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The new problem of Chinlestegophis and the origin of caecilians
(Amphibia, Gymnophionomorpha) is highly sensitive to old problems
of sampling and character construction
David Marjanović1, Hillary C. Maddin2, Jennifer C. Olori3, Michel Laurin4
1 Evolutionary Morphology, Dynamics of Nature, Museum für Naturkunde Berlin—Leibniz Institute for Evolution and Biodiversity
Science, Invalidenstraße 43, 10115 Berlin, Germany
2 Earth Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
3 Biological Sciences, State University of New York at Oswego, 30 Centennial Dr., 13126 Oswego, NY, USA
4 CR2P (Centre de Recherches en Paléontologie – Paris), CNRS/MNHN/Sorbonne Université, Muséum National d’Histoire Naturelle, 75231 Paris
cedex 05, Paris, France
https://zoobank.org/B5FBF663-BC46-439A-8DE3-BDE33D91D962
Corresponding author: David Marjanović (david.marjanovic@gmx.at)
Academic editor: Florian Witzmann ♦
Received
14 July 2023 ♦
Accepted
2 December 2023 ♦
Published
10 January 2024
Abstract
The description of the small Late Triassic temnospondyl Chinlestegophis ushered in a potentially radically new understanding of the
origins of the extant amphibian clades. Together with the fragmentary Rileymillerus, Chinlestegophis was argued to link extant cae-
cilians to Permo-Triassic stereospondyl temnospondyls rather than to frogs and salamanders (and through them to amphibamiform
temnospondyls or to brachystelechid and lysorophian “lepospondyls”). We critically review the comparative description of Chin-
lestegophis and phylogenetic analyses of previous studies. Most of the features previously interpreted to be shared by caecilians,
Chinlestegophis and/or other stereospondyls have dierent distributions than scored in the analysis. We also nd no evidence for
an incipient tentacular sulcus in Chinlestegophis, and note that its vertebrae, unreduced ribs and dermal shoulder girdle are unlike
those of any extant amphibians (nor their likely sister group, Albanerpetidae). Furthermore, the original matrices contain misscores
accreted over more than a decade that likewise inuence the results. Some features are coded as multiple redundant characters: the
double toothrow of Chinlestegophis, other stereospondyls, and caecilians is represented as seven characters. Analysis of the unmod-
ied matrix yields much less resolution than originally reported, and tree topology is altered by a small change to the taxon sample
(the addition of Albanerpetidae), limited revisions of irreproducible scores, and ordering the most obviously clinal characters; any
one of these changes removes Chinlestegophis from Lissamphibia, and conrms it as a stereospondyl.
Key Words
Amphibia, Chinlestegophis, Funcusvermis, Gymnophiona, Gymnophionomorpha, Lissamphibia, majority-rule consensus, phylo-
genetics, phylogeny
Introduction
Caecilians have a scanty fossil record (Santos et al. 2020;
Kligman et al. 2023); the earliest well-supported stem
members are Funcusvermis gilmorei Kligman et al.,
2023 (Late Triassic), and Eocaecilia micropodia Jenkins
& Walsh, 1993 (Jenkins and Walsh 1993; Early Jurassic).
Eocaecilia retains limbs and some cranial bones that are
absent in the caecilian crown group (Gymnophiona;
see Wake 2020); partial femora were also assigned to
Funcusvermis and the Early Cretaceous or, more likely,
Late Jurassic (Lasseron et al. 2019) Rubricacaecilia
monbaroni Evans & Sigogneau-Russell, 2001 (Evans
and Sigogneau-Russell 2001; Kligman et al. 2023).
Fossil Record 27 (1) 2024, 55–94|DOI 10.3897/fr.27.109555
Copyright David Marjanović et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited.
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David Marjanović et al: Dataset quality, Chinlestegophis and origin of caecilians
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Since Eocaecilia was named, a more thorough anatom-
ical study (Jenkins et al. 2007) and many phylogenetic
analyses conrmed its position along the caecilian stem
(Laurin 1998; Vallin and Laurin 2004; Maddin et al.
2012a; Pardo et al. 2017a: g. S6). However, despite the
absence of serious doubts about the status of Eocaecilia
in the literature (Evans and Sigogneau-Russell 2001;
Carroll 2007: 54; Sigurdsen and Bolt 2010: 1373;
further corroborated by Kligman et al. 2023), Pardo et
al. (2017a: abstract) stated: “The position of Eocaecilia
within tetrapod phylogeny is controversial, as it already
acquired the specialized morphology that character-
izes modern caecilians by the Jurassic.” That statement
is misleading: all phylogenetic analyses that included
Eocaecilia support its placement as a stem-caecilian;
it is the position of caecilians as a group in the context
of its ancestry among extinct tetrapods that remained
controversial.
