SUPPORTING INFORMATION
Global patterns of amphibian phylogenetic diversity
Susanne A. Fritz and Carsten Rahbek
Journal of Biogeography
Appendix S1: Construction of the global amphibian phylogeny.
Our phylogeny was compiled by hand based on a recent taxonomy by Frost (2009). To
improve phylogenetic resolution above the genus level, we followed published molecular
phylogenic studies. The family backbone followed Frost et al. (2006) with these updates:
their Amphignathodontidae and Cryptobatrachidae were included in Hemiphractidae
(Wiens et al., 2007a; Guayasamin et al., 2008), so the Nobleobatrachia consisted of the
newly defined Hemiphractidae and Meridianura; the Meridianura consisted of
Athesphatanura and Terrarana (Hedges et al., 2008), which corresponds to Frost et al.’s
(2006) Brachycephalidae; family relationships within Terrarana followed Hedges et al.
(2008); family relationships within Leptodactyliformes followed Grant et al. (2006).
Family relationships within Natatanura were from different sources: Ptychadenidae were
placed basally (Bossuyt et al., 2006; Frost et al., 2006; Van Bocxlaer et al., 2006; Wiens
et al., 2009); Africanura and Aglaioanura were preserved as valid clades (Bossuyt et al.,
2006; Van Bocxlaer et al., 2006); and the Victoranura constituted a polytomy of
Africanura, Aglaioanura, Ceratobatrachidae, Micrixalidae, Nyctibatrachidae and
Ranixalidae due to disagreement and low branch support values in the literature (Bossuyt
et al., 2006; Van Bocxlaer et al., 2006; Wiens et al., 2009). Within families, we followed
a range of published sources for between-genera relationships (Table S1).
Species were added on as within-genera polytomies, so the species-level tree
contains all currently recognized 6433 amphibian species (Frost, 2009). We assumed
monophyly of genera, and included species listed in quotes in their assigned genus (these
species are traditionally included in their assigned genus, but pending reclassification
based on phylogenetic analysis): Bufo (Anura: Bufonidae) included the species arabicus,
atukoralei, beddomii, brevirostris, dhufarensis, dodsoni, hololius, kotagamai,
koynayensis, mauritanicus, olivaceus, parietalis, pentoni, scaber, scorteccii,
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silentvalleyensis, stejnegeri, stomaticus, stuarti, sumatranus, tihamicus and valhallae;
Colostethus (Anura: Dendrobatidae) included poecilonotus and ramirezi;
Hyalinobatrachium (Anura: Centrolenidae) included eurygnathum, parvulum, and
uranoscopum; Hyla (Anura: Hylidae) included antoniichoai, helenae, imitator,
inframaculata and warreni. Exceptions to this rule followed published literature:
‘Ingerana’ baluensis (Anura, Dicroglossidae) was assigned its own genus in
Ceratobatrachidae (Frost et al., 2006), and ‘Prostherapis’ dunni (Anura, Aromobatidae)
was assigned to the genus Aromobates (Grant et al., 2006).
A short version of this description has previously been published (Olalla-Tárraga
et al., 2011), because that study used the phylogeny for some analyses published in their
Appendix S3.
Table S1 Sources of within-family phylogenetic relationships between amphibian genera.
For families not in this table, we followed Frost et al. (2006), with genera missing from
that study placed according to Frost (2009). If the position of genera was not known, they
were added into a polytomy basal to their family.
Family
Reference
Aromobatidae
Grant et al. (2006)
Brachycephalidae
Hedges et al. (2008)
Bufonidae
Van Bocxlaer et al. (2010)
Caeciliidae
Zhang & Wake (2009), Wilkinson & Nussbaum (2006)
Centrolenidae
Guayasamin et al. (2008)
Ceratobatrachidae
Wiens et al. (2009)
Ceratophryidae
Grant et al. (2006)
Craugastoridae
Hedges et al. (2008)
Cycloramphidae
Grant et al. (2006)
Dendrobatidae
Grant et al. (2006)
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Dicroglossidae
Wiens et al. (2009), Bossuyt et al. (2006), Ohler & Dubois
(2006)
Eleutherodactylidae
Hedges et al. (2008)
Hemiphractidae
Wiens et al. (2007a); corresponds to the families
Amphignathodontidae, Cryptobatrachidae and
Hemiphractidae of Frost et al. (2006)
Hylidae
Wiens et al. (2010), Smith et al. (2007), Faivovich et al.
