I recently came across some paper dealing with taxonomical revisions (land snails) claiming that a phylogenetic tree based upon COI only can provide strong and solid phylogeny of a group of species. In the same papers, a full set of essential characters (genital morphology) has been totally neglected. My results tell us this is not true. I've been told that COI phylogeny is "stronger" and more trustfull than genital morphology. What do you all think about it?
The answer as stated above is definitely NO! Fortunately in the recent years integrative approach to taxonomy became more and more widespread. This is especially useful when mitochondrial and nuclear sequences show discordant results. We have several good example for this in earthworms. E.g.
Mol Ecol Resour. 2016 Jul;16(4):883-94. doi: 10.1111/1755-0998.12517. Epub 2016 Mar 17.
Mitochondrial DNA. 2015 Dec 28:1-9. [Epub ahead of print] http://dx.doi.org/10.3109/19401736.2015.1115487
Or course no. But this strongly depends on the group. Within genus it is much more useful than for example between genera or let's say families.
Hi, Willy
I think Barna and Dilian are right. I am no expert here, but the evidence of differing results obtained when different sequences are compared tells us that we have to be very cautious. I personally think that even when phylogenies are constructed using a number of nuclear sequences, we have always to remember that even a highly supported set of relationships has elements of doubt. And Barna is right: the deeper the phylogeny, the more sceptical we should be that we have the "right" answer
Thank you Barna and thank you Robert for your interesting replies. I think we are missing the point anyhow. I'm not only questioning the absolute validity of COI phylogeny but the relationships between COI phylogeny and what genital morphology tells us. How should we handle the issue in case of conflicting results? This is my biggest puzzlement! Thank you!
Dear Jonathan,
Thank you for your reply. If morphological changes have been created for any adaptation reason, and these changes are durably transmitted to the lineage, it means that this information must originate from a stable molecular change. If so, don't you think it could be just a matter of which genes we use as markers? Why we use COI gene if it is not directly involved in speciation process? Genital morphology is the result of the expression of more that a single gene I guess.
Cheers,
Willy
I think there are a number of cases where genital morphology and at least some phylogenies inferred from molecular data do not agree. I don't have the references to hand, but try finding papers by A. Parmakelis on Mastus, and correspond with Antonio Frias Martins on Azorean Oxychilus. The former found matings between individuals with rather different genitalia, and I know that Martins (I think not fully published) has found inconsistencies between reproductive anatomy and some molecular analyses that were done for him.
Theoretically it is better to use genes which are not involved in the evolution of reproductive barriers and the adaptation to the environment, because than they are independent data sets.
Dear Willy, In my experience with veronicellid and other slugs, as well as some snail families, I have found that genital morphology is critical, and then doing molecular work to see the two methodologies support one another, and then trying to reconcile differences if they occur. Secondly using at least two (or more) genes, a mitochondrial gene like CO1 and/or 16S, plus nuclear genes such as 28S or ITS1 or ITS2. Sadly too many researchers depend exclusively on molecular analysis, as they have no knowledge of anatomy, and too often miss vital bits of data that could help in interpreting molecular results. Your choice of genes, of course, is critical in what you are trying to achieve, whether phylogeny of lower level taxonomy.
The answer as stated above is definitely NO! Fortunately in the recent years integrative approach to taxonomy became more and more widespread. This is especially useful when mitochondrial and nuclear sequences show discordant results. We have several good example for this in earthworms. E.g.
Mol Ecol Resour. 2016 Jul;16(4):883-94. doi: 10.1111/1755-0998.12517. Epub 2016 Mar 17.
Mitochondrial DNA. 2015 Dec 28:1-9. [Epub ahead of print] http://dx.doi.org/10.3109/19401736.2015.1115487
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