[Taxacom] shared derived molecular similarities

[Sergio Vargas]

hi, thanks for the answer.


hmm... I'm going to discuss protein-coding "genes" in what follows. I'm aware
of the difficulties of non-coding regions with phylogenies being
more dependent on the alignment it self than on the characters or the method
used.

>My understanding is that one is not dealing with character states, but
>four different characters that replace each other so one really does not
>know what came before.

Say you can determine the position of the amino-acids in the structure of the
protein and follow the changes at any given position of the protein in time.
The 20 amino-acids would be character-states... or?

>Even with coding genes the genes are not necessarily the same length so
>one has to invent the homologies even before theorizing the replacement.

well, I think, in principle, the problem is not so different from establishing homology
between morphological parts when one or more sections have been deleted. Perhaps a naive example,
you can still establish that a segment occurring in position 5 in species A is homologous to
segment in position 3 in species B because in sp. B segment 4 was deleted... or? I almost sure,
morphological analysis consider this valid, and is only a very simple alignment...
Also, the alignment issue has been overemphasized; is only a real problem with certain non-coding
sequences or part of some "genes" (like the loops of ribosomal RNA).

>And in practice the outgroup is often so limited in taxonomic representation as to almost be meaningless.

well this one is easy... add more outgroups... or?

>Perhaps there is a solution to the above for molecular sequences, but I
>have not yet seen it (and what of non-coding sequences?). Some molecular
>theorists admit that sequencing is, after all, unreliable and now
>salvation lies with LINE's and SINE's - once again repeating the history
>of molecular systematics which is to jump from one to another and
>another technique as problems emerge with each, but the faith holds
>true.

what do you mean by unreliable? do you mean errors (mutations) during PCR/Sequencing?

sergio