Slashdot Mirror

← Back to Stories (view on slashdot.org)

Coelacanth Genome Sequenced

Posted by Soulskill on from the elderly-base-pairs dept.

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.'"

82 comments

  1. Why Evolve by zenrandom · · Score: 3, Interesting

    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.

    1. Re:Why Evolve by djl4570 · · Score: 2

      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.

    2. Re:Why Evolve by __aaltlg1547 · · Score: 2

      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.

    3. Re:Why Evolve by Anonymous Coward · · Score: 3, Insightful

      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.

    4. Re:Why Evolve by flyneye · · Score: 1

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

      --
      *Repent!Quit Your Job!Slack Off!The World Ends Tomorrow and You May Die!
    5. Re:Why Evolve by Anonymous Coward · · Score: 0

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

      The Coela can! :)

    6. Re:Why Evolve by Anonymous Coward · · Score: 0

      No it canth...

    7. Re:Why Evolve by flyneye · · Score: 1

      dead brilliant

      --
      *Repent!Quit Your Job!Slack Off!The World Ends Tomorrow and You May Die!
  2. Really? by celocanth · · Score: 1

    ...and I didn't even notice.

    1. Re:Really? by rmdingler · · Score: 2

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

      --
      Happiness in intelligent people is the rarest thing I know.

      Ernest Hemingway

  3. That kind of longevity is awesome by GodfatherofSoul · · Score: 4, Interesting

    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!

    --
    I swear to God...I swear to God! That is NOT how you treat your human!
    1. Re:That kind of longevity is awesome by Tablizer · · Score: 3, Interesting

      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.

      --
      Table-ized A.I.
    2. Re:That kind of longevity is awesome by Anonymous Coward · · Score: 0

      Less different than you might think, sitting at the bottom of the sea. It's impressive nonetheless, I'm just saying the size and homogeneity of the ocean buffer the sort of changes you'd normal think of when talking about such long time scales.

    3. Re:That kind of longevity is awesome by Anonymous Coward · · Score: 1, Interesting

      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.

    4. Re:That kind of longevity is awesome by Joe+Snipe · · Score: 2

      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.

      --
      Sometimes, life itself is sarcasm...
    5. Re:That kind of longevity is awesome by Anonymous Coward · · Score: 0

      Maybe it's a godfish? :P

      Survival by obscurity?

    6. Re:That kind of longevity is awesome by Anonymous Coward · · Score: 0

      Alians! Fishy alians! Fishy alian überlords! Fishy alian überlords that are welcomed in Soviet Russia! Engage cruise control to honor da überlords! Iaa Iaa Coelacanth!

  4. An obvious extrapolation... by Anonymous Coward · · Score: 1

    "...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...

    1. Re:An obvious extrapolation... by LateArthurDent · · Score: 4, Interesting

      "...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.

    2. Re:An obvious extrapolation... by b4upoo · · Score: 1

      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.

    3. Re:An obvious extrapolation... by heson · · Score: 2

      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.

    4. Re:An obvious extrapolation... by cusco · · Score: 1

      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.

      --
      "Think about how stupid the average person is. Now, realise that half of them are dumber than that." - George Carlin
  5. but is the rate of genetic drift normal? by schlachter · · Score: 4, Interesting

    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.

    --
    My God can beat up your God. Just kidding...don't take offense. I know there's no God.
    1. Re:but is the rate of genetic drift normal? by Anonymous Coward · · Score: 0

      They're saying transposable elements seem to have evolved at approximately the same rate as in other vertebrate lineages.

    2. Re:but is the rate of genetic drift normal? by ncquail · · Score: 0

      They're Republicans, so of course nothing changes....

  6. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    Go to hell APK. You have no idea what you are talking about.

  7. Can Somebody Clear This Up? by sehlat · · Score: 1

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

    1. Re:Can Somebody Clear This Up? by Livius · · Score: 1

      You're thinking of overalls genome sequencing.

      Gene overalls are overalls for genes.

    2. Re:Can Somebody Clear This Up? by Anonymous Coward · · Score: 0

      you mom had genes all over her overalls!

      Oh, yea..

  8. Got bored by Anonymous Coward · · Score: 1

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

    1. Re:Got bored by Anonymous Coward · · Score: 0

      Genomes are the ultimate tl;dr.

  9. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0, Offtopic

    It's Alexander Peter Kowalski, not Jeremiah Cornelius. Google his name for more info. He's been doing this for YEARS.

  10. Re:ATTENTION SLASHDOT ADMINS ... apk by Jeremiah+Cornelius · · Score: 2, Informative

    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.

    --
    "Flyin' in just a sweet place,
    Never been known to fail..."
  11. Re:ATTENTION SLASHDOT ADMINS ... apk by interkin3tic · · Score: 5, Interesting

    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.

