I have been pondering the phylogenetic approach to taxonomy and came up with a question. How do monophyletic trees, particularly those based on molecular data, account for species of natural hybrid origin?

Any help would be appreciated

--Stephen

If one is looking at 2 trees made from 2 loci, one nuclear, the other from the chloroplast genome, then its made possible. The nuclear genome is biparentally inherited, whereas the chlorplast genome in maternally inherited in slippers. So, compare the trees, and find the mamma!

Best, Besk

Hrm using mitochondrial DNA seems like it would work and be very clever at the same time. But how do studies like Cox et. al. account for possible natural hybrid origin in creating their trees?

--Stephen

The mitochondrial genome is also maternally inherited, and harder to work with than the chloroplast genome. So, no help there. The Cox et al. study could not have completely controlled for natural introgression. Chimeric ribosomal DNAs are known (e.g., in very recent hybrids), but a phenomenon called gene conversion usually renders all ribosomal DNA copies the same as one parent or the other within an organismal group. It's hard to tell which way it goes until you do the sequencing and see if you get 2 organismal trees nested inside each other (i.e., mixed copies from bosth parents) or only one organismal tree (gene converted). Probably the best that can be hoped for from that study is the vouchered specimens and their morphology.