Let's see a show of autopods. Part 1.

The discovery of deep homology was a milestone in the history of evolutionary thought. Anatomical structures in distantly related organisms, structures with only the barest of functional similarities, were found to be constructed under the influence of remarkably similar genetic pathways. The original and classic example from 1989 involves genes controlling pattern in both insects and mammals – the famous Hox genes. Another great example emerged from the study of limb development and evolution in vertebrates, work beautifully described by Neil Shubin in Your Inner Fish.

The idea that the limbs of various animals are homologous – meaning that they are variations on a theme inherited from common ancestors – is certainly not new, with roots in the exploration of 'archetypes' by the great Sir Richard Owen. But deep homology goes, well, deeper, suggesting that even basic themes like 'limb' or 'eye' or even just 'thing-sticking-out-of-the-body-wall' can be identified and seen to be conserved throughout the biological world. And, importantly, deep homology points to genetic mechanisms that underlie basic themes, structural concepts so distinct that they would not be judged to be related by structural criteria alone. Consider, for example, limb development in vertebrates.

Tetrapod vertebrates, like humans and whales and birds, sport limbs that are recognizably homologous, built according to a plan that Neil Shubin memorably summarized as "one bone, followed by two bones, then little blobs, then fingers or toes." The parts are recognizably homologous, and so are the genetic mechanisms that assemble them. The genetic circuitry is basically the same throughout the tetrapods, with subtle distinctions that create structural differences. Bat wings and mouse forelimbs are homologous, both structurally and genetically, because both were modified from common ancestors.

So, what about "limbs" in fish? After all, fish and mice descended from a vertebrate common ancestor, and those fins in fish sure look like they could be modified into limbs. They were, of course, and that's the great story of Your Inner Fish and the wondrous fossil Tiktaalik. Get the book and/or visit the Field Museum in Chicago to learn all about it.

The development of tetrapod limbs and fish fins displays deep homology. Despite the fact that fish fins and human limbs seem structurally distinct, the developmental pathways that sculpt them are actually quite similar. A tetrapod limb (like, say, a human arm) can be divided into three anatomical segments:

Segment (technical name)	Simplified by Shubin	What we call it in humans
Stylopod	One bone	Humerus
Zeugopod	Two bones	Radius and ulna
Autopod	Little blobs and digits	Wrist and fingers

Examination of vertebrate fossils shows that fish fins and tetrapod limbs really are built on a common scaffold, and molecular developmental studies have shown that the first two segments are conserved across all vertebrates. So, a fish pectoral fin has a stylopod extending from the body, with a zeugopod connected to its end. And, amazingly, the genetic systems that control the development of those segments are homologous as well.

But the autopod is a different story. Some data suggest that the autopod is a tetrapod invention, something that developed since fish and tetrapods went their separate ways. But there are some very interesting indications that the ends of fish fins and the hands of humans develop under the control of the same genes. This would indicate that the deep homology of fins and limbs extends all the way to the end, such that human hands and rodent paws are somehow homologous to the margins of fish fins.

How could we address this question? The best approach would go like this. Take the genetic element that controls the development of mammalian digits (e.g., fingers), and look for a similar element in a fish. If you find one, then do a "molecular transplant" experiment in which you swap the two elements and see if they do the same thing. In other words, put the fish element into a mouse, and the mouse element into a fish, and see if they really have the same function.

The results of those experiments were published by Schneider and colleagues in the 2 August 2011 issue of PNAS. The article is open access, and the work was done in Neil Shubin's lab at the University of Chicago. We'll look at their data in Part 2.

[Image is adapted from Figure 4 of Schneider et al., and shows fish fins at the top, mammalian hands at the bottom, and postulated intermediates in between.]