To this controversy, Pardo et al. (2017a) added
Chinlestegophis jenkinsi, which they named and
described as a stem-caecilian from the Late Triassic
(slightly younger than Funcusvermis: Kligman et al.
2023). Their phylogenetic analyses surprisingly appeared
to anchor the caecilians (through Chinlestegophis)
within the stereospondyl temnospondyls, whereas frogs
and salamanders (i.e., batrachians) remained in a more
common placement as dissorophoid temnospondyls,
producing a new and condently delivered hypothesis
of lissamphibian origins. The captivating notion of
the problem of amphibian origins and the evolution of
specialized caecilian traits having been “solved” with
the discovery of Chinlestegophis has already permeated
popular zoology textbooks (Pough et al. 2022: gs. 9.2
and 9.5).
Although we agree that Chinlestegophis presents an
interesting mix of characters, we wish to respond to
claims Pardo et al. (2017a) made about Chinlestegophis
that were incompletely tested in that and subsequent
studies (Schoch et al. 2020; Serra Silva and Wilkinson
2021; Gee 2022; Kligman et al. 2023). We nd in Pardo
et al. (2017a), and review and evaluate below: 1) prob-
lems with the matrices used, including narrow taxon
sampling, errors and oversights in character construc-
tion and modication, and incorrect scores within the
original data sets underpinning the resulting matrices;
2) a suboptimal methodology, including reliance on a
majority-rule consensus tree and incomplete reporting
of tree statistics; and 3) qualitative problems with the
diagnostic features linking Chinlestegophis (and in
some cases Rileymillerus Bolt & Chatterjee, 2000) to
caecilians. Our reanalyses show that Chinlestegophis
in particular and stereospondyls in general currently
cannot be supported as stem-caecilians and should not
be treated as such in textbooks or in secondary anal-
yses, such as molecular estimates of divergence times
(as previously stated by Santos et al. 2020 and Kligman
et al. 2023).
Scope
Recent works have investigated selected aspects of the
work of Pardo et al. (2017a). Marjanović and Laurin
(2018) and Serra Silva and Wilkinson (2021) reana-
lyzed one of the two matrices, nding that the published
majority-rule consensus tree was a highly incomplete
presentation of the results. Kligman et al. (2023: supple-
mentary information parts 3–4) reevaluated a large
number of scores of that matrix, enlarged the taxon
sample and discussed the character states that Pardo et
al. (2017a) had used to tie caecilians to Chinlestegophis
and other stereospondyls, focusing on their distribu-
tion in stereospondyls. We focus on their distribution in
lissamphibians and so-called lepospondyls, experiment
with (and discuss) ordering characters, adding taxa and
reevaluating a dierent set of scores, and rst of all we
reanalyze the other matrix for the rst time, both without
and with a topological constraint.
Nomenclature and terminology
Our usage of the clade names Gymnophiona, Amphibia
and Lissamphibia follows Wake (2020) and Laurin et al.
(2020a, b); temnospondyl nomenclature follows Schoch
(2013, 2018), except for the names Temnospondyli,
Euskelia and Limnarchia (Yates and Warren 2000).
Whenever practicable, we applied the same set of names
to all gures. Junior synonyms are shown in parentheses,
and names that cannot be applied to a particular tree
(because of qualifying clauses or denitions that restrict
their applicability to certain phylogenetic contexts) are not
shown on that tree. Schoch (2013) gave identical deni-
tions for Stereospondyli and Stereospondylomorpha; it is
obvious that that is an accident and that the intended de-
nition for Stereospondyli can be recovered by replacing
“most” by “least”. Misspellings of genus and species
names in the matrices and gures of Pardo et al. (2017a)
are corrected. See Marjanović and Laurin (2019: 13) for
the correction of “Albanerpetontidae” to Albanerpetidae.
We use “caecilians” for crown-group caecilians
(Gymnophiona: Wake 2020) and their uncontroversial
relatives like Eocaecilia and Funcusvermis. The names
Lepospondyli and Microsauria are used here informally
for traditional groupings of taxa; the likely para- or poly-
phyly of these groupings (supported and reviewed by
Marjanović and Laurin 2019) is beyond the scope of this
work. For simplicity we present these names without
quotation marks throughout.
We use “coding” for the process of choosing and
dening the characters and their states, and “scoring” for
lling in the matrix. Observed morphology is “miscoded”
if, for example, it is represented as two redundant charac-
ters in the character sample, but “misscored” if the scores
(numbers, state symbols) in the matrix are not what they
should be according to the existing state denitions.
