Evolution Basics: Convergent Evolution and Deep Homology

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August 15, 2013 Tags: Genetics

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

Evolution Basics: Convergent Evolution and Deep Homology

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 how convergent evolution is favored by underlying homologies.

In the last post in this series, we introduced the concept of a homoplasy  – a similarity in form in two lineages that arises due to independent events. In the example we looked at last time, birds and bats independently obtained powered flight through convergent evolution – with bats arriving at membrane-based wings, and birds at feather-based wings. Since the last common ancestral population for bats and birds was a species that did not have powered flight, this is a good example of a homoplasy  – one that arose through convergent evolution.

Underneath this convergent event, however, there is a deeper connection. Bats and birds are both tetrapods – organisms with backbones and four limbs. The tetrapod body plan was already a feature of their last common ancestral population, and has been maintained in both lineages. As such, when considered strictly as a forelimb, bat wings and bird wings are homologous structures. In birds and bats, forelimbs have been shaped through natural selection for flight in different ways, but the starting point for both was a homologous structure. In other words, underneath the convergent event of powered flight in bats and birds is a deeper homology – the limb upon which both lineages independently constructed a wing. To represent this on a phylogeny, we would place the tetrapod body plan prior to the divergence of all tetrapods, and powered flight as two events on the appropriate lineages:

This pattern – convergent events with deeper homologies lurking beneath them – is one that is seen time and again in evolution. In fact, these deeper homologies improve the odds that convergent events will occur, since they provide a common basis that separate lineages can use for independent innovation. For bats and birds, adaptations leading to flight were possible because both lineages had forelimbs that could be modified, over time, from one function to another. While this example is at the anatomical level, these sorts of “predispositions” and the convergent events that arise from them can be observed at the molecular level as well.

The eyes have it

As we mentioned in the previous post in this series, camera eyes are one of the most striking examples of convergent evolution, having appeared independently in several lineages (the most common examples of which are vertebrates, cephalopods such as octopus and squid, and certain jellyfish). Camera eyes have a light-sensitive cell layer (the retina) as well as a lens that focuses light on the retina. Explaining the distribution of camera eyes among these three groups requires us to invoke three convergent events on their phylogeny (“cnidarians” are the group in which jellyfish are found):

At first glance, it seems wildly improbable that three distantly-related lineages would independently converge on such a remarkable structure as a camera eye. As it turns out, however, a key homology between all three groups greatly improved those odds – the molecules that act as light sensors.

At its most basic form, sensing of the external environment requires that the environment induce a change within cells. Accordingly, sensing light requires a light-induced change of some kind. The key molecules that perform this function in all three of the above groups are proteins called opsins and their chemical partners (a group of compounds called retinals). Each opsin protein has a retinal attached to it, and together the opsin/retinal pair acts as a light sensor. Retinals change their shape when they interact with light (i.e. absorb a photon, represented by the gamma in the diagram below). This shape change in turn alters the shape of the opsin protein attached to the retinal:

Source:  http://en.wikipedia.org/wiki/File:RetinalCisandTrans.svg

The change in shape of the opsin protein affects the flow of electrical charge in the cells responsible for sensing light, and these changes in electrical charge are what are perceived and interpreted by the brain as “light.”

The opsin/retinal system of detecting light is a very widespread system – in fact, all animals that can detect light use these molecules as the physical basis for doing so, whether they have camera eyes or other eye types (such as compound eyes, or merely patches of light-sensitive cells). This is strong evidence that the opsin / retinal system predates the divergence of the three groups we are considering:

With this knowledge in hand, we can see that the development of camera eyes in these lineages is not as improbable as we might have thought at first. In all three cases, these lineages built a camera eye around a preexisting molecular system for detecting light. The camera eyes themselves might be convergent, but they are based on a deeper underlying homology that improved the odds that they would appear through successive modifications of an ancestral system. And as we saw for bird and bat wings, there are differences between the camera eyes in these lineages that support the hypothesis that they are the result of convergent events (the most well-known example of which is that the vertebrate and cephalopod eyes have their nerve “wiring” in opposite orientations).

