Evolution in the News - September 2015
by Do-While Jones

The Octopus Genome

Not surprisingly, the octopus genome surprised evolutionists.

The August 13, 2015, issue of the British journal Nature featured a story about the newly decoded octopus genome. The abstract of their report begins by pointing out the obviously unique physical characteristics of octopi.

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. 1

So it came as no surprise when they said,

We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. 2

Unique physical characteristics must be the result of unique genetic factors. That makes perfect sense. But then they said,

Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems. 3

What is the evidence of “extensive remodelling?” How do they know the octopus DNA arose from some previous ancestor by remodeling (or remodelling in British English ) existing DNA? Did they even consider the possibility the DNA is so different because it was created from scratch, and not modified from some previous form? They should have because,

We found no evidence for hypothesized whole-genome duplications in the octopus lineage. 4

Later in the report they said,

Based primarily on chromosome number, several researchers proposed that whole-genome duplications were important in the evolution of the cephalopod body plan, paralleling the role ascribed to the independent whole-genome duplication events that occurred early in vertebrate evolution. Although this is an attractive framework for both gene family expansion and increased regulatory complexity across multiple genes, we found no evidence for it. 5

Here’s their evidence against it.

Remarkably, octopus Hox genes are not organized into clusters as in most other bilaterian genomes, but are completely atomized (Extended Data Fig. 2 and Supplementary Note 9). Although we cannot rule out whole-genome duplication followed by considerable gene loss, the extent of loss needed to support this claim would far exceed that which has been observed in other paleopolyploid lineages, and it is more plausible that chromosome number in coleoids increased by chromosome fragmentation. 6

The abstract goes on to say that they found

massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates. 7

This is significant. The division of the supposed evolutionary tree between vertebrates and invertebrates is at the base of the tree. If these large gene families existed in the supposed common ancestor of vertebrates and invertebrates, they would be in all vertebrates and invertebrates; but they aren’t. Evolutionists are forced to believe that these gene families somehow originated and enlarged late in vertebrate evolution, and also late in invertebrate evolution. What a coincidence! And, they say, this enlargement could not have happened by duplication, as was previously thought.

In the body of they article, they observe,

Soft-bodied cephalopods such as the octopus show remarkable morphological departures from the basic molluscan body plan, including dexterous arms lined with hundreds of suckers that function as specialized tactile and chemosensory organs, and an elaborate chromatophore system under direct neural control that enables rapid changes in appearance. The octopus nervous system is vastly modified in size and organization relative to other molluscs, comprising a circumesophageal brain, paired optic lobes and axial nerve cords in each arm. Together these structures contain nearly half a billion neurons, more than six times the number in a mouse brain. Extant coleoid cephalopods show extraordinarily sophisticated behaviours including complex problem solving, task-dependent conditional discrimination, observational learning and spectacular displays of camouflage. 8

Yes, Captain Obvious, an octopus is a lot more athletic and intelligent than a clam, which is not to be expected if all mollusks are closely related.

When they analyzed the protocadherin genes of octopi, they found they were more like those found in zebrafish (a vertebrate) than squid. But, they think, this is probably due to dumb luck (a.k.a. convergent evolution) because these genes had to have evolved independently in octopi, fish, and squid. Those are our words. Here are their words:

Thus both octopuses and vertebrates have independently evolved a diverse array of protocadherin genes.

A search of available transcriptome data from the longfin inshore squid Doryteuthis (formerly, Loligo) pealeii also demonstrated an expanded number of protocadherin genes (Supplementary Note 8.3). Surprisingly, our phylogenetic analyses suggest that the squid and octopus protocadherin arrays arose independently. Unlinked octopus protocadherins appear to have expanded ~135 Mya, after octopuses diverged from squid. In contrast, clustered octopus protocadherins are much more similar in sequence, either due to more recent duplications or gene conversion as found in clustered protocadherins in zebrafish and mammals.

Finally, the independent expansions and nervous system enrichment of protocadherins in coleoid cephalopods and vertebrates offers a striking example of convergent evolution between these clades at the molecular level. 9

It always seems to come down to the same argument. When genes are similar in two species that are presumed to be closely related, it is proof that they are closely related because they had to come from a common ancestor. But when genes are similar in two species that can’t be closely related, they had to have evolved independently and just happened to come out the same.

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1 Albertin, et al., Nature, 13 August 2015, “The octopus genome and the evolution of cephalopod neural and morphological novelties”, pp. 220–224, http://www.nature.com/nature/journal/v524/n7564/full/nature14668.html
2 ibid.
3 ibid.
4 ibid.
5 ibid.
6 ibid.
7 ibid.
8 ibid.
9 ibid.