Double genome sometimes creates advantages for a wild plant

_{Denyse O'Leary

March 8, 2019

Genomics, Intelligent Design, Plants

3}_{Categories
Genomics
Intelligent Design
Plants}

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Two genomes can be better than one for evolutionary adaptation, study finds — thale cress/Wikimedia Commons

Researchers studied the thale cress (an Arabadopsis relative) which can have either a single or a double genome. Genome doubling is not good news: “It’s almost always a bad thing to have too much DNA, but we think that sometimes it makes for a ‘hopeful monster’ that just might flourish.” They seem to have found one:

“These tough little plants can become little genetic adaptation machines which allows them to invade hostile environments and even thrive where others can’t. In fact, a large proportion of the most invasive plant species in the world are genome doubled, so we hypothesised that there are adaptations that occur as a result of genome duplication that we can focus on and find the genes responsible for the adaptations. To test this hypothesis in this study, we resequenced about 300 genomes of this little plant Arabidopsis arenosa,collected from 39 geographical areas across Europe, and looked for the little footprints of selection, a particular gene, that appeared helpful for adaptation to a particular area.”
“In addition to particular genes, we found something even more significant – that in the genome doubled variants the fundamental processes governing how Darwinian selection operates appear a bit different to how they are in the single genome species. That is, we found broader reasons why genome doubled populations may adapt better that go beyond the fact that they simply have more DNA or might harbour new gene variants.”
They found that in doubled genome versions of a species the linkages between neighbouring genes on the same strand of DNA are less strict. It was more common for two genes near one another on a particular piece of DNA to have different combinations of mutations than it was in single genome versions of the species. It may be that this process of ‘linkage breaking’ between neighbouring genes is more efficient in the doubled genome species because a greater variety of different combinations are present and the DNA recombines with additional partners, generating novel combinations of genes. This means that good versions of one gene can escape from bad versions of another genes in its ‘DNA neighbourhood‘, allowing Darwinian selection to occur more efficiently, purging from a population the bad versions and selecting the good. Emma Rayner, “Two genomes can be better than one for evolutionary adaptation, study finds” at Phys.org

This is very interesting but it’s not clear that it is only a Darwinian process. Genome doubling doesn’t usually work well at all in wild nature, let alone solve all kinds of problems (“This means that good versions of one gene can escape from bad versions of another genes in its ‘DNA neighbourhood‘, allowing Darwinian selection to occur more efficiently, purging from a population the bad versions and selecting the good”). There are probably other factors at work in producing the happy outcome but the researchers are not sure what they are yet.

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See also: Polyploidy: Genetic Fundamentalism Is Still Looking For A Job?

New species originated via polyploidy?

Genome doubling (polyploidy) a key factor in evolution?

