4.3. Mitochondrial vs. nuclear phylogenies
Use of nuclear genes for phylogeny reconstruction in Middle
American cichlids has certainly been informative and provided
useful insight into relationships among tribes and genera
(Chakrabarty, 2006b; López-Fernández et al., 2010; Rican et al.,
2008; Smith et al., 2008). While the days of solely mitochondrial
based phylogenies appear to be numbered, to investigate species level
questions and relationships, at least within this group of
cichlids, one may have to rely on mitochondrial genes to provide
enough variability to resolve species relationships. Given the
potentially fast rate of lineage formation in cichlids, nuclear and
even some mitochondrial genes, may be too slowly evolving to
contain phylogenetic information at present (Salzburger et al.,
2005 and references within). We find that for the 36 herichthyine
species utilized in this study there is only a 0.8% average sequence
divergence based on S7-1 sequences. López-Fernández et al. (2010)
report that for RAG2 sequences, certain species of Paraneetroplus
(including several Vieja spp.), Herichthys, as well as five other genera,
had identical intra-generic sequences. Everyone is well aware
of the caveats of solely mitochondrial based phylogenies; however,
for some studies aimed at species-level investigations there may
not be enough variation in commonly used nuclear markers to allow
for any meaningful conclusions. This certainly appears to be
the case for the present study.