Species-level phylogenetic studies require fast-evolving nucleotide positions to 
resolve relationships among close relatives, but these sites may be highly 
homoplastic and perhaps uninformative or even misleading deeper in the tree. 
Here we describe a species-level analysis of tiger beetles in the genus 
Cicindela (Coleoptera: Cicindelidae) for 132 terminal taxa and 1897 nucleotide 
positions from three regions of mtDNA, comprising 75% coverage of species 
occurring in North America. Evenly weighted parsimony analysis recovered four 
major clades representing radiations confined to North and Central America. 
Relationships near the tips were well supported but signal was contradictory at 
deeper nodes. Two major categories (3rd positions and all others) can be 
distinguished in likelihood analysis of character variation, of which only the 
fast-changing 3rd position characters were affected by saturation. However, 
their downweighting under a variety of criteria did not improve the tree 
topology at basal nodes. There was weak conflict between 3rd and non-3rd 
position characters deep in the tree, but support levels declined towards the 
root for all categories, even on trees that were reconstructed from 3rd and 
non-3rd positions separately. Statistical analysis of parsimony-based character 
transitions along branches showed a largely homogeneous distribution of change 
along the root-to-tip axis. The comparison of character transitions among the 
four major portions of the tree revealed deviations from stochastic distribution 
for the non-3rd positions, but not for 3rd positions. Hence, variability of 
functionally constrained non-3rd positions differs between clades and may be 
dependent on the character states at other sites, consistent with the covarion 
model of molecular evolution. The results suggest that some properties of 3rd 
positions are less problematic for phylogenetic reconstruction than other 
categories despite their high total homoplasy. In densely sampled data sets of 
closely related species, the disadvantages of weighting schemes according to 
homoplasy levels outweigh the benefits, showing the difficulty of devising 
meaningful weighting schemes that are applicable universally throughout the 
tree.