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Geneticists discover hidden “whole genome duplication” that may explain why some species survived mass extinctions - News & Events | Trinity College Dublin

When a mass extinction some 200 million years ago wiped out related species along with very many others, there was some reason why the common ancestor of the sturgeon and the paddle fish survived and went on to diverge into the 28 species of sturgeon (Acipenseridae) and the 2 extant and 6 extinct species of paddlefish (Acipenseridae).

Now reserchers led by Professor Aoife McLysaght and Dr Anthony Redmond from Trinity College Dublin’s School of Genetics and Microbiology, believe they have found the reason.

It was probably all due to whole genome duplication, followed by rediploidation, which gave the common ancestor an advantage in being able to evolve rapidly in the rapidly changing conditions. Genome duplication provides a spare copy of a gene which is then free to mutate without any loss of the function of the original gene. This is a natural way in which new information can arise in a genome. Gene duplication is a common feature of the evolutionary history of most species but whole genome duplication is unusual.

First a bit of background biology:

Whole genome duplication and rediploidation.

Whole genome duplication (WGD), also known as polyploidization, is a biological phenomenon in which an organism's entire set of chromosomes is duplicated. This leads to an increase in the number of chromosome sets within the cells of the organism. WGD can occur in various organisms, including plants, animals, and fungi. The process of whole genome duplication typically involves two major events: replication of the entire genome and subsequent separation of the duplicated genomes into separate cells. Here's a general overview of the process:

1. Replication: During the replication phase, the DNA in the organism's cells is duplicated, resulting in two identical copies of each chromosome. This occurs during the S phase of the cell cycle.
2. Mitosis: The cell enters mitosis, a process of cell division where the duplicated chromosomes align and separate into two daughter cells. Each daughter cell receives an identical set of chromosomes, effectively maintaining the ploidy level of the organism.
3. Cytokinesis: The final step of cell division is cytokinesis, during which the cytoplasm and organelles divide, creating two separate cells.

In the case of WGD, instead of just one round of replication and division, there is an additional round, resulting in four identical copies of each chromosome. This leads to the formation of cells with twice the number of chromosomes (tetraploidy) compared to the original organism (diploidy).

Rediploidation, on the other hand, is the process by which the duplicated chromosomes in a polyploid organism reestablish the original diploid state. It occurs through a series of genetic and cellular mechanisms over time. Here are some of the possible scenarios for rediploidation:

1. Diploidization: Over time, the duplicated chromosomes may undergo structural changes, such as rearrangements, deletions, or mutations. These changes can lead to gene loss, pseudogenization, or functional divergence. The genome stabilizes, and the duplicated chromosomes differentiate from each other.
2. Chromosome pairing and segregation: During meiosis, the process of producing gametes, chromosomes from different sets may pair and segregate normally. This can result in the formation of haploid gametes with a balanced set of chromosomes, which can then combine during fertilization to restore diploidy.
3. Chromosome elimination: In some cases, polyploid organisms may eliminate entire sets of duplicated chromosomes through a process called chromosome elimination. This occurs through mechanisms such as uniparental chromosome loss or preferential pairing and segregation of specific chromosomes during meiosis.

The specific mechanisms and timing of rediploidation can vary among different organisms and even within species. The process is complex and can take place over multiple generations. Rediploidation plays a crucial role in the evolutionary and ecological dynamics of polyploid organisms, as it allows them to adapt and diversify.

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The Trinity College news release explains the research:

Geneticists have unearthed a major event in the ancient history of sturgeons and paddlefish that has significant implications for the way we understand evolution.

They have pinpointed a previously hidden “whole genome duplication” (WGD) in the common ancestor of these species, which seemingly opened the door to genetic variations that may have conferred an advantage around the time of a major mass extinction some 200 million years ago. The big-picture finding suggests that there may be many more overlooked, shared WGDs in other species before periods of extreme environmental upheaval throughout Earth’s tumultuous history. The research, led by Professor Aoife McLysaght and Dr Anthony Redmond from Trinity College Dublin’s School of Genetics and Microbiology, has just been published in leading international journal, Nature Communications.

Whole genome duplication is exactly as it sounds – it’s a fascinating evolutionary event where an entire genome is copied and pasted so that a species suddenly has twice the genetic material as it did before. Whereas most species, like us, are ‘diploid’ – having pairs of chromosomes, one from each parent – after whole genome duplication everything is in four copies. This effectively provides a lot of raw material for mutations – and evolution – to occur. Eventually, a species genome will revert to the typical pairs through a process called rediploidisation.

