Results: Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control
region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers
obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of
phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor
resolving power; very few species’ nodes in the tree are supported by bootstrap resampling. The
AFLP phylogeny is considerably better resolved and more congruent with relationships inferred
from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops.
The AFLP data indicate a close relationship between the two spotted dolphin species and recent
ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei
lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological
expectations but the phylogenetic analysis is not.
Conclusion: For closely related, recently diverged taxa, a multi-locus genome-wide survey is
likely the most comprehensive approach currently available for phylogenetic inference.