A recent phylogenetic study, by Adam D. Leache of the University of California at Davis, of 53 out of the 90+ species in the lizard genus Sceloporus employs four nuclear genes, which were contrasted against a new mitochondrial genealogy based on six genes, revealed more conflicting than concordant relationships among the 21 defined species groups.
Perhaps the most effective means of conveying these results is to simply reproduce Figure 4 from the paper, which clearly shows the level of disagreement between the two methodologies via a multitude of skewed dotted lines. The tree derived from nuclear data is on the left, that from mitochondrial data to the right. Bear in mind that this graphic is comparing species groups, not individual species (e.g., the Sceloporus graciosus species group is comprised of the three species: S. arenicolus, S. vandenburgianus, as well as S. graciosus itself).
"The phylogenetic relationships inferred from the nuclear and mtDNA data are in strong disagreement (Fig. 4). Conflicts are not restricted to weakly supported or unresolved nodes, but include relationships that receive strong support in the separate analyses . . . . Furthermore, conflicts are found across different levels of the phylogeny and involve alternative placements for species groups and individual species. . . .
"Incongruence is not restricted to weak or unresolved nodes as might be expected under a scenario of rapid diversification . . ., but extends to conflicts involving clades receiving strong support (Fig. 4). This latter type of incongruence indicates that the nuclear genes are tracking a species history that is distinctly different from that of the mtDNA genome. . . .
"Tapping into the nuclear genome to assemble data sets containing hundreds of independent markers offers greater potential for elucidating difficult phylogenetic relationships . . ., such as those presented by Sceloporus, than does continued sequencing of the remaining genes of the mtDNA locus."
Some of the problems encountered when attempting to establish a phylogeny of Sceloporus are doubtless related to the hypothesized explosive radiation in its recent evolutionary history, which has resulted in an extensive and rapid diversification. One remarkable mechanism which could play a role in rapid diversification among such groups involves the acquisition of differing numbers of chromosomes, which would of course instantly render these groups reproductively isolated from each other:
"Variation in chromosomes numbers is a particularly interesting feature of Sceloporus, because chromosomal changes can contribute to species formation . . . . It is uncommon for members of a species group to have overlapping distributions; however, when communities of Sceloporus do form, they are generally composed of species with different chromosome numbers . . . . This pattern suggests that chromosomal rearrangements may play a key role during lineage formation by establishing genetic incompatibilities between species . . . . Whether the chromosomal changes observed in Sceloporus are adaptive is an open question, and the mechanism(s) responsible for increasing the rate of chromosome evolution in Sceloporus remain unknown."
The author additionally questions the wisdom of combining data obtained from nuclear and mitochondrial DNA for analysis, as most current studies utilizing nuclear genes are presently doing.
Leache, A.D. 2010. Species trees for spiny lizards (Genus Sceloporus): Identifying points of concordance and conflict between nuclear and mitochondrial data. Mol. Phylogent. Evol. 54(2010): 162-171. [PDF]