We enjoyed reading “The evolution of animal genomes” by Casey Dunn and Joseph Ryan. In his work, Dunn has taken a human-neutral view of animal evolution, and thus appears to be closer to the truth. We covered his work earlier in - Evolutionary Biologists to Follow Sally Leys and Casey Dunn.
With the availability of large number of genome sequences, the scientists are able to make comparative analysis and understand the roles of various gene families in building organelles, tissues and organs. One of the most surprising discoveries in those comparisons has been the lack of surprises. Human genome did not turn out to have numerous and far more complex genes and gene structures than supposedly less complex organisms, such as sponges.
As animal genome sampling has improved, the results have surprised many investigators. It was postulated that animals differ greatly in complexity, and it was expected that gene number would be correlated with these differences . Instead, genome after genome has revealed that, while genomes were radically transformed along the branch that gave rise to animals, there is far less diversity within animals in terms of gene number and other genome features than expected [5,1624,25,26]. The genomes of animals that are sometimes erroneously referred to as higher, such as vertebrates, are remarkably similar
to those that were characterized as lower, such as sea anemones and sponges. This has been considered a paradox , but it says far more about our conceptions of animals and complexity than it does about the biology of the animals themselves. It is based on biases that lead us to greatly underestimate the intricacy of many poorly studied animals  and chauvinism that leads us to overestimate vertebrate complexity , and presumes that there are a small number of common types of genome changes (such as acquisition of new protein coding genes) that underlie particular phenotypic changes.
There are two ways out of this dilemma. The first one was taken by the ENCODE project, who claimed that the human genome had other unrecognized complex parts. The other is to reject the human-centric method of understanding and look at animal evolution from bottom up. That is the approach being taken by Casey Dunn and a few others.
In the meanwhile, ENCODE backers have not given up. They are now promoting the idea that human complexity comes from splicing structures of genes and long non-coding RNAs. (check - Human Transcriptome is Extremely Complex and Snyderome is the Most Complex of All, and Alternative Splicing the New Snake Oil to Explain Human Complexity).
What if cyanobacteria wrote the bacterial history?
When researchers study bacterial evolution, a bottom up view becomes the norm rather than exception. If a scientist claims that cyanobacteria or spirochetes are more complex than all other phyla, she needs to justify it by providing extensive scientific evidence. However, one difference with animal evolution is that no researcher is cyanobacteria himself, and therefore there is no role for ‘emotional evidence’.
The situation is quite different for animal evolution, because a human-centric view is backed by government agencies supposedly promoting science. A bottom-up view can be seen as existential threat for such agencies like NHGRI. It is commendable for Dunn and others to be swimming against the current and leave a lot of research money on the table.
Distribution of sequenced animal genomes
The first figure of their review paper tells us how little attention has been given on ‘other’ animal phyla. Please note that the figure uses data from 2012, and some of the ignored branches have fully sequenced genomes now, but the proportions are very small compared to Craniata and Arthopoda.
Genome sequences are now available for hundreds of species sampled across the animal phylogeny, bringing key features of animal genome evolution into sharper focus. The field of animal evolutionary genomics has focused on identifying and classifying the diversity genomic features, reconstructing the history of evolutionary changes in animal genomes, and testing hypotheses about the evolutionary relationships of animals. The grand challenges moving forward are to connect evolutionary changes in genomes with particular evolutionary changes in phenotypes, and to determine which changes are driven by selection. This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods.