182 Population genetics and Markov chains (a) Without doing any calculations, is this a regular Markov chain? Why? (b) If the answer to (a) is yes, compute the equilibrium probability distribution p. (c) If X0 = 3, what is the eventual probability that the position of the particle is 3? 19. In the Markov chain model of random mating with mutation in a population of size .V, find P if ai = x2 - « ¥■ 0. Given an arbitrary initial probability distribution p(0), find pfl) and deduce that the stationary distribution is attained in one generation. 20. What will happen in the Markov chain model of random mating with mutation if a, ^ 0 but a2 = 0? Population growth I: birth and death processes 9.1 INTRODUCTION j ! It is clearly desirable that governments and some businesses be able to predict I future human population numbers. Not only are the total numbers of male t and female individuals of interest but also the numbers in certain categories | such as age groups. The subject which deals with population numbers and I movements is called demography. Some of the data of concern to human demographers is obtained from our ifiUing out census forms. The type of data is exemplified by that in Tables 9.1 land 9.2, In Tabic 9.1 is given the total population of Australia at various times since 1881 and Table 9.2 contains some data on births and deaths and their ■rates. Notice the drastic fall in the birth rate in the last few decades compared With an almost steady death rate. Table 9.1 Time Population of Australia (thousands)* 3 April 1881 2250.2 5 April 1891 3 177.8 31 March 1901 3 773.8 3 April 1911 4455.0 4 April 1921 5435.7 30 June 1933 6629.8 30 June 1947 7 579.4 30 June 1954 8 986.5 30 June 1961 10548.3 30 June 1966 11599.5 30 June 197! 12937.2 30 June 1979 14417.2 30 Juns 1981 14923.3 ♦Obtained from Cameron (1982} and Austral Bureau of Statistics. 184 Birth and death processes Table 9.2 Annual (average) number Annual rates per thousand Time period Births Deaths Births Deaths 1956-60 222459 86488 22.59 8.78 1961-65 232 952 95465 21.34 8.75 1964-70 240325 107 263 19,95 8.90 1971-75 253438 111216 18.99 8.32 1976 227810 112662 16.37 8.10 1977 226291 108 790 16.08 7.73 1978 224 181 108425 15.73 7.61 Deterministic model An accurate mathematical model for the growth of a population would be a very useful thing to have. There is a substantial literature on various models, as exemplified by the books of Bartlett (I960), Kcyfitz (1968), Pollard (1973) and Ludwig (1978). A first division of such models is into deterministic versus stochastic ones. In the former category there are no chance effects. Let N(t) be the population size at time t>0 and assume that the initial population size W(0) > 0 is given. The number of individuals at t is a non-negative integer, but it is convenient to assume that Nit) is a differentiable function of time. A simple differential equation for A' is obtained by letting there be bAt births and dAt deaths per individual in (f, t + At] where 6, d ^ 0 are the per capita birth and death rates. Then N(t + At) = N(t) + N(l)bAt - N(t)dAt and it follows, upon rearranging and taking the limit At -»0, that d.V cr = {b~d)N, t>0. This differential equation is called the Malthusian growth law (after Thomas Malthus, whose essay on population appeared in 1798). Its solution is |_iV(l) = N{oy-m, and once we specify JV(0) the population size N(t) is determined for all r > 0. Three qualitatively different behaviours are possible, depending on the relative magnitudes of 6 and d. These are illustrated in Fig. 9.1. It is seen that Itm N(t) • 0, b d (exponen tial growth). Simple Poisson processes 18S / b>d Figure 9.1 Population size as a function of lime for various relative magnitudes of the birth and death rates in the Malthusian growth model. Experience tells us that the times of occurrence of births and deaths are not predictable in real populations. Hence the population sizes iV = {N{l), t> 0} constitute a random process. As observed above, the number of individuals is a non-negative integer so N is a random process with a discrete stale space {0,1,2,...