Evolution basics: From Variation to Speciation, Part 4

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May 31, 2013 Tags: Genetics

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

Evolution basics: From Variation to Speciation, Part 4

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we examine the details of how allele flow became (mostly) blocked between two very recently diverged populations/species as they exploited different niches in the same geographic area.

In yesterday’s post, we introduced the idea that species can form in the same geographic location based on resource partitioning—where the two populations become increasingly suited, over time, to exploit different niches. In this post, we’ll explore this phenomenon in detail, using an example of nascent species that have formed in the very recent past, and under human observation: diversification within hawthorn flies, Rhagoletis pomonella. These flies are attracted to the unripened fruits of hawthorns, a wild relative of domestic apples (i.e. something resembling a small crabapple). Hawthorn fruit is also where hawthorn flies find their mates and lay their eggs, to allow the larvae to feed on the fruit (and cause it to spoil and fall early, with the larvae along for the ride). Hawthorn flies produce only one generation per year, and survive the winter buried as pupae. Moreover, they have a short adult lifespan, giving them only a short period to find a mate, breed, and for the females to lay eggs. This crucial period, of course, is set by the life cycle of the hawthorn—when its fruit is available for the flies to use as a food source and meeting location.  As such, natural selection (exerted by the hawthorn life cycle) acts on genetic variation relevant to hatching time in hawthorn fly populations. The timing of hatching shows heritable variation, and flies that happen to hatch near the fringes of when hawthorn fruit is available (or worse, when there is no fruit available at all) do not reproduce as successfully as do flies that hatch when hawthorn fruit is abundant. Not surprisingly, the result is that we observe populations of hawthorn flies that are well-timed with their host plants, with most members of any fly population hatching in concert with the height of fruit availability:

Hatching time is an example of a continuous trait, in contrast to a discontinuous trait. Discontinuous traits are traits that have distinct categories: black versus blue eyes,  or red versus white flowers, and so on. Many traits cannot be “binned” into such categories, but rather form a distribution in populations. Traits such as height and weight are examples of continuous traits, and the timing of hawthorn fly hatching is another. The effect that the hawthorn tree has on the hawthorn fly is an example of stabilizing selection—fruit availability is selecting against flies that fall outside the boundaries on either side (i.e. flies hatching too early, or flies hatching too late). The overall effect is to keep fly hatching matched to fruit availability, generation after generation.

Tempted by an apple

Something happened to upset this stable, balanced interaction, however: the introduction of domestic apples to North America by European colonists. As we noted above, hawthorns and apples are related plants, with somewhat similar fruits. One difference, however, was the timing of fruit development in apples compared to hawthorns: domestic apples produce fruit some weeks earlier than do hawthorns. The introduction of apples into the hawthorn fly habitat thus provided a potential food source for flies that happened to hatch on the “early” end of the spectrum:

For those “early” flies that were attracted to this new, but somewhat similar fruit in their environment, the result would be twofold: (a) finding a food source with reduced competition from members of their own species, and (b) finding a mate with similar tendencies of attraction to apples. What was previously a “losing” genetic combination (hatching too early, without sufficient food or reasonable prospects for a mate) was now a “winning” combination. As a result, “early” variants could now reproduce much more effectively than they could before, and thus increase in number over successive generations:

In other words, once apples were present, the environment was no longer selecting fly populations in a stabilizing way, but rather acting to shape variation into two subpopulations. The selection had now switched to being diversifying selection. Importantly, these two subpopulations were not diversifying only with respect to hatching time and food preference, but also (given the nature of their biology) with respect to mating preference. As the “apple” variants increased in number, they naturally bred more frequently with other “apple” variants, since they encountered their mates on apple trees. The result was a partial barrier to allele flow that would reinforce the nascent differences between the two groups over time.

While the hawthorn and apple “species” of Rhagoletis pomonella have been the subject of human interest for centuries (mostly owing to the economic impact of the apple species as a pest) geneticists are just starting to get a handle on the allele differences that were the targets of selection during the separation process. Not surprisingly, genes known from prior research to affect hatch timing show up as having different alleles in the two groups. Other candidate genes include the receptor proteins the flies use to detect odors from their target fruits—with certain alleles more tuned to apple odors, and other alleles tuned to hawthorn odors. What started out as variation within one population has now been partitioned by selection into allele combinations suited to distinct niches—and given the short timeframe in which the switch to apples occurred, it is likely that new mutations did not play a role. Rather, recombination and segregation of existing alleles of numerous genes was enough to provide genetic differences that suited some members of the original population to exploit the new opportunity. The net effect was the shifting of a few continuous traits (hatch timing, fruit odor preference) to match a new environmental niche and precipitate a barrier to allele flow.

