Evolution Basics: From Variation to Speciation, Part 2

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May 17, 2013 Tags: Genetics

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. In this post we examine how geographic barriers can arise that restrict the flow of alleles between populations, and how the founder effect can contribute to genetic differences for newly founded populations.


In yesterday’s post, we made a number of points worth summarizing here:

New alleles arise as unique events in individuals, but may become common in their population through various processes, including genetic drift and natural selection.

New alleles, should they become common in a population, may shift the average characteristics of that population.

If exchange of alleles between two populations of the same species is blocked or reduced, then average characteristics of the two populations may diverge from each other.

Given enough time, these processes may lead to differences between the two groups that are significant enough to establish them as distinct species.

With these points in hand, we are now ready to have a closer look at the various ways that genetic exchange between populations can be reduced or eliminated. We’ll start by looking at the simplest case, that of complete geographic isolation.

Geographic barriers

Geographic separation of two populations of the same species is a rapid and effective way of stopping the exchange of alleles between them. At the point of separation, the two populations are, of course, fully capable of interbreeding biologically, but prevented from doing so by physical separation. One example of geographic isolation leading to speciation that we have discussed already is the various species of finches that Darwin observed on the Galapagos islands off the coast of South America. The original finch population of the Galapagos was founded by a small group of birds that arrived on the islands from the South American mainland, most likely blown there during a storm. These birds, as a population, were biologically cut off from the source population on the mainland, since the Galapagos are hundreds of miles offshore. Once separated from the larger population, the smaller “founding” group no longer received new alleles from it, nor passed new alleles that arose back to it. Despite being two populations of the same species, they were now genetically sealed off from one another, and differences in allele frequencies began to accrue between them. These differences lead to changes in average characteristics over time, and ultimately the formation of a new species.

The founder effect

In many cases, this process of accumulating differences gets a head start right at the point of separation, due to a phenomenon known as the “founder effect.” A small founding population is very often a non-representative sample of the genetic diversity of the source population. For example, consider a hypothetical population with 36 individuals. Each individual carries two alleles of a given gene, and there are four different alleles of this gene in the population (represented by the four colors):

Note that the yellow allele is the most common, followed by the blue allele. The purple and red alleles are comparatively uncommon in this population. In fact, their rarity means that it would be unlikely for this population to have an individual with two red alleles in the next generation, for example. In order to have such an individual, two parents who were “carriers” of the red allele would have to mate, and both pass the red allele on to their offspring. This is not impossible, but in this population it would be unlikely.

Now suppose that a few members of this population start a new population on an isolated island. Only six individuals start the new population, and the alleles that they carry are not a perfect representation of the allele frequencies of the larger, source population (approximate frequencies are shown for the source population and the new “founding” population):

We can see that for the common alleles, the yellow allele has increased in frequency, and the blue allele has decreased in frequency. Despite these differences, the common alleles are reasonably similar in frequency to the source population. The rare alleles, however, have had larger shifts: the red allele is now much more common in the newly founded population, and the purple allele has been lost entirely.

Now, these changes are subtle, and changes for one gene would not likely be enough to precipitate a speciation event between the two populations. These sorts of changes could, however, be significant in the long run. Consider the red allele in the newly founded population. As this population increases in number, it will be much more likely to have individuals with two red alleles crop up in this population than in the original source population. If this genetic combination has a selective advantage, then natural selection will be able to act on it in the new population. In the source population, however, this genetic combination is much more unlikely, largely preventing natural selection from acting on this allele combination. Over time, the red allele could come to dominate the new population, but remain rare in the source population. Additionally, it is likely that the environment will be somewhat different for these two populations, leading to differences in natural selection. What might be a winning allele combination for the mainland might not be as suitable for the island environment, and vice versa.  A second issue is that the newly founded population, like any small population, is much more subject to genetic drift than the larger source population. The red allele might increase in frequency in the new population simply due to chance alone, and not due to the action of natural selection.

