We have looked in the past for ways to to identify and group organisms by using morphology and development. This proves somewhat satisfactory for identification even today, however, it has always been problematical for relationship studies. It still dictates the classification schemes encountered in textbooks and to some extent, that found in systematic studies.
This is because until recently we have had so little other evidence to use. In 1909, our earliest (then) glimpse into what the ancestors of most invertebrate body patterns found today begins with the discovery of the Burgess shale. It took years to "mine" these fossils and they became the focus of serious study in 1950s. Recently older biota have been found in China (Chengjiang) and Greenland (Sirius Passet). About the same time, we began to appreciate the function of DNA as the information molecule and now molecular evidence is accepted as the most important of all that available to classify invertebrates.
So to summarize, we have almost no fossil data for the evolution of most animals from one ancestor. In fact our understanding of animal form from fossils goes back only about 550 years ago.
The earliest morphological evidence for life is 3.5 billion years old, fossils of stromatolites (colonies of cyanobacteria) and single, undifferentiated cells, or Prokaryotes. For 1.6 billion years these simple cells were the only kind of living organism, until the arrival of Eukaryotes, or single cells with differentiated nuclei and cell organelles. Although representing a large leap in complexity, the Eukaryotes were still only single cells or cell aggregates. It was another 1.4 billion years before complex, multicellular life made an appearance in the form of the Ediacaran (Vendian) faunas. These fauna are simple in from yet only a few million years later there is an explosion in diversity in the period known as the Cambrian roughly starting about 550 million years ago.
Animals first appear in the fossil record around 580 million years ago as frond-likeforms, jellyfish-like imprints, and trace fossils. These fossils appear simultaneously on all continents, except Antarctica, and each assemblage contains roughly the same kinds.
Some of these fossils are simple blobs that are hard to interpret and could represent almost anything. Most have been classified as cnidarians, some are more worm-like with segments or appear to some systematists to be soft-bodied relatives of the arthropods. Others are less easy to interpret and may belong to extinct phyla. Vendian rocks also contain trace fossils, probably made by wormlike animals slithering over mud.
At the base of the Cambrian period about 545 million years ago, all modern phyla of animals and many algae and protists appear or radiated. This event is sometimes called the "Cambrian Explosion", because of the relatively short time (geologically speaking) over which this diversity of forms appears. We know have several sites where organisms were preserved because they were buried rapidly in a mud slide. Burgess Shale type assemblages show that this is a radiation of soft-bodied as well as skeletonized organisms or Bauplans in general. Between 60% and 80% of the fossil remains are those of soft organisms. These organisms were preserved because they were buried rapidly in a mudslide.
Most explanations for this radiation involve properties of animals themselves (intrinsic causes). These scientists feel animal life evolved to the size that suddenly resulted in a coevolutionary "war" between predator and prey, especially in armourment that would allow for easier fossilization. There are coincident events in algae and protozoans that also suggest perhaps a more ubiquitous, ecologic trigger (extrinsic causes). One possibility is oceanographic changes that increased nutrient supplies to the shallow waters, hence a radiation of trophic links in the food chains of that time. Oxygen levels were increasing for the same reason. After the glacial period, temperatures rose until by the time of the Cambrian itself the climate was warmer than it is today. We also do not know why the innovation stopped. There have been extinctions since the Cambrian but an increase in very different bauplans has not been part of any following radiation of forms. Now we have evidence from two other localities that are older. Chengiang adds many new species to a Burgress shale type setting, so sets the time for the Cambrian explosion back about 10-15 million years. Interestingly enough there are many more chordate ancestors in this biota, including organisms that today would be classified as jawless fishes.(Visit these websites if you are interested, http://en.wikipedia.org/wiki/Vetulicolia and https://en.wikipedia.org/wiki/Haikouichthys)
The Sirius Passet biota are also about 15 million years older but hint at simpler forms (perhaps living deeper?), but also give more evidence for more worm like and mollusk type of fossils. http://www.peripatus.gen.nz/paleontology/lagsirpas.html
So what is happening with respect to animal genetics to explain such an explosion?
