Coelacanth Genome Sequenced

damn_registrars writes "The lobe-finned fish described as a 'living fossil' due to its apparent lack of change for hundreds of millions of years (thought to be extinct until the 1930s) has been sequenced by an international team, including scientists from Sweden, Harvard, and MIT. The 3-billion-base-pair genome of the Coelacanth was described yesterday in the journal Nature. This paper is published in an open (non-paywalled) manner on Nature, making the full text available to all. 'We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at.'"

Comments

Why Evolve

[zenrandom]

They don't really seem to have any convincing external factors to make them evolve. I have not RTFA'd, but most things evolve because they have trouble surviving. There are so few of these things that they are endangered, but they don't have any natural predators because they apparently make anything that eats it sick... check the wikipedia article on them.

Re:Why Evolve

[djl4570]

That was my thought. Evolution requires selective pressure that causes certain traits to become assets or liabilities. The coelacanth fills an ecological niche and doesn't have much if any competition in that niche except from other coelacanths.

Re:Why Evolve

[__aaltlg1547]

That was my thought. Evolution requires selective pressure that causes certain traits to become assets or liabilities. The coelacanth fills an ecological niche and doesn't have much if any competition in that niche except from other coelacanths.

Competition from other members of the same species is supposed to be one of the major drivers of natural selection.

Re:Why Evolve

[Anonymous Coward]

But why would natural selection lead to significant evolutionary diversification if maintaining the status quo is closest to the optimal solution? In that case, wouldn't selection work to keep things more of the same? I'd suspect those fish probably aren't alone in being "genetically old", there are likely some insects and creatures like jellyfish that really haven't evolved much since some wormlike thing had the luck to spawn the first vertebrate. Thus plenty of critters we have now aren't really all that much different than the ones the dinosaurs were living with.

Re:Why Evolve

[flyneye]

Behold, a species perfectly comfortable in its environment. No motivation, probably just swims around all day gloating at its luck.

Re:Why Evolve

[flyneye]

dead brilliant

Really?

[celocanth]

...and I didn't even notice.

Re:Really?

[rmdingler]

You aren't a big noticer either, 'cuz somebody already got your extra O.

That kind of longevity is awesome

[GodfatherofSoul]

It's amazing to think that a species is so well adapted that it's survived numerous extinction events and still looks relatively the same. Three hundred million years ago, this planet would have looked like an alien world!

Re:That kind of longevity is awesome

[Tablizer]

My understanding is that it has a very efficient metabolic system that allows it to survive famines. It's comparable to some snakes: sit quiet in waiting for long periods of time with meals few and far between. Rather than compete with the newer younger faster whipper-snapper ray-finned fish, it found a nice little niche of hiding out and cruising.

Re:That kind of longevity is awesome

[Anonymous Coward]

It's preposterous to think that the ecology around this fish was changing substantially over eons, and yet this fish didn't adapt at all. Food sources were changing or going extinct, abiotic conditions were changing, predators were becoming more effective... but the coelacanth just didn't care.

It's equally preposterous to think that the ecology around this fish was UNchanging over eons, and yet that's exactly what the article suggests; "Although a static habitat and a lack of predation over evolutionary timescales could be contributing factors to a lower need for adaptation." Wow. I guess they don't have any other option - gotta come up with some story that fits the evidence, no matter how ridiculous.

Re:That kind of longevity is awesome

[Joe Snipe]

We have the ability to compare this fish to actual fossils from the time, your incredulity notwithstanding. What boggles my mind is why ancient life has so many more gene pairs than current life. It's like we are being sculpted from some master block of genes.

An obvious extrapolation...

[Anonymous Coward]

"...We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at.'"..

Which indicates that their environment has hardly changed in many million years...

Re:An obvious extrapolation...

[LateArthurDent]

"...We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at.'"..

Which indicates that their environment has hardly changed in many million years...

It can also mean they're fairly robust and can survive in a large range of environments. I think that's more likely considering the other fish sharing the same environment has evolved faster.

That said, it's not like the ocean is dominated by coelecanth, so it doesn't mean they've reached optimality or anything. Just that they're good enough to continue reproducing and surviving.

Re:An obvious extrapolation...

[b4upoo]

One wonders how these critters prosper. It may be that they taste lousy to predators or that they simply can get by in such stark environments that they don't have to compete much to get by. But if the gene sequence is available I would think we could cross breed some species and perhaps generate a fish of great use to humans. Cross breeding species seems to not be mentioned a lot but surely the scientists are trying it out. Is it so hard to do something like cross breed a trout with a bass or a catfish with a carp? One would think some great results might flow from such work.

Re:An obvious extrapolation...

[heson]

That said, it's not like the ocean is dominated by coelecanth, so it doesn't mean they've reached optimality or anything. Just that they're good enough to continue reproducing and surviving.

I would say that their genes are stuck in a local maxima where they can't evolve. Any mutation dies off or are so different that they leave the area and become a new species.

Re:An obvious extrapolation...

[cusco]

Is it so hard to do something like cross breed a trout with a bass or a catfish with a carp?