Taken together, these mechanisms can put the two populations onto different trajectories, and, over time, lead to significant differences between them. Given enough time, the differences that accrue may be enough to keep the populations separate even if they should come into contact again. If so, most biologists would classify the two populations as distinct species. While this is easier to do for species that have been separated for a long time and have accumulated significant differences (and as such no longer interbreed, or interbreed only rarely), it is notoriously difficult for more recently separated populations that are not yet fully reproductively isolated. As such, what constitutes a “true species” instead of merely a “subspecies” or “variety” is often a subject for discussion and debate between scientists, and indeed was a topic that Darwin devoted much time to in his works. The ambiguity arises out of the mechanism of slow, gradual divergence of species from a common ancestral population.

Not just differences

Given the foregoing conversation, you might be under the impression that the differences between species are the main issue. Certainly differences are vital, since ultimately it will be the accumulation of differences that will lead to new species being formed. It is important to remember, however, that for closely related species, these differences will be small in number compared to the features that remain unchanged for both groups. At the genetic level, we can illustrate this by considering a gene for which there is only one allele in the source population – perhaps an allele that has been under natural selection and has displaced all other alleles. The newly founded population will inherit only this allele, despite the small sample size of the founding group, since there are no other variants in the population. The result is that the island population will be identical to the mainland population for this trait until a mutation event (in either population) even allows for the possibility of change. For most traits, mutations will not arise, since the DNA copying mechanism is highly accurate. This will keep most traits between the two populations constant. The pattern we expect for recently diverged species, then, is one of mostly identical characteristics overlaid with only a smattering of differences. You might recall that it was exactly this pattern in its biogeographical context that caused Darwin to reflect on the possibility that species may not be stable:

“The most striking and important fact for us in regard to the inhabitants of islands, is their affinity to those of the nearest mainland, without being actually the same species. Numerous instances could be given of this fact. I will give only one, that of the Galapagos Archipelago, situated under the equator, between 500 and 600 miles from the shores of South America. Here almost every product of the land and water bears the unmistakeable stamp of the American continent. There are twenty-six land birds, and twenty-five of these are ranked by Mr. Gould as distinct species, supposed to have been created here; yet the close affinity of most of these birds to American species in every character, in their habits, gestures, and tones of voice, was manifest.”

Note that it was the combined pattern of overwhelming “affinities” (distinctive features in common) with subtle, but significant differences that Darwin observed. The birds in question were distinct species, but they retained the “unmistakeable stamp” of their heritage. It was these observations that led Darwin to hypothesize that these finch species were the product of a speciation event brought on through geographic isolation.

While geographic isolation is a straightforward situation that can lead to genetic barriers and the formation of new species, speciation can also occur without full separation. In the next post in this series, we’ll examine a case of speciation with only a partial geographic (and genetic) barrier – a case that will also demonstrate the “fuzziness” of what exactly constitutes a species.


Dennis Venema is Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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Roger A. Sawtelle - #80919

June 12th 2013


Let me try to explain what is going on from my perspective. 

Darwinian theory describes what is going on with evolution, however it largely fails to explain how and why it works.  It has the Variation of evolution down pretty well, but not Natural Selection which is the key.  It is a half truth, which is the enemy of the whole truth.  It is poor science, which is the enemy of good science.

Darwinism is more like a manual for driving a car, which is good and helpful, rather than a technical explanation which explains us how the engine and transmission works, which is the real scientific basis of the automobile.  Maybe this is because Darwin based his thinking on the how-to of agricultural breeding of plants and animals.

Ecology is the theory of how plants and animals develop naturally.  Darwinism is magical in that it does not explain how this happens.  If the universe is based on irrational magic, it does not need God, Who is rational.  

Thus Darwinism is just a semi-superficial description of how evolution happens.  A mathematical formula is not an explanation.  Ecology is the explanation.     

Lou Jost - #80922

June 12th 2013

I beg to differ. A word salad like this is not an explanation. An explanation of natural selection is,  for example, a mathematical proof that fitness controls the expected rate of change of  allele frequencies in a population. This is what population genetics provides, and which both you and GJDS refuse to even look at.

beaglelady - #80932

June 12th 2013

Lol!  Ever read The Jabberwocky, Lou?  

