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Re: Retroposon evidence for an explosive radiation of Neoaves



Hi,

happy new year everyone!

evelyn sobielski schrieb am 2012-01-05:

[...]
> Without these analyses one cannot *know* whether mere presence of a
> transposon (any kind of transposon) at an unspecified locus is an
> apomorphy, or a homoplasy. We only know a taxon has it, but it may be
> highly mobile *within* that taxon.
Please keep in mind: once inserted and fixed in the population, a RETROposon
will not "jump" like a DNA transposon. It'll stay in the same place
(witnessing the same random mutations as any non-coding DNA) and, if it's a
full length element, it might distribute copies of itself somewhere else in
the genome..

> At present the assumptions of transposing frequency in birds are
> simply guesstimates not supported by any hard data. I had the odd
> transposon (all sorts) in my taxon/locus set, and usually they were
> devoid of any pyhlogenetic pattern, or almost so. I.e. they may
> "jump" more quickly than generally supposed.
Not all genomic insertions are derived from retroposons or DNA transposons.
:-) See the comment below for distinguishing retroposon insertions from DNA
transposon insertions and from random insertions.

> In any case, the claim that "one should not BLAST retroposons" is
> dangerously untrue, at least according to the (plant) retroposon
> experts I asked.
> You need to be careful with your BLAST parameters though. Using the
> standard settings will indeed yield only nonsense. But if you account
> for partial sequence loss/gain, you will get *interesting* results...
[...]
If you BLAST a piece of non-coding DNA (potentially including a retroposon)
against a database of other pieces of non-coding DNA (e.g., GenBank's
nucleotide collection), the results will indeed be "interesting" (in most
cases not telling you anything about the type of repetitive DNA in there - it
could still be a retroposon, DNA transposon or a random insertion).
Instead, try to use one of the tools for repeat masking (e.g., Repeatmasker,
Censor) - they compare your sequence to a database of known retroposons and
DNA transposons - if you, by doing that, find an insertion that has similarity
to a retroposon (either to a full-length retroposon or to the 3'-end of a
retroposon; but be careful with those that have just a few basepairs
similarity to a middle or 5'-end part of a large retroposon - such a hit is,
in most cases, due to random sequence similarity), I'll be curious to see if
you will still have retroposon presence/absence markers "devoid of any
pyhlogenetic pattern". :-)

Best regards,
Alex