Descendant Haplogroups, and Associated Clades

GenBank (2010) is a collection of publicly available DNA sequences maintained by the National Center for Biotechnology Information. It currently contains about 7000 homo sapiens mtDNA 'full genome sequences', although some of these are complete in the coding region only. Abstracts of these sequences that list differences from the CRS are available through Ian Logan's Checker web site (Logan I, 2010). This paper describes the selection of sequences from this source that belong to Super-Haplogroup N, its subordinate haplogroups, and their clades, and how these sequences were organized into a matrix reflecting the current consensus about the phylogeny of homo sapiens mtDNA. Features of this matrix are described, the content analyzed, and a number of issues articulated relative to the use of various alleles in clade definitions. Illustrated herein is also a scheme for quantitatively assessing the quality of alleles used in the clade definitions. Products of the application of this scheme, in turn, are used as major components of a semi-automated allele encyclopedia. Finally, there is a description of the tools used to develop and maintain the matrix, perform ongoing analysis, and produce the core structure of an allele encyclopedia