Selection for the few

Having considered the genes (and their alleles) that were under selection during this speciation event, there are a few points to make. The number of genes under selection (and thus with different alleles in the two new species) will be relatively rare. Only alleles that affect traits relevant to adaptation to the new niche will be affected. Most genes will remain identical between the two populations, since they were not under diversifying selection, but continued to be under stabilizing selection for their (identical) role in both species.  For example, consider genes required for cellular energy conversion or wing development—processes that both species still need to do in the exact same way. These genes will have the same alleles (or perhaps only one allele) in both populations, since the function of these genes were not relevant to adapting to the new niche. In short, the overall pattern that speciation produces will be a small smattering of differences in alleles for the genes under selection (or genes that happened to experience drift by chance) against a backdrop of the large majority of identical genes that were not subject to selection (or drift).

Indeed, one reason we can be confident that the hawthorn and apple “specialists” of Rhagoletis pomonella are in fact the products of a recent speciation event (aside from the fact that farmers observed them as they arose) is because of the overwhelming identity between their genomes—they have only tiny differences in a handful of genes. Biologically, it’s an open question if they are in fact truly separate species, since they do continue to exchange alleles, albeit at a greatly reduced rate compared to sharing alleles within their respective populations. As we have seen for ring species, this example shows us that it is possible to observe in the present day the precise features we would predict for an ongoing, “in process” speciation event. Additionally, it shows that only a small handful of differences, derived from variation already existing within a population, can start two subpopulations on a trajectory that gradually improves the barrier to allele flow between them. Over time, these effects can lead to the formation of closely related species.

In the long run

The production of closely-related species from a common ancestral population is hardly controversial among evangelical Christians, though the mechanisms underlying such events are not commonly appreciated. What is more controversial for many, however, is the suggestion that these mechanisms also produce widely diverged species over greater spans of time. In the next post in this series, we’ll turn to some lines of evidence that support the hypothesis that highly diverse modern species are indeed derived from common ancestral populations deep in the past.

For further reading:

Schwarz, D. et al., (2009). Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics 10; 633. (http://www.biomedcentral.com/1471-2164/10/633)


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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beaglelady - #80625

May 31st 2013

Excellent, as ever. Reminds me so much of my recent Coursera course on Genetics and Evolution.  I still miss it!

glsi - #80674

June 2nd 2013

This is an interesting article; and convincing in that it appears to be built on solid, verifiable research.

I surely agree with your concluding paragraph that these type of adaptations within species are not controversial and have been shown many times over.  

I’ll await your next post to see if you can produce evidence to show how this hawthorn fly can transform into something that’s no longer a fly.  Or work backwards and show how it derives from anything that was not a fly. 

Lou Jost - #80677

June 2nd 2013

One thing you could do while you wait for Dennis’ next post is to learn about the taxonomy of some large group. More often than not, there are many borderline cases where a species cannot be unambiguously placed in any given genus, because it is intermediate between those genera. This causes us taxonomists no end of headaches (my orchids are giving me this exact headache right now). The same goes for many higher taxonomic groupings. There are almost always some weird sets of species that seem intermediate between big clear groups. When we are dealing with organisms that leave fossils, we can see that this happens because of evolution from a common ancestral group that was not as highly differentiated as the groups that descended from it. 

For example, creationists love to say a dog will never turn into a cat. But if you look at their fossil record, you find that eventually the fossils cannot be clearly classified as either a dog or a cat, and if you go back farher, there is only one group of carnivores, with some characteristics that are more cat-like, and others that are more dog-like. So you see that in fact the same common ancestor did produce both dogs and cats. And today, there are still some leftover groups that bridge the dog-cat gap, such as hyenas.

beaglelady - #80680

June 2nd 2013

True.  And aren’t there mammal-like reptiles and reptile-like mammals?

Lou Jost - #80693

June 2nd 2013

Yep, the transition from reptile to mammal is very well documented in the fossil record. See Donald Prothero’s book, which I mention below, for more examples.

glsi - #80682

June 2nd 2013

I’m quite familiar with these assertions, but without robust evidence it’s rather unconvincing.  The platypus is quite an odd thing as well, but no one has ever been able to show how it was ever anything other than a platypus.

