First, a "star tree paradox" (Steel and Matsen 2007) might also affect Bayesian methods when three or more lineages with high PP values (apparently resolved) diverge more or less simultaneously (Lewis et al. 2005; Kolaczkowski and Thornton 2006).
When using multigene sequence alignments for resolving deeply diverging relationships, misleading information due to violations of evolutionary models, bias in sequence composition, or sequence heterotachy may yield the wrong tree topology (Phillips et al. 2004; Jeffroy et al. 2006; Philippe et al. 2011b).
Recent developments in the population genetics of speciation may offer new power to resolve recently diverged lineages, however [7].
We recognise, however, the danger that also DNA-taxonomy may fail to resolve recently diverged taxa, especially if the species have ancestrally polymorphic mitochondrial haplotypes that do not sort according to subsequent speciation events [ 47].
However, continuous technical improvements observed in MRI, may resolve the dilemma between the diverging demands of high temporal resolution and high spatial resolution.
The relationships among cytosolic epimerases of eukaryotes are poorly resolved, with only recently diverging groups such as vascular plants and metazoa recovered with strong bootstrap support.
Because of a higher mutation rate, a smaller effective population and consequently a shorter coalescence time than typical autosomal loci, the uniparentally inherited mtDNA is known to be conducive to resolving phylogenetic relationships of recently diverging taxa [ 31, 32].
Mitochondrial DNA (mtDNA), as a uniparentally inherited genomic region, has higher mutation rates, as well as a smaller effective population size, than typical autosomal loci and hence has a shorter coalescence time conducive to resolving phylogenetic relationships of recently diverging species [ 4, 5].
From morphological, mitochondrial, and nuclear genetic studies, it has not been fully resolved what species diverged first in the waterbird assemblage (fig. 1).
Overall, the separated nrITS and the plastid datasets, and the total dataset are informative in resolving relationships among recently diverged nodes, but provide poor resolution and support for earlier divergences.
