First a disclaimer- I am not a taxonomist, and I am not particularly familiar with rosy boas. I'm just throwing out some ideas here.



You draw a connection here between size and relatedness, but this is not necessarily the case. I can see a few scenarios that would result in the conflict between MtDNA and morphological data.



1). The adult size of these snakes is non-genetic. The 'dwarf forms' simply live in a habitat that causes them to remain small. A number of factors could lead to this: prey is scarce or of poor quality; seasonal activity is limited; larger individuals are selectively preyed upon; individuals breed at small size or early age, diverting nutrients from growth; etc. Thus the two lineages are affected by the same factors in the southern mountains. Perhaps if the southern lineage reached farther north, it would also show regional variation in size.





2). The adult size of these snakes is genetic, but small size has evolved in parallel in the southern lineage and in southern populations of the northern lineage. Similar selective factors have resulted in similar phenotypes.



3). The converse of (2)- The adult size of these snakes is genetic, but small size is the ancestral state. Some populations of the northern lineage have evolved to larger size.



4.) The adult size of these snakes is genetic, and represents a primary division between a dwarf lineage and a large lineage. This is in actual conflict with the MtDNA data and could result in different taxonomic conclusions. Perhaps the MtDNA was skewed by incomplete sorting of mitochondrial lineages due to a recent divergence between these two lineages, or represents an earlier incomplete divergence between two lineages, followed by subsequent partial reintegration and redivergence.



5.) The converse of (4)- the southern and small northern snakes are evidence of an older incomplete divergence.



Taxonomy really has no way to deal with (4) and (5); only one split is important, the most recent one. So the following taxonomic schemes would be suitable:



Scenario 1:



Charina "Northern"

Charina "Southern"



Scenario 2:



Charina "Northern"

-----"Northern Large"

-----"Northern Small"

Charina "Southern"



Scenario 3:



same as 2



Scenario 4:



Charina "Large"

Charina "Small"



Scenario 5:



Charina "Northern"

Charina "Southern"

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