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Inferring phylogenies and distributions of upper-Andean and
Amazonian frogs from the genusPristimantis using new and
previously published sequence data.
Pristimantis acuminatus
Name: Robyn Cuthbertson
Matriculation number: 0906976c
Level 4 Honours Project
Supervisor: Dr Kathryn Elmer
Submission date: 22 March 2013
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ContentsAbstract ................................................................................................................................ 2
Introduction .......................................................................................................................... 3
Methods ................................................................................................................................ 6
Data collection .................................................................................................................. 6
Phylogenetic analyses........................................................................................................ 6
Results .................................................................................................................................. 8
Convergence assessment ................................................................................................... 8
Discussion ........................................................................................................................... 13
Phylogenetic relationships ............................................................................................... 13
Model and analyses ......................................................................................................... 17
Convergence on stationarity ............................................................................................ 18
Wider implications .......................................................................................................... 18
Acknowledgements ............................................................................................................. 20
References .......................................................................................................................... 21
Appendix I .......................................................................................................................... 28
Appendix II ........................................................................................................................ 34
Appendix III ....................................................................................................................... 36
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Abstract
The genusPristimantis is the largest of the amphibian genuses with 454 species
currently described and this number is likely to increase with more recently developed
techniques for recognition of cryptic species and the introduction of new molecular
techniques. The deep evolutionary history has been examined and the evolutionary
relationship withEleutherodactylus has been discussed by Heinicke, Duellman and Hedges
(2007), inferring thatPristimantis split from the Eleutherodactylines 37 million years ago,
with rapid speciation 24 million years ago and also with the uplift of the Andes, where
mountain building first appeared around 23 Ma, and the most pronounced peaks followed
between 12 and 4.5 Ma (Hoorn et al., 2010).
My study involved the alignment and phylogenetic analysis of 112 sequences,
followed by the investigation of the distributions of species in a selected clade. This revealed
some relationships between species which support those found by Heinicke, Duellman and
Hedges (2007) and some which differnew evolutionary relationships may be the result of
the introduction of 30 new sequences into the analyses. Wide distribution of some of the
species possibly suggest cryptic species complexes and indicate further studies need to be
done in order to fully delimitate species such asPristimantis ockendeni andPristimantis
chalceus.
The implications for my study and those similar, for example Heinicke, Duellman and
Hedges (2007), on the knowledge of evolutionary history and relationships can have an
impact on the knowledge of the methods of diversification (for example due to topographical
complexities) which in turn can give an indication of the history of the landscape. It can also
affect conservation as subdivision of distributions due to delimitation of species can change
the species conservation requirements.
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Introduction
Frogs of the genusPristimantis (Jimnez de la Espada 1870),the South American rain
frogs, are distributed mainly in Central and South America.They are nocturnal and primarily
arboreal (Kok and Kalamandeen, 2008), and are small in length like most direct developing
frogs (range from 20-50mm) (Heinicke, Duellman and Hedges, 2007).They are also
polychromatic which can cause problems in identification (Kok and Kalamandeen, 2008).
Pristimantisis widely accepted to be the most speciose genus of the Neotropical amphibia,
with an estimated species number of 454 (AmphibiaWeb 2013).This can be validated with
comparison of other genuses in the family Strabomantidae: for example the genus Oreobates
with 21 species listed, and the genusBryophrynewith just eight (AmphibiaWeb, 2013).
With the increasing availability of molecular information it has become of great
interest to researchers to utilise this information in order to infer phylogenies, the overall aim
of which is to discover the topology of the tree and infer evolutionary relationships.
However, the correct phylogenies can be affected by the model chosen to investigate the
evolutionary history (Bollback, 2002).There are a variety of different methods, each with
strengths and weaknesses (Yang and Rannala, 2012).The process of molecular phylogenetics
that is, using DNA sequences to investigate the evolutionary histories and relationships
between species (Hay, Ruvinsky, Hedges, and Maxson, 1995; Darst and Cannatella, 2003;
Fouquet et al., 2007)allows for more precise phylogenetic inference than morphological
classifications can allow.
Species concepts have been discussed recently in terms of reclassifying species, with
changes from the typical biological species concept to phylogenetic and evolutionary
http://amphibiaweb.org/cgi-bin/amphib_query?table=amphib&special=one_record&where-genus=Bryophryne&where-species=abramalagaehttp://amphibiaweb.org/cgi-bin/amphib_query?table=amphib&special=one_record&where-genus=Bryophryne&where-species=abramalagaehttp://amphibiaweb.org/cgi-bin/amphib_query?table=amphib&special=one_record&where-genus=Bryophryne&where-species=abramalagaehttp://amphibiaweb.org/cgi-bin/amphib_query?table=amphib&special=one_record&where-genus=Bryophryne&where-species=abramalagae8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
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species concepts (Hanken, 1999). South America has many areas of high species diversity
(Myers 2000), with important protected areas such as Manu in Peru and Madidi in Bolivia to
preserve niche biodiversity hotspots (Padial and de la Riva, 2009).There are numerous
hypotheses as to why these areas of diversity exist, such as riverine barriers (Gascon,
Lougheed and Bogart, 1996) and paleogeographic characteristics (Rsnen et al., 1996;
Hughes and Eastwood, 2006).Wang et al., (2009) discuss two causes of speciation: firstly,
where geographic and physical landscape barriers restrict the movement of individuals and so
constrain gene flow between populations, in turn causing genetic drift and/or selection to
result in divergence of phenotype and secondly, where gene flow against immigrant
phenotypes is the result of natural or sexual selection, which causes divergence, and
demonstrates that geographic isolation, although thought to be the primary reason for
diversification and speciation, may not be as fundamental a theory as previously thought.
Generally, it is established that geography has had a major impact on species diversity in
South America, especially in the Andes and Amazonia (Elmer, Dvila and Lougheed, 2007).
Recently Heinicke, Duellman and Hedges (2007) refined the Eleutherodactylines into
three cladesMiddle American, the Caribbean, and finally the South American clade.It is
the later in whichPristimantisis included, and it has been inferred that this genus split from
the rest of the Eleutherodactylines 37 million years ago (Heinicke, Duellman and Hedges,
2007).The range ofPristimantisis central to the Andes, caused by changes in plate tectonics
in the Palaeocene 65-34 million years ago (Hoorn et al., 2010).In terms of geological history
this is very recent and it is apparent thatPristimantisbecame speciose in a short space of
evolutionary time, diversifying rapidly from 24 million years ago (Heinicke, Duellman and
Hedges, 2007).This idea is supported by changes in climate resulting in genetic isolation
resulting in further speciation of the species and the pronounced uplift of the Andes in the last
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124.5 million years (Hoorn et al., 2010).The genus invaded Central America on at least 11
separate occasions, and some of these occurred before the suggested closing of the Isthmus of
Panama (Pinto-Sanchez et al., 2012) around 3 million years ago (Heinicke, Duellman and
Hedges, 2007)for example,Pristimantis ridenswas also established in Central America
before the presence of the land bridge (Wang, Crawford and Bermingham, 2008), again
consistent with the hypothesis of rapid radiation from South America.Arguments for high
diversity of poison frogs in the Amazon basin due to rapid dispersal from neighbouring areas
have also been made (Santos et al., 2009) and so this may also have occurred in Pristimantis.
It is clear that even the current estimations ofPristimantis species numbers may be
lower than the actual number of species present (Fouquet et al, 2007; Lehr, Moravec and
Gagliardi Irrutia,2010) due to unexplored regions, polymorphic species, cryptic species and
species that have extremely similar morphologies.Recent analyses of species in the
Pristimantisgenus include those by Elmer and Cannatella (2008), Siqueira et al., (2008),
Padial and de la Riva (2009), and Arteaga-Navarro and Guayasamin (2011), and with further
work done in the area of phylogenetics and more scientific exploration in the region it is
likely that there will be a continuation of these redefinitions of relationships in the genus.
This study will attempt to determine the phylogenies of the South American clade of
Pristimantis using recently acquired and previously-published sequence data, and
comparisons with other papers will be made in order to infer the likelihood of the accuracy of
results. Using Bayesian analyses, I will closer inspect a single clade in terms of altitude - in
doing so I aim to understand better the patterns of diversity and species richness of the genus
and investigate possible multi-complexes of species.
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Methods
Data collection
This study used data from 121 sequences of 12S ribosomal RNA (12S) and 16S
ribosomal RNA (16S) mitochondrial genes.Of these, 30 were new sequences were provided
by Dr Kathryn Elmer (see Appendix II) and 91 were published sequences were downloaded
from NCBI database (see Appendix I).The South American clade group formed by Heinicke
et al., 2007 (species numbers 162-248) was the source for which accession numbers were
chosen and the outgroup was selected from the same study (see Appendix I).
Phylogenetic analyses
The removal of one outgroup species and the joining of 12S and 16S sequences from
the same species resulted in a total of 112 sequences analysed with a total of 1017 sites.The
sequences were aligned using the default settings of the ClustalW option in Geneious 6.0.6
(Biomatters, 2012), where the cost matrix used was IUB, the gap open cost was 15, and the
gap extend cost was 6.66. MEGA 5.1 was used to extend the flanking regions of the
sequences in order to make them the same length as 12S and 16S sequences have hyper
variable regions which cannot be aligned.Ambiguous regions in the alignment were then
removed using Gblocks 0.91b (Castresana, 2000), in which the default block parameters
were: minimum number of sequences for a conserved position: 9; minimum number of
sequences for a flank position: 14; maximum number of contiguous non-conserved positions:
8; minimum length for a block: 10; allowed gap positions: 0.The resulting alignment was
comprised of 1017 sites.The MrBayes plugin (Hulsenbeck and Ronquist, 2001) in Geneious
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6.0.6 was used to perform Bayesian analyses to reconstruct phylogenies with the GTR + I +
model of evolution (adhering to the methods used by Heinicke, Duellman and Hedges, 2007).
Two parallel runs of the Monte Carlo Markov chain algorithm were conducted with
1,100,000 generations (chain lengths) each.The burn-in length was 160,000 and branch
lengths were unconstrained.The subsampling frequency was 200.
The posterior output was examined to assess the convergence of likelihoods onto the
stationary distribution of the two separate runs.A 50% consensus tree was formed using the
resulting raw tree data (11002 trees) in Geneious 6.0.6 (Biomatters, 2012).The posterior
probability (or clade credibility) values for the branch nodes were examined. Inferred
relationships were examined.
A clade encompassing 32 sequences was chosen for further analysisthis clade was
chosen based on the high proportion of new sequence data and species of interest included.
For this clade, the altitudinal ranges were obtained from AmphibiaWeb (2013), IUCN (2012)
and from the individually collected specimen information.A bar graph was created to
compare these altitudinal rangesto further investigate their biodiversity and possible
relationships.
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Results
Convergence assessment
The parameter estimates included the log likelihood score (LnL), total tree length
(TL), the 4 stationary state frequencies (piT, piA, piG, and piC) and the 6 reversible
substitution rates (rA-T, rA-G, rA-C, rC-G, rC-T, and rG-T), and the shape of the gamma
distribution of rate variation across sites (alpha). The comparison of these parameters from
each of the 2 runs shows that the results of each run were similarasides from the
autocorrelation time which increased fairly substantially. The correlation graph shows a
random distribution, or white noiseof points.The density and relative density graphs for
each run show similar patterns.The trace and sample trace was stochastic around the mean.
These indicate convergence on stationarity in the Bayesian analyses and tree space by
MCMC (see Appendix III).
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Phylogeny assessment
Fig. 1: 50% consensus tree from 11002 raw trees created using the MrBayes plugin in Geneious 6.0.6. (Biomatters 2012)
showing the inferred phylogenies of 111Pristimantis species sequences and 1outgroup sequence. Bayesian posterior
probability values are shown.
