Multilocus phylogeny of alligator lizards (Elgaria, Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses.

The increased availability of nuclear DNA sequence data has led to a better appreciation of the role and frequency of introgressive hybridization and subsequent mitochondrial capture in misleading phylogenetic hypotheses based on mtDNA sequence data alone. Relationships among members of the alligator lizard genus Elgaria have been addressed with morphology, allozyme and mtDNA sequence data with discordant results. In this study, we use seven nuclear loci (total of 5.9kb) and ∼3kb of mtDNA to infer the phylogenetic relationships among Elgaria species and test whether the discordance among previous phylogenetic hypotheses is due to introgression and mtDNA capture. While gene tree topologies varied among the different loci, we recovered a well-resolved coalescent-based species tree. Contrary to our expectations, the nDNA-only species tree does not support the sister relationship between E. kingii and E. panamintina inferred from the previous allozyme study. Nevertheless, we found evidence for possible mitochondrial capture in two unexpected situations. The first instance of mtDNA capture involves E. paucicarinata from the Cape Region of Baja California. MtDNA recovered a clade comprising E. paucicarinata and the other two peninsular endemics, while the nDNA-only species tree recovered E. paucicarinata as sister to the continental E. kingii. We hypothesize that this discordance is the result of ancient mitochondrial capture rather than incomplete lineage sorting. Additionally, analyses of nDNA recovered E. panamintina as sister to an E. multicarinata North lineage, whereas the mtDNA gene tree recovers E. panamintina nested within a southern E. multicarinata clade. We hypothesize that this discordance also may be due to mitochondrial capture. Additionally, hybridization between these two lineages may have resulted in geographically limited nuclear introgression. Divergence dating analyses suggest that oviparous Elgaria species diverged within a relatively narrow timeframe from the late Miocene to early Pliocene. We find that accounting for introgressed alleles is important when inferring phylogenetic relationships when using coalescent-based approaches.