The Cambrian explosion is still about 300 million years later than the molecular data suggest that animals originated, leaving an enormous period of time without a fossil record. Perhaps, the first animals were small, unskeletonized, or destroyed by geologic processes. Examining rRNA sequences supports an explosion of sorts. DNA and RNA sequence analyses indicate that diversification started earlier but support that diversification occurred rapidly on a geological scale. In fact, most of the classification you will learn for invertebrates in this courses rest on comparative rRNA sequence analysis. When we are comparing the DNA sequences that code for r or ribosomal RNAs we are looking for random changes that occur through copying errors that do not really affect the structure of the ribosomes. If truely random, than the longer the time that divides two organisms that evolved from an ancestor, the more changes we expect and so differences in sequences in the two organisms. Answer question three.
Why not compare structural gene sequences, or those genes that code for eyes, livers, the structures that make up a body? After all we do use what organisms look like to tell them apart.
Most of the information about the inappropriateness of this approach is coming from a field know as evo-devo.
Evo-devo
All changes in an organism involve changes in development as well as genes.
Many differences in diversity may involve simple differences in the amount of refinement or growth of a "parts" (modules) or timing in development.
Let us take a real example and then use an analogy to show how a small difference in timing can explain this difference in real species.
Plains zebra-------------------------------------------Grevy's zebra Zebras differ in pattern of stripes.
Just imagine painting stripes on a ballon at different times as you are blowing it up. If you paint them on early, you will get broad stripes. Iif you paint them on later, you will get narrow stripes.
So surprising it is small differences in timing and spatial expression of genes not different genes that may explain the diversity we find today.
Please view the following three movies. Double click on the center of the movie of choice for it to play.
The first hint about the important role of differential expression came when we could decode the human and several other animal genomes. Answer question 4.
We begin to realize that most organisms share similar structural genes and it is only a matter of which are switched on and when that explains the diversity we see.
So for a more formal explanation by one of the leading scientists in this area, view the third film.
Examples of similar genes---The hox genes.
Most of the work to date is on homeobox genes, (or a gene coding for a protein with a particular DNA binding motif known as the homeodomain) that controls axis and overall positioning and are highly conserved in evolutionary time. They encode transcription factors that act as molecular markers for the position of cells along the major body axis.
Example of similarity in some developmental genes:
If you compare a single hox gene (MSX gene) from sea urchins and mice: both of them consist of about 180 nucleotides, and both code for a protein of about 60 amino acids. The sequence of amino acids in the sea urchin and the mouse differ only in a single amino acid. The rest have remained the same over 600 million years of evolution.
Hox genes are so amazingly conservative that geneticists do all sorts of weird things like remove a hox eye gene from a fly and replace it with the equivalent human hox gene and produce an absolutely normal fly with a compound eye.
Example of a difference in body plan that a small change in the expression of a regulatory gene can make.The difference between an insect and a crustacean can be explained mainly by differences in Ubx expression, a regulatory gene.
This conservatism has a major implication, it means that hox gene clusters probably evolved only once and so all animals evolved from a single ancestor. It also substantiates a radiation over a relatively short geological timespan, although it might have taken place before the Cambrian.
However, it does not indicate anything about the bauplan of that ancestor because hox gene clusters can be lost as well as added.
We will need more information on the next level of regulatory genes, the ones beyond those that control the overall pattern. We need to know more about genes that control what specific organ, develops at a specific time and place to eventually be able to explain the diversity we see in animals. However, it is obvious that differences in structural genes or structure itself will not tell us much about how the diversity we see in animal forms today evolved.
Take home messages.
By Cambrian have major body or bauplans or so all basic genes. Evolution since then has mostly tinkered with variation within a bauplan. So animals have gotten more diverse, but not usually by the appearance of radically new bauplans. The new phylogeny will be based on what we find out how development is controlled and changed not only to get different bauplans, but variations of a bauplan through time.