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Altitude(metersabovesealevel)
Altitudinal assessment
Fig 2: Comparison of altitudinal distributions of species in the clade encompassing species fromP.orestes toP. diadematus QCAZ18015. For published data, the altitudinal range was taken from IUCN(2012) and AmphibiaWeb (2013), and for new sequence data the altitude where the individual waslocated was taken from the active specimen information sheet provided by K. Elmer.
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Distribution assessment
P.ockendeni: P.simonbolivari:
P.cajamarcensis: P.orestes:
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P.ceuthospilus: P. luteolateralis:
P. chalceus:
Fig 3. Distributions of 7 species ofPristimantis (P. ockendeni, P. ceuthospilus, P. simonbolivari, P.
cajamarcensis, P. chalceus, P. luteolateralis, andP. orestes), from the clade encompassing speciesfromP. orestestoP. diadematus, with altitudinal distributions above 1500m.a.s.l. All images from
IUCN (2012). Species with altitudinal distributions above 1500m.a.s.l were chosen as occurrences atthese altitudes are generally rarer and investigation into their distribution could possibly show multi-
complexes of species.
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Discussion
Phylogenetic relationships
74 of the 99 posterior probability values (75%) in the 50% consensus tree were over
80%, indicating the high likelihood of relationships in the majority of the nodes.However,
there are several incidences where the posterior probability values were less than 70%,
including several of the basal relationships.Unfortunately, because of low support, the deep
relationships of these species cannot be confidently confirmed with this analysis. These deep
relationships are likely to be ancient, and confidence in these phylogenies could mean a better
understanding of the evolutionary histories of the genus overall.
There is one occurance of phylogenetic polytomythese occur where there is a lack
of information, the inability to determine the branching order, or possibly speciation events
that occured at once (Garland and Diaz-Uriarte, 1999).In this case there is phylogenetic
polytomy ofP.nigrovittattus (QCAZ25789).I believe this was due to errors in the analysis
rather than speciation from the rest of the species involved at the same time as the outgroup
Phrynopys bracki.
The new sequencePristimantis altamazonicus QCAZ25382 was grouped separately
from the other 2 newP.altamazonicus and the 1 published sequence ofP.almatazonicus -
instead it was grouped withP.diadematus.This may have been due to discrepancies in
sequence analysis, but as the distributions of the species are similar it is also possible that the
inconsistent sequence ofP. altamazonicus was simply mis-identified and should be namedP.
diadematus. This sequence was also found at a higher altitude than the rest of the species in
theP. diadematus cladethis could indicate that it is in fact a different species altogether,
but further analyses would be needed to investigate this.
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P.sp.QCAZ 25588 and P.sp.QCAZ 25582 are likely to be the same species as there
was high support for a close relationship and they were also found in the same area.The most
closely related species according to my analyses isPristimantis ockendeni.Heinicke,
Duellman and Hedges (2007) analysis found that the closest relative toP.ockendeniwasP.
unistrigatusthis species was found in the similar position in my analyses but was not more
closely related to P.sp.QCAZ 25588 and P.sp.QCAZ 25582 compared toP.ockendeni (see
Fig.4).With the wide distribution and the recognition thatP. ockendeniis yet to be fully
delimited is likely thatP.sp (QCAZ25582 and QCAZ25588) are that of one of the species
that has been or is yet to be delimited fromPristimantis ockendeni.
Fig. 4. Simple representation of the comparison of relationships betweenPristimantisockendeni,Pristimantis unistrigatus and two unidentifiedPristimantis species in my own analysis and the
analysis of Heinicke, Duellman and Hedges (2007).
It is likely that the sequenceP.sp.QCAZ25392 isP.conspicillatus due to the high
posterior probabiliy values for their relationship.The inferred relationships ofP.condor, P.
conspicillatus (QCAZ18007, QCAZ25392) andP.croceoinguinis(QCAZ25544) are similar
to the inferred relationships proposed by Pinto-Snchez (2012) (see Fig.5).They also find
thatP.malkiniis the sister species toP.citrogasterwith relatively high support, but my
Bayesian analysis showedP.malkinito be more closely related toP.lirellus andP.imitatrix,
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with higher support.It is less similar to the relationships proposed by Heinicke, Duellman
and Hedges (2007); they showP.croceoinguinis to be a sister species toP.citrogaster, and
P.condor to be a derived species, whereas my analyses showP.citrogaster andP.
croceoinguinis to be sister species (see Fig.6). With a follow-up study I would consider
removing theP.croceoinguinissequence from the analysis in order to see if the relationships
betweenP.condor, P.conspicillatus and P.citrogasterremained the sameif so we could
conclude that these relationships are more likely to be correct than those proposed by
Heinicke, Duellman and Hedges (2007).
Fig.5.Simple representation of the comparison of relationships between 3 species of Pristimantis inmy own analysis and the analysis of Pinto- Snchez (2012)P conspicillatushere includes the
sequencesP.sp.QCAZ18007, QCAZ25392 and the published sequence ofP.conspicillatus.
Fig.6.Simple representation of the comparison of relationships between 4 species of Pristimantis inmy own analysis and the analysis of Heinicke, Duellman and Hedges (2007)
With further investigation of the species listed in Heinicke, Duellman and Hedges
(2007) asPristimantis sp.AY326002, I found that this sequence is listed as an
Eleutherodactylus species on NCBI.However, this was defined by Darst and Canatella
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(2004) before the analyses done by Heinicke, Duelmann and Hedges (2007), and so I
currently accept the laters definition of the sequence.
P.acuminatusandP.lacrimosuswere not included in the study by Heinicke,
Duellman and Hedges (2007) nor by Pinto-Sanchez et al.,(2007)it is possible that this
study reveals newly discovered relationships, but it would be useful for further
investigations of the relationships between these species and those surrounding them in the
inferred phylogenies as the posterior probability value for splitting ofP.lacrimosuswas
extremely low (52.3) and so this relationship cannot be established with confidence.