Lou Jost - #80692

June 2nd 2013

Sorry, it doesn’t sound like you are familiar with this at all. Look at Donald Prothero’s book, “Evolution: what the fossils say and why it matters”, for some nice examples of step-by-step transitions into very different animals.

glsi - #80703

June 2nd 2013

Back at you, brother:

“If my theory be true, numberless intermediate varieties, linking most closely all the species of the same group together, must assuredly have existed. ... evidence of their former existence could be found only amongst fossil remains, which are preserved ..., in an extremely imperfect and intermittent record. ... Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory” 


“There is another and allied difficulty, which is much graver. I allude to the manner in which numbers of species of the same group suddenly appear in the lowest known fossiliferous rocks. Most of the arguments which have convinced me that all the existing species of (he same group have descended from one progenitor apply with nearly equal force to the earliest known species. For instance, I cannot doubt that all the Silurian trilobites have descended from some one crustacean, which must have lived long before the Silurian age, and which probably differed greatly from any known animal” 

“If numerous species, belonging to the same genera or families, have-really started into life all at once, the fact would be fatal to the theory of descent with slow modification through natural selection. For the development of a group of forms, all of which have descended from some one progenitor, must have been an extremely slow process; and the progenitors must have lived long ages before their modified descendants . ... To the question why we do not find records of these vast primordial periods, I can give no satisfactory answer. ... the difficulty of understanding the absence of vast piles of fossiliferous strata ... is very great”—C. Darwin

I haven’t seen the book you’re referring to, but I’ve seen many others.  None of them show the “vast piles” and transitional forms necessary to make this theory believable and that’s around 150 years of intensive searching after Darwin.  So no, I doubt the book you refer to is going to present some large number of transitional forms I haven’t already heard about.  Sorry about that!

Lou Jost - #80704

June 2nd 2013

You must not have looked very hard. There are thousands, tens of thousands, of intermediate forms. Look at the book I mentioned, or any similar one. There is also the enormous pile of genetic and biogeographical evidence for common descent, much of it available here on this website. I encourage you to check the very well-written resource pages available here by clicking on “Resources” at the top of this page.

glsi - #80705

June 2nd 2013

Despite your unfounded assertions,  I’ve read quite a bit.  Evidently what’s convincing as a transitional form to you is not to me.  I’ve read Shubin’s book, for example, on Tiktaalik and I think it’s greatly exaggerated probably for the sake of careerism.  It’s a fish, and most of the rest claims are inferred based upon Shubin’s hopes and dreams and what he desperately wants to see.  Perhaps you may accept inferences as proof, but I do not.

And yes, I’ve even read the Resource stuff at this website.  Take a look at the Cambrian Explosion section.  It concludes with a 5 sentence paragraph which claims the Cambrian fossils are “providing the answers”.  I think that’s really laughable.  Where is the answer part?

Lou Jost - #80716

June 3rd 2013

Before I can answer, I have to know more about your assumptions and beliefs. Do you deny common descent?

glsi - #80750

June 4th 2013

Read Behe, Noble, Margulis and Dembski.   They are coming from different points of view and yet they all present powerful challenges to Darwinism.  Check out the recent calculations by evolutionary biologists Sharov and Gordon who  say there isn’t anywhere near enough geologic time for present living forms to have evolved on Earth.


These and many other challenges tell me that much of Darwinism and NeoDarwinism is grossly off the mark.  I think people believe in it only because there are few other competing scientific theories available.


I don’t claim to know what happened.  There seems to be some evidence including DNA  evidence which seems to support common descent.  Much other evidence such as enormous periods of stasis in the fossil record(e.g., the horseshoe crab) and the sudden emergence of new large and complex life forms I think confound and probably falsify Darwinism’s primary prediction of slow, gradual change.  (and punctuated equilibrium is extremely unconvincing as an answer to this).


The DNA evidence is perplexing, and I believe it’s perplexing to the most astute scientists judging by the constantly changing thinking on subjects like pseudogenes.  A strand of DNA is described as dwarfing the abilities of our most advanced computers and I believe it is still poorly understood by science.  And I don’t believe a strand of DNA ever invented itself by Darwinian processes via some unnamed chemical process.  That would be a violation of all known chemistry.  Nor do I believe that anyone understands how organs such as a complex eye could have been produced via mutations/selection starting with a sea sponge in the PreCambrian/Cambrian.  No, BioLogos cannot convincingly claim that the fossils are providing the answers on this.  The fossils are instead providing gulfs of mystery.