PNG - #80935

June 12th 2013

Alice comes to mind more and more as I watch these exchanges. Curioser and curioser.

beaglelady - #80942

June 12th 2013

Exactly, PNG.

‘When I use a word,’ Humpty Dumpty said, in a rather scornful tone, ‘it means just what I choose it to mean, neither more nor less.’

PNG - #80937

June 12th 2013

Lou, could you give the ref. for the Wagner paper, if there is one different from the PLOS Comp Biol ref you gave above. Thanks.

Lou Jost - #80943

June 12th 2013

PNG, the JSTOR link for the other paper, “The role of randomness in Darwinian evolution”, is


but you can find it (and other interesting things) free at Wagner’s university website:


Roger A. Sawtelle - #80974

June 12th 2013

Lou wrote:

fitness controls the expected rate of change

If fitness controls something, it must be an agent.  Is it? 

If it is, how does it control the expected rate of change of alleles? 

Lou Jost - #80979

June 12th 2013

Thanks for the good question. Let me explain the relation between natural selection and fitness by a specific example.

Suppose we have organisms with non-overlapping generations, to make the math easier. And suppose they are haploid (just one set of chromosomes) to simplify the math even more. Maybe an annual moss. Suppose at a locus there are two alleles, X and Y. Suppose we measure the average number of viable spores produced by organisms with allele X, and they make 4 spores on average. Let’s say organisms carrying allele Y make 1 spore on the average (maybe Allele X improves nitrogen uptake compared to Allele Y, accounting for the increased reproductive success of bearers of allele X). Those numbers, multiplied by the probability that the individual survives to make its spores, are the fitnesses of the alleles. To simplify things, I assume that individuals, once sprouted, always survive to adulthood and make their spores.

Suppose at the moment there are 2000 organisms with Allele X, and 8000 organisms with Allele Y.  Thus the relative proportion of Allele X in the population is 2000/10000 = 0.2. How much will the proportion of Allele X change in the next generation?

The number of spores carrying Allele X equals 2000 * 4 =  8000. The number of spores carrying Allele Y equals 8000*1 = 8000. So now in the next generation, any given young plant would have an equal chance of coming from a spore carrying Allele X or a spore carrying Allele Y. The frequency of Allele X in this generation will therefore increase to about 0.5 (8000/16000) from its previous value of 0.2. It will continue to increase in each subsequent generation, on the average.

The expected rate of change in allele frequency per generation was determined by its relative fitness, the reproductive success rate of the organisms carrying the allele relative to that of organisms carrying the other allele (or relative to the average reproductive success rate of individuals in the population). It is simple math, nothing mysterious or magical, and this is the essence of natural selection. For diploid organisms the math is just slightly more complicated. For simple situations we can derive formulas for how the frequency of a given allele is expected to change as a function of time, and what its equilibrium frequency will be after a long time has passed.

I have ignored the random component of generation-to-generation frequency change in this simple example. Even if there are exactly equal numbers of spores for Allele X and Allele Y, as in this example, it is extremely unlikely that the actual number of baby plants would be split exactly evenly between the two types. It is a binomial sampling process (drawing from the cloud of 16000 spores) with variance Npq where N is population size, p is frequency of Allele X, and q is frequency of allele Y. The variance is negligible when N is large, but not when N is small. This is the source of “genetic drift”, and it too is nothing mysterious and can be quantified exactly.

GJDS - #80982

June 12th 2013

Even in this simplified ‘example’ you are showing the ‘kindergarten’ class something that has been understood for (almost) COUNTLESS generations - which is the capacity for bio-species of variation and adapatation to the particular ecological niche, and the interpedendence therein. And selective breeding has been praccticed for a long time (note axiomatic, not predictive).

Puting numbers for a statistical treatment is just that, and claiming something else is simply ‘slight of hand’.

I will illustrate with a simple but scientific example - the structure of benzene was a mystery and myths had probably been circulated (including dreams of snake swallowing its tail) - but along comes the (real) theory of covalent bonding, and a mountain of measurements to determine its bond lengths, electron density, delocalised nature, and indeed everything down to the wave function and exact bond lengths - and virtually any predictive power needed for aromatic structures in any system (including those in the bio-world).