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Abbreviations
AMNH FARB Collection of Fossil Amphibians,
Reptiles and Birds at the American
Museum of Natural History (New York).
app. appendix (of cited works).
CI consistency index.
MPT most parsimonious tree.
MRC majority-rule consensus.
OTU operational taxonomic unit (a line in a
data matrix).
RC rescaled consistency index.
RI retention index.
supp. inf. supplementary information (of cited
works).
Matrices, methodologies, and missteps
Matrix history and taxon sampling
Pardo et al. (2017a) analyzed two matrices: a taxo-
nomically broader, unpublished dataset, and an
expanded, published matrix focused on the position of
Chinlestegophis and Rileymillerus within temnospon-
dyls. The originally unpublished matrix (see Suppl.
material 1 for a NEXUS le), which generated the trees
shown in Pardo et al. (2017a: g. S6), contains 319 char-
acters (27 of them parsimony-uninformative, including
ve constant ones) and 71 OTUs; it is based on the matrix
of Maddin et al. (2012a), with additions of characters and
taxa from Huttenlocker et al. (2013) and several new
ones. Those earlier matrices are based on that of Anderson
et al. (2008a), but subsequently proposed corrections to
that matrix (Marjanović and Laurin 2009; Skutschas and
Martin 2011; Sigurdsen and Green 2011) were neither
included in the resulting composite matrix nor addressed
in the text by Pardo et al. (2017a) or any of the references
therein. Those changes have considerable inuence on
the resulting tree topology, as exemplied in Fig. 1.
The published matrix (Pardo et al. 2017a: supporting
information part D), which generated the trees shown in
Pardo et al. (2017a: g. 2, 3, S7), has 345 characters (23
parsimony-uninformative) and 76 OTUs. It is built on
the unpublished matrix by the deletion of most non-tem-
nospondyl taxa and the addition of characters and taxa
taken primarily from Schoch (2013)—see Gee (2022) for
a thorough discussion of that lineage of matrices.
It is, of course, common practice to modify and expand
existing data sets, and underlying errors are frequently
perpetuated into later generations of matrices when rst-
hand reassessment of specimens is infeasible, detailed
comparison to the literature is deemed too time-con-
suming, or the full history of characters becomes
obscured over time, leading to dierent meanings of
the same character for dierent taxa that were added or
revised at dierent times (Marjanović and Laurin 2019;
Gee 2021, 2022). In those cases, conservative practice is
to accept preexisting descriptions and scores as reliable.
However, over many iterations of matrices, substantial
errors can and do accumulate—this is a known and perva-
sive problem with large data matrices that are recycled
in consecutive studies (Simões et al. 2017; Laurin and
Piñeiro 2018; Marjanović and Laurin 2019; Gee 2021,
2022; Kligman et al. 2023: supp. inf. part 4; and see our
Discussion section).
The merging of existing matrices can also generate
additional problems related to redundant characters
and states. As an example, multiple characters related
to the lower jaw in the published matrix of Pardo et
al. (2017a) carry redundancy (in particular characters
147, 148, 146, 272, 273, 322, 344; see full evaluation
below), and because each is strongly associated with
specialized morphologies mainly observed in caecilians,
they may, even when correctly scored, generate bias by
inating support for the purported relationship between
Chinlestegophis and caecilians. Moreover, as characters
are merged, moved, modied, and added, it becomes
increasingly easy to overlook simple mechanical errors,
such as state 26(2) being mentioned neither in the list of
state labels within the matrix le nor in the character list
despite all three states being scored for numerous taxa in
the matrix (Pardo et al. 2017a: SI appendix parts C, D).
Robust analyses also may be thwarted by constraints
related to the original taxon sampling of the underlying
matrices; in other words, matrices compiled by other
authors were (implicitly or explicitly) constructed with
the intent to apply them to specic problems, and thus
any clade may be densely or sparsely sampled depending
on the question that was originally addressed, rather than
on questions of later interest. Inserting new taxa may be
dicult if additional variation is not easily accommo-
dated without major character revisions, and this may
limit which taxa can be speedily added. The matrix of
Anderson et al. (2008a) is slightly modied from that
of Anderson (2007), which is a merger of a matrix that
sampled lepospondyls (Anderson 2001) and a matrix that
sampled amphibamiform temnospondyls (Anderson et
al. 2008b). As a result, all descendants of the matrix of
Anderson et al. (2008a), including the unpublished matrix
of Pardo et al. (2017a), sample lepospondyls, amphibam-
iforms, and very little in between; in the case of Pardo
et al. (2017a: g. S6), other than the amphibamiforms
and the added taxa Chinlestegophis and Rileymillerus,
taxa include only seven other temnospondyl OTUs
(some composite), the colosteid Greererpeton, lepo-
spondyls, the diadectomorph pan-amniote Limnoscelis,
the seymouriamorph Seymouria and the anthracosaur
Proterogyrinus. The taxon sample is completed by the
designated outgroup Acanthostega, the earliest well-un-
derstood limbed vertebrate.