Lou Jost - #80760

June 5th 2013

Thanks for your answer. I suggest you read enough to realize that Behe and Dembski are fringe figures whose mathematical work has been at least partly disproven. Noble (and Behe and Margulis) accepts common descent. Noble is not anti-evolution.

To argue against common descent of, say mammals, is like arguing for a flat earth. Someone who doesn’t believe in common descent, knowing the evidence, is not going to be open to evidence-based discussion of anything else regarding evolution, so I prefer not to waste time on such discussions. However, if you can accept common descent, then the argument is about how evolution happens, not whether it happens, and certainly there are plenty of legitimate and interesting questions about that.

glsi - #80770

June 5th 2013

That’s okay; sometimes the best stuff comes out of the fringe.  When you have a theory with as many holes as Darwinism has you need the fringe.

Anyhow, thanks, but I don’t want to waste your time either.  I’ll just keep pointing out the empty claims BioLogos is making with their “answers” to the Cambrian explosion and other subjects.

Lou Jost - #80774

June 5th 2013


melanogaster - #80758

June 5th 2013

“Despite your unfounded assertions,  I’ve read quite a bit.”

From what you’ve written, there’s no evidence that you understand any of it. “It’s a fish” is a dead giveaway.

beaglelady - #80765

June 5th 2013

A fish? Try “Fishapod”

glsi - #80798

June 6th 2013

Yeah, Shubin called it that and I’m sure he’s thrilled whenever anyone takes the bait.  UC Berkeley’s evolution site says it’s a fish.  It’s got fins and gills and whenever anyone claims it had lungs it’s a hoot because that’s all just wishful speculation and conjecture.  The artists’ drawings are funny too because they always show it with 2 back leg appendages.  Funny because they never found the whole back end of the thing.

 Poor Shubin made a big point of saying he knew in advance exactly where to look for it in the geologic strata and now it turns out they’ve found terapod tracks millions of years earlier.  Whoops.  Guess it wasn’t the missing transitionary link he was looking for after all.  Wrong strata!

beaglelady - #80799

June 6th 2013

Let us look at the whole quote in from UC Berkeley in context:

Tiktaalik, of course. Pronounced tik-TAA-lik, this 375 million year old fossil splashed across headlines as soon as its discovery was announced in April of 2006. Unearthed in Arctic Canada by a team of researchers led by Neil Shubin, Edward Daeschler, and Farish Jenkins, Tiktaalik is technically a fish, complete with scales and gills — but it has the flattened head of a crocodile and unusual fins. Its fins have thin ray bones for paddling like most fishes’, but they also have sturdy interior bones that would have allowed Tiktaalik to prop itself up in shallow water and use its limbs for support as most four-legged animals do. Those fins and a suite of other characteristics set Tiktaalik apart as something special; it has a combination of features that show the evolutionary transition between swimming fish and their descendents, the four-legged vertebrates — a clade which includes amphibians, dinosaurs, birds, mammals, and of course, humans.

So hardly simply a fish, is it? Shubin made a prediction on  where to look, he looked, and he found it.  A transitional fossil. He spent a long time camped out in the Arctic doing the hard work of science.  Instead of sitting on his bum, scoffing.  


glsi - #80801

June 6th 2013


Thanks for that clarification.  You’re right, they call it “technically” a fish.  What they’re saying there is that they know the pop-sci books like Shubin’s are calling it a fishopod, but they’re Berkeley and they can’t be caught calling it something they’re going to get burned on.  They wish they could, but, dang, it’s a fish!

melanogaster - #80807

June 7th 2013


Your emphasis on labeling of huge taxonomic groups over examining evidence is silly.

The evidence tells us that the most recent common ancestor of all mammals and (only some) fish was a fish.

So what’s your point, other than to push the tedious creationist falsehoods that evolution is linear, not branching, and that it happens to individuals, not populations?

In your fly challenge below, in which you pretend that evolution involves one individual transforming (which has nothing to do with evolutionary theory), how broad is the taxonomic group that corresponds to the term “fly”?

beaglelady - #80809

June 7th 2013

“Fishapod” is a nickname. 

glsi - #80824

June 7th 2013

Exactly.  A nickname for a fish meant to pretend that it’s not a fish.  Probably very effective on “Yahoo News” type audiences.

melanogaster - #80832

June 8th 2013

The evidence tells us that the most recent common ancestor of all mammals and (only some) fish was a fish.

What’s preventing you from understanding this basic point?

beaglelady - #80835

June 8th 2013

I see you enjoy being silly.

melanogaster - #80759

June 5th 2013

“I’ll await your next post to see if you can produce evidence to show how this hawthorn fly can transform into something that’s no longer a fly.”