Hearing is believing

A second example of “molecular predisposition” leading to convergence can be seen in the molecular machinery underlying a different form of sensory perception – the ultrasonic hearing required for echolocation in bats and toothed whales. Both groups use highly tuned echolocation for navigation and seeking prey in an environment where visual perception is limited or lacking altogether. The evidence that the development of echolocation in these two very divergent groups of mammals is due to convergent evolution is strong – no other mammals more closely related to either group has such an ability.

The cellular / molecular basis for detecting sound in mammals is a set of cells in the ear that extend hair-like projections (called cilia) that vibrate in response to different wavelengths of sound.  Cilia also change their length and vibratory properties in response to different auditory stimuli. The vibrations are used to change the flow of electrical charge in these cells, eventually leading to nervous system signals that the brain perceives as sound. All mammals use a protein called prestin as part of the auditory system. Prestin is a “motor protein” that can change cell shape by moving internal structures around – and mammals use it for modifying cilia in response to sound.

The cilia/prestin system is known to predate all mammals, so it is not surprising that toothed whales and bats use this system for hearing. What is interesting, however, is that in these groups the prestin protein has been independently shaped through natural selection to be tuned to high frequency (ultrasonic) sound more useful for echolocation. In fact, in a phylogeny restricted to prestin sequences, bat prestins and toothed whale prestins appear to be the most closely related to each other – a finding wildly at odds with the species tree for bats and whales. Further examination, however, shows that these striking similarities are the result of convergent evolution, not a more recent shared ancestry. In both cases, the prestin protein was available to become attuned to ultrasonic wavelengths, and similar (though not identical) mutation events in both lineages were selected for along the way – an additional example of a “deep homology” favoring independent convergent events.

Summing up: evolution as a non-random process

One common misconception I encounter about evolution is that it is predominantly a random process – one that is mainly influenced by chance events. While we have already shown that evolution has a strongly non-random component (natural selection), this discussion of convergent evolution further demonstrates that evolution is repeatable in certain important ways. When natural selection affects distantly-related groups in a similar fashion, we often observe similar outcomes. These similar outcomes are in many cases favored by prior history (homology) and arrived at through similar, but not identical paths (demonstrating that contingency and chance are present as well). Evolution is thus a balance of contingent events (mutations and other chance events) and emphatically non-contingent events (selection, convergent evolution).

In the next post in this series, we’ll return to bat echolocation to explore how evolution of one species can be greatly shaped by another species in close relationship with it – a phenomenon known as coevolution


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Roger A. Sawtelle - #82453

August 15th 2013


Thank you for this excellent essay.

One problem with it is that you say quite rightly that natural selection, the other basic component of evolution along with variation, is not random and is the cause of convergent evolution, but you along with no one else has yet explained how natural selection works.

How can one say that natural selection is non-random if we do not know how it works?  As I have said many times natural selection is a key component of evolution, so how can we say we understand evolution if we do not understand how natural selection works?

I have given my explanation of how natural selection works in a non-random manner only to have it rejected without explanation.  Where do you stand on ecological natural selection?     

Dennis Venema - #82455

August 15th 2013

Hi Roger,

Natural selection is a straightforward concept that we covered early on in this series, e.g.

In a nutshell,

(a) mutations occur without respect to the fitness they confer on the organism, which provides a population with genetic variation,

(b) not all variants in a given environment reproduce at the same frequency, and

(c) given (a) and (b), some variants will tend to become more common over time, and others less common, and

(d) as a result the average characteristics of a population may shift over time.

That’s it.

Dennis Venema - #82456

August 15th 2013

Sorry, the link didn’t work. Here it is:


Roger A. Sawtelle - #82461

August 16th 2013


What you have given us is a bare description of what happens without any information about why it happens.  I do not consider this good modern science.  It is more like the tide charts which can give us an exact record of the tides and can be used to predict the tides but say nothing about gravity which causes the tides. 

You also refered us to Darwin who used Malthusian population theory, survival of the fitest, as the basis of his understanding of natural selection.  As you know this point of view has been widely discredited, but Darwinism and science still clings to it.   