The more narrowly focused published matrix of
Pardo et al. (2017a) omits almost all taxa not sampled
by Schoch (2013), retaining only temnospondyls,
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David Marjanović et al: Dataset quality, Chinlestegophis and origin of caecilians
58
Acanthostega
Greererpeton
Eryops
Balanerpeton
Dendrerpetidae
Ecolsonia
Acheloma
Tambachia
Branchiosauridae
Micromelerpetidae
Tersomius
Micropholis
Eoscopus
Doleserpeton
Gerobatrachus
Platyrhinops
Amphibamus
Proterogyrinus
Seymouria baylorensis
Limnoscelis
Adelogyrinus
Microbrachis
“Asaphestera” (chimeric)
Tuditanus
Hapsidopareion
Saxonerpeton
Pantylus
Stegotretus
Pelodosotis
Micraroter
Batropetes
Rhynchonkos
Cardiocephalus sternbergi
Cardiocephalus peabodyi
Euryodus primus
Euryodus dalyae
Utaherpeton
Scincosaurus
Sauropleura scalaris
Ptyonius
Urocordylus
Keraterpeton galvani
Batrachiderpeton
Diceratosaurus
Diplocaulus magnicornis
Diploceraspis
Oestocephalus
Phlegethontia
Brachydectes
Eocaecilia
Albanerpetidae
salamanders
Triadobatrachus
frogs
46
37 76
83
91
30
50
35
41
35
25
52
–
–
–
–
–
–
7
–
19
–
30
28
68
44
29
77
52
47
68
67
52
19
12
100
69
88
83
50
93 75
96
17
22
32
70 88 97
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
4
5
5
≥ 5
≥ 5
4
≥ 5
4
≥5
≥5
Liss-
amphibia
Amphibia
(Lepospondyli)
Temnospondyli
Amphibamiformes?
“microsaurs”
Aïstopoda
“nectrideans”
Tetrapoda
Figure 1. Strict consensus of the four MPTs obtained by Marjanović & Laurin (2009: electronic supplementary material 2) from
their modied version of the matrix of Anderson et al. (2008a) with ordering of clinal characters. Note that contrary to Anderson
et al. (2008a), who had found extant amphibians to be diphyletic, with the stem-caecilian Eocaecilia among lepospondyls but
Albanerpetidae, “salamanders”, Triadobatrachus and “frogs” among temnospondyls, Lissamphibia is found as a clade (cyan
rectangle) and placed among lepospondyls (orange rectangle). The temnospondyl Gerobatrachus, interpreted as a member of the
batrachian stem by Anderson et al. (2008a), i.e., closest to frogs and salamanders, is marked with a purple rectangle and white font.
The names of extant taxa are in boldface; “frogs” and “salamanders” are composites. The application of the name Amphibamiformes
is unclear due to the absence of Dissorophus. Numbers below internodes are bootstrap percentages (in bold if 50 or higher; “–”
indicates clades contradicted by the bootstrap tree, always by clades with bootstrap percentages of 40 or less), numbers above
internodes are Bremer values. Some or all of the Bremer values shown as “≥ 5” are probably 5 (Marjanović and Laurin 2009). Note
that “Asaphestera” as used here is a chimera of the amniote Asaphestera, the microsaur Steenerpeton Mann et al., 2020, and an
indeterminate lower jaw; most of the material belongs to Steenerpeton, however (Mann et al. 2020). The Dendrerpetidae OTU was
originally called “Dendrerpeton” but is mostly based on its apparently close relative Dendrysekos.
Fossil Record 27 (1) 2024, 55–94
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59
lissamphibians, and the same two outgroups as Schoch
(2013), Proterogyrinus and Greererpeton. The stated
reason for this drastic omission of taxa, which eliminated
all lepospondyls, Seymouria and Limnoscelis, was to
reduce calculation time for the Bayesian analysis (Pardo
et al. 2017a: E5394), after analysis of the unpublished
matrix suggested that Chinlestegophis and lissamphib-
ians nested within Temnospondyli.