Fig.7.Simple representation of the comparison of relationships between 5 species of Pristimantis in
my own analysis and the analysis of Heinicke, Duellman and Hedges (2007).
The 32 species wide clade that was used for altitudinal analyses was chosen as it
encompasses some of the species that have been most recently studied, namelyP.achuar, P.
altamnis, andP.kichwarum (and the previously mentionedP.sp.)and the majority of the
information included in this clade was from the new sequences.
The distribution map forP.ockendenishows a vast range, but this species is
undergoing scrutinisation. The small distributions of the recently delimitedP.kichwarum, P.
altamnis andP.achuarby Elmer and Canatella (2008) indicate that any occurence ofP.
ockendeniwhich has a large distribution should be studied further as the presence of cryptic
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species, each with a smaller seperate distribution, is likely. This may also be true of other
species with wide distributions.
The distribution ofP. chalceus appears to be vast, but of the 25 localities in Ecuador,
20 of them occur below 1000m.a.s.l. (AmphibiaWeb, 2013) and so those at higher altitudes
are probably uncommon. Even so, this wide distribution could indicate that the species name
is an umbrella termfor species that have yet to be delimited. All the sampling was
performed in Ecuador, but for species which appear to have distributions which need to be
further defined sampling further afield would be useful as individuals in those areas may give
an indication of further delimited species.
Model and analyses
Each model available for phylogenetic analyses has its weaknesses.The GTR + I +
model was chosen as it is more parameter rich than models such as the Jukes Cantor model
(Hulsenbeck, Ronquist, Neilson and Bollback, 2001) and has been used in a number of
studies involving phylogenetic relationships (Heinicke, Duellman and Hedges 2007; Santos
et al., 2009; Pinto-Sanchez et al., 2012) and as the comparisons would involve two of these
studies it was beneficial for the same model to be used.It has a relaxed assumption of equal
base frequencies.The I symbol indicates that the base frequencies are stationary, and the
symbol indicates a gamma distribution of rates for sites (Neilson, Lohman and Sullivan,
2001).The MCMC (Markov chain Monte Carlo) algorithm is used by MrBayes to estimate
the posterior probabilities of trees (Hulsenbeck and Ronquist, 2001) and is useful as it takes
phylogenetic uncertainty into account.However, it has been shown that even the widely used
Bayesian methods may not be fully accurate but may be too liberal, especially if the model
used is not complex enough (Suzuki, Glazko and Nei, 2002).With more time, analyses such
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as maximum likelihood and bootstrap probability would be performed to deduce any
discrepancies that may have occurred due to the use of the model and Bayesian methods
chosen.
Convergence on stationarity
The output results show convergence on stationarity when addressing the correlation,
density and trace plots of the runs.The shape of the correlation graph showed no affinity for
increasing or decreasing over time, with a white noise pattern of points, another indication
of convergence. Similarly, initially the shape of the trace and sample trace graphs are
stochastic around the mean, showing that variation of the likelihood around the mean is high,
but then nearing the end of the analysis it varies less so indicating the approach to
stationarity.With analyses run for a longer period of time it is likely that the variation around
the mean would decrease further and give greater confidence in the output.
The standard deviation of the mean was 0.915 and 1.083 for run 1 and run 2 respectivelyit
is expected that during analysis this value should approach 0.Overall, the likelihood of
reaching stationarity in this project was high, but with a repetition of the analysis the program
should be run for longer in order for better confidence in this respect.
Wider implications
As well as the inferrred deep evolutionary history of the genus, assessing the
distribution ofPristimantis is useful in determining which diversification hypotheses is most
likely to be correct - for example, it has been stated that diversification was ancient and due
to tectonic events (with the formation of the Andes) rather than climatic change (Elmer,
Dvila and Lougheed, 2007; Heinicke, Duellman and Hedges, 2007).
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The importance of conservation is amplified by studies similar to my own as it is
difficult to know what real damage anthropogenic practices may have on undiscovered
cryptic species as rapid declines continue (Stuart et al., 2004, Bickford et al., 2007). For
example, the subdivision of wide distribution ranges into multiple smaller regions due to the
occurrence of newly delimited species can intensify the pressure on each new species, or
mean that different conservation practices are needed (Kohler et al., 2005)this may be true
for the example in this study ofPristimantis ockendeni. Globally, 1933 species of amphibians
are listed on the IUCN Red List of Threatened Species as Vulnerable, Endangered or
Critically Endangered (IUCN, 2012) due to known practices such as habitat destruction and
fragmentation, infectious disease, and many enigmatic declines (Stuart et al., 2004). The
continued efforts to revise the taxonomy of thePristimantis genus will enhance the
knowledge of species requirements and the knowledge of the genus overall.
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Acknowledgements
I would like to thank Dr Kathryn Elmer for her continued support throughout my time
working on this project. Her knowledge of the subject was indeed an inspiration and gave me
drive to learn more about the subject. I would also like to thank Roderic Page for his
knowledge of the program Geneious and Roman Biek for the access to the licence for the
same program, and Hans Recknagel for his insight into the program Gblocks and for his
assistance when things were not going smoothly. I would also like to thank Isabel Coombs
for the use of the laptop used for the majority of the preliminary analyses. Thanks also to my
friends and family for putting up with my stress-filled messages and phone calls.
Title page photo credit: Santiago R.Ron, Museo de Zoologa, Universidad Catlica del
Ecuador.
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References
AmphibiaWeb: Information on amphibian biology and conservation.[web application].
2013.Berkeley, California: AmphibiaWeb.Available at
Accessed 15 February 2013
Arteaga-Navarro, A.F., and Guayasamin, J.M., 2011.A new frog of the genusPristimantis
(Amphibia: Strabomantidae) from the high Andes of Southeastern Ecuador,
discovered using morphological and molecular data.Zootaxa,2876, 17-29.
Bickford, D., Lohman, D.J., Sodhi, N., S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K.
K., and Das, I., 2007.Cryptic species as a window on diversity and conservation.