You also quote Darwin using the phrase “the struggle for existence” and he also used the phrase “the war of nature” to describe evolution.  From this we receive Dawkins’ Selfish Gene.  Is life a war which produces selfish individuals?

Again I am not saying that evolution and natural selection do not exist, and do not happen.  I am saying that our understanding of how they happen is flawed and incomplete.  It is time to update our science. 

E. O. Wilson and group selection are going in the right direction.  So is Denis Noble. 

Ecology helps us to understand how life forms change and evolve when the environment changes.  We can see that species usually die out, not because they can no longer compete, but because their ecological niche disappears.  

When we leave ecology out of evolution we 1) have a very incomplete understanding of how it works that distorts our perception of Life, and 2) do not have an important tool that we need to face this uncertain period of environmental change.


David Sirrine - #82465

August 16th 2013

@Roger A. Sawtelle: Did you get lost looking for a forum where the participants are debating modes of evolution?

Chip - #82466

August 16th 2013

Hi Dennis,

I’m wondering if you could provide a suitable positive synonym for “non-random.”  Words like “planned,” “intended,” or perhaps “deliberate” occur to me (and to my thesaurus), but I’m wondering what you think.  Thanks. 

Dennis Venema - #82477

August 16th 2013

Hi Chip,

I think you’re confusing “random” with “ateleological”. Your proposed synonyms only work if you take “random” in that sense. The sense that I was speaking to was not “without purpose” but rather “unpredictable” (though, as my physicist colleageues like to point out, a random system is predictable, but I digress - the point is that often folks use “random” in the sense of “unpredictable”.)

I use a positive synonym in the post itself - “repeatable.” Other choices could be “constrained”,  “predicatable”, “biased”, “skewed”, et cetera. The point is that evolution is not a free-for-all.

Roger A. Sawtelle - #82470

August 16th 2013


This essay ie primarily about Natural Selection.  To wit:

While we have already shown that evolution has a strongly non-random component (natural selection), this discussion of convergent evolution further demonstrates that evolution is repeatable in certain important ways. When natural selection affects distantly-related groups in a similar fashion, we often observe similar outcomes.

My problem is that Dennis and others talk about Natural Selection as if it were a scientifically documented process, which it is not. 

If you would care to elucidate as to how natural selection enables bats to fly, please do so. 


Dennis Venema - #82478

August 16th 2013

Hi Roger,

Natural selection is amply demonstrated with experimental evidence. To argue that natural selection doesn’t exist is to argue that all genetic variants reproduce with equal success in all environments, which is manifestly not the case.

Roger A. Sawtelle - #82481

August 17th 2013


I have been asking for experimental evidence on these pages for years with no result.

I have never claimed that Natural Selection does not exist, but only Darwinian science has not understood it properly.

In a sense the problem is not reproduction, at least in most situations.  The problem is survival.  Moths which are not able to trick echolocation are certainly able to reproduce, but many will not be able to reproduce,

The question is cause and effect.  Is there a reason or cause why some are more “fit” than others, or is this some magical, mysterious non-scientific process? 

I say there is a cause behind natural selection, which is ecology and it is only because there is a cause we can say that it is not random, and it is rational and intelligible.  Darwinian theory says that there is no identifiable cause behind natural selection, so while it seems to be non-random, it is not intelligible, scientific, and rational because there is no identifiable cause and effect. 

Also Darwinian natural selection is circular because it has no cause and effect.  Fitness is not the result of a process, but is determined by reproduction.  Reproductive rates can be used to determine the effectiveness of adaption. 

Natural Selection as used by Darwinians is not an explanation, but a Black Box or Deus ex machine to explain something without giving an explanation. 

Roger A. Sawtelle - #82482

August 17th 2013


Let me try to give you an idea what non-random means. 

Random means caused by chance or without rational cause.

Mutations are random in that they are created by chance events.  In a sense they have causes, but the cause is by chance.  Nota Bene:  Not all variations are caused by mutations or by chance.  Many possible variations, like the color of hair, are already present in the genome.  

Non-Random that is an event which had a rational, non-chance cause.  History is generally indeterminate because we cannot predict how it will happen, because it is so complex.  However, when we look at it in retrospect we have a good idea why events took place and they do have rational intelligible cause, rather than chance.  

