Identification of Cenocrons - Evolutionary Biogeography - page 280

whereas interior haplotypes are those that are connected to two or
more haplotypes. Set j = 0.
b. Pick a tip haplotype that is not part of any j + 1-step network.
c. Identify the interior haplotype with which it is connected by j + 1 nucle-
otide differences.
d. Identify all tip haplotypes connected to that interior haplotype by j + 1
nucleotide differences.
e. The set of such tip and interior haplotypes constitutes a j + 1-step
clade.
f. If there are tip haplotypes remaining that are not part of a j + 1-step
clade, return to Step b.
g. Identify any internal j -step clades that are not part of a j + 1-step clade
and are separated by j + 1 steps.
h. Designate these clades as terminal and return to Step b.
i. Increase j by one and return to Step b.
3. Represent the phylogroups on a map and calculate the following:
a. The clade distance ( D c ): average distance of each haplotype in the
particularcladefromthecenterofitsgeographicdistribution,measured
as the great circle distance, to represent the distribution of the
phylogroups.
b. The nested clade distance ( D n ): average distance of the center of dis-
tribution for this haplotype from the center of distribution for the haplo-
type within which it is nested.
c. The average distance between D c and D n for the terminal phylogroups
in order to identify whether they are structured geographically.
4. Use a statistical test to evaluate whether the haplotypes of the nested
clades are distributed randomly. If this hypothesis is rejected, it means that
there is a significant geographic association between them.
Software TCS 1.18 (Clement et al. 2000) and GeoDis (Posada et al. 2000).
Empirical Applications Many phylogeographic papers have been pub-
lished in recent decades; this is a nonexhaustive list: Arnaiz-Villena et
al. (2001), Ávila et al. (2006), Avise (1989, 1992), Avise et al. (1992),
Ball and Avise (1992), Bermingham and Martin (1998), Bernatchez (2001),