(2005)
Hylodidae
Grant et al. (2006)
Hynobiidae
Subfamily relationships according to Frost (2009);
relationships within Hynobiinae followed Zhang et al. (2006)
Ichthyophiidae
Frost (2009)
Leptodactylidae
Grant et al. (2006)
Leiuperidae
Grant et al. (2006)
Mantellidae
Subfamily relationships according to Wiens et al. (2009);
relationships within Mantellinae followed Glaw & Vences
(2006)
Megophryidae
Delorme et al. (2006); relationships within Leptobrachiinae
followed Fu & Bi (2007)
Microhylidae
Genera unassigned to subfamilies were included in a
polytomy basal to the family; subfamily relationships mostly
followed Van Bocxlaer et al. (2006), but also consider Frost et
al. (2006) and the reanalysis of their data as well as original
data in van der Meijden et al. (2007)1; relationships within
Asterophryninae followed Köhler & Günther (2008)2;
relationships within Cophylinae followed original data from
van der Meijden et al. (2007) and Wollenberg et al. (2008)3;
relationships within Gastrophryninae followed Frost et al.
(2006) and the original data in van der Meijden et al. (2007);
relationships within Microhylinae followed Van Bocxlaer et
al. (2006), with missing taxa added according to van der
Meijden et al. (2007) and Frost et al. (2006)
Pipidae
Frost et al. (2006), with Pseudhymenochirus added as the
sister genus of Hymenochirus following Cannatella & Trueb
(1988)
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Plethodontidae
Subfamily relationships were unresolved (Frost, 2009);
relationships within Plethodontinae and Spelerpinae followed
Vieites et al. (2007), within Bolitoglossinae they followed
Wiens et al. (2007b)
Ptychadenidae
Wiens et al. (2009)
Pyxicephalidae
Wiens et al. (2009), Scott (2005)
Ranidae
Wiens et al. (2009), Stuart (2008), Che et al. (2007)
Rhacophoridae
Wiens et al. (2009), Li et al. (2008)
Salamandridae
Zhang et al. (2008)
Strabomantidae
Hedges et al. (2008)
1
Phrynomerinae was the sister group to all microhylids assigned to subfamily [Van Bocxlaer et
al. (2006); reanalysis of Frost et al.’s (2006) data in van der Meijden et al. (2007)]; the sister
clade to Phrynomerinae formed a polytomy, consisting of Otophryninae, Scaphiophryninae,
Hoplophryninae, Gastrophryninae and an unnamed clade, because the published topologies
differed widely and none recovered basal relationships with high support; the unnamed clade,
which was supported by Van Boxclaer et al. (2006) and van der Meijden et al. (2007), consisted
of two clades as follows: (Melanobatrachinae + (Kalophryninae + Cophylinae)) +
(Asterophryninae + (Dyscophinae + Microhylinae)).
2
Genera not sampled: Pherohapsis was placed in a basal polytomy, Mantophryne was placed
following Frost (2009).
3
Madecassophryne was not sampled in either of these, so was placed in a polytomy at the root.
4
Appendix S2: Representation of the global amphibian genus-level phylogeny.
Figure S1 Representation of the genus-level global amphibian phylogeny, constructed as
described in Appendix S1. Chosen clades (mostly families) are labelled above the branch
leading to their most recent common ancestor.
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Appendix S3: Results of all analyses rerun with the global amphibian phylogeny
from Pyron & Wiens (2011).
