Journal of Biogeography
SUPPORTING INFORMATION
Partitioning taxon, phylogenetic and functional beta diversity
into replacement and richness difference components
Pedro Cardoso, François Rigal, José C. Carvalho, Mikael Fortelius,
Paulo A.V. Borges, Janos Podani and Denes Schmera
Appendix S1 Phylogenetic and functional analysis of Christmas Island rats.
The extinction of two endemic Rattus species
(R. macleari and R. nativitatis) from Christmas
Island (Australia) is a well-known example of
island extinctions due to invasive species. Both
endemics were abundant before the black rat
(R. rattus) introduction in 1899 and, probably
due to the spread of an infectious trypanosome,
both went extinct shortly thereafter (Wyatt et al.,
2008). Isolating the phylogenetic tree for these
three species alone using the software TREESNATCHER (Laubach et al., 2012), the extinct R. nativitatis is the sister taxon to both congenerics,
therefore encompassing the most unique phylogenetic information (Wyatt et al., 2008; Fig. S1).
Being the only fossorial and probably
diurnal species, R. nativitatis was also most
unique in terms of functional traits (Table S1).
We calculated Euclidean distances and built
a functional tree using UPGMA (the unweighted
pair group method with arithmetic mean). We
then calculated βtotal, βrepl, βrich, βjtu, βjne, βsor, βsim
and βsne (for definitions not in this paper, see
Baselga, 2010, 2012; Leprieur et al., 2012; Villé-
Figure S1 Phylogenetic tree for the Rattus species
of Christmas Island.
ger et al., 2013), for taxon, phylogenetic and functional data comparing the fauna before and after
the extinction period (Table S2).
Although there are no species in common
before and after the invasion/extinction event,
because there are parts of the phylogenetic tree
and functional traits that were in fact preserved
(although by a cosmopolitan species), the phylogenetic and functional turnover is not complete
Table S1 Functional characteristics used to quantify functional diversity of Christmas Island rats (data from
Andrews, 1909; Lamoreux, 2009a,b).
Food
Rattus macleari
Rattus nativitatis
Rattus rattus
Vertical strata
Activity period
Plants/fruits
Animals
Soil
Trees
Day
Night
1
1
1
0
0
1
1
1
1
1
0
1
0
1
0
1
1
1
Table S2 Beta diversity values of comparisons pre- and post-extinction of endemic Rattus species in Christmas
Island with the introduction of Rattus rattus. βtotal and βsor = total dissimilarity; βrepl, βjtu and βsim = dissimilarity
derived from true turnover, i.e. replacement; βrich, βjne and βsne = dissimilarity derived from richness difference.
Tβ
Pβ
Fβ
βtotal
βrepl
βrich
βjtu
βjne
βsor
βsim
βsne
1.000
0.936
0.911
0.667
0.582
0.549
0.333
0.355
0.363
1.000
0.901
0.861
0.000
0.035
0.050
1.000
0.880
0.837
1.000
0.820
0.756
0.000
0.060
0.081
(Tβtotal = 1; P/Fβtotal < 1). Additionally, as species,
phylogenetic data and functional traits were effectively lost, part of the total dissimilarity is not
due to replacement (βtotal > βrepl) but is instead
reflected in richness differences on all dimensions (βrich > 0).
While our framework reflects the overall
loss of one species (Tβrich = 0.333), the previous
methods (Baselga, 2010, 2012; Leprieur et al.,
2012; Villéger et al., 2013) claim that two species
were completely replaced by a single species
(Tβjtu = Tβsim = 1), with no beta attributable to
richness differences (Tβjne = Tβsne = 0). While the
new method reflects the loss of major phylogenetic information with the extinction of the most
unique species (Pβrich = 0.355), this loss is identified as minor by the previous methods (Pβjne <
Pβsne = 0.060). Finally, the loss of a functionally
unique species is proportionally reflected by the
new framework (Fβrich = 0.363), contrary to the
previous methods (Fβjne < Fβsne = 0.081).
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