Confusion is the typical reaction when you tell somebody you're a phylogeneticist . Sometimes though, us phylogeneticists chance upon someone who's been waiting weeks, months, or even years to consult someone from our profession. For me this tends to happen when I strike up conversations with strangers while waiting in line at my local coffee shop. My most recent experience with coffee shop phylogenetics involved a guinea pig lover with a pressing question about where her beloved pets fall in the tree of life. She was particularly eager to get my thoughts the a rumor circulating among fellow afficionados that the guinea pig is not a rodent (apparently, some guinea pig fans would like to distance themselves from the less-ruputable mouse and rat lovers). I laughed and said "Of course, the guinea pig is a rodent. How else would you explain all of their stunning similarities, like the precence of constantly growing upper incisors?" When I tried to track down the source of her information, however, I was stunned to learn of the guinea pig battles that raged among phylogeneticists in the early to mid-1990s.
Things kicked off in 1991 with a parsimony analysis of amino acid sequence data published in Nature by Graur et al. suggesting that mouse-like rodents (myomorphs) were more closely related to primates than they were to guinea pigs (hystricomorphs). Hasegawa et al. responded immediately, showing that monophyly of rodents (myomorphs + hystricomorphs) was supported by maximum likelihood-based analyses and suggesting that the unusual myomorphs + primates inference was due to parsimony's inability to deal with unequal evolutionary rates. In a '92 response, Graur's group stood their ground, arguing that Hasegawa et al.'s results were an anomaly resulting from maximum likelihood analyses of highly divergent, "nonconservative" proteins. Graur continued to discuss the distinctness of guinea pigs and lobbied to have the Hystricomorpha recognized as a distinct order representing "one of the most ancient branches in eutherian evolutionary history." In a '93 PNAS paper, Martignetti and Brosius used the presence of a neural specific small cytoplasmic RNA (BC1 RNA) in guinea pigs and other rodents - but not in other mammals - to argue for inclusion of guinea pigs with rodents. Additional phylogenetic analyses of DNA sequence data by Hasegawa's group in '94 and Frye and Hedges in '95 further supported the guinea pigs as rodents hypothesis. By '96, even Graur had changed his tune and was considering the Hystricognathi a suborder of Rodentia (my knowledge of this history if obviously incomplete and he may have addressed this point more direclty elsewhere).
Just when the dust had settled, things blew up again with the publication of a Nature paper by D'Erchia titled simply "The Guinea Pig is Not a Rodent". Although this paper rejected rodent monophyly, it suggested a rather different tree than that of Graur et al. (1991). This time, the New York Times even got involved. Of course, Hasegawa's group rallied once again to dismiss the guinea pig is not a rodent argument, arguing that, at the very least, there simply wasn't enough support to overturn the traditional classification (a point that was reinforced by similar conclusions from Philippe). Where do things stand now? Suffice to say that nearly everything published over the last 10 years has strongly supported inclusion of gunea pigs in a monophyletic rodentia (e.g., Prasad et al.'s recent phylogenomic analysis fo mammals). In any case, the guinea pig wars represent an interesting historical anecdote and a powerful example of the symptoms that can result when systematists are engaged in intense debate over the value of different types of data (morphological versus molecular) and different types of phylogenetic methods (parsimony versus maximum likelihood).
Sorry guinea pig lovers: you're living with a rodent whether you like it or not.