165shown in the second type of profiles based on the measure qPD(T)) over the three
decades.
When species/lineage abundances are discounted (q = 0 in the left panels of
Fig. 4b), both lineage richness (based on the measure^0 DT()) and total branch
lengths (based on the measure^0 PD(T),i.e.,Faith’sPD)exhibittheexpectedorder-
ing: Decade I > Decade II > Decade III. When species/lineage abundances are
counted (i.e. q = 1 and 2 in Fig. 4b), the profiles for Decades I and II cross because
the assemblage of Decade II has more even abundant species than that of Decade I
(see the first type of profiles for T = 0 and Fig. 3a, b). Note that if the time-depth is
greater than 6 Myr (including the age of the root), then all the abundance-sensitive
phylogenetic measures for the three assemblages are very close because most of the
dominant species began to diverge around 6 Myr (Fig. 3b). This also explains the
closeness of the three profiles in the first type of profile for T = 7.9 Myr (the right
panel in Fig. 4a).
Fig. 3 (a) The phylogenetic tree of 52 rockfish species of the genus Sebastes (Hyde and Vetter
2007 ) and the species relative abundances in three assemblages: 1980s (Decade I), 1990s (Decade
II) and 2000s (Decade III). The age of the root is T = 7.9 Myr. (b) A sub-tree contains only the
dominant species (those with relative abundance >8 % in at least one assemblage), and these spe-
cies are marked in figure (a). All six species are shared by the three assemblages and four of them
divergedaround 6 Myrago(i.e.,theyhavebeeninisolatedlineagesfor 6 Myr)(SeePavoineetal.
( 2009 ) for details)
Phylogenetic Diversity Measures and Their Decomposition: A Framework Based...