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Molecular systematics has revolutionized traditional plant systematics and classification.
Molecular systematics has dramatically changed the ideas about the phylogenetic relationships of the lophophorate lineages, ectoproct bryozoans, brachiopods and phoronids.
The challenge of deep molecular systematics has been to determine the relationships among these well-defined groups.
Rigorous application of molecular systematics has done much to clarify relationships of the bryophytes (Renzaglia et al. 2007; Goffinet and Shaw 2008).
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Phylogeography and molecular systematics have been of great utility for delimiting the species boundaries of morphologically cryptic taxa [ 1- 3] and understanding the origins of diversity both at and below the species level [ 4- 7].
The recent development in molecular taxonomy and systematics has uncovered a rich diversity of cryptic species, in particular for nocturnal mammals [ 3- 8].
The use of molecular genetic data in phylogenetic systematics has revolutionized this field of research in that several taxonomic groupings defined by traditional taxonomic approaches have been rejected by molecular data.
In the absence of a molecular species concept, most microbial eukaryotic systematics has been based on morphological data to delineate species, and the characters used have often been restricted to features that are visible with light microscopy.
From the seminal comprehensive study of Hennig [ 1], to the impressive descriptive work of Kristensen [ 2, 3], to the increasingly common molecular approaches [ 4- 14], Insecta class systematics has been a challenging field of study.
To use EST data in molecular systematics, sequences have been initially BLASTed against a protein sequence database, e.g., the non-redundant protein database at NCBI, and the highest scoring hits are taken to tentatively annotate the EST sequences [ 20].
In the last decades, traditional morphological systematics has been augmented by novel molecular phylogenetics.
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