In article 4siv at unix1.sncc.lsu.edu, xxia1 at unix1.sncc.lsu.edu (Xuhua Xia) writes:
[most of a very interesting post deleted]
>The lineage effect refers to the phenomenon that the same clock,
>e.g., the same (the "sameness" is hard to define) protein-coding
>gene, ticks at different evolutionary lineage.
Isn't orthology your "sameness" ?
Two genes are homologous if they share a common ancestor.
Two homologous genes are paralogous if they diverged after a duplication
event in the genome.
Two homologous genes are orthologous if diverged after a speciation event.
This of course ignores modular evolution of genes.
>Does the detection of a lineage effect hurt the concept of
>molecular clock? It could, if the effect is rather dramatic, and if
>it is found in almost all genes.
If a lineage effect exists (as it seems to in murids (rodents ?)) it should
in my understanding affect all genes.