How should we treat hybrids in a taxonomic scheme?

There are many plant genera that have long been considered to involve extensive hybridization, as indeed there are also for vertebrates (eg. Lepus, Salmo). These genera form complexes of taxa that apparently intergrade due to individuals that are phenotypically and genotypically intermediate. One such plant genus is Nicotiana (tobacco).

In 1954 Thomas Harper Goodspeed published a summary of his lifetime's work on this genus, consolidating his data concerning morphology, cytology, genetics, distribution and taxonomy. While this work was not universally well received, especially the taxonomy (eg. DeWolf 1957), it does contain one interesting diagram, which is an evolutionary network summarizing his ideas on the phylogeny of the genus.

Since the relationships are complex, so is the diagram. However, basically, Part A summarizes the relationships among some of the species, while Part B summarizes the rest along with "centroids" representing the species from Part A. The different orbital rings represent hypothetical ancestors of the various groups, with the groups having different numbers of chromosomes.

As Knapp et al. (2004) have noted: "Amphidiploid (allotetraploid) hybridization is common in the genus and appears to be unrelated to human intervention; both the tobaccos of commerce as well as several other species and species groups are amphidiploid hybrids." An amphidiploid is an interspecific hybrid having a complete diploid chromosome set from each parent. It is this hybridization that creates the complexity among the tobacco taxa, and its nature is summarized by Chase et al. (2003).

Goodpseed's hybridization network is a fascinating early attempt to represent evolutionary complexity, irrespective of what one thinks about his methodology, which is never satisfactorily explained. The existence of subjectively determined hypothetical ancestors is probably the most worrisome aspect.

However, apart from drawing attention to the existence of the network, I wish to raise a point about how to turn this complexity into a classification. Goodspeed (1947) had a go at this, as did Goodspeed (1954). However, more importantly Knapp et al. (2004) made a more recent attempt, and they had this to say:

We retain Goodspeed's sectional classification as the basic framework for this new classification, understanding that different ways of treating hybrids in phylogenetic classifications have been proposed. 

In this sectional classification we have placed all amphidiploid species in sections separate from their progenitor taxa because they represent fusion of two distinct genomes, and based on studies such as Kenton & al. (1993) we know that these genomic interactions create new traits and permit movement into new habitats.

The classification is based on a phylogenetic tree onto which the authors have plotted reticulations representing hybridization (see below). Those taxonomic sections that are represented in the tree-like parts of the phylogeny can thereby be considered to be monophyletic, but those sections consisting of hybrids cannot.

Summary of the classification of Nicotiana, showing diploid species and their sectional classification.
Sections of allotetraploid origin are indicated by dashed lines from both of their parental lineages.

My question is this: Is this really the best way of treating hybrids taxonomically? It looks a bit like an attempt to sweep all of the problems together into separate piles, and then simply labelling them "problem piles".

Mind you, in this particular example all of the hybrids in any one section are hypothesized to have had the same lineages as parents, so there is some coherence to each section. However, unless we hypothesize a single hybrid origin for  each section the component species cannot be considered to have a unique common ancestor, which all of the non-hybrid sections do have. In this sense the sections are not directly comparable.

References

Chase M.W., Knapp S., Cox A.V., Clarkson J.J., Butsko Y., Joseph J., Savolainen V., Parokonny A.S. (2003) Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Annals of Botany 92: 107-127.

DeWolf G.P. (1957) Review of Goodspeed (1954). The Southwestern Naturalist 2: 177-179.

Goodspeed T.H. (1947) On the evolution of the genus Nicotiana. Proceedings of the National Academy of Sciences of the USA 33: 158-171.

Goodspeed T.H. (1954) The genus Nicotiana: origins, relationships and evolution of its species in the light of their distribution, morphology and cytogenetics. Chronica Botanica 16: 1-536.

Knapp S., Chase M.W., Clarkson J.J. (2004) Nomenclatural changes and a new sectional classification in Nicotiana (Solanaceae). Taxon 53: 73-82.