In short, Pardo et al. (2017a) rst tested the phylo-
genetic position of Chinlestegophis and the similar
Rileymillerus (Bolt and Chatterjee 2000) “coarsely”
by adding them to a matrix that sampled lepospondyls,
amphibamiforms, a few other extinct taxa, and lissam-
phibians. Chinlestegophis and Rileymillerus were found
as temnospondyls close to, but outside, Amphibamiformes
(Pardo et al. 2017a: g. S6). Accepting the result that
Chinlestegophis, Rileymillerus and lissamphibians were
temnospondyls, Pardo et al. (2017a) zoomed in by adding
them to a matrix that sampled temnospondyls (and temno-
spondyl-related characters) more broadly, but omitted
most other extinct clades. The question of whether caeci-
lians are lepospondyls or stereospondyl temnospondyls
was never adequately tested; the unpublished matrix
lacks stereospondyls and uses unrevised scores for lepo-
spondyls that were previously criticized (Marjanović and
Laurin 2009; Sigurdsen and Green 2011; Skutschas and
Martin 2011), whereas the published one lacks lepospon-
dyls altogether.
The published matrix further lacks representation
of Albanerpetidae (a member or the sister group of
Lissamphibia), despite their presence in the unpublished
matrix. Daza et al. (2020) added Albanerpetidae (as a
composite taxon with new data) back into the published
matrix of Pardo et al. (2017a) and analyzed the result with
implied weighting. They found caecilians and batrachians
as sister taxa, followed by Karauridae as the next more
distant relative, then Albanerpetidae, then the branchio-
saurid Apateon and then the rest of Amphibamiformes.
Chinlestegophis and Rileymillerus instead formed the
sister-group of Brachyopoidea within Stereospondyli
(Daza et al. 2020: g. 4E, S14). Clearly, omitting
Albanerpetidae had a large eect on the resulting rela-
tionships among extinct taxa and extant amphibians.
Phylogeny inferred from parsimony
The original parsimony analysis of the published matrix
yielded 882 shortest trees (Pardo et al. 2017a; and see
below). As often occurs, the strict consensus was poorly
resolved. To remedy this, Pardo et al. (2017a: g. S7B)
produced a majority-rule consensus (MRC) tree and
used it as the basis for comparison with the tree resulting
from a Bayesian analysis of the same matrix (their g.
2C = S7A). Both the MRC and Bayesian trees show
batrachians as amphibamiforms, but caecilians as stereo-
spondyls closest to Chinlestegophis, and Rileymillerus as
sister to caecilians + Chinlestegophis. However, none of
the 28 nodes that separate caecilians from batrachians +
karaurids have 50% or higher bootstrap support, and none
(even the basal caecilian node) occurs in 100% of the
shortest trees (Pardo et al. 2017a: g. S7B). We stress that
the percentage of MPTs in which a given node occurs,
as long as it is not 0 or 100, is not a support measure
in a parsimony analysis (e.g., Serra Silva and Wilkinson
2021; Kligman et al. 2023: supp. inf. part 3); all MPTs are
equally parsimonious, and therefore equally optimal by
the sole criterion the analysis used. Therefore, the MRC
tree provides an incomplete picture of the results of any
parsimony analysis, even if there is only a single island
of MPTs (see below). Indeed, a fully resolved MRC is
not even necessarily identical to any MPT (J. Felsenstein,
pers. comm. to D. M. 2017).
Investigating that problem specically, Serra Silva and
Wilkinson (2021) reevaluated the full diversity of MPTs
supported by the published matrix of Pardo et al. (2017a),
noting in their introductory paragraph that “[d]espite
concerns that summarizing MPTs with the majority-rule
consensus is potentially misleading […], some workers
still use the majority-rule method as if it were unprob-
lematic (e.g. […] Pardo et al. 2017[a]).” After briey
describing the reanalysis by Marjanović and Laurin (2018:
57–58; 2019: 144, g. 30I–K), they demonstrated why
the MRC is misleading in the specic case of Pardo et al.
(2017a), and why it is important to inspect individual trees
when the strict consensus is unsatisfactorily resolved: the
882 trees form islands which are each highly congruent
internally, but very dierent from each other. More than
half of the MPTs belong to a single island; therefore, the
overall MRC (Pardo et al. 2017a: g. S7B) is almost
entirely identical (Serra Silva and Wilkinson 2021: g. 2)
to the MRC of that one island and fails to represent the
MPTs on the other equally parsimonious islands.
Of the other islands, one (gured by Marjanović
and Laurin 2019: g. 30I; Serra Silva and Wilkinson
2021: g. 3c) agrees with the most popular hypothesis
of lissamphibian origins, which is also supported by the
previously unpublished matrix of Pardo et al. (2017a:
g. S6): that Lissamphibia (including Eocaecilia but
excluding Chinlestegophis and Rileymillerus) nests inside
Amphibamiformes, close to Gerobatrachus (Atkins et al.