Trends in Ecology and Evolution, 22(3), 148-155.
Biomatters, 2012. Geneious 6.0.6., available from
Bollback, J.P., 2002.Bayesian Model Adequacy and Choice in Phylogenetics.Molecular
Biology and Evolution, 19(7), 1171-1180
Castresana, J., 2000. Selection of conserved blocks from multiple alignments for their use in
phylogenetic analysis.Molecular Biology and Evolution17, 540-552.
Elmer, K.R., and Cannatella, D.C., 2008.Three new species of leaflitter frogs from the
upper Amazon forests: cryptic diversity withinPristimantis ockendeni(Anura:
Strabomantidae) in Ecuador.Zootaxa, 1784, 11-38
Elmer, K. R., Dvila, J. A., and Lougheed, S. C., 2007. Cryptic diversity and deep divergence
in an upper Amazonian leaflitter frog,Eleutherodactylus ockendeni.BMC
Evolutionary Biology, 7, 247-261
8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
23/39
22
Fouquet, A., Gilles, A., Vences, M., Marty, C., and Blanc, M., 2007.Underestimation of
Species Richness in Neotropical Frogs Revealed by mtDNA Analyses.PLoS ONE,
Vol 2 (10): e1109.doi:10.1371/journal.pone.0001109
Garland Jr., T., and Daz-Uriarte,R., 1999.Polytomies and Phylogenetically Independent
Contrasts: Examination of the Bounded Degrees of Freedom Approach.Systematic
Biology, 48(3), 547-558
Gascon, C., Lougheed, S.C., and Bogart, J.P., 1996.Genetic and morphological variation in
Vanzolinius discodactylus: a direct test of the riverine barrier hypothesis.Biotropica,
28, 376-387
Hanken, J., 1999.Why are there so many new amphibian species when amphibians are
declining? Trends in Ecology and Evolution, 14(1), 7-8
Hay, J.M., Ruvinsky, I., Hedges, S.B., and Maxson, L.R., 1995.Phylogenetic
Relationships of Amphibian Families Inferred from DNA Sequences of Mitochondrial
12S and 16S Ribosomal RNA Genes.Molecular Biology and Evolution, 12(5), 928-
937
Heinicke, M.P., Duellman, W.E., and Hedges, S.B., 2007. Major Caribbean and Central
American frog faunas originated by ancient oceanic dispersal.Proceedings of the
National Academy of Sciences of the United States of America, 104(24), 10092-10097
Hoorne, C., Wesselingh, F.P., ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J.,
Sanmartin, I., Sanchez-Meseguer, A., Anderson, C.L., Figueiredo, J.P., Jaramillo,
C., Riff, D., Negri, F.R., Hooghiemstra, H., Lundberg, J., Stadler, T., Sarkinen, T.,
http://sysbio.oxfordjournals.org/search?author1=Ram%C3%B3n+D%C3%ADaz-Uriarte&sortspec=date&submit=Submithttp://sysbio.oxfordjournals.org/search?author1=Ram%C3%B3n+D%C3%ADaz-Uriarte&sortspec=date&submit=Submit8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
24/39
23
and Anntonelli, A., 2010.Amazonia Through Time: Andean Uplift, Climate Change,
Landscape Evolution, and Biodiversity.Science, 330(927), 927-931
Hughes.C., and Eastwood.R., 2006.Island radiation on a continental scale: Exceptional
rates of plant diversification after uplift of the Andes.Proceedings of the National
Academy of Sciences of the United States of America, 103, 10334-10339
Hulsenbeck, J.P., and Ronquist, F., 2001.MrBayes: Bayesian inference of phylogeny.
Bioinformatics, 17, 754-755.
Hulsenbeck, J.P., Ronquist, F., Neilson, R., and Bollback, J.P., 2001.Bayesian Inference of
Phylogeny and Its Impact on Evolutionary Biology.Science, 294, 2310-2314
IUCN 2012.IUCN Red List of Threatened Species.Version 2012.2..
Accessed15 February 2013
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis cajamarcensis.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis ceuthospilus.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis chalceus.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
http://www.iucnredlist.org/http://www.iucnredlist.org/http://www.iucnredlist.org/http://www.iucnredlist.org/http://www.iucnredlist.org/http://www.iucnredlist.org/8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
25/39
24
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis luteolateralis.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis ockendeni.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis orestes.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
IUCN (International Union for Conservation of Nature), Conservation International &
NatureServe, 2004.Pristimantis simonbolivari.In: IUCN 2012.IUCN Red List of
Threatened Species.Version 2012.2
Kass, R. W., Carlin, B. P., Gelman, A. and Neal, R. M., 1998. Markov Chain Monte Carlo in
Practice: A Roundtable Discussion. The American Statistician, 52(2), 93-100
Khler, J., Vietes, D.R., Bonett, R.M., Garca, F.H., Glaw, F., Steinke, D., and Vences,
M., 2005.New Amphibians and Global Conservation: A Boost in Species Discoveries
in a Highly Endangered Vertebrate Group.Bioscience, 55(8), 693-696
Kok, P.J.R., and Kalamandeen, M., 2008.Introduction to the taxonomy of the amphibians
of Kaieteur National Park, Guyana.ABC Taxa, 5, 238-243
8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
26/39
25
Lehr, E., Moravec, J., and Gagliardi Urrutia, L.A.G., 2010.A new species ofPristimantis
(Anura: Strabomantidae) from the Amazonian lowlands of northern Peru.
Salamandra, 46(4), 197-203
Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B., and Kent, J., 2000.
Biodiversity hotspots for conservation priorities.Nature, 403, 853-858.
Neilson, M., Lohman, K., and Sulliovan, J., 2001.Phylogeography of the tailed frog
(Ascaphus truei): Implications for the biogeography of the Pacific Northwest.
