what do you think about phylogenetic studies based on molecular markers which draw toplogies for speciation patterns of organisms? Can gene(s) tree(s) reflect the evolution as is?
I think that the border between gene and species tree is quite obvious as they may not coincide to each other. What do you mean in "paraphyly can not be easily ignored"?
Not only the observation that different genes carry different information and thus their analysis results in different evolutionary scenarios is a problem. Furthermore the shape of a cladogram is likely to be influenced by extinctions - maybe even more than by speciation. Intermediates are lost through extinction and branches get longer and longer. This causes the phylogenetic signal to erode. Of course we do not know much about extinct taxa and thus a phylogenetic tree or cladogram can never show the "real" historical evolution. Trees are approximations, nothing more but nothing less. Good luck!
a gene tree reflect the evolution of its own, it will not give clear full views on the organism evolution.
comparison is the term that is been utilised for studies and if important contributor is absent in study it not provide correct tree but still it can indicates like a mile stone or a signboard.
In my point of view Evolution is not an individual's game its due to the surrounding that make or force the individual/species to change so to understand it its important to study all.
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