You concede that ‘evolution’ is in need of improvement (which is probably the first sensible thing you have said until now) and yet you will stubbornly refuse to provide an example of the certainty you endlessly claim in your myriad of posts - my above example is based on the theory of chemical bonding, which is defined as an exchange of electron density between atoms, and in the case of benzene, the hybridization of carbon, the sigma bonds with hydrogen, and the delocalised pi bonds. This theory has been described (scemantics), has been stated mathematically (the wave equation), has been applied in an endless number of cases, and has provided the foundation for virtually all scientific work involving chemical compounds and structures (all of nature).

Since you make the gradiose claims re Darwin, just give a paragraph describing the theory of natural selection (not variations withing a given ecosystem) expound it so that even your simpleton example may show us the workings of this theory - and formation of new species no less.

Populations can be treated statistically by building a data base and treating it using given statistics - this has been demonstrated in a paper in Nature - you may prefer a treatment using your allele frequency, of others may prefer a data base of reproductive rates, historical trends, death, births, migrations and so on. Provided the data base is sound, the statistical treatment can be found for the treatment required. As a sicentist, you should understand that and admit to it.

Lou Jost - #80989

June 12th 2013

“axiomatic, not predictive” No, it is predictive. We measure the fitness first, and with this in hand we predict the future trajectory of the population.

GJDS - #81018

June 13th 2013

Lou, I will give you free business advice that will make you an overnight billionaire; if you can do what you claim, predict fitness from whatever manipulation you use, just bring your predictive mathematical model to breeders of race horses - once you provide them with fitness for race horses to win, they will drown you with billions of dollars - just how cool would that be?

Don’t be shy, just ring up any breeder of race horses and you will be the ultimate winner - I am not kidding you!!!!

beaglelady - #81055

June 14th 2013

Horse breeders already breed Thoroughbreds for speed and stamina. Quarter horses are bred for speed at short distances.    If  a trait is at all heritable, breeders can select for that trait.   Breeders don’t even need to know squat about genes and inheritance;  as a matter of fact,  people  have been selecting for desired traits in plants and animals  long before they knew a thing about genetics.   So yes, you can breed a faster race horse.  And so can other breeders.  However, there are other factors that determine whether your horse will win, so it’s still a horse race.   

GJDS - #81057

June 14th 2013

Missing the point of these discussions seems a talent by some of you lot - but I will eventually get used to it, so I will try again - yes, I made the point by using selective breeding when this ‘discussion’ started. The additional point is that of predicting the fitness (for whatever purpose, but the example of racing horses is humorous and involves a lot of money). THUS, if Lou, or you, or anyone, has a scientificaly developed program, based on a solid ‘law of science’ that is mathematically constructed to PREDICT such fitness, it could be worth a LOT of money. My point has always been that natural selection has NEVER been such a scientific law, while your friend Lou states that it is (as he has said - but I will let the fruitfly obsess with Lou’s or my quotes). THUS no maths that would scientifically show fittness via natural selection - I really really hope my remarks are clear and not considered insulting or non-scientific. 

beaglelady - #81059

June 14th 2013

Huh? I was simply pointing out that breeders can and do select for faster horses.  They all do. And then the horses compete against each other.  There is a lot of money involved.   A top sire can earn millions of dollars for his owner in stud fees.  But there are many, many, many, many  factors that determine which horses in a race finish in the money.   So your “challenge” to Lou is too simplistic.  

beaglelady - #81064

June 14th 2013

I don’t know if this would qualify as a “law of science” to you, but plant and animal breeders do have  the “breeder’s equation.” Every heard of it?

Lou Jost - #80985

June 12th 2013

I pointed out that we can measure reproductive success objectively, in this case we can count the average number of spores produced by plants with either allele.

This number, which can be objectively measured, allows us to predict the expected values of allele frequencies for future generations. In particular, it shows the now-obvious fact that alleles which give an organism a reproductive advantage will  increase their relative frequency in the population, on the average, and the expected rate of increase per generation can be calculated if we know the relative fitnesses, as in my example.

