Sunday, 5 November 2017

Gene Duplication Gave Us Spiders

Common house spider, Parasteatoda tepidariorum
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution | BMC Biology | Full Text

For creationists still trying to get away with the absurd claim that mutations are always harmful and that no new information can arise in the genome because of the second law of thermodynamics, this is another of those bad news stories.

No! I'm not joking! They really do claim that! Creationists think nothing of claiming an observable thing can't happen, knowing that their willing dupes won't go and check. They'll no doubt continue to claim it even after this paper showing how the scorpions and arachnids have evidence of whole genome duplication in a common ancestor about 400 million years ago.

A similar things appears to have happened in an ancestor of the horseshoe crab, not once but twice. Similarly, there were two whole genome duplications in the early evolution of vertebrates.

In collaboration with scientists from the U.K., Europe, Japan and the United States, researchers at the Human Genome Sequencing Center at Baylor College of Medicine have discovered a whole genome duplication during the evolution of spiders and scorpions. The study appears in BMC Biology.

What makes this especially pleasing is that the lead author, Dr Alistair P. McGregor, is Professor of evolutionary developmental biology at Oxford Brookes University, my old alma mater, where I studies Applied Biology in the days when being able to analyse a species' genome was but a pipe dream. Even in those days, writing up the results of some lab work with the conclusion that "this is all to hard for me to understand so it must be magic", would have resulted in a swift ejection from the course. Mind you, if I had submitted that to an American diploma mill Bible college, with maybe a couple of random Bible quotes, with the appropriate fee, I'd probably have been awarded a 'doctorate' in 'Creation Science' or some such worthless piece of paper.

Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.

Results
We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.

Conclusions
Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, HarshaVardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica Garb, Luis B. Gonzalez, Vanessa L. Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel S. T. Hughes, Ralf Janssen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Christian L. B. Paese, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, John H. Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpic, Jean-François Flot, Nico Posnien, Stephen Richards, Alistair P. McGregor
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
BMC Biology
, 2017, Volume 15, Number 1, Page 1

Copyright © McGregor et al. 2017
Published open access

While most of the new genetic material generated by whole genome duplication is subsequently lost, some of the new gene copies can evolve new functions and may contribute to the diversification of shape, size, physiology and behavior of animals. Comparing the whole genome duplication in spiders and scorpions with the independent events in vertebrates reveals a striking similarity. In both cases, duplicated clusters of Hox genes have been retained. These are very important genes that regulate development of body structures in all animals, and therefore can cause evolutionary changes in animal body plans.

Dr. Alistair McGregor, Lead author.
Professor of evolutionary developmental biology
Oxford Brookes University.
The thing about gene or, in this case, whole genome duplication, is that they create opportunities for evolution by creating spare genes that can mutate without loss of the function still being provided by the originals. This study also shows that even duplicated hox genes, which, because of their controlling function are normally highly conserved, differ in when and where they express, suggesting they have been adapted for a different function.

There is also scope for exaptation of these genes for a new purpose. In the case of whole gene duplication, it's like having the entire genome to experiment with without harming the individual. Only if a mutation created something harmful would this be detrimental, and then it would be rapidly removed from the species gene pool. On the other hand, if something beneficial arose, it would spread throughout the gene pool.

Whole genome duplication is thus a major driver of evolutionary radiation and diversification. It is a mutation which not only need not be harmful but which, if it doesn't create new information as opposed to duplicated information, it created the opportunity for new information to arise by harmless mutation in the duplicated genes.

Once again, and I seem to be saying this for almost every science paper these days, a piece of research refutes creationism quite incidentally and without any intention on the part of the authors. Creationism is now so detached from reality that almost the slightest whiff of a verifiable fact refutes it.

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