2019; Daza et al. 2020: g. 4D/S13; Schoch et al. 2020;
Kligman et al. 2023). It further diers from the largest
island in that the karaurids occupy their usual position as
stem-salamanders (corroborated by Jones et al. 2022), not
the entirely novel one on the batrachian stem found on the
largest island. Moreover, on the stereospondyl side of the
tree, Chinlestegophis and Rileymillerus form the sister-
group of Brachyopoidea, rather than being nested in it as
on the largest island.
Another island (Marjanović and Laurin 2019: g.
30K; Serra Silva and Wilkinson 2021: g. 3b) shows
Lissamphibia as the sister-group of Chinlestegophis +
Rileymillerus, together nested within Stereospondyli next
to Brachyopoidea. Yet another island (Marjanović and
Laurin 2019: g. 30I; Serra Silva and Wilkinson 2021:
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David Marjanović et al: Dataset quality, Chinlestegophis and origin of caecilians
60
g. 3a) positions Lissamphibia next to Gerobatrachus
within Amphibamiformes, and Chinlestegophis is nested
within the caecilians as the sister-group of Eocaecilia,
while Rileymillerus is placed among the stereospondyls
as the sister-group of Brachyopoidea.
In other words, parsimony analysis of the published
matrix of Pardo et al. (2017a) supports positions within
Amphibamiformes or Stereospondyli equally strongly for
Chinlestegophis, the undoubted caecilians, and Batrachia
(including Karauridae).
Bayesian inference of phylogeny
With the result of the parsimony analysis of the published
matrix wholly inconclusive, an argument can still be
made that the topology shown in g. S7B of Pardo et
al. (2017a) should be preferred over the equally parsi-
monious alternatives because it is congruent with the
result of the Bayesian analysis of the same matrix, which
is the only result gured in the main paper (Pardo et al.
2017a: gs 2B, C, 3, S7A). However, Bayesian inference
as a method of phylogenetic analysis of paleontological
matrices has its own sources of error.
The supposed problem of common branch lengths
for all characters in previous simulations, pointed out by
Golobo et al. (2017, 2018) and given great weight by
Marjanović and Laurin (2019: 98), seems not to be one
of them; it was accounted for by the two latest treatments
of the question of how best to analyze morphological
data (Puttick et al. 2018; Keating et al. 2020) and found
to be irrelevant. Yet, those two studies did not simulate
any missing data, and the misuse of the MRC to repre-
sent the results of parsimony analyses by Puttick et al.
(2018) will overestimate the precision but underestimate
the accuracy of parsimony, as Keating et al. (2020: g. 5)
demonstrated. Furthermore, the homoplasy distributions
in the matrices simulated by Puttick et al. (2018), and
probably Keating et al. (2020) as well, do not encompass
cases like the matrix of Marjanović and Laurin (2019)
at the very least, and evidently not the matrix of Pardo
et al. (2017a) either—given the multiple starkly dierent
topologies that it supports as equally parsimonious.
Even more importantly, as paleontological matrices
generally do (contrary to the implication by King
[2020]), the matrix of Pardo et al. (2017a) contains
multiple conicting signals as well as large amounts of
missing data. That combination is known to present a
major problem for parametric methods in phylogenetics,
including Bayesian inference, whereas parsimony (a
non-parametric method) is immune to that particular
issue (Simmons 2014; King 2019). Specically, when
character conict is present (and at least one terminal
branch has a positive length), parametric methods give
much greater weight to the signal present in characters
that are sampled for all taxa than to the signal present
in incompletely sampled characters, even if very little
information is missing (Simmons 2014; King 2019).
Given that there is no reason to assume a correlation
between homoplasy and preservation, we regard
this as a aw of parametric methods for paleontolog-
ical applications.
We also would like to draw attention to gure 1 of
Mongiardino Koch et al. (2021), in which the propor-
tion of quartets in a simulation study that are accurately
resolved by undated Bayesian inference (as used by
Pardo et al. 2017a) increases when the amount of missing
data also increases, or in other words decreases when
accurate data are added. Although this startling result
is not statistically signicant, it seems that undated
Bayesian inference was, in that case, right for the wrong
reasons, and is likely to be wrong for the same reasons in
other circumstances.
Further, by default, parsimony is somewhat less vulner-
able than parametric methods to the long-known problem
of heterotachy (Crotty et al. 2019, and references therein).