and

Life continues to ignore what evolution experts say

Comments

Yes, they're saying that the didn't use thale cress, but a close relative. " native UK plant Arabidopsis, or thale cress," is a nounal phrase (albeit a bit of a monster).Bob O'H_{March 10, 2019
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Bob O'H at 1, thanks for the clarification. The description of the study at Phys.org reads "The research team used a close relative of the native UK plant Arabidopsis, or thale cress, which can have either a single or a double genome. " We are not in a position to contest their description of the plant.News_{March 9, 2019
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As to:
Two genomes can be better than one for evolutionary adaptation, study finds - March 4, 2019 Excerpt: Whole genome duplication (genome doubling or polyploidy) happens in all kingdoms of life and is most common in plants. It can occur during a type of cell division called 'meiosis' and is very common in crops that we eat including, wheat, apples, bananas, oats, strawberries, sugar and brassicas like cauliflower. It can also occur in the most aggressive cancers and is associated with cancer progression, so it is important to understand what factors stabilise genome duplication as well as how genome doubled populations evolve. Associate Professor Levi Yant said: "Understanding how that strange state of having 'too much DNA', which clearly causes initial problems, can be overcome – and even turned into an evolutionary positive – is a big scientific question. It's almost always a bad thing to have too much DNA, but we think that sometimes it makes for a 'hopeful monster' that just might flourish. https://phys.org/news/2019-03-genomes-evolutionary.html
So they admit that polyploidy is almost always a 'bad thing' but they hope that it might make a 'hopeful monster' that just might flourish? Hmmm actually, when looking at the evidence without their 'Darwinian rose colored glasses' on, this is actually another confirming evidence for the overall thesis of Dr. Behe's new book "Darwin Devolves":
The First Rule of Adaptive Evolution: "Break or blunt any functional gene whose loss would increase the number of a species's offspring" - Michael Behe - Darwin Devolves; Feb. 2019 - - cover page for Table of Contents “Behe introduces new molecular-level facts that sink the Darwinian view of life once and for all: Darwinian mechanism sometimes helps survival of an organism but always by damaging or breaking genes. The conclusion is clear: life is the product of a mind.” (Matti Leisola, DSc, professor emeritus of bioprocess engineering at Aalto University, Finland) https://www.amazon.com/Darwin-Devolves-Science-Challenges-Evolution/dp/0062842617/
Of related note: John Sanford, a leading expert in plant genetics, examines the Polyploidy (Gene/Chromosome Duplication) claims of Darwinists in Appendix 4 of his book “Genetic Entropy and the mystery of the Genome”, and finds their claims wanting.
“What about polyploidy plants? It has been claimed that since some plants are polyploidy (having double the normal chromosome numbers), this proves that duplication must be beneficial and must increase information. Polyploidy was my special area of study during my Ph.D. thesis. Interestingly, it makes a great deal of difference how a polyploid arises. If somatic (body) cells are treated with the chemical called colchicine, cell division is disrupted , resulting in chromosome doubling – but no new information arises. The plants that result are almost always very stunted, morphologically distorted, and generally sterile. The reason for this should be obvious – the plants must waste twice as much energy to make twice as much DNA, but with no new genetic information! The nucleus is also roughly twice as large, disrupting proper cell shape and cell size. In fact, the plants actually have less information than before, because a great deal of the information which controls gene regulation depends on gene dosage (copy number). Loss of regulatory control is loss of information. This is really the same reason why an extra chromosome causes Down’s Syndrome. Thousands of genes become improperly regulated, because of extra genic copies. If somatic polyploidization is consistently deleterious, why are there any polyploidy plants at all – such as potatoes? The reason is that polyploidy can arise by a different process – which is called sexual polyploidization.This happens when a unreduced sperm unites with a unreduced egg. In this special case, all of the information within the two parents is combined into the offspring, and there can be a net gain of information within that single individual. But there is no more total information within the population. the information within the two parents was simply pooled. In such a case we are seeing pooling of information, but not any new information.”,,, “in some special cases, the extra level of gene backup within a polyploidy can outweigh the problems of disrupted gene regulation and reduced fertility – and so can result in a type of “net gain”. But such a “net gain” is more accurately described as a net reduction in the rate of degeneration.” John Sanford – Genetic Entropy & The Mystery of the Genome – pages 191-192 –
As well, Dr. Wolf-Ekkehard Lönnig, (retired) Senior Scientist (Biology) at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, has also done extensive research on plant breeding and is also, to put it mildly, unimpressed with Darwinian claims of speciation:
Peer-Reviewed Research Paper on Plant Biology Favorably Cites Intelligent Design and Challenges Darwinian Evolution – Casey Luskin December 29, 2010 Excerpt: Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment instead of regularly producing a range of new systematic species… (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) http://www.evolutionnews.org/2010/12/peer-reviewed_research_paper_o042191.html Dr. Wolf-Ekkehard Lönnig, (retired) Senior Scientist (Biology), Max Planck Institute for Plant Breeding Research, Emeritus, Cologne, Germany.
bornagain77_{March 9, 2019
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thale cress (an Arabadopsis relative)
Thale cress is an Arabidopsis - Arabidopsis thaliana to be exact. The common name for species in the study - A. arenosa - is sand rock-cress.Bob O'H_{March 9, 2019
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