Oolon Colluphid
03-04-2009, 01:59 PM
Just spotted this. It's a bit technical, so I'll try to Wiki any bits I can (and put in some breaks and snip the refs for ease of reading), but it's pretty cool (unless you're a creationist)...
Large number of ultraconserved elements were already present in the jawed vertebrate ancestor
Molecular Biology and Evolution 2009 Mar; 26(3):487-90.
Stephen (2008) identified 13,736 ultraconserved elements (http://en.wikipedia.org/wiki/Conserved_sequence) (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes.
In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes.
These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.
Mammalian genomes contain thousands of highly conserved sequences that are under evolutionary selection. Surprisingly, a major portion of them are located in the noncoding regions of the genomes. Functional assays of such conserved noncoding sequences have indicated that many of them function as transcriptional regulatory elements (http://en.wikipedia.org/wiki/Transcriptional_regulation).
Because the amount of noncoding sequences shows a broad correlation with the developmental complexity of eukaryotes, it has been hypothesized that noncoding sequences have played an important role in the evolution of complex developmental programs and phenotypic diversity of organisms.
Therefore, investigations of the evolution of the conserved mammalian sequences in other vertebrate lineages should provide useful insights into the origin and the role of these elements in the evolution of phenotypic diversity of vertebrates.
In a recent study, Stephen et al. (2008) identified 13,736 ultraconserved elements (UCEs) in the human genome that are identical over 100 bp in at least three out of five placental mammals (human, mouse, rat, dog, and cow) and investigated the evolution of these sequences in opossum, chicken, frog, and fugu genomes. They found that about 40% of these eutherian UCEs were present before the speciation of ray-finned fishes; 30% appeared first in the tetrapod ancestor; 18% arose in the amniote ancestor; and 10% evolved in the therian ancestor (fig. 1).
In addition, they found that the substitution rate in the UCEs that first appeared in ray-finned fishes reduced significantly in the frog and chicken lineages compared with the fish lineage. It was therefore hypothesized that the UCEs were exapted to perform novel functions in tetrapods. The alternative hypothesis that these elements were present in the ancestral vertebrate and have evolved rapidly in teleost fishes was rejected because it is less parsimonious.
In this study, we investigated the presence of eutherian UCEs in a cartilaginous fish, the elephant shark (Callorhinchus milii), for which a 1.4x coverage genome sequence was recently generated. Cartilaginous fishes are the oldest group of living jawed vertebrates that diverged from bony vertebrates (ray-finned fishes, coelacanths, lungfishes, and tetrapods) 528 MYA.
Surprisingly, our study showed that a majority of UCEs were in fact present in the common ancestor of jawed vertebrates and that the ancient UCEs have accumulated substitutions at a higher rate in teleost fishes, so much so that one-third of them have diverged beyond recognition.
[...]
Together, these data indicate that the UCEs have been evolving rapidly in the teleost fish lineage. The absence of a large number of ancient UCEs in teleost fishes is consistent with our previous observation that a significant number (65%) of ancient conserved noncoding elements (>70% identical across >100 bp) present in the elephant shark and human have diverged beyond recognition in teleost fishes.
Teleost fishes, remember, includes us tetrapods.
Science in action, folks. This paper uses new data to disprove a hypothesis that had previously seemed plausible.
ETA: Edited to strike the above. More science in action. Thanks for catching my errant fish, Ray. Careless talk costs credibility. The thought process, if you can call it that, was: teleost = bony fish, and we're bony fish, therefore... That is, I read 'teleost' and thought 'osteichthyes', thrown off by their mention of tetrapods.
Bloody fish. I'll stick to me hominins in future...
Large number of ultraconserved elements were already present in the jawed vertebrate ancestor
Molecular Biology and Evolution 2009 Mar; 26(3):487-90.
Stephen (2008) identified 13,736 ultraconserved elements (http://en.wikipedia.org/wiki/Conserved_sequence) (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes.
In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes.
These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.
Mammalian genomes contain thousands of highly conserved sequences that are under evolutionary selection. Surprisingly, a major portion of them are located in the noncoding regions of the genomes. Functional assays of such conserved noncoding sequences have indicated that many of them function as transcriptional regulatory elements (http://en.wikipedia.org/wiki/Transcriptional_regulation).
Because the amount of noncoding sequences shows a broad correlation with the developmental complexity of eukaryotes, it has been hypothesized that noncoding sequences have played an important role in the evolution of complex developmental programs and phenotypic diversity of organisms.
Therefore, investigations of the evolution of the conserved mammalian sequences in other vertebrate lineages should provide useful insights into the origin and the role of these elements in the evolution of phenotypic diversity of vertebrates.
In a recent study, Stephen et al. (2008) identified 13,736 ultraconserved elements (UCEs) in the human genome that are identical over 100 bp in at least three out of five placental mammals (human, mouse, rat, dog, and cow) and investigated the evolution of these sequences in opossum, chicken, frog, and fugu genomes. They found that about 40% of these eutherian UCEs were present before the speciation of ray-finned fishes; 30% appeared first in the tetrapod ancestor; 18% arose in the amniote ancestor; and 10% evolved in the therian ancestor (fig. 1).
In addition, they found that the substitution rate in the UCEs that first appeared in ray-finned fishes reduced significantly in the frog and chicken lineages compared with the fish lineage. It was therefore hypothesized that the UCEs were exapted to perform novel functions in tetrapods. The alternative hypothesis that these elements were present in the ancestral vertebrate and have evolved rapidly in teleost fishes was rejected because it is less parsimonious.
In this study, we investigated the presence of eutherian UCEs in a cartilaginous fish, the elephant shark (Callorhinchus milii), for which a 1.4x coverage genome sequence was recently generated. Cartilaginous fishes are the oldest group of living jawed vertebrates that diverged from bony vertebrates (ray-finned fishes, coelacanths, lungfishes, and tetrapods) 528 MYA.
Surprisingly, our study showed that a majority of UCEs were in fact present in the common ancestor of jawed vertebrates and that the ancient UCEs have accumulated substitutions at a higher rate in teleost fishes, so much so that one-third of them have diverged beyond recognition.
[...]
Together, these data indicate that the UCEs have been evolving rapidly in the teleost fish lineage. The absence of a large number of ancient UCEs in teleost fishes is consistent with our previous observation that a significant number (65%) of ancient conserved noncoding elements (>70% identical across >100 bp) present in the elephant shark and human have diverged beyond recognition in teleost fishes.
Teleost fishes, remember, includes us tetrapods.
Science in action, folks. This paper uses new data to disprove a hypothesis that had previously seemed plausible.
ETA: Edited to strike the above. More science in action. Thanks for catching my errant fish, Ray. Careless talk costs credibility. The thought process, if you can call it that, was: teleost = bony fish, and we're bony fish, therefore... That is, I read 'teleost' and thought 'osteichthyes', thrown off by their mention of tetrapods.
Bloody fish. I'll stick to me hominins in future...