Why choose the taxonomic label “fly,” gist? Let’s see how well-read you are.

fly:Drosophila melanogaster::________:Homo sapiens.

Can you fill in the blank?

Gary Friedman - #80685

June 2nd 2013

I am not sure I am addressing my question within the appropriate discussion forum, but here it is.

I am a physicist who has been attempting to study the theory of evolution by natural selection. In physics, a theory must produce falsifiable predictions, not just predictions that are consistent with the theory. A prediction is falsifiable if its falsity can be observed in principle, although it may be difficult or impractial to do so for the time being. Falsifiable predictions need not be deterministic. They may involve prediction of probabilities, expected values or some other statistics, for example.

Now, here is my question. I have read in a number of popular and more formal books and papers on the theory of evolution that Darwin’s hypothesis of natural selection has been used numerous times to make predictions, but most predictions I have actually found could not be classified as falsifiable. Can someone please provide precise reference or direct description of a falsifiable prediction based on the natural selection hypothesis? Please, do not provide references to the falsifiable predictions of decsent with variations. I found a number of those. Thank you very much.


Lou Jost - #80702

June 2nd 2013

Can you be more specific? You mention that you understand the falsifiability of common descent, right? What aspect of natural selection do you think lacks falsifiability? Fitness can be measured independently, and then we can see how allele frequencies should change over time as a function of their relative fitness. This is a quantitative prediction that can be falsified.

Gary Friedman - #80711

June 3rd 2013

Lou, thanks for the response. Unfortunately for me, I can’t understand it. Let me try to explain my difficulties.

Let us say we assume that the hypothesis of descent with variations is true. It follows that, should I take an organism and some of its direct descendants, I will see some features (of phenotype or genotype) that are common to both. An observation that shows nothing in common between an organism and its direct descendants would falsify this prediction. As far as I know, we have not had any observations that found nothing in common between an organism and its descendants. Therefore, we have not falsified the hypothesis of descent with variations and have a very good reason to keep using this hypothesis for other predictions.

Now, I want to know if similar falsifiable predictions have been made for the hypothesis of natural selection as a mechanism by which all life on earth actually evolves. What falsifiable predictions based on the hypothesis of natural selection have been made and reported in the literature? I would like to find actual references (with page numbers, etc) to such predictions?

As far as your suggestion of predicting allele frequencies based on fittness, I do not see how it is a prediction based on the hypothesis of natural selection. This prediction is based on the hypothesis that allele frequencies determine fittness. It follows from the the hypothesis of “genetic determinism”, but does not implicate “the environment” in any processes that determine changes in fittness or in allele frequencies. As far as I know, natural selection implicates “the enviornment” as the selection agent and fittness is a measure of reproductive success which may or may not be determined solely by “the environment”. Am I wrong in my understanding? If so, I woud really appreaciate it if you could direct me to appropriate references (with page numbers) to help me correct my misunderstanding. Thanks again



Lou Jost - #80714

June 3rd 2013

“This prediction is based on the hypothesis that allele frequencies determine fittness” No, it is based on the fitness conferred by individual alleles. For example, suppose in a given environment, individuals with two copies of allele A have on average 10 babies per generation, and individuals with one copy of A and one copy of B have 12 babies, and individuals with two copies of B have 1 baby. These things can be measured empirically.  Then we can predict the average rate of change and the final equilibrium frequencies of the allele composition of the population, assuming random mating (an assumption that can also be tested) and a few other things.

Lou Jost - #80715

June 3rd 2013

Fitness of an allele is determined by the environment and the rest of the genome. When fitness of an allele is measured, this includes the component of the genome that is tightly linked to the allele of interest.

melanogaster - #80757

June 5th 2013

Gary, have you considered differences instead of common features? If you did, I think things would be much clearer.

Jeremy Blakey - #80713

June 3rd 2013

Hamilton’s rule (Hamilton, W. D. (1964). “The Genetical Evolution of Social Behavior”. Journal of Theoretical Biology 7 (1): 1–16.) provides a falsifiable prediction of natural selection. It would be reasonably straightforward to falsify this by showing that the relative value of altruistic behaviour is not related to genetic relatedness. There’s lots of evidence for kin selection; the most cogent critiques of it evoke a non-kin multilevel selection model, which is also testable.

In general, lots of things in behavioural ecology (ESS models, ESS and full genetic models of sexual selection, optimal foraging, life history strategies etc. etc.) provide falsifiable predictions based on selection.

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