Yes, they're different species, they can't mate successfully. If you actually mean splicing genes from different species together to make a chimera of some kind I'm sure that some are trying it, but plants and insects are a lot easier to work with and more profitable.

but is the rate of genetic drift normal?

[schlachter]

I get that there may be low selection pressure. Are they claiming that there's also a slower rate of genetic drift? That would be interesting. I just assumed that drift would happen similarly across species, perhaps with some minor variation for body temp, metabolism, habitat (i.e. radiation exposure), etc.

Can Somebody Clear This Up?

[sehlat]

"genes overall". I wasn't aware my overalls HAD genes!

Re:Can Somebody Clear This Up?

[Livius]

You're thinking of overalls genome sequencing.

Gene overalls are overalls for genes.

Got bored

[Anonymous Coward]

after reading the first 20000 base pairs. Yawn...

Re:ATTENTION SLASHDOT ADMINS ... apk

[Jeremiah Cornelius]

I always post/repost this under my own flag, and never sail the seas of LULZ with another pseudonym or anon posting.

Never.

I was here before you. I was here before there were "logins".

I will be here - long after you've gone - adding value to conversations and spicing others with provocative and sometimes unpopular opinions.

Re:ATTENTION SLASHDOT ADMINS ... apk

[interkin3tic]

Why not just prevent posts from ACs, new accounts, or accounts with negative karma from going up for, I dunno, half an hour on a story?

Or maybe reorder comments so that they're by score and not first posted by default? Maybe don't jump right into it. There's this little website called reddit that does it that way, maybe slashdot should wait and see if that catches on before making the jump. Maybe people really like completely off-topic posts as the first thing they see?

I get the feeling that slashdot is trolling me these days. They're still updating stuff, but not bothering to fix that.

Re:ATTENTION SLASHDOT ADMINS ... apk

[Tablizer]

We ARE out to get you and we ate your cat at 4am last night. We also replaced your cheese with moldy cheese and broke the threads on your toothpaste cap so that it doesn't seal.

We decided to be evil because being evil is more fun, and we like warm weather and hate harp music.

-Slashdot Management

Au Contraire!

[rmdingler]

I believe they are cousins of the lungfish, so their evolutionary spawn may have escaped notice since they are no longer sea-bound.

Pass me the Coelacanth sharpener

[Dynamoo]

Sadly no longer a Googlewhack.

Genetic Curmudgeon

[Mystakaphoros]

*shakes its non-evolved fist* Those damned kids...

If Coelacanth had a front porch, it'd be stealing our baseballs and yelling at us.

Coelacanth Provokes Tidal Waves

[Alejux]

It's a known fact here in Brazil.

Woah

[wakeboarder]

The first time I read it I thought it said Cthulhu genome sequenced, now that would be impressive.

Re:ATTENTION SLASHDOT ADMINS ... apk

[Joe Snipe]

This guy will be the death of slashdot. He is seriously about to remove your icon from my favorites folder.

Re:ATTENTION SLASHDOT ADMINS ... apk

[Gregg Alan]

I'm a little bummed that you might be right.

How do they measure that?

[__aaltlg1547]

The article was pretty sketchy on details. How do they establish how fast coelecanth genes are changing? It's not like they can break open a package of 300 million year old coelecanths and sequence the ancient genome. You have to compare it to other modern animals.

Re:How do they measure that?

[drunken_boxer777]

I don't know how strong your biology, specifically genetics, background is, but they do explain how they established the rate of change (the second paragraph under the heading "The slowly evolving coelacanth"). I will try to keep my explanation of that second paragraph succinct and simplified, so it might not satisfy your curiosity. But, you can also consult the methods, which are in a linked PDF document (bottom of page 8, through to page 10).

Due to random copying errors during DNA replication, a base pair substitution can occur in a gene. The rate at which these substitutions occurs in a population is relatively fixed, and low. These mutations accumulate over time in a population. If you compare the sequence differences between two species you can estimate how long ago they diverged based on the mutation rate.

The authors compared the degree of difference between the coelacanth genome and the genomes of three cartilaginous fishes. They did the same for the lungfish, chicken, and mammalian genomes. Now look at Figure 1. The ancestor of the coelacanth, lungfish, chicken, and mammals diverged from the ancestor of the cartilaginous fishes at the same time. Therefore, if the coelacanth et al. genomes evolved at the same rate, the degree of difference from the genomes of the cartilaginous fishes should be the same. It is not: the rate of divergence is lower for the coelacanth.

News value?

[tulcod]

I fail to see how this article is worthy of being on the front page. Sure, the fish itself was an interesting find in 1938, but we have been sequencing DNA for years now - what's so special about this paper?

Re:ATTENTION SLASHDOT ADMINS ... apk

[deimtee]

Every other slashdot poster is truncated at 20 or 30 lines with a "read the rest of this comment" link.
Why aren't this troll's posts truncated?

Re:ATTENTION SLASHDOT ADMINS ... apk

[flyneye]

You're an AC and you say you have impersonators?
For every man who would be king....

Re:ATTENTION SLASHDOT ADMINS ... apk

[flyneye]

Sheeit, boy,I could be your projenitor, whatcher mama look like?