Spatial patterns for species richness when using the subset of amphibian species in the
Pyron & Wiens tree were very similar to global species richness (Fig. S2a, Pearson
correlation coefficient r = 0.984). Equally, spatial patterns for most of the phylogenetic
diversity indices were similar when calculated on our tree (Fig. 1b–e) or on the Pyron &
Wiens one (Fig. S2b–e) (see also Table 1 and main text). Values of Faith’s (1992)
phylogenetic diversity (PD), total taxonomic distinctness (TTD) and average taxonomic
distinctness (AvTD) across grid cells correlated well when calculated on the two different
trees, but less so those for mean root distance (MRD) (Table 1, Fig. S3). Relationships of
the different phylogenetic diversity indices with global species richness across grid cells
did not change substantially when the Pyron & Wiens tree was used (Figs 1f–i, S2f–i).
As with the results for our tree, we mapped residuals from the relationships of
global species richness with Faith’s PD and TTD calculated on the Pyron & Wiens tree
(Fig. S4; LOESS regressions with 11920.9 equivalent d.f.: Faith’s PD, residual sum of
squares = 958.0; TTD, residual sum of squares = 21785.6). Spatial patterns of these
residuals were closely correlated for the two phylogenies (Faith’s PD, r = 0.828; TTD, r
= 0.851), and overlap of cells identified as unusual areas was high between the two
phylogenies (Faith’s PD: 827 of 1179 cells, 70%; TTD: 763 of 1179 cells, 65%).
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Figure S2 Global maps of (a) amphibian species richness for the subset of 2792 species
in the Pyron & Wiens tree and (b–e) four indices of amphibian phylogenetic diversity
calculated on the Pyron & Wiens phylogeny, and graphs (f–i) of the relationship of each
phylogenetic diversity index with global species richness (6111 species in total) across
grid cells. Phylogenetic diversity indices were: (b,f) Faith’s (1992) phylogenetic diversity
(Faith’s PD), (c,g) total taxonomic diversity (TTD), (d,h) average taxonomic diversity
(AvTD), and (e,i) mean root distance (MRD). Red lines in (f–i) were fitted to the data by
local regression models with nonparametric smoothing. Colour scales in (a–e) are based
on 30 equal-interval categories labelled with median values; the first and last categories
are larger and labelled with the minimum and maximum value. Maps use the Behrmann
projection.
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Figure S3 Scatterplots of four indices of phylogenetic diversity calculated within grid
cells on two different phylogenies, our global amphibian supertree and the Pyron &
Wiens phylogeny: (a) Faith’s (1992) phylogenetic diversity (Faith’s PD), (b) total
taxonomic diversity (TTD), (c) average taxonomic diversity (AvTD), and (d) mean root
distance (MRD). Broken lines are the 1:1 line (intercept a = 0, slope b = 1). Solid lines
are fitted regression lines as follows: (a) a = 12.45, b = 0.63, R2 = 0.95; (b) a = 9.52, b =
0.86, R2 = 0.94; (c) a = –3.98, b = 0.86, R2 = 0.85; (d) a = 0.03, b = 0.67, R2 = 0.56.
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Figure S4 Global maps of residuals from a local regression model of (a) Faith’s (1992)
phylogenetic diversity (Faith’s PD) and (b) total taxonomic diversity (TTD) against
species richness, using the Pyron & Wiens phylogeny. Colour scales are based on equalinterval categories centred on zero and labelled with median values; the first and last
categories are larger and labelled with the minimum and maximum value. Maps use the
Behrmann projection.
(a)
(b)
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REFERENCES
Bossuyt, F., Brown, R.M., Hillis, D.M., Cannatella, D.C. & Milinkovitch, M.C. (2006)
Phylogeny and biogeography of a cosmopolitan frog radiation: Late Cretaceous
diversification resulted in continent-scale endemism in the family Ranidae.
Systematic Biology, 55, 579-594.
Cannatella, D.C. & Trueb, L. (1988) Evolution of pipoid frogs: morphology and
phylogenetic relationships of Pseudhymenochirus. Journal of Herpetology, 22,
439-456.