We’ve known about whole genome duplication and rediploidisation for a long time but what is new, and exciting, is that we have shown that the time it takes for the second part of the process to complete is very important. In this case, it took a long, long time – so long that some gene duplications appear to be species-specific, occurring after the two species went their separate ways on the tree of life.

As a result, the ancient original whole genome duplication that happened before the species had separated had been missed until now. We believe the same thing might have happened in many other species lineages and that is important given the possibility that it generated genomic conditions that helped the species survive mass extinctions.

Professor Aoife McLysaght

Genetically, sturgeons and paddlefish show evidence of shared and non-shared gene duplications that were themselves derived from the ancient WGD, which, when timestamped to just over 250 million years ago places it just before the Permian-Triassic mass extinction that wiped out over half of the families of all living things.

This would seem to add more weight to the theory that WGD events provide species with more of an evolutionary canvas to work with; more genetic material means more capacity for variations over a given time, and that in turn increases the chance of some conferring an advantage to cope with difficult or changing environmental conditions. These would certainly have been in evidence during the period of rediploidisation that overlapped with the Triassic-Jurassic mass extinction around 200 million years ago.

Multiple whole genome duplication events famously occurred in our ancient early vertebrate ancestors and these have shaped the landscape of our modern human genome. Our findings are exciting because as well as shining a light on sturgeon and paddlefish genome evolution, they provide a comparative snapshot of how our early vertebrate ancestors genome and duplicated genes evolved after these doubling events.

Dr Anthony Redmond

The team's findings are published, open access, in Nature Communications

Fig. 1: Scenarios of WGD and rediploidization timing relative to the Sturgeon-Paddlefish divergence and their expected topologies for ohnolog-pair gene trees.

Scenario 1 is the widely accepted hypothesis of independent WGD events in the sturgeon and paddlefish lineages. Scenario 2 is a shared ancestral WGD with complete rediploidization prior to lineage divergence. Scenario 3 extends Scenario 2 by considering the possibility of speciation happening during a prolonged, asynchronous rediploidization process following a shared WGD event. In this case genes rediploidizing prior to speciation will follow the gene tree expected under scenario 2 while those rediploidizing after speciation (i.e. lineage-specific rediploidization) will follow the gene tree expected under Scenario 1. This is distinguishable from independent small-scale duplication using the expectation that ohnolog pairs largely retain ancestral collinearity between non-overlapping duplicate chromosomal regions. Rediploidization events and associated gene trees after the sturgeon-paddlefish speciation are shown in red, those preceding speciation are shown in blue.

Redmond, A.K., Casey, D., Gundappa, M.K. et al. (2023)

Abstract

Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to a preponderance of duplicate genes with independent histories. Here we show that although there is indeed a plurality of apparently independent gene duplications, these derive from a shared genome duplication event occurring well over 200 million years ago, likely close to the Permian-Triassic mass extinction period. This was followed by a prolonged process of reversion to stable diploid inheritance (rediploidization), that may have promoted survival during the Triassic-Jurassic mass extinction. We show that the sharing of this WGD is masked by the fact that paddlefish and sturgeon lineage divergence occurred before rediploidization had proceeded even half-way. Thus, for most genes the resolution to diploidy was lineage-specific. Because genes are only truly duplicated once diploid inheritance is established, the paddlefish and sturgeon genomes are thus a mosaic of shared and non-shared gene duplications resulting from a shared genome duplication event.

Redmond, Anthony K.; Casey, Dearbhaile; Gundappa, Manu Kumar; Macqueen, Daniel J.; McLysaght, Aoife
Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Nature Communications 14(1); 2879. DOI: 10.1038/s41467-023-38714-z

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Let's recap the creationist fallacies, false claims and downright lies this piece of research quite incidentally refutes:

1. No new genetic intervention can arise naturally: This paper shows not only that it can but has done by a perfectly natural process not requiring magic or the intervention of hypothecated but unevidenced supernatural magician(s), by the simple process of gene duplication and repurposing of the 'spare' copies.
2. All mutations are deleterious and therefore 'devolutionary' (© Michael J Behe): Unless you call surviving a mass extinction by being able to evolve rapidly in rapidly changing conditions a disadvantage, then this paper give the lie to that claim.
3. Mainstream biologists are abandoning the Theory of Evolution and turning to Creationist superstitions for answers: The authors show no evidence of that risible claim and appear to believe the facts are best explained by an evolutionary process.
4. Creationists claim Earth is just a few thousand years old: (the actual age varies according to the argument they are trying to win). The mass extinction described in this paper happened more than 200 million years ago.

Creationism is, of course, childish nonsense, daily refuted by mainstream science without intention, simply by revealing the facts, which are, as always, completely at odds with creationist claims.

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