HI Gregiore, 

This is a topic that has taken my attention for sometime, morphological vs molecular. With many people holding polarized views. 

It also comes from what your view of a species is. There are cases of morphologically distinct but molecular identification and vice versa. 

Certain organisms are classified as different 'species' but have the same DNA barcode and also the converse. 

If one is to go down the molecular route than it is a basic requirement to use mitochondrial and nuclear genes but certain fungi do not contain mitochondria. 

If going down the morphological route it is suggested that habitat preference ought to be taken into account also. Then there is the possibility of subspecies, ecotypes etc but not everybody agrees with. I'm a little on the fence at the moment (after having been solidly in the molecular camp). 

Very interested to hear your views and those of others. Hopefully this will provide for a fruitful discussion. 

HI Gregiore, 

This is a topic that has taken my attention for sometime, morphological vs molecular. With many people holding polarized views. 

It also comes from what your view of a species is. There are cases of morphologically distinct but molecular identification and vice versa. 

Certain organisms are classified as different 'species' but have the same DNA barcode and also the converse. 

If one is to go down the molecular route than it is a basic requirement to use mitochondrial and nuclear genes but certain fungi do not contain mitochondria. 

If going down the morphological route it is suggested that habitat preference ought to be taken into account also. Then there is the possibility of subspecies, ecotypes etc but not everybody agrees with. I'm a little on the fence at the moment (after having been solidly in the molecular camp). 

Very interested to hear your views and those of others. Hopefully this will provide for a fruitful discussion. 

Hi Gregiore,

I see you say species community, are you studying related species within the same family or genus or species assemblages in a community?

If your specimens are thought to belong to the same family/genus based on morphology or behavior and no previous studies have been done I would suggest an integrative approach.

If you use only one method you are less certain that your results are correct, if you get congruent results based on several methods you are more certain. An approach including morphology and multi gene analysis is in many cases optimal.

Convergent or parallel evolution can drive unrelated or not closely related taxa, towards a similar morphology due to similar behavior, diet or habitat. Also molecular phylogenetics have shown several cases where distinct morphotypes are one species or species thought to be one species is in reality a cryptic species complex. So basing your research on only morphology you may mistake convergence for descent form a common ancestor.

As Asif said, a barcode or a gene can be identical between groups seen as different species; the way to solve this is to do a multi gene analysis to see if your specimens are distinct or the same for more than one gene. So if you base your analysis on only one gene and that one is extremely conserved for that taxa, you may overlook species that are unique by other genes, behavior or morphology.

Additionally the method you analyse your genetic data by may cause different results, so many try additional methods to test their data, for example Bayesian analysis is prone to too high supports, so many supplement it by doing an additional Maximum likelihood analysis.

Of course all this depends on taxonomic level, if you are trying to separate species I would go with morphology + two common genes for the group analyzed with Bayesian + Maximum Likelihood.

Some examples form sea slugs

Hope this helps.

Article Ohnheiser, L. T. & Malaquias, M. A. E. 2013. Systematic revi...

Article Systematic revision of the genus Scaphander (Gastropoda, Cep...

Article Speciation in the dark: Diversification and biogeography of ...

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Hi, 

First of all, thanks you for your very informative answers.

I study how phylogenetic diversity (at sensus lato) differs among various community of wild bees. So my specimens belong to different family but in the same superfamily Apoidea. 

My view of this, is that instinctively trees based on morphology  can be a good proxy from molecular tree cause it's only based on a taxonomic classification, there are some polytomies at very little levels like subgenus. But there is also no numerical proof that the morphometric is a good proxy from molecular approach. So your both answers make me advance in my scientific mind.

Thanks 

Hi Gregiore,

I don't kown too much about the studies relates to the insects, while I think if you want to study the difference of phylogenetic diversity among different communities, a tree should be constructed based on the DNA barcodes.

Best wishes!

Wumei

To go from empirical to philosophical, what is an accurate phylogeny? Without a time machine we can never know is what the "true" phylogeny. As mentioned above,  perhaps our best route to inference of phylogeny is through multiple data sets. Congruence of these data, and thus the phylogenies derived from them, would suggest a phylogenetic hypothesis that at least explains most of the evidence available. 

It depends on the taxa studied, if you will build a tree for distant species phylogenetically can study the HOX genes, if the taxa studied are fairly closely related species phylogenetically can analyze the 16S gene, if we study taxa of the same species can be done by building a phylogenetic several types of markers but again it depends on the goal. If you want answers about breast-way through building a phylogenetic evolution is made by the study of mtDNA (including mammals) for paternal route markers are used in the Y chromosome, the study by microsatellite (at least 20 markers in 20 unrelated individuals) remains an acceptable study is interesting, but the top is currently using the SNP for the phylogenetic construction. For the morphological markers used for phylogenetic building back strength especially if the tree is compared with another carried out by molecular markers.

 Yes surely with many datasets we should find if there are some differences between the different phylogenetic reconstruction methods (ML, Bayesian, NJ, UPGMA, ...). And clearly it is a good question to know what is an accurate phylogeny if we have no proven reference. And clearly we have a multitude of phylogenetic trees cause its depends n phylgenetic recnstruction and also the basal data which are the considered genes.