Evolution, 55(1), 147-160
Padial, J.M., and de la Riva, I., 2009.Integrative taxonomy reveals cryptic Amazonian
species ofPristimantis (Anrua: Strabomantidae).Zoological Journal of the Linnean
Society, 155(1), 97-122
Pinto-Snchez, N.R.,Ibez, R., Madrin, S., Sanjur, O.I., Bermingham, E., and
Crawford, A.J.,2012.The Great American Biotic Interchange in frogs: Multiple and
early colonization of Central America by the South American genusPristimantis
(Anura: Craugastoridae).Molecular Phylogenetics and Evolution.62, 954-972
Pyron, R.A., and Wiens, J.J., 2011.A large-scale phylogeny of Amphibia including over
2800 species, and revised classification of extant frogs, salamanders, and caecilians.
Molecular Phylogenetics and Evolution, 61(2), 543-583
Rsnen, M.E., Linna, A.M., Santos, J.C.R., and Negri, F.R., 1995.Late Miocene tidal
deposits in the Amazonian foreland basin.Science, 269, 386-390
8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
27/39
26
Ron, S.R., Guayasamin, J.M., and Yanez-Munoz, M.H., 2013.AmphibiaWeb
Ecuador.Version 2013.0.Museum of Zoology, Catholic University of Ecuador.
Available at:
Accessed 13 February 2013
Ronquist, F., Huelsenbeck, J.P., and van der Mark, P., 2005.MrBayes 3.1 Manual, Draft
5/26/2005 [online] Available at
Accessed 9 March 2012
Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H,, Canese, K., Chetvernin, V.,
Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L, Y.,
Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D. J., Madden, T.L., Maglott,
D.R., Miller, V., Mizrachi, I., Ostell, J., Pruitt, K.D., Schuler, G.D., Sequeira, E.,
Sherry, S.,T, Shumway, M., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusova, T.
A., Wagner, L., Yaschenko, E., and Ye, J., (2009).Database resources of the National
Center for Biotechnology Information.Nucleic Acids Res.2009 Jan;37(Database
issue):D5-15.Epub 2008 Oct 21.
Siqueira, S., Aguiar Jr, O., Strssmann, C., Del-Grande, M.L., Recco-Piemtel, S.M., 2008.
Chromosomal analysis of three Brazilian eleutherodactyline frogs (Anura:
Terrarana), with suggestion of a new species.Zootaxa, 1860, 51-59
8/13/2019 Hons Project - Robyn Cuthbertson - Inferring Phylogenies and Distributions of Upper-Andean and Amazonian Frogs
28/39
27
Stuart, N.S., Chanson, J.S., Cox, N.A., Young, B.E., Rodrigues, A.S.L., Fischman, D.
L., and Waller, R.W., 2004.Status and Trends of Amphibian Declines and
Extinctions Worldwide.Science, 306, 1783-1786
Suzuki, Y., Glazko, G.V., and Nei, M., 2002.Overcredibility of molecular phylogenies
obtained by Bayesian phylogenetics.Proceedings of the National Academy of
Sciences of the United States of America.99(25), 16138-16143
Wang, I.J., and Summers, K., 2009.Genetic structure is correlated with phenotypic
divergence rather than geographic isolation in the highly polymorphic strawberry
poison-dart frog.Molecular Ecology, 19(3), 447-458
Wang, I.J., Crawford,A.J., and Bermingham, E., 2008.Phylogeography of the Pygmy Rain
Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central
America.Molecular Phylogenetics and Evolution, 47(3), 992-1004
Yang, Z., and Rannala, B., 2012.Molecular phylogenetics: principles and practice.Nature
Reviews Genetics, 13, 303-314
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Appendix I: Table of species names and accession numbers used (Heinicke,
Duellman and Hedges, 2007).
No.
Species Origin
Museum
voucher
Lab tissue
number
Genbank accession no.
12S 16S
162
Pristimantis Heinicke,Duellman andHedges (2007) KU218116 267231 EF493518walkeri
163
Pristimantis Heinicke,Duellman and
Hedges (2007) KU177807 267863 EF493517luteolateralis
164
Pristimantis Heinicke,Duellman andHedges (2007) KU177821 267864 EF493351parvillus
165
Pristimantis Heinicke,Duellman andHedges (2007) KU177638 267865 EF493675chalceus
166
Pristimantis Heinicke,Duellman and
Hedges (2007) KU222023 267253 EF493519ockendeni
167
Pristimantis Heinicke,Duellman andHedges (2007) KU218057 267227 EF493387unistrigatus
168
Pristimantis Heinicke,Duellman andHedges (2007) KU217845 267211 EF493823 EF493663cajamarcensis
169
Pristimantis Heinicke,
Duellman andHedges (2007) KU212216 267198 EF493520ceuthospilus
170
Pristimantis Heinicke,Duellman andHedges (2007) KU212226 267200 EF493521lirellus
171
Pristimantis Heinicke,Duellman and
Hedges (2007) KU215476 267205 EF493824 EF493667imitatrix
172
Pristimantis Heinicke,Duellman and
Hedges (2007) KU217862 267213 EF493669 EF493665croceoinguinis
173
PristimantisHeinicke,
Duellman andHedges (2007) KU215460 267204 EF493670altamazonicus
174
Pristimantis Heinicke,Duellman and
Hedges (2007) KU218257 267249 EF493388orestes
175
Pristimantis Heinicke,Duellman and
Hedges (2007) KU218254 267248 EF493671simonbolivari
176
Pristimantis Heinicke,Duellman andHedges (2007) KU218035 267224 EF493348riveti
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177
Pristimantis Heinicke,Duellman andHedges (2007) KU218096 267228 EF493389versicolor
178
