[continued from previous message]   
      
   > 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.   
      
   Birds may in fact be different (though croc introns evolve even more   
   slowly). Still, have you tried within mammalian orders or some higher   
   groups?   
      
   As for birds and introns:   
      
   Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C. K. Bowie,   
   Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett,   
   Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H.   
   Sheldon,David W. Steadman, Christopher C. Witt, and Edward L. Braun.   
   Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes   
   Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2013,   
   419-444.   
      
   Sushma Reddy, Rebecca T. Kimball, Akanksha Pandey, Peter A. Hosner,   
   Michael J. Braun, Shannon J. Hackett, Kin-Lan Han, John Harshman,   
   Christopher J. Huddleston, Sarah Kingston, Ben D. Marks, Kathleen J.   
   Miglia, William S. Moore, Frederick H. Sheldon, Christopher C. Witt,   
   Tamaki Yuri, and Edward L. Braun. Why Do Phylogenomic Data Sets Yield   
   Conflicting Trees? Data Type Influences the Avian Tree of Life more than   
   Taxon Sampling. 2017. Systematic Biology 66(5).   
      
   Jena Chojnowski, Rebecca Kimball, Edward Louis Braun. Introns outperform   
   exons in analyses of basal avian phylogeny using clathrin heavy chain   
   genes. 2008. Gene 410(1):89-96.   
      
   Shannon J. Hackett, Rebecca T. Kimball, Sushma Reddy, Rauri C. K. Bowie,   
   Edward L. Braun, Michael J. Braun, Jena L. Chojnowski, W. Andrew Cox,   
   Kin-Lan Han, John Harshman, Christopher J. Huddleston, Ben D. Marks,   
   Kathleen J. Miglia, William S. Moore, Frederick H. Sheldon, David W.   
   Steadman, Christopher C. Witt, Tamaki Yuri, A Phylogenomic Study of   
   Birds Reveals Their Evolutionary History. 2008. Science 320:1768-1768.   
      
   >>> 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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