That problem was solved, but currently the solution is
implemented in only one program, which only performs
maximum-likelihood analysis and cannot deal with most
features of morphological data (Crotty et al. 2019); a
solution remains unavailable for Bayesian inference. On
the empirical side, Palci et al. (2019) recovered a plau-
sible topology of total-group snakes when they analyzed
their dataset with parsimony, but a highly implausible
one, requiring ecologically unmotivated reversals, by
Bayesian inference. Thus, we strongly emphasize the
conclusion of Marjanović and Laurin (2019: 96–99) that
the accuracy of the matrix is much more important than
the method of analysis, because no method can compen-
sate for misscoring or miscoding of morphological data,
a major issue we document for the matrix published and
relied upon by Pardo et al. (2017a).
Materials and methods
As noted above, Pardo et al. (2017a) performed analyses
of two matrices (one published, one unpublished) with
similar character samples but dierent taxon samples.
The originally unpublished matrix was kindly shared
with us by J. Pardo and A. Huttenlocker, and we publish
it here: Suppl. material 1 contains the unaltered matrix
in a NEXUS le, with an added PAUP command block
that replicates our analyses of it (called a1 and a2 below)
when the le is executed in PAUP*. All of our analyses
(Table 1) were run in PAUP* 4.0a169 (Swoord 2021)
for Windows. This includes bootstrap analyses to test the
results of selected phylogenetic analyses for robustness;
we have relied not only on the bootstrap trees, which we
present as gures, but also on the lists of bipartitions in
the PAUP* output (Suppl. material 2: tables S1–S4). The
published matrix was modied in Mesquite versions up
to 3.70 (Maddison and Maddison 2021). The Kishino/
Hasegawa, Templeton and winning-sites tests were
employed to assess whether constrained and uncon-
strained trees resulting from the previously unpublished
matrix are signicantly dierent; all three tests are avail-
able in PAUP*.
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61
As described below, for some of our analyses of the
published matrix, we added Albanerpetidae from Daza et
al. (2020, based mainly on Yaksha Daza et al., 2020) rather
than from Schoch et al. (2020, based on Celtedens ibericus
McGowan & Evans, 1995, with a few additions from
Shirerpeton Matsumoto & Evans, 2018). We did not add
Funcusvermis for any analyses; we consider the eects of
adding Funcusvermis suciently tested by Kligman et al.
(2023), who added it to their revision of the matrix of Schoch
et al. (2020), which was itself an expansion and slight revi-
sion of the published matrix of Pardo et al. (2017a).
Analyses of the unpublished matrix of Pardo et
al. (2017a)
We reanalyzed the originally unpublished matrix (asso-
ciated with gure S6 of Pardo et al. 2017a) to determine
how many steps are needed to change the results. Two
analyses were performed: one (a1) unconstrained, to
replicate the original results, and one (a2) constrained to
nd Eocaecilia closer to the lepospondyl Carrolla than to
the temnospondyl Doleserpeton, de facto enforcing the
“lepospondyl hypothesis” of lissamphibian origins (but
not any particular version of it) to enable us to compare
the number of necessary extra steps. (The constraint also
allows the “polyphyly hypothesis” that was supported by
earlier versions of that matrix, most recently Huttenlocker
et al. [2013].)
In both analyses, all characters were unordered, and no
changes were made to the matrix. The search parameters
were as follows: 10,000 random addition sequence repli-
cates (far more than proved necessary) were performed
holding one tree at each step, followed by branch swap-
ping using TBR (tree bisection and reconnection) with
a reconnection limit of 8 and a limit of 50 million
Table 1. Overview of analyses and results presented here.
Analysis Our
gure
Base matrix of
Pardo et al. (2017a)
Modications from
Pardo et al. (2017a)
Ordering
of clinal
characters
inf.
char.