Pristimantis Heinicke,Duellman and
Hedges (2007) KU218025 267222 EF493349
phoxocephalus
179
Pristimantis Heinicke,Duellman andHedges (2007) KU218052 267225 EF493673spinosus
180
Pristimantis Heinicke,Duellman andHedges (2007) KU217863 267214 EF493672cryophilius
181
Pristimantis Heinicke,Duellman and
Hedges (2007) KU219788 267250 EF493674rhodoplichus
182
Pristimantis Heinicke,Duellman and
Hedges (2007) KU219796 267251 EF493377 EF493668wiensi
183
Pristimantis Heinicke,Duellman andHedges (2007) KU212293 267202 EF493825 EF493367petrobardus
184
Pristimantis Heinicke,Duellman andHedges (2007)
MHNSMWED56846 267438 EF493826 E F493664melanogaster
185
Pristimantis Heinicke,Duellman and
Hedges (2007) n/a n/a AM039709 AM039641simonsii
186
Pristimantis Heinicke,
Duellman andHedges (2007) KU177637 267866 EF493524appendiculatus
187
Pristimantis Heinicke,Duellman andHedges (2007) KU218028 267223 EF493680pycnodermis
188
Pristimantis Heinicke,Duellman andHedges (2007) KU179090 267867 EF493522dissimulatus
189
Pristimantis Heinicke,Duellman andHedges (2007) KU177658 267868 EF493523calcarulatus
190
Pristimantis Heinicke,
Duellman andHedges (2007) KU218021 267221 EF493679orcesi
191
Pristimantis Heinicke,Duellman andHedges (2007) KU218002 267217 EF493676glandulosus
192
Pristimantis Heinicke,Duellman andHedges (2007) KU218015 267218 EF493677inusitatus
193
Pristimantis Heinicke,Duellman andHedges (2007) KU217786 267207 EF493678acerus
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194
Pristimantis Heinicke,Duellman andHedges (2007) KU212220 267199 EF493681schultei
195
Pristimantis Heinicke,Duellman and
Hedges (2007) KU291702 171051 EF493351
bromeliaceus
196
Pristimantis Heinicke,Duellman andHedges (2007) KU218147 267246 EF493525subsigillatus
197
Pristimantis Heinicke,Duellman andHedges (2007) KU177812 267869 EF493526nyctophylax
198
Pristimantis Heinicke,Duellman andHedges (2007) No voucher 266036 EF493692shrevei
199
Pristimantis Heinicke,Duellman and
Hedges (2007) BWMC6918 266624 EF493527euphronides
200
Pristimantis Heinicke,Duellman andHedges (2007) No voucher 102308 EF493691rozei
201
Pristimantis Heinicke,Duellman andHedges (2007) KU218109 267230 EF493511gentryi
202
Pristimantis Heinicke,Duellman and
Hedges (2007) KU218013 267229 EF493512truebae
203
Pristimantis Heinicke,
Duellman andHedges (2007) KU217871 267215 EF493513curtipes
204
Pristimantis Heinicke,Duellman andHedges (2007) KU177972 267870 EF493689vertebralis
205
Pristimantis Heinicke,Duellman andHedges (2007) KU217836 267210 EF493350buckleyi
206
Pristimantis Heinicke,Duellman andHedges (2007) KU217991 267216 EF493688devillei
207
Pristimantis Heinicke,
Duellman andHedges (2007) KU177847 267871 EF493687surdus
208
Pristimantis Heinicke,Duellman andHedges (2007) KU179374 267872 EF493690quinquagesimus
209
Pristimantis Heinicke,Duellman andHedges (2007)
n/aKU217998
n/aKU21799
8 AY326003duellmani
210
Pristimantis Heinicke,Duellman and
Hedges (2007) KU177861 267873 EF493514thymalopsoides
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211
Pristimantis Heinicke,Duellman andHedges (2007) KU208508 267439 EF493682ocreatus
212
Pristimantis Heinicke,Duellman and
Hedges (2007) KU218030 267441 EF493683
pyrrhomerus
213
Pristimantis Heinicke,Duellman andHedges (2007) KU218234 267247 EF493515festae
214
Pristimantis Heinicke,Duellman andHedges (2007) KU218227 267437 EF493684leoni
215
Pristimantis Heinicke,Duellman and
Hedges (2007) QCAZ12410 267646 EF493686verecundus
216
Pristimantis Heinicke,Duellman and
Hedges (2007) KU177684 267874 EF493685celator
217
Pristimantis Heinicke,Duellman andHedges (2007) n/a n/a AY326007chloronotus
218
Pristimantis Heinicke,Duellman andHedges (2007) QCAZ16428 267644 EF493516thymelensis
219
Pristimantis Heinicke,Duellman andHedges (2007) n/a n/a AY326005supernatis
220
Pristimantis Heinicke,
Duellman andHedges (2007) n/a n/a AY326002sp.
221
Pristimantis Heinicke,Duellman andHedges (2007) USNM33609 101646 EF493699urichi
222
Pristimantis Heinicke,Duellman andHedges (2007) KU218016 267219 EF493698latidiscus
223
Pristimantis Heinicke,Duellman andHedges (2007) QCAZ17101 267635 EF493354colomai
224
Pristimantis Heinicke,
Duellman andHedges (2007)
AMNHA12444 267876 EF493697cruentus
225
Pristimantis Heinicke,Duellman andHedges (2007)
AMNHA124551 267877 EF493355ridens
226
Pristimantis Heinicke,Duellman andHedges (2007) KU177252 267878 EF493528cremnobates
227
Pristimantis Heinicke,Duellman andHedges (2007) n/a n/a AY326004w-nigrum
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228
Pristimantis Heinicke,Duellman andHedges (2007) KU217830 267209 EF493696actites
229
Pristimantis Heinicke,Duellman and
Hedges (2007) KU222001 267252 EF493695
lanthanites
230
Pristimantis Heinicke,Duellman andHedges (2007) KU177730 267879 EF493693 EF493666crenunguis
231
Pristimantis Heinicke,Duellman andHedges (2007) QCAZ19771 267640 EF493694labiosus
232
Pristimantis Heinicke,Duellman and
Hedges (2007)
MHNSMLR
4341 266049 EF493356sp.
