Hox and Rocks July 7, 2000

Remember the old days when we were all taught the progression of life on Earth. You know, bacteria to fungi to jellyfish to starfish to fish to insects to reptiles to mammals. H. G. Wells described 'The Age of Fishes', The Age of Reptiles', and 'The Age of Mammals' in his 1920 book 'A Short History of the World'. The Peabody Museum at Yale has one of the most famous murals created in the last century. It portrays 'The Age of the Reptiles'.There is always a definite progression from simple to complex, with the obvious implication that we were at the top. Now this old view was changed over the course of time, particularly recently.

Fish existed during the 'Age of Fish' and continue to exist. Mammals were around when Dinosaurs ruled the Earth. But there were not very many families of mammals and those that did exist were not very diverse. They formed the 'stem' of the mammalian lineage. After the Dinosaurs were removed from the scene, there was a huge explosion in the diversity of mammalian forms, called the 'crown' because of the shape the phylogenetic tree takes on. This is a pretty common phenomenon. Most people simply extended this 'stem-crown' model back in time.

Fewer crowns and fewer stems and simpler life until we get to the first advanced animal, sometime shortly before the Cambrian Era. Well, recent molecular data indicate that this view is wrong. Ancestors of every form of complex animal life were already in existence by then. The last 500 million years have really only seen modifications of the set of genes that were already in existence. The reason we see so many genes in common between humans and Drosophila is because they had already been developed by the last common ancestor of both. This ancestor already had a fairly complex set of genes.

One of the greatest events in life on earth, at least from our perspective, was the creation of the Bilateria. These organisms all share bilateral symmetry, at least during some stage of their life cycle. They also have 3 layers of cells (endoderm, ectoderm and mesoderm). The simplest multicellular organisms, non-Bilaterians such as Radiata, only have 2 layers. They have simple structures with an open gut. Both layers of cells are usually exposed to surrounding nutrients with little need for complex circulatory systems. The addition of a third cell layer in Bilateria permits a large increase in multicellular complexity but also creates new requirements for metabolic processes. Not all cells can be exposed to nutrients, necessitating complex systems of cell communication and transport.

The old view was that the Bilateria also started simple and gained complexity over the course of hundreds of millions of years. This view has persisted since the first examinations of basic body shapes over 200 years ago. Phylogenetic trees based on morphology and development show a gradual increase in complexity as one moves up the tree (usually culminating in us at the top). So, let's examine this one (This is shown in section A). It shows the 'family' tree of Bilateria. Simple at the bottom, complex at the top. One sees a pretty long tree with lots of short branches.

Work back from Vertebrates. We have branches at the Cephalochordates, then the Urochordates, the Hemichordates, the Echinoderms, all of which are in a group called Deuterosomes. There are then branches at the Lophophorates, the Protosomes, the Pseudocoelomates, and finally the Acoelomates. These are all branches just in the Bilateria, animals that display bilateral symmetry during their life.Each level down describes animals that are simpler, with less complex body morphologies and more similarities to non-Bilaterians.

So, there were 9 branching events since the last common ancestor of vertebrates and Radiata. One can easily envision, as many scientists did, that there would be many years between each branching event, allowing plenty of time for mutations to create new control features that allowed new, and more complex body types. Well, recent data indicate that this view is incorrect. Tremendously so.

For you see, molecular data indicate that instead of 5 branches between the last common ancestor of Deuterosomes and Radiata, there are only 2. Incredibly, the tree of life may be very simple. The best set of data use rRNA sequences. This is a good choice, since all eukaryotic cells have rRNA. Yet, when these sequences are examined using the best and most modern algorithms, all the members of Bilateria fell into just 3 groups, the Deuterosomes, the Lophotrocozoans and the Ecdysozoans. Compare the new phylogeny with the old (This is shown in section B.). Several groups of organisms have been moved around and the overall tree rearranged. (This data is reviewed by Adoutte et al. in a recent PNAS article.)

Arthropods and Annelids have been put in similar groups since Cuvier first described them almost 200 hundred years ago. This was done based on the similarity in the segmentation of their bodies. Yet Annelids and Molluscs, which are not segmented, also display a similar, spiral cleavage of the embryo. Now, rRNA data show the similarity of Annelids and Molluscs, placing them in the Lophotrocozoans. So we can now use spiral cleavage as a more important determinant of group phylogeny than segmentation.

Nematodes are another group whose phylogeny changes tremendously. They now fall into the same group as Arthropods. In fact, the only group that has not undergone major reorganization is our own, the Deuterosomes. Probably since we have studied this group the most, being a parochial species. The biggest change in the group is in the branching of Echinoderms. In the old tree, Echinoderms branched off the direct path to Vertebrates. In the new tree, they form a sister group. This could have major implications regarding how Vertebrates originated. The data indicate that the branching of Deuterosomes from the Protosomes occurred first, suggesting that our branch in one of the oldest in Bilateria.