} and a continuous parameter set {t»0}. The models we will consider do not contain very many elements of reality. They are nevertheless interesting because they may be solved exactly and provide a starting point for more complicated models. 9.2 SIMPLE POISSON PROCESSES The random processes discussed in this section are of fundamental importance even though, as will be seen, their use as population growth models is very limited. The following process has a different parameterization from that defined in Chapter 3. Definition A collection of random variables N = {A(r), r > 0} is called a simple Poisson process with intensity J. if the following hold: (I) A'(0) = 0. (ii) For any collection of times 0 «S t0 < t ,<...< r„_ i < t„ < the random variables A'(tt) - N(lk _k = 1,2,..., n, are mutually independent. (iii) For any pair of times OsStj < f2, the random variable A'(i2) —/V^) is Poisson distributed with parameter X(/2 - f,). Condition (i) is a convenient initialization. The quantity ANk — fV(tk) - N(tk-1) is the change or increment in the process in the time interval 186 Birth and death processes ('k-i> fJ- Condition (ii) says that the increments in disjoint (non-overlappjng) time intervals are independent. Condition (iii) gives the probability law of the increments. Then Markov chains in continuous time 187 Pr{Jr(t2)-W(t1) = li} = q(t2-tijye-*"- k = 0,l,2,... and in particular, choosing tL = 0 and t2 = r>0 we have, since W(0)-0. fe = 0,l,2... Pr{JV(ŕ) = ŕ) (9.1) The mean and variance of N(t) are therefore E(N((f) = yax(N{t)) = Xt. Sample paths What does a typical realization of a simple Poisson process look like? To get some insight, let Af be a very small time increment and consider the increment &N(t)-N(t + &t)-N(t). The probability law of this increment is Pr {AA'(t) = k] 1 - Mi + o(A£), it = 0 Mr + o(Ar), k-1 o(Aí), k >Z (9.2) We see therefore that when Ar is very small, N(t + Ar) is most likely to be the same as A'(r), with probability iAt that it is one larger, and there is a negligible chance that it differs by more than one from N(t). We may conclude that sample paths are right-continuous step functions with discontinuities of magnitude unity - sec Fig. 9.2. Note that equation (9.2) can be used as a definition and the probability law of the increments derived from it-see Fxercise 2. The simple Poisson process is called simple because all of its jumps have the same magnitude - unity in the above case. This contrasts with compound Poisson processes in which jumps may be any of several magnitudes (see for example Parzen, 1962). To relate the Poisson process to a growth model wc imagine that each time a new individual is born, N(t) jumps up by unity. Thus N(t) records the number of births in (0,t], i.e. up to and including time t and {N(t), t>0} may be regarded as a birth process, ff in Fig. 9.2 we place a cross on the f-axis at each N(t| Figure- 9.2 Two representative sample paths for a simple Poisson process. The mean value function At is also indicated. jump of W(t) we obtain a collection of points. Thus there is a close relationship between the simple Poisson processes of this section and the Poisson point processes of Section 3.4. This is elaborated on in the exercises. Poisson processes, though dearly limited as population growth models, find many other applications. Some were mentioned in Chapter 3. Furthermore they may result when several sparse point processes, not themselves Poisson, are pooled together. This makes them useful in diverse areas (TuckweU, 1981). 9.3 MARKOV CHAINS IN CONTINUOUS TIMF In Chapter 8 we encountered Markov random processes which take on discrete values and have a discrete parameter set. Markov processes of that kind are called Markov chains. However, Markov processes in continuous time and with discrete state space are also called Markov chains. Usually we mention that they have continuous parameter set when we refer to them in order to distinguish them from the former kind of process. If X = [X(i], t S 0} is such a process, the Markov properly may be written, with t0 0} with initial value lV(0) = no>0, subject to the evolutionary laws (9.4)-(9.6). Define the transition probabilities p„(l) = Pr(JV(t) = «|N(0) = no}, B0>0, t>0, and note that these arc stationary. Our aim is first to