233
Pristimantis Heinicke,Duellman and
Hedges (2007) QCAZ28448 267636 EF493529conspicillatus
234
Pristimantis Heinicke,Duellman andHedges (2007) KU217857 267212 EF493701condor
235
Pristimantis Heinicke,Duellman andHedges (2007) KU212278 267201 EF493700citriogaster
236
Pristimantis Heinicke,Duellman and
Hedges (2007) KU217809 267208 EF493827 EF493660achatinus
237
Pristimantis Heinicke,
Duellman andHedges (2007) KU218019 267220 EF493392lymani
238
Pristimantis Heinicke,Duellman andHedges (2007)
MHNSM9298 266046 EF493703fenestratus
239
Pristimantis Heinicke,Duellman andHedges (2007) KU291638 171021 EF493702bipunctatus
240
Pristimantis Heinicke,Duellman and
Hedges (2007)
MHNSM100
71 266052 EF493393skydmainos
241
Pristimantis Heinicke,
Duellman andHedges (2007) KU215493 267206 EF493353toftae
242
Pristimantis Heinicke,Duellman andHedges (2007) KU173492 267875 EF493706rhabdolaemus
243
Pristimantis Heinicke,Duellman andHedges (2007) n/a n/a AY843586pluvicanorus
244
Pristimantis Heinicke,Duellman andHedges (2007) KU291635 171098 EF493705sagittulus
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245
Pristimantis Heinicke,Duellman andHedges (2007) KU291659 171080 EF493704stictogaster
246
Pristimantis Heinicke,Duellman and
Hedges (2007) KU291627 171070 EF493390
aniptopalmatus
247
Pristimantis Heinicke,Duellman andHedges (2007)
MHNSM9267 266050 EF493707peruvianus
248
Pristimantis Heinicke,Duellman andHedges (2007) KU177680 267880 EF493391caprifer
.....
260
Phrynopus Heinicke,Duellman andHedges (2007)
USNM286919 171045 EF493709bracki
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Appendix II: New sequence information provided by Dr Kathryn Elmer
Species nameQCAZnumber
Locality Latitude LongitudeElevation(m.a.s.l)
Pristimantisachuar
25457 Kapawi lodge S 0232'32" W 7651'50" 239
Pristimantis
achuarholotype25463 Kapawi lodge S 0232'32" W 7651'50" 239
Pristimantis
acuminatus16748 EC Yasuni S 040' 36'' W 7623'43'' 230
Pristimantis
acuminatus19664 EC Yasuni S 040' 36'' W 7623'43'' 230
Pristimantis
altamazonicus25382 FMT S 0121'26" W 7751'73" 973
Pristimantis
altamazonicus 25407 La Selva S 0029'89" W 7622'43" 245
Pristimantisaltamazonicus
25535 Kapawi lodge S 0232'32" W 7551'50" 239
Pristimantis
altamnis25808
Comunidad
AsociacinChonta Yacu
N 0006.69 W 7722.46 610
Pristimantis
conspicillatus18007
Estacion
BiologicaJatun Sacha,Napo
S 0104'840" W 7736502 419
Pristimantiscroceoinguinis
18231
Shaime,
Zamora-
ChinchipeS 0418'92" W 7839'84" 907
Pristimantis
croceoinguinis25544 Kapawi lodge S 0232'32" W 7551'50" 239
Pristimantis
diadematus18014
EstacionBiologica
Jatun Sacha,Napo
S 0104'840" W 7736502 419
Pristimantis
diadematus18015
EstacionBiologica
Jatun Sacha,Napo
S 0104'841" W 7736503 420
Pristimantis
diadematus18017
EstacionBiologica
Jatun Sacha,Napo
S 0104'842" W 7736504 421
Pristimantis
kichwarum25579
Estacion
BiologicaJatun Sacha,Napo
S 0103.740 W 7736879 390
Pristimantis
lacrimosus15982 Azuela S 010'00" W 7739'00" unknown
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Pristimantis
lanthanites25389 La Selva S 0029'89" W 7622'43" 245
Pristimantis
librarius25589 Auca 14 Rd S 0041'85" W 7643'79" 255
Pristimantismalkini
25444
Estacion
BiologicaJatun Sacha,Napo
S 0104'840" W 7736'502" 419
Pristimantis
martiae25403 La Selva S 0029'89" W 7622'43" 245
Pristimantis
nigrovitattus25789 Lumbaqui N 0006'69" W 7722'46" 610
Pristimantis
ockendeni25576 Cuyabeno S 0000'8" W 7610'4" 230
Pristimantis
ockendeni25768
EstacionBiologica
Jatun Sacha,Napo
S 0104'840" W 7736'502" 419
Pristimantis sp. 18233Shaime,
Zamora-Chinchipe
S 0418'92" W 7839'84" 907
Pristimantis sp. 18235Shaime,
Zamora-Chinchipe
S 0418'93" W 7839'85" 908
Pristimantis sp. 18236Shaime,Zamora-Chinchipe
S 0418'94" W 7839'86" 909
Pristimantis sp. 25392 La Selva S 0029'89" W 7622'43" 245
Pristimantis sp. 25582 Auca 14 Rd S 0041'85" W 7643'79" 255
Pristimantis sp. 25588 Auca 14 Rd S 0041'86" W 7643'80" 256
Pristimantis
variabilis28430 Cuyabeno S 0000'8" W 7610'4" 230
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Appendix III: Output tables and graphs from MrBayes (Hulsenbeck and
Ronquist, 2001)
Table 1.Summary statistics produced from the MrBayes analysis.
Summary statistic LnL_run1 LnL_run2
Mean -17914.636 -17911.164
Standard deviation of mean 0.915 1.083
Median -17914.23 -17911.767
95% HPD lower -17938.889 -17938.827
95% HPD upper -17892.597 -17882.131
Auto-correlation time (ACT) 5380.765 5153.555
Effective sample size (ESS) 173.804 181.467
Fig.S1.Correlation of LnL_run1 and LnL_run2.
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Fig. S2.Comparison of density between LnL_run1 and LnL_run2.
Fig. S3. Comparison of relative density between LnL_run1 and LnL_run2.
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Fig. S4. Trace plot
Fig. S5. Trace plot (sample only)