[continued from previous message]   
      
   tried to do it decades ago (I had a post doc with cattle) and for most   
   introns you could not match up mouse and human or cattle and human   
   introns.  There was some highly conserved sequences in some introns, but   
   they were likely regulatory sequences.  Blast would not match up the   
   mouse and human tyrosinase intron, and under relaxed conditions it would   
   produce short matches, but a lot of the short matches were with other   
   chromosomes and not the intron sequence.   
      
   Further on I do determine that avian introns are more conserved.  I   
   worked with chicken sequence for decades and never bothered to look at   
   the intron sequences because of my experience with mammals.   
      
   I worked on an intron sequence that was highly conserved between birds   
   and mammals it was the regulatory sequence for sonic hedge hog but it   
   was in an intron of a neighboring gene.  SNP in the enhancer regulatory   
   sequence in both mammals and birds resulted in extra digits.   
      
   >   
   > Introns of course vary in evolutionary rate, both across taxa and within   
   > genomes. But I think the usefulness of introns even in mammal phylogeny   
   > is generally underrated.   
      
   Try to match up the mammalian introns.  I gave the example of Tyrosinase   
   intron 1.  BLAST would not match it up so it is less than 55% similarity   
   between mice and humans.   
      
   >   
   >   
   >> I checked the same Tyrosinase intron sequence that could not be   
   >> matched up between mice and humans for chickens and pigeons, and about   
   >> 1/3 of the sequence was likely not good for phylogenetic analysis (60%   
   >> similarity with multiple indels to make those matches) but the other   
   >> 2/3 was as high as 80% similar for 60 bp stretches with only a few   
   >> indels, so you could pick intron sequences that you could still   
   >> align.  I wouldn't like to maximize sequence similarity by inserting   
   >> indels for intron sequence.   
   >   
   > Why not? The indels are there, and generally easy to align. They can   
   > often be used as informative characters.   
      
   Because once you get down to around 75% similarity placing the indels in   
   the sequence likely produces spurious matches in the sequence flanking   
   the indel.  Some analyses that use sequence with indels remove the   
   affected sequence and some surrounding sequence from the analysis.  If   
   you just count the indel as a single event you would likely be making   
   spurious matches in the surrounding sequence immediately flanking the   
   indel because the indel is inserted where it maximizes the similarity   
   and not where it may have actually occurred.   
      
   >   
   >> The conserved regions likely averaged 75% similarity. You'd likely   
   >> need to implement some type of transition/transversion analysis to   
   >> estimate double hits, and have some estimate for the rate of change   
   >> for nonconserved sites relative to the conserved sequences.   
   >   
   > I recommend a maximum likelihood model.   
      
   I used to use ML in Felsenstein's philip back in the 1980's.  I was   
   working with nematodes and other invertebrates and was usually dealing   
   with divergent sequences.   
      
   Ron Okimoto   
      
   >   
   >> Divergence estimate between mice and humans is around 90 million   
   >> years, and between chickens and pigeons is around 89 million years   
   >> (estimates that I got from google).   
   >>   
   >> Ron Okimoto   
   >>   
   >>>   
   >>>>>> The additional sequence that Luskin is beefing about was sequence   
   >>>>>> that we could not obtain in all taxa, and it is still sequence   
   >>>>>> that can't be accurately compared between the taxa with complete   
   >>>>>> genome sequences because of the repetitive nature of the sequence   
   >>>>>> and the rapid copy number variations between species and the rapid   
   >>>>>> evolution of the sequence of the heterochromatin repeats.   
   >>>>>>   
   >>>>>> Luskin is literally beefing about something that never mattered,   
   >>>>>> and still does not matter.   
   >>>>>>   
   >>>>>> The mitochondrial DNA sequence is 8.9% different between chimps   
   >>>>>> and humans and still indicates that chimps are the most closely   
   >>>>>> related species to humans.  In the 1980's mitochondrial DNA was   
   >>>>>> the first sequence used to determine that of the other great apes   
   >>>>>> chimps were our closest relative.  It wasn't the 1% genomic coding   
   >>>>>> sequence difference. For the tyrosinase sequence that I used in   
   >>>>>> the above analysis both gorilla and chimps are 99% similar (16   
   >>>>>> mismatches with Gorilla and 20 mismatches with chimps) by blast   
   >>>>>> alignment.   
   >>>>>>   
   >>>>>> Ron Okimoto   
   >>>>>>   
   >>>>>>   
   >>>>>   
   >>>>   
   >>>   
   >>   
   >   
      
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