Che, J., Pang, J., Zhao, H., Wu, G., Zhao, E. & Zhang, Y. (2007) Phylogeny of Ranidae
(Anura: Ranidae) inferred from mitochondrial and nuclear sequences. Molecular
Phylogenetics and Evolution, 43, 1-13.
Delorme, M., Dubois, A., Grosjean, S. & Ohler, A. (2006) The new ergotaxonomy of the
family Megophryidae (Amphibia, Anura). Alytes, 24, 6-21.
Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological
Conservation, 61, 1-10.
Faivovich, J., Haddad, C.F.B., Garcia, P.C.A., Frost, D.R., Campbell, J.A. & Wheeler,
W.C. (2005) Systematic review of the frog family Hylidae, with special reference
to Hylinae: phylogenetic analysis and taxonomic revision. Bulletin of the
American Museum of Natural History, 294, 1-240.
Frost, D.R. (2009) Amphibian species of the world: an online reference. Version 5.3.
American Museum of Natural History, New York. Available at:
http://research.amnh.org/herpetology/amphibia/index.php (accessed May–June
2009).
Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., De Sá, R.O.,
Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A.,
Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M.
& Wheeler, W.C. (2006) The amphibian tree of life. Bulletin of the American
Museum of Natural History, 297, 1-370.
Fu, J. & Bi, K. (2007) A phylogeny of the high-elevation Tibetan megophryid frogs and
evidence for the multiple origins of reversed sexual size dimorphism. Journal of
Zoology, 273, 315-325.
15
Glaw, F. & Vences, M. (2006) Phylogeny and genus-level classification of mantellid
frogs (Amphibia, Anura). Organisms Diversity & Evolution, 6, 236-253.
Grant, T., Frost, D.R., Caldwell, J.P., Gagliardo, R., Haddad, C.F.B., Kok, P.J.R., Means,
D.B., Noonan, B.P., Schargel, W.E. & Wheeler, W.C. (2006) Phylogenetic
systematics of dart-poison frogs and their relatives (Amphibia: Athesphatanura:
Dendrobatidae). Bulletin of the American Museum of Natural History, 299, 1-262.
Guayasamin, J.M., Castroviejo-Fisher, S., Ayarzagüena, J., Trueb, L. & Vilà, C. (2008)
Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial
and nuclear genes. Molecular Phylogenetics and Evolution, 48, 574-595.
Hedges, S.B., Duellman, W.E. & Heinicke, M.P. (2008) New World direct-developing
frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, and
conservation. Zootaxa, 1737, 1-182.
Köhler, F. & Günther, R. (2008) The radiation of microhylid frogs (Amphibia: Anura) on
New Guinea: a mitochondrial phylogeny reveals parallel evolution of
morphological and life history traits and disproves the current morphology-based
classification. Molecular Phylogenetics and Evolution, 47, 353-365.
Li, J., Che, J., Bain, R.H., Zhao, E. & Zhang, Y. (2008) Molecular phylogeny of
Rhacophoridae (Anura): a framework of taxonomic reassignment of species
within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus.
Molecular Phylogenetics and Evolution, 48, 302-312.
van der Meijden, A., Vences, M., Hoegg, S., Boistel, R., Channing, A. & Meyer, A.
(2007) Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae)
and a discussion of competing hypotheses concerning their biogeographical
origins. Molecular Phylogenetics and Evolution, 44, 1017-1030.
Ohler, A. & Dubois, A. (2006) Phylogenetic relationships and generic taxonomy of the
tribe Paini (Amphibia, Anura, Ranidae, Dicroglossinae), with diagnoses of two
new genera. Zoosystema, 28, 769-784.
Olalla-Tárraga, M.Á., McInnes, L., Bini, L.M., Diniz-Filho, J.A.F., Fritz, S.A., Hawkins,
B.A., Hortal, J., Orme, C.D.L., Rahbek, C., Rodríguez, M.Á. & Purvis, A. (2011)
Climatic niche conservatism and the evolutionary dynamics in species range
16
boundaries: global congruence across mammals and amphibians. Journal of
Biogeography, 38, 2237-2247.