  12. Re:ATTENTION SLASHDOT ADMINS ... apk by Tablizer · · Score: 1, Offtopic

    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

    --
    Table-ized A.I.
  13. Au Contraire! by rmdingler · · Score: 1

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

    --
    Happiness in intelligent people is the rarest thing I know.

    Ernest Hemingway

  14. Pass me the Coelacanth sharpener by Dynamoo · · Score: 1

    Sadly no longer a Googlewhack.

    --
    Never email donotemail@WeAreSpammers.com
  15. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    bullshit http://slashdot.org/comments.pl?sid=3581857&cid=43276741 caught you you fucking troll

  16. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    Shut up, Paul.

  17. DISPROVE MY POINTS EFFETE TROLL... apk by Anonymous Coward · · Score: 0

    See here, explains it all -> http://tech.slashdot.org/comments.pl?sid=3561925&cid=43223585

    * :)

    I.E./Summary: Trolls had a challenge put to them to validly disprove my points in the post I just replied to - result? Trolls FAIL... lol!

    APK

    P.S.=> That's what makes me LAUGH harder than ANYTHING ELSE on this forums (full of "FUD" spreading trolls) - When you hit trolls with facts & truths they CANNOT disprove validly on computing tech based grounds, this is the result - Applying unjustifiable downmods to effetely & vainly *try* to "hide" my posts & facts/truths they extoll!

    Hahaha... lol, man: Happens nearly every single time I post such lists (proving how ineffectual these trolls are), only showing how solid my posts of that nature are...

    Ah yes "geek angst" @ it's 'finest' (not), vs. facts & truths = downmod by /. weak trolls!

    ... apk

  18. It's not I folks: It's Jeremiah Cornelius... apk by Anonymous Coward · · Score: 0

    THIS is why he's doing it & proof of it, here -> http://interviews.slashdot.org/comments.pl?sid=3585927&cid=43295193 when others pointed out Jeremiah Cornelius forgot to submit one of the "first post spams" masquerading as myself as AC, & mistakenly submitted one of the impersonations of myself as his registered 'luser' name here on /. forums.

    Pretty pitiful actually, but like every up to no good idiot does? He screwed up & submitted it under his registered 'luser' name here.

    * Jeremiah Cornelius: DO YOURSELF, and the rest of us, A GIANT FAVOR MAN: Seek professional psychiatric help!

    (Since Jeremiah Cornelius obviously can't get over the fact he made a spelling error on what it is HE ALLEGEDLY DID FOR A LIVING? That's not MY fault... it's HIS!)

    APK

    P.S.=> I seriously must have dusted JC (in his mind @ least) for his BAD spelling error & it "got his goat"...

    I.E.-> Catching what he claimed to do as a job, for YEARS he left "PENETRATION" (correct) spelled as "PENTRATION" (incorrect) on his resume on LinkedIn & I pointed it out as he & his friends trolled me as usual (webmistressrachel, gmhowell, & crew (probably ALL JC no doubt using alterate emails or TOR to do it as a possible - I've caught "them & theirs" doing it before, ala Barbara, not Barbie = TomHudson (same person))).

    So THAT is what has gotten his goat in a technical debate & his "geek angst" could only come up with *trying* to "impersonate me" in every news thread on /. for the month of March 2013 so far!

    (Just to attempt to 'discredit me' as a spammer here obviously)

    Doing so, by posting that "$10,000 challenge" &/or reposts of my old posts on hosts file value to end users into EVERY SINGLE NEWS ARTICLE POSTED on /. ...

    It's all I can think of that *might* cause such a mentally troubled 'reaction' like the Jeremiah Cornelius is doing & there's NO QUESTION he's the one doing this spamming of nearly every posted article masquerading as myself...!

    ... apk

  19. Jeremiah Cornelius by Anonymous Coward · · Score: 0

    I don't whether Jeremiah Cornelius is the ThinkAboutYourBreathing troll, but frankly I applaud whoever it is, since while they are poking you with a stick, it saves the rest of us from the bother of doing it.

    I also note that you've adopted the modus operandus of the SeekProfessionalHelp troll, which presumbaly means that approach must have particularly needled you. I guess it got under your skin because somewhere deep inside, you know that you are seriously ill and do need professional help. So I applaud myself, because I am the SPH troll. :)

    Oh, and you need to seek professional help btw.

  20. YOU CAN'T DISPROVE MY POINTS... apk by Anonymous Coward · · Score: 0

    See here, explains it all -> http://tech.slashdot.org/comments.pl?sid=3561925&cid=43223585

    * :)

    I.E./Summary: Trolls had a challenge put to them to validly disprove my points in the post I just replied to - result? Trolls FAIL... lol!

    APK

    P.S.=> That's what makes me LAUGH harder than ANYTHING ELSE on this forums (full of "FUD" spreading trolls) - When you hit trolls with facts & truths they CANNOT disprove validly on computing tech based grounds, this is the result - Applying unjustifiable downmods to effetely & vainly *try* to "hide" my posts & facts/truths they extoll!

