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Of Mice, Men, and Coelacanths

December 11, 2006
Intelligent Design
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Alternate title: The Sound of the Tree of Life Exploding

Explosion
Comparing the sequence to other species also turned up a big surprise. When the researchers compared the human ultraconserved element to all the DNA sequences in the public database GenBank, the closest match was to DNA from the coelacanth…

Okay, so maybe it didn’t explode but some branches are bent and something is definitely fishy here. Rubin, Haussler, and Bejerano sure do turn up some interesting things. Our closest relative on the tree of life according to ultra-conserved DNA is a fish that’s been around unchanged for at least 360 million years.


Mobile DNA part of evolution’s toolbox
Thursday, May 4, 2006
Written by Howard Hughes Medical Institute

“The big question is whether this is a special case or whether it’s the tip of the iceberg,” says Haussler. A report on the research is published in the May 4, 2006, issue of the journal Nature.

Haussler and his colleagues were led to the discovery through their work on the ultraconserved elements of the genome. One ultraconserved element in particular caught their eye. “We were very interested in this sequence, because it had a number of copies elsewhere in the genome,” says postdoc Gill Bejerano, who is the first author of the study. Close copies of the sequence were ubiquitous in amphibians, birds, and mammals, indicating that it served an important function. “We found it in every species for which we have genomes, from frogs to humans,” says Bejerano.

Comparing the sequence to other species also turned up a big surprise. When the researchers compared the human ultraconserved element to all the DNA sequences in the public database GenBank, the closest match was to DNA from the coelacanth—an ancient fish thought to have gone extinct millions of years ago until a live specimen was caught in 1938 off the east coast of South Africa. The coelacanth is a descendant of the ancient marine organism that gave rise to the terrestrial vertebrates more than 360 million years ago. Humans are therefore separated from the coelacanth by hundreds of millions of years of evolution, yet the two organisms still share critical DNA sequences.

Read the whole article at the link above.

Comments
Tb - sorry, I miscalculated. Your number is surely correct -- until tomorrow. Patrick, when I look at a bush, it forks just like a tree. It seems, however, that you and your article are not talking about a "very busy" tree, but a tree-like structure that doesn't simply fork as you climb up from the roots to the leaves. Rather it seems to show a tangled mess that resists a fork-based mapping. Alas, this particular thread started by showing that we are more Coelacanthlike than mouselike. I understand that the cytochrome C, of Denton fame, also shows that the rattle-snake is more human-like than snake-like. I believe that it shows to be more human-like than mouse-like even. 1+1 = 36. I'll never finish my lunch.bFast
December 11, 2006
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GeoMor
I am not really sure what problem is being pointed out here. The ultraconserved elements are by definition shared almost exactly among the mammals. If you start to look for them further out, you hit some fish — which is not itself surprising, since mammals evolved from fishlike ancestors.
Well, you don't expect the coelacanth and the human to have the highest degree of identity on a gene or that kind of homology with a fluke. This is why the author said,
Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered.
BTW, how does a sequence get horizontally transferred from fluke to human?Jehu
December 11, 2006
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Shared information in divergent lines where none is expected? Color me not surprised. Still looking for someone to compare the sugar glider and the squirrel but this will do for now Oh, and for those who missed it: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0040352 The tree of life is not exactly "exploding" but it is getting bushy even considering the included bias in interpreting the evidence: “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes.” EDIT: Added a "not" between is and exactly and clarified my sentence...Patrick
December 11, 2006
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Sorry for the grammar, but gotta catch a flight soon! My first two sentences in #6 are two separate ideas! And I didn't mean to say any sequence cannot be ultraconserved since back then (but I don't believe in back then), but that if there were other species closer to should have a more similar sequence to us, than should the fluke.jpark320
December 11, 2006
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No, if it was a "transposable element" as you say you would think that there would be some incredible modification since the time fluke and humans were related. Those things, whether exapted or not shouldn't stay ultraconserved (not merely conserved) only in flukes to humans, but across the multiple species amphibians, reptiles, and other primates. Tree of life is exploding b/c it skipped all the other "ancient" and related "organisms" and suddenly is found conserved on a very recent branch. In other words an ultraconserved sequence we have should be in our "close relatives" primates ~ b/c they've been ultraconserved so you'd expect primates who we have supposedly recently branched off from to be the closest match. But guess what you have to go back no to just the primate/hominid split, reptile/mammal split, but some place way back w/the flukes. So start yelling "TIMBERRRR!!!!"jpark320
December 11, 2006
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I am not really sure what problem is being pointed out here. The ultraconserved elements are by definition shared almost exactly among the mammals. If you start to look for them further out, you hit some fish -- which is not itself surprising, since mammals evolved from fishlike ancestors. The surprising thing was that the matching sequence in fish is a known transposable element, whereas in mammals it seems to have taken exapted into some other role. But none of this relates to the tree of life exploding...?GeoMor
December 11, 2006
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Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered.
Just out of curiosity how does DNA get horizontally transferred from a fluke worm to a human?Jehu
December 11, 2006
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bFast@ 1+1 = 42! Meaning of Life and all, you know! I think I am growing gills!tb
December 11, 2006
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1 + 1 = 47bFast
December 11, 2006
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Related article http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1518811
Finally, we note that there is a single strong match in one distant organism: the human blood fluke (Schistosoma japonicum). This instance shares 88% sequence identity with the core region SINE3 over 72 bp (see Fig. 15, which is published as supporting information on the PNAS web site). Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered. Resolving this question will require extensive genomic sequence from platyhelminthes. If the element in blood flukes does represent vertical descent from a common ancestor, then the core element must be very old indeed.
DaveScot
December 11, 2006
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