Nowhere does that article suggest that horizontal gene transfer is common in animals. As I said, it occurs but is not common. You can find a balanced (and later) assessment here. Relevant snippet: ‘The results suggest that “if we use the same yardstick to measure a variety of model organisms, it’s possible to say that mammalian genomes have also been subjected to low levels of HGT, although it happened only on very rare occasions at the early stages of evolution.’"
Read the paper. “On the other hand, regions corresponding to exons I and V were not identified in the guinea pig Lgulono-y-lactone oxidase gene homologue”, and “The regions corresponding to the rat GLO gene exons except for exons I and V were identified in the guinea pig gene, and their sequences were determined.” They didn’t show that exon 1 was missing: they failed to find exon 1. (They examined the sequence for exon 5 and showed that it wasn’t present, but did not do the same for exon 1.) Since they were searching for the gene by physically hybridizing the DNA, it would have been impossible for them to find exon 1, given how divergent the GP and mouse exons are.
As I said, I didn’t find anything. The finding was done by the comparative genomics folks at UC Santa Cruz. I just downloaded the files. They do their cross-species alignment using whole-genome sequence and the tool BLASTZ. That approach is dramatically more sensitive than the GP study (which was done 20+ years ago), and also more sensitive than the search that missed human exon 5, which used BLAST rather than BLASTZ.
true. i reffer to a different tree made by different (regular)genes, and not about lgt. we know that its very common that some genes tell different story. see this paper for example:
2)evolution cant explain how this lgt happan in animals. so even one event is a problem to the evolution senario.
fair enough. but still- why this result have not publish in a peer review article? why the new article from 2011 doesnt fix this? where is the peer review?
here is an example of 2 mutations without a commondescent:
and even in the gulo one rat share one base with chimp.
Sure, single-gene studies are noisy, but that is easily addressed by using more sequence. Incomplete lineage sorting means that closely spaced branches don’t actually have a unique tree, but that is expected and also easily dealt with. There are indeed real problems with ordering deep branches that are fairly close together: there simply isn’t enough information to determine the tree. But none of that changes the fact that DNA routinely produces reliable trees; it just means that there are well-known spots in the trees where the precise order is uncertain.
Sure it can (or rather, biology can – it’s not really the job of evolution). There are multiple plausible mechanisms for HGT in animals, several of which have been observed in intermediate states.
Because it’s trivial. Basically, no one cares. With whole-genome databases readily available, no one is going to go back and update all of the single-gene sequencing studies in the literature.
Which mutation do you mean? (It’s hardly surprising that the same mutation occurs independently in multiple lines, by the way. What we’re looking for is convergent mutations that happen more frequently than you would expect by chance.)
there is a lot of problems with this method that we can discuss about. but the main point is that this tree isnt evidence for a commondescent more then a commondesginer.
can you give an explanation for lets say this one:
about the uox pseudogene- i reffer to those mutations:
" One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications"-
and the mutation at codon 107:
“The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation”
Sure it is. Common designers routinely violate hierarchical trees. In fact, that’s an important component of intelligent design – any software engineer can tell you that good design involves reusing components across diverse applications.
That’s an interesting one. It will take me a while to dig out the sequence to look at it.
That’s not an interesting one. That a recurring mutation at a “CG” dinucleotide, better known as a CpG. That particular combination of nucleotides mutates to T at a very high rate (because the C in that pair is usually methylated, and methylated C spontaneously deaminates to thymine). They’re routinely discarded from many comparative analyses because recurrent mutations are so common at such sites. So multiple independent mutations at this site are not surprising. (Something I believe is mentioned in the paper somewhere.)
Where there is little horizontal gene transfer, living things do not routinely violate hierarchical trees.
False. You can’t just lump all mutations together; you have to try to understand what you’re looking at. Highly mutable sites will frequently appear as multiple mutations in different parts of the tree. Other kinds of mutation will rarely appear independently in different parts of the tree. That’s the actual expectation of common descent – not that all mutations should follow the tree perfectly. And that’s what we see.
ok. lets check this. take for example the tetrapod evolution. the phylogenetic tree base on molecular evidence show one tree and the fossil one show another. i also gave this one:
“This family tree is backed up by reams of genomic and morphological data, and is well accepted by the palaeontological community. Yet, says Peterson, the tree is all wrong.”
and i can show you a lot more examples.
true according to evolution. but then the main argument that shared mutations is evidence for a commondescent is false. because there is a lot of examples for a shared mutations without a commondescent.
Chimpanzees are the same as humans there, and gibbons look similar. The anomaly is that gorillas and orangutans share a chunk of sequence not found in humans/chimps or the more distantly related gibbons, even though gorillas are more closely related to humans than they are to orangutans.
You may recall that I previously said that deletions tend to occur where there are stretches of nearly identical, duplicated sequence. (The same is also true of duplications, by the way.) And that’s what we’ve got here. Gorillas and orangutans have three (nearly identical) copies of an 8-base-pair repeat, while humans and gibbons have two. (Specifically, it’s a direct tandem repeat, meaning that the copies go in the same direction and are placed next to one another.) This should indeed be a hotspot for both insertions and deletions of copies of the repeat, and finding violations of the tree here is not surprising. I wouldn’t want to venture a guess as to whether it was two independent duplications in orangs and gorillas, or two independent deletions in gibbons and the human/chimp ancestor, that led to the incongruity. More distantly related primates (monkeys and prosimians) have only one copy of that segment, so it was probably first duplicated in an early ape.
We expect to find some disagreements at the cutting edge of science. At the time of the Nature article, Peterson had not yet accumulated enough data or performed enough analysis to even publish an article on the implications of miRNA for mammalian phylogeny. So how does the article somehow disprove our understanding of the standard phylogeny?
Second, Peterson does not for a second think that his analysis, such as it was/is, disproves evolution. He is looking to refine the phylogeny; he does not contend that miRNA deals a blow to the theory of descent with modification from common ancestors.
