2R or not 2R: Testing hypotheses of genome duplication …

Personally, I have a certain epistemological sympathy for the position taken in this paper in the sense that I believe that, as a matter of principle, the piecemeal duplication model should be the null hypothesis of (in this case, vertebrate) genome evolution that has to be falsified in favor of WGD scenarios. I doubt that the current statistical argument for such falsification is overwhelming so that 2R is to be accepted as the final verdict. However, I also think that the evidence in support of 2R is rather diverse and rather substantial, so it needs to be addressed seriously rather than summarily dismissed, primarily, on the basis of the high complexity of primitive metazoan genomes which is not a logically consistent argument against 2R. I believe that, for a really critical assessment of the 2R hypothesis, the evolutionary genomics literature, and in particular, the evidence claimed in support of 2R should be examined in considerably greater detail and more carefully, with special attention to the underlying assumptions of the statistical models employed in the respective studies.

For example, the 2R quadrupling of ..

If we’re scientists, we’re looking for natural processes, that’s what real scientists are doing.

Cosmic censorship hypothesis - Wikipedia

Initial attempts to unravel the evolutionary aspects of our own genome have borne out highly controversial results. Some has suggested that drastic events (2 rounds of whole genome duplication/2R hypothesis) at the base of vertebrate lineage led to the greater genetic complexity in modern vertebrate genome whereas other researchers rejected the 2R hypothesis at all and suggested a continuous mode of small scale duplications (segmental/gene cluster). These alternative scenarios of vertebrate genome evolution are largely based on data from human and few other vertebrate and invertebrate genomes. The recent availability of additional vertebrate and invertebrate genomes has provided an unprecedented insight into the core evolutionary processes that had shaped our genome, deep in the history of life. Surveying of newly sequenced genomes from the deepest branches of life has revealed that many components of the genetic toolkit seen in modern vertebrates arose and diversified deep in animal history even before the origin of chordates. Indeed the origin and evolution of vertebrates is partly accompanied by an increase in gene number, for instance one coherent HOX cluster in amphioxus like invertebrate to four or more HOX clusters in modern vertebrates. However, neither can we take this subtle increase in gene number as an only causative factor for evolution of phenotypic complexity in modern vertebrates nor we can take it as a reflection of whole genome duplication events early in their history. In depth analysis of the genomic data from recently diverged primate species on markedly different phenotypic trajectories provides valuable clues to ancient genomic events. These data supports the notion that small scale duplications and rearrangements have remained a pervasive phenomenon, driving the vertebrate evolution both at phenotypic and genotypic level, throughout their history. I conclude, therefore, that the comparative genomic data from species that diverged early in metazoan evolution (such as Cnidarian-bilaterian) as well as from the very recently diverged animals (such as primates among vertebrates) provides no evidence in favor of the ancestral tetraploidy in vertebrates. In fact it appears that the 2R hypothesis is an artifact, invoked by the lack of phylogenetic breadth in the genome sequence data in early years of genomic era.

10.1139/facets-2017-0063 - FACETS Journal

This is a critical overview of the 2R hypothesis (two rounds of whole genome duplication) on the origin of vertebrates. The conclusion that, to a large extent, is based on the unexpected genomic complexity of organizationally simple animals, such as sea anemone, and on the modest number of 2-fold and, particularly, 4-fold paralogons in vertebrate genomes, is that there is currently no basis to accept the 2R hypothesis. Instead, it is proposed that the vertebrate genome evolved by relatively small, regional duplications.

You can believe that if you want. But do you have any examples of this actually happening?
This hypothesis proposes that polyploidy furnished the raw material necessary for evolution, through the production of genetic redundancy.

5.8 The Field Equations - MathPages

I have questioned the validity of arguments adduced in support of Ohno's view that the complexity of vertebrate genomes originated by means of whole genome duplications. Instead, the hypothesis presented here suggests that the animal genomes evolved through small-scale duplication events scattered at different times over the history of life. This hypothesis is testable in the light of currently available extensive genomic data form an expanding range of vertebrate and invertebrate animals: 1) through comparison of total gene number and gene family size differences among modern vertebrate and basal invertebrate (for instance, sea anemone/sea urchin) genomes; 2) by estimating the fraction of vertebrate chromosomes occupied by three or four fold paralogy regions; 3) by conducting the phylogenetic analysis of multigene families with three or more of their representatives residing on four-fold paralogy regions (paralogons) in the human genome; 4) by estimating the genome evolutionary scenario of very recently diverged vertebrate species (for instance, primates among vertebrates). Evaluating the correlation between the organismal complexity and gene duplications may also be helpful in testing the validity of two main competing hypotheses [] (small-scale duplication versus 2R hypothesis).

These hypotheses approximate those of the mechanism proposed by Lynch and Conery (2000), called “subfunctionalization”.

Block duplication is a known but ..

PZ is not giving us any principles. He’s asking for a free diplomatic pass of immunity, if you will. And I’m saying really there’s very little we know about origin of life that currently qualifies as science. And let’s improve that. That is what I’m saying.

And I said ‘you know what, I’ve got the same question Bryan has. I’m going to let science settle this for me.’ And I went down the rabbit hole.

2R or not 2R is not the question anymore

Statistical testing of vertebrate genome evolutionary scenarios is often based on comparative observations from few vertebrate and highly derived invertebrate genomes, and thus could inadvertently lead to unfounded conclusions. Therefore, I recommend that future statistical approaches to test hypothesis concerning vertebrate genome evolution, should take into account the newly sequenced genomes of basal metazoan animals and recently diverged vertebrate species (for instance primates).