Appendix S2. Additional Phylogenetic Procedures and Results
Phylogenetic Procedures
As described in the main text, we used Pyron & Wiens’ (2011) phylogenetic
hypothesis, the largest estimate of extant amphibian phylogeny to the moment.
However, this phylogeny still lacks 1820 of the 3017 amphibians that should be
considered in any conservation study. These species that are “missing” from the base
tree are hereafter referred as “Phylogenetic Uncertain Taxa” or PUT. To include a PUT
in the analysis it has to be inserted in the phylogeny. The insertion starts by defining the
most derived consensus clade (MDCC) to which each PUT unquestionably belongs.
Our primary sources of information to identify the MDCC of each PUT were the
Amphibian Species of the World (ASW; Frost, 2011) and the Amphibian Web (AW)
databases. We compiled all the relevant information available in these databases,
including the cited taxonomic and phylogenetic literature.
For example, Pyron & Wiens’ (2011) phylogeny contains only one
representative of the genus Adelophryne (Adelophryne gutturosa). Available
information in ASW concerning Adelophryne relationship with other taxa suggests that
the genus is monophyletic (Hedges et al., 2008; Pyron and Wiens, 2011; Fouquet et al.,
2012). However, there is no agreement about the relationship between PUT species that
are member of the genus (A. adiastola, A. baturitensis, A. maranguapensis, A.
pachydactyla and A. patamona). Thus, we assigned Adelophryne gutturosa as the
MDCC of all PUT in the genus Adelophryne. PUT with very poor information, such as
Adelastes hylonomos and Altigius alios, were assigned to a MDCC following the
taxonomy presented at ASW and AW, which is the family Microhylidae (sensu Pyron
& Wiens, 2011, since it is strongly supported) in this case. Consensus taxonomic groups
such as Dendropsophus microcephalus group and Dendropsophus rubicundulus group
were also acknowledged and used as MDCC when necessary. Conversely, all
information in ASW and AW that suggest possible relationship but is also uncertain,
such as “possibly the sister-taxon”, was not considered, and a more basal MDCC was
defined. In the figure 1 we show the entire phylogeny, where species present in Pyron
and Wiens’ (2011) are shown in black, and PUT are highlighted in red and assigned to
their respective MDCC.
Figure 1. The phylogeny of the 3027 New World anurans. Species
present in Pyron & Wiens’ (2011) phylogeny are presented in black.
Phylogenetically uncertain taxa (PUT) are shown in red, placed
polytomically in their respective Most Derived Consensus Clade
(MDCC).
Once all PUT are assigned to their respective MDCC, we employed a Monte
Carlo procedure (Rangel et al. 2013) that is similar to approaches described and used by
Housworth and Martins (2001), Day et al. (2008), FitzJohn et al. (2009) and Kuhn et al.
(2011). The procedure allows the generation of a possible phylogeny by assuming
random placement of PUT within their MDCC (or “constrained phylogeny” in
Housworth and Martins, 2001). Once a PUT is inserted in a random branch of the
MDCC, its own branch length is randomly sampled from a Gaussian distribution with
mean and standard deviation defined based on the distribution of branch lengths within
the MDCC. The algorithm iterates until all PUT have been inserted within the clade
defined by its MDCC, which produces a fully resolved phylogeny. The fully resolved
phylogeny is then used in our analysis of EH loss, and results of the analysis are stored.
Finally, the entire procedure is replicated, with a new sampled phylogeny. The variation
in the results obtained from the replicates of the analysis using different phylogenies is
caused by phylogenetic uncertainty.
Software PAM (Rangel & Diniz-Filho 2013), which implements the
phylogenetic uncertainty procedure described above is available under request. Also,
one of us is currently working on a R package to be released in the first semester of
2013. Finally, the PUT insertion procedure is also available through an web-based
interface available at: http://wsmartins.net/webtrex/
Additional results
Species richness of amphibians is highly patterned across the Western Hemisphere
and evolutionary history (EH), as measured by the sum of branches connecting a pool of
species to the root of the phylogenetic tree, follows the same pattern (r=0.97, p<0.001)
(Fig. 2). High values of richness (Fig. 2a) and EH (Fig. 2b) are concentrated in South
America and a portion of Central America, specifically on Brazil, Bolivia, Ecuador,
Colombia, Panamá and Costa Rica. Species richness ranged from 1 and 160 species per
cell (average 25 species). However, only 151 cells (4% of the total), located in the
Amazon and Atlantic Forests, show richness values greater than 100 species (Fig. 2a).
Grid cells with 30 species or less (70%) are concentrated in temperate region.
Figure 2. Spatial pattern in species richness (a) and evolutionary
history (EH) (b).
We observed a similar pattern in the magnitude of difference between Random
and IUCN scenarios measured by the Sub-optimality index and the Partial suboptimality indexes. Following the richness of threatened species, high negative t values
are located along Central America, Caribbean and northern Andes for all proportions of
species evaluated. However, several cells with positive t value in the ISB analyzes
showed values of t nearly zero in PISB analyses. Nevertheless, Brazilian Atlantic forest
still showed cells with positive t values for the Partial sub-optimality index comprising
threatened and DD species (PISB_DD, Fig. 3b), indicating that DD species display an
important role for the rate of EH loss in these region.
Figure 3. Values of t for each cell with more than four species. (a) t
values for the Partial sub-optimality index comprising only the
proportion of threatened species of the cell (PISB index); (b) t values for
the Partial sub-optimality index comprising threatened and DD species
(PISB_DD index).
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