find equations governin g the evolution in time of p, and then to solve them. To obtain a differential equation for p„ we seek a relation between p„(t) and P,(t -+ At). If N(t + At) = n>n0 then, ignoring the possibility of more than one birth, we must have W) = \n and no births in (t,l + At], \n - 1 and one birth in (t,t +- At]. Dropping reference to the initial state, the law of total probability gives Pr {N(t + At) •= n] = Pr {JV(t + At) = n|JV(t) - "} x Pr{JV(t) = n} + Pr{JV(f + Ar) = n|N(t) = n-l} xPr{AT(i) = n-l}. <9-7) In symbols this is written, using (9.4) and (9.5), p„(t + At) = (1 - AnAf)p„(t) I* ■ l)Atp„ - ,(t) + o(At), n > na. 190 Birth and death processes This rearranges to pjjt + &t)-pjjt) A[(»-l)p,-1(t)-«p,(t)] + o(Ar) At ■ At Taking the limit Ar->0 we obtain the required equation dp, it = 4.(n - 1)p, n = na + 1, n0 + 2,. since o(A[)/A( -»0 as At -> 0 by definition. When n - n0 there is no possibility that the population was n0- 1 so (9.7) becomes Pr {N(t + At) = n0} - Pr {JV(< + At) = n„ | AT(f) = fl0} Pr {JV(t) = »„} which leads to IT"-*1* (9.9) Initial conditions Equations (9.8) and (9.9) are first-order differential equations in time. To solve them the values of p„(0) are needed and since an initial population of n0 individuals was assumed, we have P„(0) = fl, n = n0, (0, n > n„. Solutions of the differential-difference equations The solution of (9.9) with initial value unity is Armed with this knowledge of pn(, we can now find p„a + 1. The differential equation (9.8) is, with n = n0 + 1, dr (9.10) This will be recognized as a linear first-order differential equation in standard form (see any first-year calculus text). Its integrating factor is eM"°+111 and in Exercise 10 it is shown that p„o + 1(0 = "o?"""n'(i e-*^. (9.11) Having obtained pBo+1 we can solve the equation for p„0+2, etc. In general we obtain for the probability that there have been a total number of* births at t, Pro **M = h„ + k - 1 k = 0,1,1. (9.12) as will be verified in Exercise 11. The Yule process 191 It can be seen that p„„(r) is an exponentially decaying function of time. If we define as the time of the first birth and observe that pB(r) is the probability of no birth in (0,1] wc get Pr{T, >t}=e-'h°', or equivalenlly Pr{r1 of failure at each trial. Let the random variable X, be the number of trials up to and including the rth success, r = 1,2.....Then it is easily seen that the distribution of Xr is given by -o fc = r,r+ l,r + 2,. (9.15) the smallest possible value ofjf, being ?■ since there must be at least r (rials to obtain r successes. The mean and variance of Xr are found to be (see Exercise 13), E(JQ = Var(XJ = We now put j — n0 + k in (9.12) to get '/-I Pr{AT(r) = j} = This is seen to be a negative binomial distribution as in (9.15) with parameters r = n0, p = e~",q = 1 — e~u. Thus we quickly see that the mean and variance of the population in the Yule process arc E(N(t)) = n0e>' Vai(W(r)) = Ho 1 individuals to start with, since individuals act independently, Pr {population is unchanged at t) = Pr{n0 failures in n0 trials} = {e~xJa = e~Xno', this being an exact result. Also, when n0 ■ 1 let the mean and variance of the population be denoted by /j, and o\ which are given by px=e"'(i-«■■")• When n0 > 1 we may at any time divide the population into n0 groups, those in each group being descendants of one of the original individuals. The number in each group is a random variable and it follows that the population at time f is the sum of n0 independent and identically distributed random variables each having mean /z, and variance a\. By the central limit theorem we see that for large ;i0 and any t, the random variable N(t) is approximately normal with mean n0pt and variance n0a\. Hence we may estimate with reasonable accuracy the probability that the population lies within prescribed limits (see exercises). 