The ID Report

Robert Deyes
ARN Correspondent

Writing over a decade ago, UCLA biologists Laura Maley and Charles Marshall noted how genetic sequence comparisons carried out between different animal phyletic groups can lead to significantly different interpretations of evolutionary relationships depending on which species is chosen to represent each group (Ref 1). Such a finding should raise concern amongst protagonists of molecular systematics who today use sequence data to determine evolutionary relationships. Yale University's Gavin Naylor showed just how inaccurate such comparisons could be in the context of the vertebrate evolutionary tree (Ref 2). Mitochondrial DNA sequence analyses of 19 different taxa generated an astounding result- frogs and fish were clustered in the same clade as chickens even though "strong morphological and fossil evidence" did not show these as being in any way related by a common ancestor (Ref 2). The same mitochondrial DNA sequences placed echinoderms- which include starfish and sea urchins- in closer proximity to the vertebrates than amphioxus even though, being a chordate, we would expect amphioxus to be closer (Ref 2). That is, if we give the evolutionary tree any credibility.

Given such anomalies, one should be cautious about stating what we really do know about the evolutionary relationships between different classes of vertebrates. Nevertheless molecular biologist Thomas Sakmar and his colleagues from the Rockefeller University seemingly threw caution to the wind several years later when they redesigned the rhodopsin molecule- a visual, light perceiving pigment that is ubiquitous throughout nature (Ref 3). By taking DNA sequences from rhodopsin in alligators, birds, frogs and fish, Sakmar and his colleagues used what we supposedly know about evolutionary relationships between these animals to construct a theoretical 240 million year-old form of rhodopsin. Belinda Chang, one of Sakmar's collaborators, summarized the research

"Using our knowledge of how these vertebrates are related to each other, the sequence alignment and a model of how often certain types of genetic changes occur over time, we calculated the most likely gene sequence"(Ref 3).

A review on this controversial work drew the following conclusion

" [Chang et al provided] a statistical method to work out what the ancestral archosaurs' rhodopsin was like by using knowledge about the evolutionary relationships between living animals related to the archosaurs, and what we know about how sequences of chemicals in a molecule change over time"(Ref 4)

What Sakmar and his team demonstrated was that the novel rhodopsin protein was functional in monkey cells and that it was light sensitive when bound to vitamin A (Ref 3). Moreover it responded to light in the red region of the visible spectrum. This in itself was a masterful achievement. What they did not show was that archosaurs- the supposed evolutionary ancestors of birds and reptiles- would have carried this particular genetic sequence of rhodopsin. Yet this was heavily implied from Chang's conclusion that birds, which also carry a red-light sensitive rhodopsin pigment- had "retained more of the ancestral characteristics than some of the other vertebrates" (Ref 4).

Other similar studies have been carried out aimed at trying to ascertain what ancestral genes and genomes would have looked like. Speaking at the 2004 Genome Sequence Analysis Conference (GSAC), genome diversity biologist Stephen O'Brien described work currently in progress to decipher an ancestral mammalian genome (Ref 5). The common ancestor that O'Brien described is believed to have existed some time before the catastrophic demise of the dinosaurs in the so-called K-T event- one of the greatest extinction events the earth has ever known. Small mammals are thought to have roamed the earth before the K-T event running beneath the feet of dinosaurs (Ref 5). With the dinosaurs' demise, there arose a new ecological background in which a plethora of evolutionary niches were made vacant. So the story goes, mammals filled these niches by evolving into the many forms that we see alive today (Ref 5).

At the same conference, biologist Dario Boffelli told of how humans are distantly related to Ciona- a sessile filter feeder more commonly known as a sea squirt that is today believed to lie at the base of the vertebrate evolutionary tree (Ref 6). The predominant evolutionary mechanism assumed to have operated in bringing about all diversity from the sea squirt is that of natural selection. So it is that within this context we can understand evolutionary biologist Leo Goodstadt's assertion that "genomes are lab books of giant evolutionary experiments" as meaning evolution through undirected, natural causes (Ref 7). Such an assertion is stymied by the fact that not only do we not have any evidence for a common natural ancestor for all vertebrates but we do not have any evidence that natural causes can bring about gross-level evolutionary diversity be it through natural selection on gene fusions and gene duplications, the appearance of pseudogenes, frame shift mutations or any other genetic mechanisms that were identified at the conference (Ref 7).

The take-home message from such a conflict is that in addition to critically scrutinizing current theories on how mammals and archosaurs supposedly coexisted we should also be carefully examining what we do and do not know about the vertebrate sequence. We seem so intent on placing all of life within an assumed evolutionary framework that, even when genetic differences are inconsistent with supposed taxonomic proximity, we explain away these differences simply on the basis of different rates of evolution. Indeed Goodstadt finished his list of bold claims by asserting that "high or low rates [of genetic change] say it all" (Ref 7). With such sweeping generalizations, who can refute anything?

References
1. Laura E Maley and Charles R Marshall (1998), The Coming of Age of Molecular Systematics, Science Volume 279 pp.505-506

2. Michael Balter (1997), Morphologists Learn To Live With Molecular Upstarts, Science Volume 276 p.1032

3. Dinosaur ancestor's vision possibly nocturnal Researchers recreate 240-million year old protein in test tube
http://runews.rockefeller.edu/index.php?page=engine&id=118

4. Sanjida O'Connell, 'What the dino saw', The Guardian Thursday November 28, 2002, http://www.guardian.co.uk/science/2002/nov/28/dinosaurs.research

5. Stephen O'Brien (2004), Landscape of Comparative Genomics in Mammals, Genome Sequencing & Analysis Conference, 2004

6. Dario Boffelli (2004), Phylogenetic Shadowing to annotate the Human Genome, Genome Sequencing & Analysis Conference, 2004

7. Leo Goodstadt (2004), Gene Evolution and Our Place in the Phylogenetic Tree, Genome Sequencing & Analysis Conference, 2004