That is all there is to the much-vilified process of natural selection. There is nothing to argue about here. It is inevitable.

This kind of example does not deal with speciation, which usually involves  multiple populations with leaky barriers between them. You can see my mathematical analysis of the process of genetic divergence between such populations in my article,

Jost, L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026.

That is not the traditional analysis; it applies some new mathematical concepts. For background on the relationship between diversity and differentiation measures, which is essential for understanding this problem, see:

Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88:2427-2439.

GJDS - #80986

June 12th 2013

Your statement “that is all to natural selection” should be taken up by others and I suspect (if anyone else believes this) no-one (least of all me) would bother (wasting/using my time) with this subject. I recommend an intorductory course in Phylosophy of Science (I have mentioned Rosenberg often enough on this site) - these scholars give Darwin a better ‘trot’ than you, and even show why his thinking had been taken up and proved popular (to summarise Rosenberg - Darwin removed teleology and purpose in nature). You will also find out why the semantic theory has proven so inadequate scientifically (and not because biology is a soft science, what ever that may mean), as (to summarise) it works for some models and does not work for others - a very sharp criticism of any scientifc theory.

Meanwhile send your papers to those who care to read them - perhaps the next step in this banal exchange is for me to send you my papers?

I have given this remark to the mega-monstrosity (fruit fly) and to you - show anyone (not only lucky me) that there is a scientific theory (not all that it is and what is axiomatic) termed natural selection - note I have shown you mine (chemical bonding), since you and beaglelady know who are real scientists, simply show me yours.

Lou Jost - #80987

June 12th 2013

You asked for me to ” show us the workings of this theory - and formation of new species no less” so I directed you to my analysis of the stochastic process underlying genetic divergence between subdivided populations. Hope you will see exactly what makes populations diverge, even in the absence of natural selection. That is an important point. But if you don’t want to learn about that, don’t read it.

GJDS - #80993

June 12th 2013

Crumbs - what is the point of these exchanges with you - now you set yourself as a teacher while ignoring a huge amount of thought and discussion on the thing that ‘just works for you’ - do you even understand what stochastic methods are? Teacher, learn something first before presuming so much.

GJDS - #80994

June 12th 2013

Just to ptove to beaglelady that I enjoy the fairy tales on this site (but not the tap dancing unless she serves that ale), I submit the following:

Humpty dumpty sat on his wall

Darwin sat next to him, before his fall,

Saying, “Humpty old son, can you now see it all?”


As humpty fell to the ground

Darwin, hearing a sound

Said, “Humpty, you unfit scoundrel,


Natural selection will

Put your bit and pieces

Together again.


(Note: Darwin had little patience

With all the king’s horses and all the king’s men)

Roger A. Sawtelle - #80997

June 13th 2013

Lou wrote:

I pointed out that we can measure reproductive success objectively, in this case we can count the average number of spores produced by plants with either allele.

The question is not measurement, but prediction.  One can predict and determine how far a object will travel by knowing forces and trajectory. 

One can only measure the reproductive success of a plant or animal through observation, that is we measure the productive success of a plant by measuring its reproduction.  We can predict future success from current success.  Very profound.      

Darwinism from The Origin claims to the status of the Newtonian natural sciences.  It is not, but this false understanding has distorted the scientific view of reality and life.  Of course Newton was wrong too about the nature of matter and energy, so this is a double error. 

Fitness is not a force like gravity.  Fitness is a quality, the quality of being fit, which is an adjective.  Therefore fitness is not a thing that can control anythiong.  Fitness is an idea or word salad to use a phrase.  As Popper stated some time ago, “survival of the fittest” is not a theory but a circular statement.   

Three Cheers for GJDS.  Thank you. 

beaglelady - #81003

June 13th 2013


Are you asking yourself just what kind of bizarre world you have wandered into?   LOL!

Lou Jost - #81004

June 13th 2013

Yes, and I am beginning to wonder where is the door….and can I lock it on my way out???