9.6 A SIMPLE DEATH PROCESS In this rather macabre continuous time Markov chain, individuals persist only until they die and there are no replacements. The assumptions are similar to A simple death process 195 those in the birth process of the previous two sections, but now each individual, if still alive at time t, is removed in (t,t + AQ with probability pAt + o(Af). Again we are interested in finding the transition probabilities p„(l) = Pr {N(t) - n\N(0) = n0], n = »0t n0 - 1,..., 2,1,0. We could proceed via differential-difference equations for />„ but there is a more expeditious method. The case of one individual Let us assume n0 = I. Now p^t) is the probability that this single individual is still alive at I and we see that Pl(t + At) = p,(0(l - pAt) + o(At) (9.16) since 1 — ^Af is the probability that the individual did not die in (t,t + At]. From (9.16) it quickly follows that dp, t>0. The solution with initial value p,(0) = 1 is just The initial population size is A'(0) = n0 > 1 If there are n0 individuals at t = 0, the number alive at t is a binomial random variable with parameters n0 and p,(t). Therefore we have immediately n = n0, no-l,...,l,0. Also E(N(t)) = n0e-'u, which corresponds to a Malthusian growth law with d - p and b = 0, and Var(JV(t)) = n0e-"(l -«-<"). Extinction In this pure death process the population either remains constant or it decreases. It may eventually reach zero in which case we say that the population has gone extinct. The probability that the population is extinct at time f is Pr{JV(0-0|JV(0) = Ho}=(l-e T>^1 as t-»oo. 196 Birth and death processes 1.0 Prob. exrincl- 0.5 Figure 9.5 Probabilities that the population is extinct at t, versus t for various initial populations with n = 0.5. Thus extinction is inevitable in this model. In Fig. 9.5 are shown the probabilities of extinction versus time for various initial populations. 9.7 SIMPLE BIRTH AND DEATH PROCESS We now combine the ideas of the Yule process and the simple death process of the previous section. Let there be n0 individuals initially and N(t) at time t. In [t,t + At] an individual has an offspring with probability AAt + o(Af) and dies with probability nAt + o(At). Using the same kind of reasoning as in Section 9.4 for the population birth probabilities we find that Pr {one birth in (t, r + At] | AT(t) = n} = XnAt + o(At) Pr {one death in (t, t + Ai]\N(t) = n} = finAt + o(At) Pr {no change in population size in (t, t + At]\N(t) - n} = 1 — {X + n)nAt + o(Ar). The ways to obtain a population size n at time t + At are, if n> 1, N{t) = n-\ and one birth in (t,l + At] N(t) = n and no change in (t, t + At] N(t) = n + 1 and one death in (t, t + At]. Hence pjf + At) = Pn-^Mn - l)At + p„(i)ri - (A + n)nAt\ + P»-iW/<(" + l)Ai + o(Af). Simple birth and death process 197 It quickly follows that = M.n - l)pn-1 - (* + (ti»P* + Mn + l)Pn +: R>1. If n = 0 we have simply and the initial conditions are P„(0) dpa dt (9.17) (9.18) • f'l, n = n0, ~[0, n#n„. The system of equations (9.17) and (9.18) cannot be solved recursively as could the equations for the simple birth (Yule) process as there is no place to get started. The probability generating function of N(t) By definition, the probability generating function of N(t) is <£(s,t)= £ pMf. n = 0 This can be shown (see Exercise 16) to satisfy the first-order partial differential equation dt os which is to be solved with the initial condition -JHs.O^s"0. (9-20) It may be shown (see, for example, Pollard, 1973; Bailey, 1964) and it will be verified in Exercise 17, that the solution of (9.19) and (9.20) is where Ás — n Ms)- s-1 (9.21) (9.22) The probability of extinction A few sample paths of the simple birth and death process are shown in Fig. 9.6. The state space is the set of all non-negative integers {(), 1,2,...} and the state 0 198 Birth and death processes N(t) Realization ol the extinction —*- 1 time Figure 9.6 Two representative sample paths of a birth and death process. Here N(0) = 6 and one path is shown on which the population goes extinct is clearly absorbing. A sample path may terminate at 0 which corresponds to extinction of the population. We can easily find the probability that extinction has occurred at or before time t from the probability generating function. This is just Pr {N(t) - 01 N(0) - n„} = p0(f) = 0(0, r). From (9.22) we have ij/(0) = ji and thence, from (9.21), a — fie k^p.. (9.23) When /. = p. the following expression is obtained by taking the appropriate limit in (9.23): fX kt + 1 X-ii. (9.24) In the limit t-»oo, p. we may still talk of the random variable T, the extinction time, However, we then have Pr{r <»}-(£)", so we must also have Clearly in these cases T has no finite moments and, because its probability mass is not all concentrated on (0, oo) we say it is not a 'proper' random variable. 