Biodiversity Conservation and Phylogenetic Systematics

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The numerator is the same as that in CT 2 N(), revealing that the similarity

index UT 2 N() also quantifies the node-by-node resemblance among the N

abundance sets {zik; i∈BT̅}, k = 1, 2, ..., N; but here the denominator (for the

purpose of normalization) is different and takes a regional perspective.

3. A class of phylogenetic homogeneity measures

ST

DT N

N

qN

q

()

/()/

/

=.

-

-

11

11

b

(12b)

This measure is linear in the proportion of regional phylogenetic diversity con-
tained in a typical assemblage.
(3a) For q = 0, it reduces to the “phylo-Jaccard” measure U̅ 0 N (T), i.e.,
ST 00 NN()=UT().
(3b) For q = 1, this measure does not reduce to the “phylo-Horn” overlap
measure.
(3c) For q = 2, this measure is identical to CT 2 N(), the “phylo-Morisita-Horn”
similarity measure, i.e., ST 22 NN()=CT().

4. A class of measures of the complement of “phylogenetic turnover rate”:

VT

NDT

N

DT

qN N

qq

()

() ()

=.

-

-

=-

-

-

bb

1

1

1

(^1)
(12c)
This measure in linear in the phylogenetic beta diversity and the corresponding
differentiation measure ëéqDTb()- 11 ùû/()N- quantifies the relative branch
turnover rate per assemblage.
(4a) For q = 0, the measure VT 0 N() is identical to the “phylo-Sørensen” mea-
sure, i.e., VT 00 NN()=CT().
(4b) For q = 1, this measure does not reduce to the “phylo-Horn” overlap
measure.
(4c) For q = 2, this measure is identical to U̅ 2 N (T), the “phylo-regional-overlap”
measure. That is, VT 22 NN()=UT().
As with the phylogenetic diversity measures, all the above similarity or differentia-
tion measures are functions of two parameters: the sensitivity parameter q and the
time perspective T. Thus, for each measure, we suggest using the two types of pro-
files described in section “PhylogeneticHillnumbersandrelatedmeasures” for the
two major similarity measures CTqN() and U̅qN(T) (or their complements) to convey
complete information about the similarity or differentiation of a set of assemblages.
An example showing the two types of profiles is given in section “An example”.
The lineage excess qqDTga()- DT() and the phylogenetic diversity excess
qqPD TPDT
ga()- () can be interpreted as the effective number of regional lineages
Phylogenetic Diversity Measures and Their Decomposition: A Framework Based...