User:Berton/APG

Criticism on this classification:
 * Angiosperm Phylogeny Group
 * It is just for to be based on chloroplast genes that the main reason which this classification should be rejected because it analyses the plastid genome (thus an allogenome), a cyanobacteria, a co-evolutional being, a symbiont, and not the plant genome per se (by itself).
 * It is regarded chaotic (since it makes changes so radically, that soon, will be better that we use only the common names rather than scientific names).
 * It is anti-Linnaean (since it uses Cladistics, that is, does not fit in Linnaean taxonomic categories).
 * It is anti-Taxonomic (since it is corrosive to major taxa, like Family).

A classification only gone back to the past, only cladogenetic (of the lumper kind), that denies the evolution as anagenesis (= paraphyly), that does not present morphological synapomorphies (impractical) is a classification totally useless and a loss of time that will only leads to the increase of the confusion and without a doubt it should be rejected.

The study of genome of the chloroplast has been disturbed for the fact of this genome it is uniparentally inherited and this on the one hand technically facilitates the analysis, on the other hand, it changes the phylogeny inference, consisting of paraphylogeny. (see "This is conclusive evidence that chloroplast DNA is inherited in a maternal manner.")

Citing Whittemore & Schaal 1991: "The demonstration that chloroplast DNA in natural populations may be acquired from distantly related organisms, so that relationships shown by this molecule may not be representative of the genome as a whole, suggests that chloroplast DNA data must be used with caution in cladistic studies of plant relationships where hybridization may occur. It is difficult to determine how common introgressive plastid exchange may be in plants, since many published studies of chloroplast DNA variation are based on very small samples, often only one individual per species." (also cited by Arnold 2007 [in Kindle version on location 779]).

According to Steane et al. 1999:"Finally, one criticism of the cpDNA-based phylogenies centers on the uniparental mode of chloroplast inheritance (Harris and Ingram, 1991 ; Mogensen, 1996 ). Phylogenetic reconstructions based on cytoplasmically inherited genomes may be susceptible to significant error from hybridization and introgression or lineage sorting (Rieseberg and Soltis, 1991 ; Doyle, 1992 ). Comparisons of trees derived from nuclear DNA with those derived from cpDNA may assist in the identification of such problems, as well as providing corroborative evidence of relationships hypothesized by cpDNA data."

Another evidence (among many others): "A long history of hybridization and introgression in the evolution of Betula has made the use of chloroplast genes to infer interspecific relationships prone to errors....In the chloroplast matK gene tree, most North American species [of Betula] formed a clade, as did the Eurasian species (Järvinen et al. 2004), implying that chloroplast capture may have occurred during the early diversification of Betula, thus rendering sequences of the chloroplast genome inappropriate for resolving interspecific relationships (Li, unpublished data)".

For more sources on this topic:Rieseberg & Soltis and Okuyama et al.

It is already a well-known fact that the genetic research of APG, mainly APG I, is based almost thoroughly on genetic material of plastid, that not even it is a plant, and it was already demonstrated in several works that there is incongruence among the data of the cpDNA and those of nuclear material.

APG has its blame parcel in destroying the stability of Taxonomy and it makes it in the worst way: through molecular research in organelles that are endosymbionts.

"Chloroplast genes have been used extensively in plant cladistic studies. Chloroplasts are semi-independent organelles that can become disassociated from their normal nuclear genome (Rieseberg and Soltis, 1991 ). Consequently, a particular chloroplast gene may or may not be a reliable indicator of the overall genome of the species in which it is found, depending on its history.

Cronn et al. 2002 analyzed molecular characters in diploid species of Gossypium belonging to the various chromosomal genome groups (A, B, D, etc.). They used three types of DNA and one or more genes in each type: ribosomal DNA (one gene), other chromosome segments (11 loci), and cpDNA (four genes). The cladograms for the 12 loci in the two types of nuclear DNA are in agreement with the other evidence concerning phylogeny of Gossypium. But the cladograms for the four chloroplast genes are incongruent with this evidence and give incorrect phylogenetic indications." from Grant, Verne 2003 . Thus the studies based on chloroplast DNA are evaluations of the endosymbiont genome that has inheritance pattern different from the plant genome (host).

Observe that: Bacteria of the genus Agrobacterium have developed a special mechanism that allows transfer of genes from the bacterium to higher plant chromosomes. It is well known for its ability to transfer DNA between itself and plants, and for this reason it has become an important tool for plant improvement by genetic engineering.

Williams et al. (2007) also highlight the growing evidence that quorum sensing crosses the prokaryotic–eukaryotic boundary—a recurring theme throughout the other contributions to this issue.

Other "allogenomes": DNA transposons, retrotransposons, retrovirus, B chromosomes, plasmids, other endosymbionts; moreover most of DNA is junk DNA.

So after all these confused factors for the genetic research that this no doubt it should be subordinated to the morphological research, that is a field of the solid knowledge and not subject to "jack-in-the-box factors" (surprise factor) as the already mentioned. APG provoked an unprecedented crisis in the history of the Taxonomy when giving priority for the genetic research and relegating to second plan the morphological research. Kubitzki system has been making something very different having a balance between the two research types and it is for that reason that should be considered better.

Changing point of view about APG
An important addendum: With a new article DE Soltis et al. 2011 (APG IV ?) based on analyses from 17 genes extracted from 3 genomes e much more sampling of the plants (taxa), I considere that there was a great advance in phylogenetic treatment of Angiospermae.

But I accept the structural schema (topology) only, for the interpretation still we have a long way.

Even I accepting this structure I should say that it is insufficiently bi-dimensional when should to be at least tri-dimensional.

For me it is very difficult to accept that highly heterogeneous paraphyletic taxa might be transformed into a single monophyletic taxon sensu lato, with no clear morphological synapomorphies and apparently denying the divergent evolution (anagenesis).

Well, the APG V is on the way...and APG VI, etc...