Jumping genes: Cross species transfer of genes has driven evolution


#1

Dr. Swamidass, comments please. Is this a new and surprising result? Does it fit into the neutral theory of evolution?


#2

For example, Professor Adelson says, 25% of the genome of cows and sheep is derived from jumping genes.

Well whatever your faults you continue to show yourself to be a most useful mammal for posting articles friendly to positions which I hold. This article for example is very amenable to creationist interpretations.


#3

That’s the great thing about science, one day your new result is the greatest insight in the history of mankind, then the next day it is proven wrong by the next greatest insight in the history of mankind. All truth in science is provisional.


#4

Here is the whole paper if interested. Don’t get too excited as the gene transfer happened 160 million years ago.


#5

Thank you for the link. I will try to contain myself.


#6

One by one:

  1. Not new or surprising. This is an incremental advance, misreported, about something we have known for a very long time.

  2. Not only does it fit with neutral theory, it is because of neutral theory that they can infer the cross species transfer of transposons (“genes” in this case is a misnomer, and only helpful to alliterate with “jumping”).

I’ve already mentioned this several time before. Just a few examples:

There are several much more detailed discussions over at biologos too.

It is very true that many creationists think that, especially because its being misreported. You forget, however, that I already mentioned this in my PSCF paper too! About 45% of the human genome is transposons. The fact of the matter is that we know how and why they are everywhere. We know how they jump between species. They are the remnants of ancient viruses. That is how they moved between species.

Then exaptation. They become useful for other purposes. This is among the most important and well known mechanisms of evolutionary change.

It is also very strong evidence for common descent.

I’m still not sure what there is to contain. Isn’t it important to understand it first? This is one of the most well known examples of genomic evidence for common descent. This data is not your friend if you are looking evidence against evolution.


#7

There speaks wisdom… unless, of course, the next greatest insight is in your PhD student’s thesis and would put your rumoured Nobel prize for the last greatest out of the running. In that case, you might decide the new insight was pseudoscience!


#8

@swamidass well one of my first thoughts is what a nightmare these things could make of your Bottleneck of Two research. A huge amount of time must be devoted just to that task. It hurts my head to even think about it, but I guess that’s where they super-computers come in handy.

A link from a Christadelphian blog? Please tell me you are not a “Christadelphian”. My brother-in-law was once involved with one- I consider them a cult well outside of orthodoxy.

I am old enough to remember when evolutionary science insisted that known mechanisms were able to explain everything without any idea that genes in sponges could wind up in mammals and nothing in between. I don’t think this was “predicted” so much as once it was discovered the theory was modified to take it into account. And that is fine. It is how science is supposed to work and I do wish the theologians would do the same with their branch of science. But it was not something evolutionary science predicted. Nor is it “common descent” for those HTs.

I think if you will look at the paper it is talking about something different than what you are referring to. They are talking about a class of genetic elements that are NOT normally thought to make such jumps, which they call L1, and use a class which are known to do so as sort of a control.

BovB retrotransposons provide an excellent example of HT: divergent species contain highly similar BovB sequences and the analysis of various insect species has revealed plausible vectors of transfer [8, 11]. In contrast, L1 elements are believed to be only vertically inherited [16]. We hypothesise that the very presence of L1s in today’s mammals is due to an ancient HT event.

Yet later in the paper their research concludes…

In contrast to BovBs, there is no strong evidence to suggest ongoing L1 HT in mammals.

And yet despite this note the last sentence…

Three criteria are typically used to detect HT candidates: (1) a patchy distribution of the TE across the tree of life; (2) unusually high TE sequence similarity between divergent taxa; and (3) phylogenetic inconsistencies between TE tree topology and species relationships

Even within mammals, there are noticeable differences in copy number; for example, bats and equids have a very low number of full-length BovBs (< 50 per genome) compared to the thousands found in ruminants and Afrotherian mammals. The low copy number here is TE-specific rather than species-specific; there are many L1s in bats and equids.

Some of their findings are just bizarre. I wouldn’t call it support for special creation per se, but this is not “common descent” as it is commonly understood…

Our mining of BovB sequences further revealed two concurrent BovB subgroups in bats and frogs. Two frog species (Xenopus laevis and Xenopus tropicalis) each contain a single intact BovB sequence > 2 kb in length (and numerous fragments), but these two sequences are very different and correlate with the two distinct BovB subgroups observed in bats (Fig. 2b). This seems to indicate at least two independent insertion events, somehow connecting Xenopus laevis with the ‘horse-like’ BovB group, and Xenopus tropicalis with the bat-specific BovB group (most similar to the BovBa-1_EF consensus from RepBase [20]). Without intermediary species, it is difficult to infer the chain of events that led to these patterns.

And other than a couple of L1s sneaking into ruminants because they match up so well with more transmittable forms (BovB) they think this process stopped in mammals. But if something was happening way back when and not happening now, then we cannot say that extrapolation of existing evolutionary mechanisms produced all the change we see. Something happened 160 million years ago and has not (in that manner) happened again in mammals. I know there are different ways to look at things but that seemingly non-repeated event sounds more like special creation than evolution from where I am standing.


#9

@Revealed_Cosmology (& @swamidass )

These matters were touched upon by Venema and Buggs… because it is a normal activity that happens every generation, it is part of the mutation rate.

One would have to imagine that dramatically different rates of transpositions are somehow a hazard … when in fact, the low rate of occurrence seems to be more of a “nudge” to the basic numbers than a crucial determinant.


#10

I am not a Christadelphian. That post is 100% science.

A lot of crazy stuff like that is said in the public, even now. That is not what scientists in the field have been saying. Don’t judge the field by self-appointed spokesmen with an agenda.

Nope. I did not make a mistake there. L1 is the same LINE-1, and are well known transposable elements. Maybe the biologist in the room knows some biology :wink:.

How do you know this? Do you have a solid grasp of the history of the vast evolutionary literature?

How do you know that? I might be better to ask how we came to have confidence in this.

It is common descent as it is understood in science, with is certainly not what is commonly understood. Wouldn’t it be great if we encouraged students to actually learn modern evolutionary theory? Then it could be commonly understood!

Bizzare? Welcome to my world. Science is nonintutive, and biology papers are a tangle of complex both-ands. That is how biology works.

Sigh. Maybe start by reading up on what Transposons actually are. Maybe take a course on them.


#11

@Revealed_Cosmology

The question is less about “the original source of what is getting moved around” …
and more about
"when is it likely that something was transposed [regardless of what was the ultimate source of the original string of molecules] - - based on flags and markers (which would disqualify some populations and some time periods from consideration).