Chip - #82489

August 19th 2013

Re:  82477


Thanks for the response.  A couple follow-ups.  


1. I’d respond by saying that I have the idea that evolution is linked to purposelessness because that’s what’s most often communicated by evolution’s most prominent advocates.  To provide just one of the many possible examples, Coyne quotes Futuyma in his blog:

[Darwin’s] alternative to intelligent design was design by the completely mindless process of natural selection, according to which organisms possessing variations that enhance survival or reproduction replace those less suitably endowed, which therefore survive or reproduce in lesser degree. This process cannot have a goal, any more than erosion has the goal of forming canyons, for the future cannot cause material events in the present. Thus the concepts of goals or purposes have no place in biology (or any other of the natural sciences), except in studies of human behavior. (p. 282)


2. Are you saying then that evolution does exhibit purpose/teleology?  If so: 

a.  What is its purpose and how do you know this? 

b.  How would you correct the understanding that is exhibited by most mainstream evolution advocates (as in the example cited above)? 


3. If non-random means repeatable, doesn’t “repeatable” in scientific parlance typically refer to the sameness of outcomes when multiple versions of the same experiment are performed?  For example, I have some kind of system or process, provide an input to that system and measure the result.  When I repeat the experiment, I get the same outcome; thus, repeatability. How does this apply to your wing-development example? Are you suggesting that if we were able to “rewind the tape” back to the precursor of the modern bat (whatever it was) and start again from that point, that the modern bat would inevitably develop (even though this could never really be tested)?  Alternatively, was Gould incorrect when he famously hypothesized that “rewinding the tape” would produce an outcome different than what we have now?

Dennis Venema - #82530

August 28th 2013

Hi Chip,

Sorry for the wait - life has been full lately.

I’m not claiming that evolution is teleological from a scientific standpoint. In my view, science is not well suited to detecting purpose and meaning. That’s not to say it isn’t there - Scripture is abundantly clear that what we call “natural phenomenon” is in fact brimming with God’s plans and purposes - but I don’t think science has the ability to test for it.

I think most mainstream promoters of evolution have moved away from claiming that science has demonstrated the ateleology of evolution. Organizations like National Association of Biology Teachers and the NCSE come to mind here.

As for the “repeatable” aspect, don’t forget that evolution is a mix of contigency and non-contingency. Have you ever played the game “Settlers of Catan”? Games of Settlers are somewhat predictable (certain rolls of the die are more common than others, certain combinations of resources are best for achiving certain goals), and certain aspects are contingent (which rolls of the die actually occur, regardless of their probability, choices made by other players). Skilled Settlers gamers know how to maximize their chances of success, but relatively uncommon or downright rare events (especially early in the game) can seriously upend even the most skilled player. Evolution is like this - often repeatable in broad terms, but rarely precisely “repeatable” in the sense of a controlled experiment.

Roger A. Sawtelle - #82491

August 19th 2013



It is clear that erosion does have the purpose of creating a river bed to take river water into the sea.  Whether that riverbed forms a canyon or not depends on the topography.  Purpose does have a place in natural science.

Roger A. Sawtelle - #82512

August 24th 2013


Good news.

There is an article in the 8/22 edition of the New York Times entitled As Humans Change Landscape Some Animals’ Brains Change Too that speaks to this question.  It describes a new study involving recent changes in the skulls of 10 small mammals. 

It includes this finding: 

In this disrupted environment, animals that were better at learning new things were more likely to survive and have offspring.

I would have written it to say “In this altered environment” or “In this more complex environment,” but the finding is clear, changes in the environment produce changes in life forms, which is my point.   

Roger A. Sawtelle - #82533

August 29th 2013

Dennis wrote:

I think most mainstream promoters of evolution have moved away from claiming that science has demonstrated the ateleology of evolution. Organizations like National Association of Biology Teachers and the NCSE come to mind here.


Could you please provide a reference?  Not that I question your statement, but not all of us have easy access to this type of information. 

If the “mainstream,” as opposed to Dawkins & Dennett, has moved away from ateleology, this could be a breaktrough to reconciliation that I for one have been looking for.



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