Additionally, there are fewer branches in the new phylogeny and they are consequently much longer. Instead of a gradually branching tree, with different animals representing intermediate states of complexity, the branches occur much earlier and there are no apparent intermediate steps. In fact, the new data indicate that ALL animals seen today, and in the fossil record, came from just 2 major branching events: the first splitting the Protosomes and Deuterosomes; and the second splitting the Protosomes. And we have very good fossil data demonstrating that members of ALL 3 major groups were already present shortly before the Cambrian. So, the branching events must have occurred before this time.

Thirty years ago or so, Britten and Davidson proposed that development was controlled by a series of master-slave genes. The complex and diverse shapes that many organisms took were due to the timely expression of a set of genes forming a network. The assumption was that more complex animals had more complex control systems; simple animals had simple control systems. Is this seen in the molecular data?

Nope. Or at least not to the extent expected. The basic set of genes found in the earliest Bilaterians were actually already pretty complex. The set of genes that define Bilateria more than any other are the Hox genes. These genes determine the anterior-posterior (i.e. head-tail) organization of cellular morphology. Obviously a major difference between a radially symmetrical organism and a bilateral one is the possession of a head and a tail. In the old view, the expectation was that simple Bilateria would have simple Hox genetic organization and more complex animals would have more complex ones. Again, this is not the case.

There are up to 13 different types of Hox genes found in Bilateria, falling into just a few classes describing the head, the tail and the center of an animal. Their linear order directly corresponds to the organization of the organism from head to tail (i.e. the anterior modifying genes are close together followed by the genes which modify the central region followed by those that modify the posterior).

Now simple forms of the Hox gene cluster are seen in simpler organisms outside the Bilateria. A primordial Hox gene has been described in Porifera but there is no expanded gene cluster, simply a copy or two of a primitive gene. More complex Radiata have 2 or 3 genes in the Hox cluster. But the Hox genes are expanded in all groups of the Bilateria to 7 or more copies.

de Rosa et al. examined the Hox genes from wide range of Bilateria. The old view would expect to see a simple Hox gene organization in simple Bilateria and more complex in more complex Bilateria. Not the case. Putting together a phylogenetic tree based on the new view reveals something very interesting. It appears that ALL Bilateria have members of ALL the basic Hox genes. The 'simplest' Bilaterians have quite complex sets of Hox genes. For this to occur, the last common ancestor of ALL the Bilateria must have had copies of most of the Hox genes. This paper estimates that at least 7 of the Hox genes would be represented in the last common ancestor of the Bilateria.

We have fossil data from the Cambrian period, over 500 million years ago, showing the existence of members of each major group in the Bilateria. So, at that time, all the basic genes were in place to create all the diversity we have seen in the last 500 million years. There was not a gradual progression from simple to complex body plans, with intermediate steps. From the earliest fossils we have, all the pieces were already in place. The last 500 million years have simply seen modifications in this basic set, although these modifications can result in quite complex organisms.

So, when did all this complexity originate? When did Urbilateria, the last common anscestor of all Bilaterians, arise? Fossil and genetic data indicate that this had to be before the Cambrian. There is some data using molecular clocks that this event occurred 50-100 million years before the Cambrian. Right about at the time of.... the Snowball Earth episodes!!

So, an attractive theory is that the periods of extreme cold that covered the Earth were the drivers for the creation of the Bilaterians. A major aspect of many animals in these groups is the existence of set aside cells and of a larval stage. That is, cells that are only useful during certain periods of development, to be kept or discarded as needed. Perhaps the extreme conditions found during the Snowball Earth episodes created niches for animals with a more complex architecture than could be created with just 2 layers of cells. Perhaps the climate was such that there was a very short 'summer' each year. The ability to exist in two forms, larval and adult, could be very useful in a world where there was such an extreme change in climate. Many bacteria respond to extremes by forming spores, waiting for a time when conditions allow rapid growth. Perhaps a property of Urbilateria was its ability to accomplish a morphological change for similar reasons.

It seems that more and more of the molecular data we generate provide increasing understanding of how animals evolved. DNA sequencing has long given us indications of microevolution, the small incremental changes seen from one generation to another. Now it is giving us more intriguing information dealing with macroevolution, the large changes that separate one group from another. It seems that much of the genome that determines who we are and how we look had already been developed long before the time of the Cambrian Explosion. This explains why some many of the genomes we have examined are similar. The branches that lead to them occurred AFTER the basic developmental genes had come into existence.

The old view held that there was little life of interest before the Cambrian explosion. It now appears that this was deceptive, due to the dearth of useful fossils. Genomic knowledge is requiring scientists to investigate the nature of life before the Cambian age. I believe that the genomic data we are generating today will more rapidly tell us about where we came from than it will tell us about where we are going. Hox will help explain the rocks sooner than it will open the (human) cloning locks. Cute, huh.