Even though this wasn't a major point in the last post, i want to disagree anyway:
To suggest that the genes unique to the human or fugu lineages are not 'the point of real interest' is in error. While it is absolutely true that sequence differences and gene expressivity are highly of interest, any genetic difference between species should be considered a candidate for causing important phenotypic differences. The presence/absence of unique, 'new' genes in one species relative to another is at least as radical as altering the expression of a gene relative to its homologue.
More importantly, though, the process of duplication provides the necessary material for functional divergence and ecological adaptation (and even speciation): Selection and drift can alter the function of genes to produce adaptation, but how can a new function evolve without losing the old one? Duplication is one important way.
It is the duplication of genes, chromosomes, and whole genomes that facilitates increases in organismal complexity through evolution.
The original article that started all of this is a bit misleading; the relevant point isn't that the pufferfish is extra-ordinarily similar to humans. In fact, Fugu's genome is as similar to humans as one would expect for its phylogenetic position! The neat thing is that its lineage has lost large amounts of non-coding DNA, leaving 'just genes'.
This is convenient because a big problem in comparative genomics is trying to just identify the genes. If we have a vertebrate genomic sequence that is fully annotated (ie. where all genes have been identified), this can be used as a reference point for studying the architecture and evolution of the human genome. Additionally, assembly of all the sequenced fragments of the human genome is generally quite difficult because much of the 'junk DNA' is made up of repetitive elements, leading to many possible overlapping contiguous sequences. Fugu has no repetitive sequeneces to speak of, so assembly is straightforward. Thats it.
Yes humans may have lost some genes and gained some relative to Fugu--and yes, these will be involved in making humans human, or making Fugu Fugu. In this respect the common genes are boring. However, the main point is that Fugu is a vertebrate--and vertebrates are all quite similar physiologically, biochemically, and therefore genomically.
As a final note, more DNA doesn't necessarily mean 'more information' if large parts of the sequence are "junk", or don't do anything. Contrariwise, elements of the so-called 'junk DNA' have been shown to play a role in affecting gene-expression (since they can contain transcription-factor binding sites)..and it is differences in gene-expression levels that are thought to frequently be responsible for the sorts of morphological differences that lead to ecological adaptation, and perhaps even speciation. In this respect, "junk DNA" can be more important than the actual genes--which is quite contrary to most people's intuition. This is more or less a modern incarnation of King and Wilson's "regulatory hypothesis" which suggests that humans are so morphologically and behaviourally different from chimps because of differences in gene-expression (though we are ~99% similar when it comes to our *gene* sequences).
Slashdot Mirror
To suggest that the genes unique to the human or fugu lineages are not 'the point of real interest' is in error. While it is absolutely true that sequence differences and gene expressivity are highly of interest, any genetic difference between species should be considered a candidate for causing important phenotypic differences. The presence/absence of unique, 'new' genes in one species relative to another is at least as radical as altering the expression of a gene relative to its homologue.
More importantly, though, the process of duplication provides the necessary material for functional divergence and ecological adaptation (and even speciation): Selection and drift can alter the function of genes to produce adaptation, but how can a new function evolve without losing the old one? Duplication is one important way. It is the duplication of genes, chromosomes, and whole genomes that facilitates increases in organismal complexity through evolution.
The original article that started all of this is a bit misleading; the relevant point isn't that the pufferfish is extra-ordinarily similar to humans. In fact, Fugu's genome is as similar to humans as one would expect for its phylogenetic position! The neat thing is that its lineage has lost large amounts of non-coding DNA, leaving 'just genes'. This is convenient because a big problem in comparative genomics is trying to just identify the genes. If we have a vertebrate genomic sequence that is fully annotated (ie. where all genes have been identified), this can be used as a reference point for studying the architecture and evolution of the human genome. Additionally, assembly of all the sequenced fragments of the human genome is generally quite difficult because much of the 'junk DNA' is made up of repetitive elements, leading to many possible overlapping contiguous sequences. Fugu has no repetitive sequeneces to speak of, so assembly is straightforward. Thats it. Yes humans may have lost some genes and gained some relative to Fugu--and yes, these will be involved in making humans human, or making Fugu Fugu. In this respect the common genes are boring. However, the main point is that Fugu is a vertebrate--and vertebrates are all quite similar physiologically, biochemically, and therefore genomically. As a final note, more DNA doesn't necessarily mean 'more information' if large parts of the sequence are "junk", or don't do anything. Contrariwise, elements of the so-called 'junk DNA' have been shown to play a role in affecting gene-expression (since they can contain transcription-factor binding sites)..and it is differences in gene-expression levels that are thought to frequently be responsible for the sorts of morphological differences that lead to ecological adaptation, and perhaps even speciation. In this respect, "junk DNA" can be more important than the actual genes--which is quite contrary to most people's intuition. This is more or less a modern incarnation of King and Wilson's "regulatory hypothesis" which suggests that humans are so morphologically and behaviourally different from chimps because of differences in gene-expression (though we are ~99% similar when it comes to our *gene* sequences).