, the
probability that it becomes homozygous at or before the tth generation,and
y = lim, . Vtthat it ultimatelybecomes homozygous. The chance that fixation
will occur precisely at time t can be shown to be greatestwhen Ft-_ contains
only one representativeof one of the alleles,and least when they are presentin
equal numbers.Hence
1 )t 2t (1 )t 2t+1

^(~~~~~-a'^ ))"-
A mathematicalstudy of thefounderprincipleof evolutionarygenetics 125

Supposethat for some k, yk is known, then

Y= Yk + (1 - yk)Yk+ + (1 - Y)(l - Yk+I)7k+2 +

>=Y + -)
(1 )k+i
_- 1 )\ (

(14) ( 1 k+2

Y-k + (Y) [ ) 1 1 -

By computation,the probabilitiesthat a givenallele, say A will be fixedby the kth

generationhavebeenobtainedup to k = 5, and aregivenin TableIV.

Probabilitiesof the fixation of A after t generationsof randommating, for the
k 1 2 3 4 5

i Yk .062500 .088997 .099550 .103808 .105536

Takingk = 5 in (14) leads to

1 y > 0.105598,

whichin the presentcase is only slightlylargerthan I 75. Using the 62 technique

(Aitken, 1926) a numerical approximationto ly may be obtained from the
terms given in Table IV. Applying the method to I72, i73 and I74 gives
Iy = 0.10669, and applying it to I73, I74 and Iy5 gives Iy = 0.10672, which
is thereforeprobably correct to 5 decimal places. Acceptingthis the moments
of Y conditionalon absorptionnot having taken place may be calculatedfrom
(10) and (13),
t2 = 0.06643, r/4 = 0.00982, P2 = 2.23.

For a populationof 2t individualswhichhas evolved through t generationsof

random mating at constant size, the probabilityof fixation is approximately
1-(1-(1/2)t+1)' (Moran, 1962, Chapter 4), and this approaches zero very
quickly as t increases.

4. A fullystochasticmodel
A simplefully stochasticmodel is obtainedby lettingthe numberof offspring
of each individual be, not a constant, but a Poisson variable. Bartlett (1937,
Formula(7b))obtainedthe variancesof the numbersof heterozygotesin successive
generations,(without conditioning on the population as a whole remaining
non-extinct).For the case where(i) the Poissonmeanis unityand hencethe mean
populationsize is constant,(ii) the numberof generationssufficientlylargefor the
probabilitythat the heterozygousoffspringof a given individualwill not have
been eliminatedto be given by the asympoticformula derivede.g. by Harris
(1963, p. 18),Formula 9.5), and (iii) the founder population so large that the
chance of completeextinctionis negligible,Bartlettalso showedhow the proba-
bility that the population should consist entirely of homozygotes could be
In the remainderof this sectionI presentsome numericalvalues relatingto the
results of three generationsof mating,for a populationinitiatedby a single in-
dividualand havinga mean rate of increaseof 2, and for a populationinitiated
by 8 individuals,and having a mean rate of increaseof unity. If the numberof
offspringof each individualis a Poisson variablewith mean 2, and the offspring
of a heterozygoteare AA, Aa, aa with probabilities1/4, 1/2, 1/4. The trivariate
stochasticprocessgivingthe numbersof the threetypesin successivegenerationsis
a multi-type Galton-Watson process (Harris, 1963, Ch. 2) with generating

f '(S, S2, S3)= exp2(sl - 1)

f2(sl,s2,s3) = exp2 s + + 3-

f3 (s1, s2,s3) = exp2s3- 1).

Taking the generatingfunction for Fo as s2, that for Ft may be obtainedby

multivariatefunctionaliteration.Fromit, the probabilitiesthat variouscombina-
tions of classes will have no representativesmay be computed.The probability
of completeextinctionturnsout to be 0.192975.On multiplyingup the remaining
probabilities,the probabilitythat a population,given that it is still in existence
after three generations,consists entirelyof AA's, or entirely of homozygotes,
may be calculated.The comparablestationarypopulationis obtainedby taking
the mean number of offspringas one instead of two, and startingwith eight
heterozygotes.In this case the chanceof total extinctionin F3 is much smaller,
0.023558.In Table V a numberof probabilitiesrelatingto the F3's of various
models consideredare collected together.
A mathematicalstudyof thefounderprincipleof evolutionarygenetics 127

I am gratefulto Mr. J. G. Skellamfor severalhelpfulsuggestionsmade in the
course of this work, and to Mr. K. Lakhaniand Mr. D. Spaldingfor assistance
in computation.


Some fixation and elimination probabilitiesfor variousmodelsconsidered.For

stochastic growth models probabilities are conditionalon complete extinction
not having occurred.

Probabilitythat F3 consistsentirelyof:
(i) AA's (ii) homozygotes
Deterministicreproduction 0.0838 0.4835
Stochasticreproduction 0.1580 0.4555

Deterministicreproduction 0.0013 0.3436
Stochasticreproduction 0.0645 0.3222

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