Category Archives: deep homology

Evolution Follows the Path of Least Resistance

Over at Jerry Coyne’s blog, biologist Greg Mayer wrote:

One of the most important lessons of comparative anatomy is that evolution usually proceeds by the modification of pre-existing structures (or, stated more precisely, the modification of the pre-existing developmental programs that produce those structures). Certain changes are easier to evolve because the developmental system can be modified to produce them—evolution follows the developmental path of least resistance. In terms of the skeleton of vertebrates, this means that most evolutionary changes are reduction, fusion, loss, lengthening, shortening, thickening,  and narrowing of bones. Evolution uses what’s already there, and rarely do wholly new structures arise.  (from “Tinkering with elephants’ feet”)

All of this is true, yet we can proceed beyond this conventional thinking and ask a couple of questions:

WHY does evolution follow the developmental path of least resistance?

WHAT are the implications of evolution following the developmental path of least resistance?

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The Adherens Junction Homology Goes Deep

Now that we have seen that VOLCADRAFT_41528  (from Volvox carteri ) is likely to be homologous to human beta catenin, it becomes reasonable to propose that something very similar to beta-catenin existed in the last common ancestor of all eukaryotes.

However, if we are going to make this rather radical claim, it would help if we could find homologs in other lineages.  So let me begin by pointing out that homologs of human beta catenin exist in all three basal metazoan lineages: Trichoplax, sponges, and comb jellies.  Among metazoans, the beta catenin sequence is strongly conserved.  For example, 340/592 (58%) of the positions have identical amino acids when sponge sequence is aligned with human sequence.

So beta-catenins are universally present among metazoans and found in the multicellular algae, Volvox.  But what about true unicellular organisms?

If you go back to the table I posted a few days ago, we do have one such example – Trypanosoma brucei, a protozoan that causes African sleeping sickness, has a protein that has similar amino acids in 90/204 (45%) positions.  But the E value for this match is only 2.00E-06.  Smaller than 1e-04, but not that much.  The bunnah wants more crunch in his carrot.

To better resolve this issue, I simply took the next logical step – I used the Volvox homolog to BLAST other green algae and various protozoan lineages.  The results are shown in the below table:

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Front-loading and Convergent Recruitment

The beauty of the front-loading hypothesis is that it unites the two aspects of evolution that are quite friendly to teleology – deep homology and convergence.  As I just explained:

That is, the globin-fold itself is a preadaptation and it is this preadaptative state that restricts possibilities as evolution is much more likely to tap into and exploit this poised, pre-existing state than stumble upon some other possible solution that would be harder to reach.  In other words, a significant factor to convergence can be attributed to deep homology, where ancient ancestral states effectively “constrain” where evolution goes.


front-loading expects an intrinsic dimension, where deep homology constrains evolution by functioning as a preadaptation.

This logic is all tied to one of the predictions of front-loading:

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Bunnah Gets it Right Again

Back in Feb 2009, the hypothesis of front-loading evolution allowed me to raise an unconventional perspective on convergence – perhaps many examples of convergence are a consequence of intrinsic constraints rather than purely environmental factors.

Then in June 2009, I added some more support to this prediction in the form of a mitochondrial protein called Tom40. Then I added a ribosomal protein. Then in Jan 2010, there was more support, this time in the form of prestin. A couple of months later, more support came from the VEGF receptors.  Again and again, examples of convergence were being explained by factors intrinsic to organisms (preadaptations) and not merely the environment and similar selection pressures.

And let’s not forget that last month, I noted yet another striking example of support:

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Convergence as a Function of Preadaptation

Let’s build on the convergence between vertebrates and cephalopods.  This time, let me quote some excerpts from the following article: Squid vascular endothelial growth factor receptor: a shared molecular signature in the convergent evolution of closed circulatory systems by Masa-aki Yoshida, Shuichi Shigeno, Kazuhiko Tsuneki, and Hidetaka Furuyaa (in EVOLUTION & DEVELOPMENT 12:1, 25–33 (2010)).

First, the researchers lay the groundwork for the convergence of these two systems:

Metazoan animals have evolved an incredible diversity of hearts and heart-like structures. The most elaborate case in invertebrates is observed in coleoid cephalopods: they exhibit an elaborate closed circulatory system (Schipp 1987; Budelmann et al. 1997). Their heart possesses a kind of advanced output structure similar to that of the human heart, which differs largely from molluscan typical nonendothelium primitive chambered hearts (see Kling and Schipp 1987; Schipp 1987). Neither morphological nor molecular data give strong support to a close phylogenetic relationship between vertebrates and cephalopods, suggesting that the closed circulatory systems and complicated hearts were formed independently in each lineage, and have converged during their evolution.


Their cardiovascular system is considerably similar to vertebrates in several respects such as high oxygen binding capacity, high concentrations of proteins, and short circulation time (Schipp 1987). Each vessel in the cephalopod is constructed similarly to vertebrate vessels, with an endothelial lining on a basement membrane (Budelmann et al. 1997), although the cephalopod blood vessel lining does not have the cellular junction typical among vertebrate species. Most invertebrates have no endothelium in their vascular walls so the cephalopods are unusual in that they are invertebrates with vertebrate type blood vessels. As the other molluscs have open vascular system, the peculiar blood vessel configuration in the cephalopods is in all probability secondarily developed similarly to the vertebrate among chordates (Ruppert and Carle 1983).

Then, they find something really cool.

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Recursive front-loading

Since prestin represents a splendid example of convergent evolution at the molecular level, which in turn, supports the position that the blind watchmaker can be guided, one has to wonder about the origin of prestin itself.

To these ends, I have run across the following paper:

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7690-5.

Expression of prestin-homologous solute carrier (SLC26) in auditory organs of nonmammalian vertebrates and insects.

Weber T, Gopfert MC, Winter H, Zimmermann U, Kohler H, Meier A, Hendrich O, Rohbock K, Robert D, Knipper M.

Prestin, the fifth member of the anion transporter family SLC26, is the outer hair cell molecular motor thought to be responsible for active mechanical amplification in the mammalian cochlea. Active amplification is present in a variety of other auditory systems, yet the prevailing view is that prestin is a motor molecule unique to mammalian ears. Here we identify prestin-related SLC26 proteins that are expressed in the auditory organs of nonmammalian vertebrates and insects. Sequence comparisons revealed the presence of SLC26 proteins in fish (Danio, GenBank accession no. AY278118, and Anguilla, GenBank accession no. BAC16761), mosquitoes (Anopheles, GenBank accession nos. EAA07232 and EAA07052), and flies (Drosophila, GenBank accession no. AAF49285). The fly and zebrafish homologues were cloned and, by using in situ hybridization, shown to be expressed in the auditory organs. In mosquitoes, in turn, the expression of prestin homologues was demonstrated for the auditory organ by using highly specific riboprobes against rat prestin. We conclude that prestin-related SLC26 proteins are widespread, possibly ancestral, constituents of auditory organs and are likely to serve salient roles in mammals and across taxa.

Fascinating.  So homologs of prestin have not only been identified in both other vertebrates and non-vertebrates, but are also expressed in their auditory organs.  Okay, so we can say that a prestin-like protein was already in place to carry out auditory function in the last common ancestor of mammals and insects.  That’s some pretty deep homology.  But does it go further?

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