    Hahaha... lol, man: Happens nearly every single time I post such lists (proving how ineffectual these trolls are), only showing how solid my posts of that nature are...

    Ah yes "geek angst" @ it's 'finest' (not), vs. facts & truths = downmod by /. weak trolls!

    ... apk

  21. Genetic Curmudgeon by Mystakaphoros · · Score: 2
    *shakes its non-evolved fist* Those damned kids...

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

  22. Coelacanth Provokes Tidal Waves by Alejux · · Score: 1

    It's a known fact here in Brazil.

  23. 'Sweden' by Anonymous Coward · · Score: 0

    I didn't realise 'Sweden' was a university.

  24. Woah by wakeboarder · · Score: 4, Funny

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

  25. Re:ATTENTION SLASHDOT ADMINS ... apk by Joe+Snipe · · Score: 1

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

    --
    Sometimes, life itself is sarcasm...
  26. Re:ATTENTION SLASHDOT ADMINS ... apk by Gregg+Alan · · Score: 1

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

    --
    Here before all but 8486 of you.
  27. How do they measure that? by __aaltlg1547 · · Score: 3, Interesting

    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.

    1. Re:How do they measure that? by drunken_boxer777 · · Score: 1

      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.

  28. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

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

    About HOSTS files?

  29. News value? by tulcod · · Score: 1

    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?

    1. Re:News value? by Anonymous Coward · · Score: 0

      Maybe because "Genes in coelacanths are evolving more slowly than in other organisms". But we would rather have an article about Facebook or "Why you need xyz".

  30. Re:ATTENTION SLASHDOT ADMINS ... apk by deimtee · · Score: 1

    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?

    --
    I'm guessing that wasn't on their radar screen...
  31. Re:ATTENTION SLASHDOT ADMINS ... apk by flyneye · · Score: 1

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

    --
    *Repent!Quit Your Job!Slack Off!The World Ends Tomorrow and You May Die!
  32. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    Slashdot, like its progenitor BSD, is dead. Quit wasting energy on it and move on.

  33. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    funny you think my name is paul you fucking worthless troll.

  34. You're a troll Jeremiah Cornelius by Anonymous Coward · · Score: 0

    Keep embarassing yourself Jeremiah Cornelius http://slashdot.org/comments.pl?sid=3581857&cid=43276741 since you posted that using your registered username by mistake (instead of your usual anonymous coward submissions by the 100's the past 2-3 months now on slashdot) giving away it's you spamming this forums almost constantly, just as you have in the post I just replied to.

    1. Re:You're a troll Jeremiah Cornelius by Anonymous Coward · · Score: 0

      Hello Paul.

  35. Re:ATTENTION SLASHDOT ADMINS ... apk by Anonymous Coward · · Score: 0

    "Robbing Peter to pay Paul". Look it up, retard. Paul = APK pretending not to be Peter.

  36. Jeremiah Cornelius: Grow up by Anonymous Coward · · Score: 0

    Keep embarassing yourself Jeremiah Cornelius http://slashdot.org/comments.pl?sid=3581857&cid=43276741 since you posted that using your registered username by mistake (instead of your usual anonymous coward submissions by the 100's the past 2-3 months now on slashdot) giving away it's you spamming this forums almost constantly, just as you have in the post I just replied to.

    1. Re:Jeremiah Cornelius: Grow up by Anonymous Coward · · Score: 0

      Hello, Paul.

  37. Re:ATTENTION SLASHDOT ADMINS ... apk by flyneye · · Score: 1

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

    --
    *Repent!Quit Your Job!Slack Off!The World Ends Tomorrow and You May Die!
  38. Seek help by Anonymous Coward · · Score: 0

    You didnt addres my points. Seek help,

  39. Re:DISPROVE MY POINTS TROLL... apk by Anonymous Coward · · Score: 0

    Alexis, you are a terrible, terrible person. Please stop crapping all over Slashdot, so we don't have to see your trite. Disprove your points? Your idiocy isn't even worth the time.

  40. Your "so-called 'points'" got blown away by Anonymous Coward · · Score: 0

    "You didnt addres my points. Seek help," - by Anonymous Coward on Saturday April 20, 2013 @09:29PM (#43507063)

    Easily, per my subject-line above, here -> http://hardware.slashdot.org/comments.pl?sid=3674733&cid=43530007 (and I certainly didn't need any help to do it either (whereas you clearly do in things technical in computing)).

    * :)

    Now, you just KNOW I've just GOTTA say it (keeping with tradition & as-per-my-usual inimitable style of course):

    THIS?

    This was just "too, Too, TOO EASY - just '2ez'"... per my subject-line & the link above lol!

    APK

    P.S.=> It always is, vs. "technically challenged" mere /. ac trolls...

    ... apk

    1. Re:Your "so-called 'points'" got blown away by Anonymous Coward · · Score: 0

      I'm so confused about who's replying to who here.