Pyron, R.A. & Wiens, J.J. (2011) A large-scale phylogeny of Amphibia including over
2800 species, and a revised classification of extant frogs, salamanders, and
caecilians. Molecular Phylogenetics and Evolution, 61, 543-583.
Scott, E. (2005) A phylogeny of ranid frogs (Anura: Ranoidea: Ranidae), based on a
simultaneous analysis of morphological and molecular data. Cladistics, 21, 507574.
Smith, S.A., Arif, S., Nieto Montes de Oca, A. & Wiens, J.J. (2007) A phylogenetic hot
spot for evolutionary novelty in Middle American treefrogs. Evolution, 61, 20752085.
Stuart, B.L. (2008) The phylogenetic problem of Huia (Amphibia: Ranidae). Molecular
Phylogenetics and Evolution, 46, 49-60.
Van Bocxlaer, I., Roelants, K., Biju, S.D., Nagaraju, J. & Bossuyt, F. (2006) Late
Cretaceous vicariance in Gondwanan amphibians. PLoS ONE, 1, e74.
Van Bocxlaer, I., Loader, S.P., Roelants, K., Biju, S.D., Menegon, M. & Bossuyt, F.
(2010) Gradual adaptation toward a range-expansion phenotype initiated the
global radiation of toads. Science, 327, 679.
Vieites, D.R., Min, M. & Wake, D.B. (2007) Rapid diversification and dispersal during
periods of global warming by plethodontid salamanders. Proceedings of the
National Academy of Sciences USA, 104, 19903-19907.
Wiens, J.J., Kuczynski, C.A., Duellman, W.E. & Reeder, T.W. (2007a) Loss and reevolution of complex life cycles in marsupial frogs: does ancestral trait
reconstruction mislead? Evolution, 61, 1886-1899.
Wiens, J.J., Parra-Olea, G., García-París, M. & Wake, D.B. (2007b) Phylogenetic history
underlies elevational biodiversity patterns in tropical salamanders. Proceedings of
the Royal Society B: Biological Sciences, 274, 919-928.
Wiens, J.J., Sukumaran, J., Pyron, R.A. & Brown, R.M. (2009) Evolutionary and
biogeographic origins of high tropical diversity in Old World frogs (Ranidae).
Evolution, 63, 1217-1231.
17
Wiens, J.J., Kuczynski, C.A., Hua, X. & Moen, D.S. (2010) An expanded phylogeny of
treefrogs (Hylidae) based on nuclear and mitochondrial sequence data. Molecular
Phylogenetics and Evolution, 55, 871-882.
Wilkinson, M. & Nussbaum, R.A. (2006) Caecilian phylogeny and classification.
Reproductive biology and phylogeny of Gymnophiona (caecilians) (ed. by J.-M.
Exbrayat), pp. 39-78. Science Publishers, Enfield, NH.
Wollenberg, K.C., Vieites, D.R., van der Meijden, A., Glaw, F., Cannatella, D.C. &
Vences, M. (2008) Patterns of endemism and species richness in Malagasy
cophyline frogs support a key role of mountainous areas for speciation. Evolution,
62, 1890-1907.
Zhang, P. & Wake, M.H. (2009) A mitogenomic perspective on the phylogeny and
biogeography of living caecilians (Amphibia: Gymnophiona). Molecular
Phylogenetics and Evolution, 53, 479-491.
Zhang, P., Papenfuss, T.J., Wake, M.H., Qu, L. & Wake, D.B. (2008) Phylogeny and
biogeography of the family Salamandridae (Amphibia: Caudata) inferred from
complete mitochondrial genomes. Molecular Phylogenetics and Evolution, 49,
586-597.
Zhang, P., Chen, Y., Zhou, H., Liu, Y., Wang, X., Papenfuss, T.J., Wake, D.B. & Qu, L.
(2006) Phylogeny, evolution, and biogeography of Asiatic salamanders
(Hynobiidae). Proceedings of the National Academy of Sciences USA, 103, 73607365.
18