A recent study (Ruane et al 2014) attempts to clarify the admittedly messy phylogeny of the Western Hemisphere's colubrid snake species known as Milk Snakes (Lampropeltis triangulum). The previous monograph on this complex (Williams 1978, revised 1988) was completed in the era before the pervasiveness of phylogenetics (as well as "subspecies denial") and was based entirely on morphological characteristics. Williams envisioned a single species, widely distributed from southern Canada to northern South America, composed of 25 subspecies, all of which, except for the northeastern-most two, sport a similar ringed, tricolored pattern (ostensibly a Batesian mimicry of coral snakes). This monograph was a distillation of Williams' doctoral dissertation and suffered from a number of problems, for which it was appropriately taken to task by Greene (1979). Nevertheless, it has served as the working paradigm for this complex for the past 35 years or so, despite the number and quality of subspecies that it espoused.
Having ruminated upon both the recent paper and Dr. Ruane's dissertation, from which it is derived (available ] HERE, thanks to Bob Hansen), I have reached the conclusion that it's far from the final word on the subject. Admittedly, it appears to offer reasonable solutions to some of the problems within the complex, especially so with respect to the relationships of the tropical forms. However, regarding the Nearctic forms, it is essentially replacing one unsatisfactory paradigm (Williams 1978, 1988) with another. Restricting my comments to those forms found along and to the north of the U.S.-Mexican border, since those are the only ones I am familiar with, I'll enumerate my reservations below. These, of course, are merely my opinions - feel free to enlighten me!
1) Poorly defined taxon boundaries - Since it is obvious that most of us would have to resort to the current paper's range maps to identify which "species" of milk snake we were dealing with, it is unfortunate that the authors chose to propose altering the taxonomy of the group without better establishing the geographic boundaries of each taxon. For example: in south Texas and adjacent Mexico the Rio Grande is mapped as the boundary between the putative "Lampropeltis annulata" and the adjacent "L. gentilis" even though they actually had no specimens/tissue samples from that area. Considering that the type locality for Kennicott's L. annulata is Matamoros, Tamaulipas (i.e., across that little stream from Brownsville, Texas), plus the fact that the natural environments on either side of the river are virtually identical for many miles in any direction (i.e., the Tamualipan Biotic Province [Dice 1943]), it is highly improbable that snakes from the respective vicinities of Brownsville and Matamoros belong to different, discrete species or that they belong to a stable hybrid population. Additionally, despite a strongly recurrent tendency for proposals emanating from certain phylogenetics labs to postulate rivers as barriers to various species' distributions, the Rio Grande does not appear to be - or ever have been - much of a barrier to most species of herps.
2) Lack of sympatry among alleged species
My second reservation with this new milk snake revision is that the geographic distribution of these purported "species" is troubling. One of the "acid tests" of whether closely related forms are discrete species or not has always been if they are found in sympatry with each other - if they are sympatric then they must have developed some form of reproductive isolation and are therefore distinct species. As mapped in this study, the ranges of the three U.S. milk snake "species" are contiguous, fitting together like tiles (parapatry*), with little or no overlap.
Most fully discrete, broadly distributed, species, however, have ranges that overlap widely and even occur in broad sympatry in many areas. In much of the country it's possible to find three species of Lampropeltis occurring together; none of these three milk snake "species," however, exhibit this behavior amongst themselves (except for a small area in the southern Appalachians where the Eastern Milk Snake ["Lampropeltis triangulum"]and the Scarlet Kingsnake ["L. elapsoides"] apparently occur sympatrically - but not syntopically). Elsewhere they commonly "hybridize" (intergrade?) only at the contact points on the periphery of their respective ranges, which also means that they are routinely exchanging genes within these peripheral zones; according to several species concepts, that would make them the same species. Hybridization between actual full species occurring sympatrically is a relatively rare phenomenon (as it must be if they are to retain their discreteness).
Even with the Scarlet Kingsnake ("Lampropeltis elapsoides"), which I consider the most likely candidate for full species status among the three US "species", I have to wonder why the other "full species," of milk snake, "L. triangulum" (sensu stricto) from the north and "L. gentilis" from the west, have not occupied more of the range of "L. elapsoides." If they are, in fact, fully discrete and independently evolving lineages, why don't they occur more broadly sympatric with the Scarlet Kingsnake ("L. elapsoides"), much as Prairie/Mole Kingsnakes (L. calligaster) and Common Kingsnakes (L. getula [sensu lato]) do? Of course, in order to do so they would have to have had developed some sort of reproductive isolation mechanism to maintain their distinctness.
*Parapatric speciation - Theoretically speciation can occur in populations that are distributed parapatrically, at least according to Coyne and Orr in their book Speciation (2004), but in order for this to happen the amount of genetic exchange between adjacent populations must be extremely limited, not to the pervasive extent one commonly sees in intergrade zones of bordering subspecies. In fact, Coyne and Orr were hard-pressed to find unequivocal examples where parapatric speciation had definitely occurred in any form of animal.