9.8 MEAN AND VARIANCE FOR THE BIRTH AND DEATH PROCESS The expected number of individuals at time t is m(t) = £[/V(r)[rV(0) = no]= £ np„(t) = £ np„(t)- We will find a differential equation for m(t). We have dm A dp„ dr=„?,"^ and on substituting from the differential-difference equation (9.17) we get -JT = £ "M" _ 1 >P« - 1 ~ (>- + f)"Pn + f(» + 1)P. * 11 which rearranges to dm dt = /.[(»-l)V,+'K«- l)P.-i -U +P) I "2P« n-l »-1 "-1 +n £ (» +1)2/>„+1-/< £ ('i+!)/>„+,. 200 Birth and death processes A relabeling of indices with n' = n — 1 in sums involving p„_i and with n" = ii -r 1 in sums involving p„+ ( yields dm dt 1 In the first three sums here, terms from it, n', n" = 2 and onward cancel and leave — (X + ujp; + Xpl - npx. Thus dm dr : = - Wi + X £ "'P.--f I n"P»- n' = 0 v - 2 or simply dm (X — pi)m. With initial condition m(0) — n0 the solution is m(t)-nc,e'A-""7| This is the same as the deterministic result (Malthusian law) of Section 9.1 with the birth rate b replaced by I and the death rate d replaced by pi. The second moment of N(t), M(f)= £ n-p„(f) can be shown to satisfy d;\J — = 2(X-u)M + (l + u)M, M(0) = rc02, (9.25) as will be seen in Exercise 19. The variance of the population in the birth and death process may then be shown to be Vai (JV(() | iV(0) = «„) = «, (* + M) X fit. In the special case /. = p., Var(Af(f)|/V(0) = n0) = 2^n„t. An alternative method of finding the moments of N(t) is to use the moment generating function (sec Exercise 20). Exercises 201 Birth and death processes have recently become very important in studies of how ions move across cell membranes. In the simplest model there are just two states for an ion channel - open and closed. The channel slays in each state for an exponentially distributed time before making a transition to the other stale. It is hoped that a study of such continuous lime Markov chain models will elucidate the mechanisms by which molecules of the membrane interact with various drugs. For details of this fascinating application see Colquhoun and Hawkes (1977), Hille (1984) and Tuckwell (1988). REFERENCES Bailey, N.T.J. (1964). Tlte Elements of Stochastic Processes. Wiley, New York. Bartlett, M. S. (1960). Stochastic Population Models. Methuen, London. Cameron, R.J. (cd.) (1982). Year Book Australia. Australian Bureau of Statistics, Canberra. Colquhoun, D. and Hawkes, A.G. (1977). Relaxations and fluctuations of membrane currents that flow through drug operated channels. Proc. R. Soc. Land. B., 199, 231-62. Furry, W.H. (193 7). On fluctuation phenomena in the passage of high-energy electrons through lead. Phys. Rev., 52, 569-81. Hille, B. (1984). Ionic Channels of Excitable Membranes. Sinauer, Sunderland, Mass. Keyfitz, N. (1968). Introduction to the Mathematics of Populations. Addison-Wesley. Reading, Mass. Ludwig, D. (1978). Stochastic Papulation Jheories. Springer, New York, Parzen, E. (1962). Stochastic Processes. HoJden-Day, San Francisco. Pielou, E. C. (1969). An Introduction to Mathematical Ecology. Wiley, New York. Pollard, J.H, (1973). Mathematical Models for the Growth of Human Populations. Cambridge University Press, London. Tuckwell, H.C. (1981). Poisson processes in biology. In Stochastic Nonlinear Systems. Springer-Vcrlag, Berlin, pp. 162-71. Tuckwell, H.C. (1988). Stochastic Processes in the Newosciences. SIAM, Philadelphia. Yule, G.U. (1924). A mathematical theory of evolution based upon the conclusions of Dr J.C. Willis, F.R.S. Phil. Trans. Roy. Soc. Land. B., 213. 21-87. EXERCISES 1. Using the birth and death rates for 1966 given in Table 9.2 and the 1966 population of Australia given in Table 9.1, estimate the 1971 population, Compare with the actual population in 1971. Is the discrepancy in the direction you would expect? Why? 2. In a simple Poisson process, let p„(t)-Pr{N{l) = n\N{0)= 0}. Use the relations Pr{AiV(t) = fc} - 1 - Mr + o(At), XAt + o(Af), o(At), k = 0. k = l. k>2.