Nielsen and Beaumont (2009; pp. 1037-1038) provide a wonderfully succinct description of NCPA. Given a sample of haplotypes at a given genetic locus, the user first identifies an estimate of the haplotype network for the sample. He or she then hierarchically agglomerates sets of haplotypes separated by 1, 2, 3, . . ., etc. mutational steps. Next, the user calculates statistics describing the geographic dispersion within clades and between nested clades, and compares these statistics to those obtained by permuting geographical information among samples - retaining the distances from the clades with significant statistics for comparison to an inference key. Inferences liable to result from the procedure include such things as range expansion, long distance migration, and geographic fragmentation.
However, the method has received some pointed criticism as well, most notably from Lacey Knowles at the
How do the readers of this blog perceive the current standing of NCPA? Furthermore, but on a much more philosophical note, how do readers view the kind of heated exchange partaken of by Knowles (2008) and Templeton (2009)? Is it true (to paraphrase A. N. Whitehead) that the clash of ideas is more of an opportunity than a calamity?
Note: For other fun exchanges in the recent literature among people I know, please check out: Downhower et al. (2009) and the response by Langerhans and Gifford (2009); or Bokma (2008), and the reply by Rabosky and Lovette (2008).