Science Literature

Genome sequencing has allowed families of genes to be mapped across the phyla, and it is presumed that the presence of a specific gene in different animal groups signifies a shared common ancestor. Over the years, it has become apparent that many significant genes are widely shared in the animal kingdom, and this blog is concerned with two more cases recently published.

Pax genes are typically linked to eye development, although they have a variety of other functions. Pax-6 is regarded as a master control gene known to turn on eye development in the arthropoda, the mollusca, and the vertebrata. The new work extends the analysis to a jellyfish.

"Here we have isolated three Pax genes (Pax-A, Pax-B, and Pax-E) from Cladonema radiatum, a hydrozoan jellyfish with elaborate eyes. Cladonema Pax-A is strongly expressed in the retina, whereas Pax-B and Pax-E are highly expressed in the manubrium, the feeding and reproductive organ."

A model for the monophyletic evolutionary origin of all animal eyes (Source here)

The significance is found in the phylogenetic analysis. The vertebrata belong to the chordata, which are deuterostomes. Arthropoda are ecdysozoans, whereas mollusca are lophotrochozoans: these groups are considered to have a common ancestry in the protostomes. The deuterostomes and protostomes have bilateral symmetry and so, it was concluded, the Pax gene originated, at least, with bilateral animals. The new research brings jellyfish into the picture, which are cnidarians having radial symmetry. This pushes the ancestry of Pax genes back before the inferred Cnidaria-Bilateria separation - well into the Precambrian. This is why the authors of the research paper claim that eyes did not evolve independently many times, but that the evidence points to "the monophyletic evolutionary origin of all animal eyes". This means that the regulatory gene controlling the development of highly complex vision systems evolved long before the need for advanced vision systems. Hence the authors offer the distinctly un-Darwinian interpretation of evolution before adaptation:

"We then propose that during the early evolution of animals, distinct classes of Pax genes, which may have played redundant roles at that time, were flexibly deployed for eye development in different animal lineages."

A similar argument has been made for a gene called BOULE, which is linked to sperm production in humans. This gene has been found also in mice, chickens, snails and sea urchins where it appears to perform a similar function: it is expressed in the testis. When the gene is deleted in mice, it results in sterility due to a lack of sperm. According to the press release:

"This is the first clear evidence that suggests our ability to produce sperm is very ancient, probably originating at the dawn of animal evolution 600 million years ago," said Eugene Xu, assistant professor of obstetrics and gynecology at Feinberg. "This finding suggests that all animal sperm production likely comes from a common prototype." [. . .] "Our findings also show that humans, despite how complex we are, across the evolutionary lines all the way to flies, which are very simple, still have one fundamental element that's shared," Xu said. "It's really surprising because sperm production gets pounded by natural selection," he said. "It tends to change due to strong selective pressures for sperm-specific genes to evolve. There is extra pressure to be a super male to improve reproductive success. This is the one sex-specific element that didn't change across species. This must be so important that it can't change."

The reality is that these examples are representative of many more cases. The findings are not unusual - they are typical. In a recent interview, molecular biologist John Mattick refers to one of the great surprises of the genome projects, one "that very few people have commented on because of their background assumptions".

"[This] is that both the number and range of protein-coding genes have remained largely the same since the base of the metazoan radiation. Caenorhabditis elegans, which is a worm of only 1,000 cells, has almost precisely the same number of protein-coding genes as a human - about 20,000 is the latest estimate - and most of those genes encode similar functions. So the basic parts set for animal development was established several hundred million years ago. In fact, I understand the sponge genome also encodes most, if not all, of the key protein families that are involved in regulating development. Now C. elegans has only got 1,000 cells - a few muscle cells, a few nerve cells, and a gut. We humans have 30 trillion to 100 trillion cells, and the complexity of our body plan organization - including all of the muscles in the face that reflect the range of human emotions, the different bones and organs, and the brain - is enormous."

The implication of this are many. Since the protein-coding DNA has not changed much, we should consider, at least, whether the non-coding DNA is the key to understanding animal complexity - that part of the genome commonly termed "Junk DNA". Mattick puts it like this:

"Since the protein-coding repertoire (notwithstanding some clade-specific innovations) has remained relatively static, the differences in developmental complexity must be due to an expansion of the accompanying regulatory architecture, which presumably lies outside the protein-coding sequences. Now, interestingly, that problem, I think, has been swept under the intellectual carpet because of the relatively facile and widely accepted assumption, which has not been challenged, nor justified, that the combinatorics of transcription factors provide an explosive number of regulatory possibilities - with enough capacity in the system to program anything from a worm to human. But you certainly need to have a more complex regulatory framework to get to a more complex organism, and the astounding thing is that the only thing that does scale with complexity - because the number of genes does not - is the extent of the non-protein-coding genome."

So, we have immensely complex protein coding systems that are relatively static across the phyla and non-coding DNA sequences that are so complex that most biologists are not yet able to recognise them as carrying biological information. The fundamental problem here is the Darwinian mindset that dominates evolutionary biology: the data is being force-fit into an inappropriate conceptual model. Biologists are, of course, free to develop hypotheses to explain the observations, but when we find "redundant roles" for genes and when there is talk of pre-adaptation - we really do need to question what's going on! Is this a good example of Kuhn's 'normal science' and of 'saving the paradigm'? By contrast, ID biologists find that these genome studies fit well into a design matrix, and that design inferences stimulate numerous avenues for research.

Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish
Hiroshi Suga, Patrick Tschopp, Daria F. Graziussi, Michael Stierwald, Volker Schmid, and Walter J. Gehring
Proceedings of the National Academy of Sciences USA, Published online before print July 26, 2010, doi: 10.1073/pnas.1008389107

Abstract: Pax transcription factors are involved in a variety of developmental processes in bilaterians, including eye development, a role typically assigned to Pax-6. Although no true Pax-6 gene has been found in nonbilateral animals, some jellyfish have eyes with complex structures. In the cubozoan jellyfish Tripedalia, Pax-B, an ortholog of vertebrate Pax-2/5/8, had been proposed as a regulator of eye development. Here we have isolated three Pax genes (Pax-A, Pax-B, and Pax-E) from Cladonema radiatum, a hydrozoan jellyfish with elaborate eyes. Cladonema Pax-A is strongly expressed in the retina, whereas Pax-B and Pax-E are highly expressed in the manubrium, the feeding and reproductive organ. [. . .] Phylogenetic analysis indicates that Pax-6, Pax-B, and Pax-A belong to different Pax subfamilies, which diverged at the latest before the Cnidaria-Bilateria separation. We argue that our data, showing the involvement of Pax genes in hydrozoan eye development as in bilaterians, supports the monophyletic evolutionary origin of all animal eyes. We then propose that during the early evolution of animals, distinct classes of Pax genes, which may have played redundant roles at that time, were flexibly deployed for eye development in different animal lineages.

Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function
Chirag Shah, Michael J. W. VanGompel, Villian Naeem, Yanmei Chen, Terrance Lee, Nicholas Angeloni, Yin Wang, Eugene Yujun Xu.
PLoS Genetics, July 2010, 6(7): e1001022. doi:10.1371/journal.pgen.1001022

Abstract: Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. [. . .] This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis.

Non-coding RNAs and eukaryotic evolution - a personal view
John Mattick
BMC Biology, 2010; 8: 67 | doi: 10.1186/1741-7007-8-67.

In this interview, [John Mattick] explains why he thinks non-coding RNA is fundamental to eukaryotic evolution.