In my moss example, we could actually deduce the fitness of each allele from first principles, if we knew enough details. We could measure how much nitrogen it takes to make a spore, and how much additional nitrogen Allele X lets into the moss compared to Allele Y, and how much nitrogen there is in the average substrate. From this information we could actually estimate how many more spores would be produced by carriers of X compared to carriers of Y.  Thus we can, in principle, even deduce the fitness from first principles, and even if that is too hard to do in any particular case, we can still deduce the future trajectory of the population from independently-measured fitnesses. Just like Roger demands.

Roger thinks my example is not very profound, and I agree that natural selection is a very simple mathematical consequence of differential reproduction. So why does he deny it is predictive of the future trajectory of the system?

And I can’t even begin to figure out how to answer GJDS’s rants, which always point out how stupid and wrong I am, but never tell me what exactly is wrong…..

beaglelady - #81007

June 13th 2013

Roger’s main objective is to promote his book and ideas.   I think GJ just hates the idea of evolution. 

Lou Jost - #81010

June 13th 2013

I’d like to think that there must be some way to explain this so they would agree.

melanogaster - #81044

June 13th 2013

Silly man…

GJDS - #81012

June 13th 2013

Beaglelady must have her say, even though it is very rude to speak on my behalf - you poor souls - I criticise your prophet Darwin and off you go with your mindless chatter. But beaglelady seems oddly ignorant of what makes for good manners, so this self appointed commentator just goes on and on and on….! 

From a scientific perspective, I am probably showing more respect for Darwin’s contribution than any of you, but not the defference and adoration that you lot a bent on. An extremely complex ‘concept’ or whatever, is not a simple ‘something’ that can be treated using simple maths. Perhaps beaglelady with her online course in 101 evolution is the type of comfort that Lou needs as he sees rants behind every ‘verbal bush’.

I will again make the same statement for lou’s sake - just put your comments out there and do not respond to mine - even fruitfly got the message - why can’t the self-confessed (how stupid and wrong) atheist do the same?

melanogaster - #81047

June 13th 2013

“Beaglelady must have her say, even though it is very rude to speak on my behalf…”

She didn’t. It’s far more rude for you to accuse her of something she didn’t do.

“… - you poor souls - I criticise your prophet Darwin and off you go with your mindless chatter. But beaglelady seems oddly ignorant of what makes for good manners, so this self appointed commentator just goes on and on and on….!”

You’re projecting.

“I will again make the same statement for lou’s sake - just put your comments out there and do not respond to mine -”

It’s a forum. Anyone can respond to anyone else’s comments.

I think that any sane person could contrast Lou’s comments with yours and easily see who is the rude one engaging in mindless chatter.

GJDS - #81049

June 14th 2013

Say it again Sam - perhaps you should mine quotes from my previous posts and you will again display the ‘sanity’ you espouse to the world out there ..... poor souls indeed ....

beaglelady - #81054

June 14th 2013

It was an excellent course,  offered by Duke University.  And it was free!  The professor, Mohamed Noor, was outstanding. It will be offered again in January 2014.  Students can take it for credit if they want that option.  What’s not to like?



Roger A. Sawtelle - #81017

June 13th 2013

If you are serious about coming to a meeting of the minds, stop the ad hominem attacks and stick to scientific arguments, if you can understand them.

I thought Jon got us off to a good start with the remarkable video lecture by Denis Noble.  However Lou and Beagle Lady have failed to respond to this presentation even though it clearly refuted Dawkins and NeoDarwinism. 

The facts are clear.  Fitness does not control natural selection.  Relative fitness may, but relative fitness is based on the ability of life forms to adapt to their environment.  Since it is the changing environment which brings on evolutionary change, it is the ecology which determines evolutionary change, not DNA.

Also one can learn to manipulate the math without understanding the science behind the math.  GJDS had a good example of this.  For many years people have been making good calendars and charting the tides without understanding gravity.     


Lou Jost - #81066

June 14th 2013

You are right about my slowness to respond to the Noble video. I have been reading his papers though. In what I have seen so far, his views on natural selection would not differ from any other biologists’ views regarding the example I just gave. After I have read enough to comment further on his ideas, I will.

Roger A. Sawtelle - #81052

June 14th 2013

Please do not respond to ad hominem comments with ad hominem comments.

Two wrongs do not make a right.

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