Molecular systematics and phylogenetics towards species delimitation

The science of taxonomy reflects our way of perception of the diverse units of life as
it encompasses identification, description, and nomenclature of species. Taxonomy is
often associated with molecular systematics, i.e. the employment of molecular
genetics tools to infer phylogenetic relationships among individuals and species, and
the use of such information to classify species and to provide insight into an
organism’s natural history and evolutionary processes. The latter is related to
cladistics or phylogenetic systematics, through which a phylogenetic tree is
reconstructed based on the affinity and dissimilarity of the share-derived characters of
the organisms under study. Phylogenetic trees show the evolutionary, ancestor–
descendant relationships among OTUs, and unveil the patterns of relationships among
them. Based on the type of data (character states or distance matrix), a variety of
phylogenetic trees can be applied with Maximum parsimony, Maximum likelihood
and Bayesian inference to pilot (for a thorough review see Yang & Rannala, 2012).
The role of molecular tools in molecular and phylogenetic systematics is
invaluable; they have assisted and accelerated species identification, diagnosis of new
species, and species delimitation; revealed cryptic species complexes; and shed light
into species evolution and biology (Rubinoff, 2006). The most popular molecular tool
is the ‘DNA barcode’, i.e. the retrieval of a short DNA sequence from a standard part
of the genome (gene-specific region) of the study specimen (Folmer et al., 1994;
Hebert et al., 2003; Hajibabaei et al., 2007). Mitochondrial DNA (mtDNA) has taken
precedence over other molecular markers because it is maternally inherited (haploid)
lacking recombination, less prone to degradation, easy to isolate and assay (high
number of copies with limited sample required), and it is quite variable among
individuals (evolution rate is 5-10 times faster than in nuclear DNA) (Avise et al.,
1987). MtDNA deficiencies (reduced effective population size and introgression,
maternal inheritance, lacking of recombination, inconsistent mutation rate,
heteroplasmy and compounding evolutionary processes; Moritz & Cicero, 2004;
Rubinoff, 2006) should also be considered when inferring species diagnosis and
delimitation, as mtDNA may result to false positive or negative signals when used
alone.
In addition to the above, species inference from molecular data transcends over
morphological/ physiological traits for several reasons (see Table 1; Graur & Li,
2000). In order to conclude on species delimitation and infer evolutionary
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