Length
of MPTs
Topology
– 1 – n/a yes 212 1264 Marjanović & Laurin (2009: supplementary gure), matrix modied
from Anderson et al. (2008a), clinal characters ordered; LH:
Lissamphibia next to Brachydectes (Lysorophia), Gerobatrachus in
Amphibamiformes
a1 2 unpublished: SM 1 None no 292 1450 as in Pardo et al. (2017a: g. S6B)
a2 3 unpublished: SM 1 constraint de facto
for LH
no 292 1454 LH; Lissamphibia contains Gerobatrachus, positions of
Chinlestegophis + Rileymillerus as in a1
b – published: SM 3 None no 322 1514 ve islands: Lissamphibia, when present, in Amphibamiformes or
Stereospondyli; Chinlestegophis in Gymnophionomorpha and/or
Stereospondyli; gures in Serra Silva & Wilkinson (2021: g. 2–4),
simplied gures in Marjanović & Laurin (2019: g. 30I–K), only
one island gured by Pardo et al. (2017a: g. S7B)
bootstrap
of b
4published: SM 3 None no 322 n/a Diphyly of modern amphibians: Karauridae + Batrachia next to
Gerobatrachus (43%), caecilians next to Chinlestegophis (52%) in
Stereospondyli
c 5 published: SM 3 addition of
Albanerpetidae from
Daza et al. (2020)
no 329 1565 as in Daza et al. (2020: g. S14) except for slightly lower resolution;
(Albanerpetidae (Karauridae, Lissamphibia)) in Amphibamiformes,
Chinlestegophis + Rileymillerus in Stereospondyli
d1 6 published: SM 4 None yes 324 1554 Lissamphibia next to Chinlestegophis + Rileymillerus in
Stereospondyli
bootstrap
of d1
7published: SM 4 None yes 324 n/a Lissamphibia (46%) next to Chinlestegophis + Rileymillerus
(29%); Chinlestegophis as gymnophionomorph not compatible with
bootstrap tree (44%)
d2 8 published: SM 4 Albanerpetidae yes 329 1605 Lissamphibia in Amphibamiformes (closer to Apateon than to
Doleserpeton or Gerobatrachus), Chinlestegophis and Rileymillerus
in Stereospondyli
bootstrap
of d2
9published: SM 4 Albanerpetidae yes 329 n/a Lissamphibia (52%) next to Chinlestegophis + Rileymillerus
(27%); Chinlestegophis as gymnophionomorph not compatible with
bootstrap tree (40%)
e1 10–12 published: SM 5 corrections of
characters and scores
no 319 1514 seven islands: Lissamphibia either next to Gerobatrachus in
Amphibamiformes or next to Chinlestegophis + Rileymillerus in
Stereospondyli
e2 13, 14 published: SM 6 corrections of
characters and scores
yes 321 1558 Lissamphibia next to Chinlestegophis + Rileymillerus in
Stereospondyli
e3 15 published: SM 5 corrections;
Albanerpetidae
no 326 1564 (Albanerpetidae (Karauridae, Lissamphibia)) in Amphibamiformes,
Chinlestegophis + Rileymillerus in Stereospondyli
e4 16, 17 published: SM 6 corrections;
Albanerpetidae
yes 326 1601 three islands; Lissamphibia always in Amphibamiformes (closer to
Apateon than Doleserpeton or Gerobatrachus), Chinlestegophis +
Rileymillerus in Stereospondyli
bootstrap
of e4
18 published: SM 6 corrections;
Albanerpetidae
yes 326 n/a Lissamphibia (77%) in Amphibamiformes (Dissorophoidea:
35%), Chinlestegophis + Rileymillerus in Stereospondyli (34%);
Chinlestegophis + Rileymillerus as gymnophionomorphs (15%)
or next to Lissamphibia (29%), let alone Lissamphibia in
Stereospondyli (10%), not compatible with bootstrap tree
inf. char. = number of parsimony-informative characters; LH = “lepospondyl hypothesis” of lissamphibian origins (Eocaecilia closer to Carrolla than to Doleserpeton);
SM = Supplementary material le that contains the matrix and the settings for the analysis in question.
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rearrangements per replicate (which was never hit);
steepest descent was not in eect; unlimited automatic
increases on the Maxtrees setting; branches collapsed if
maximum branch length was 0.
Analyses of the unmodied previously
published matrix
We reanalyzed (analysis b) an unrevised version of the
published matrix of Pardo et al. (2017a: supporting
information part D; basis for their gures 2, 3 and S7) to
verify its replicability and to further inspect the results.
We computed consensus trees for each island, rather
than for the entire sample of MPTs; unlike Serra Silva
and Wilkinson (2021), who computed the MRC of each
island, we used the strict consensus. The search settings
were as above, except for the use of only 1000 unlim-
ited replicates.
We also present a bootstrap analysis of this matrix
(200 bootstrap replicates, each with 500 addition
sequence replicates limited to 10 million rearrangements)
to enable a better understanding of its support for various
hypotheses. Most bootstrap values returned by Pardo et
al. (2017a: g. S7B) were below 50% and not originally
published; however, clades supported by moderate boot-
strap values (e.g., 45%) may still be better supported than
any single alternative.
Addition of Albanerpetidae to the previously
published matrix
Daza et al. (2020: g. 4E, S14) added Albanerpetidae—
as a composite OTU based mainly on Yaksha, the new
albanerpetid they described—to the published matrix of
Pardo et al. (2017a) and analyzed the resulting matrix
with implied weighting, using concavity values (k)
ranging from 10 to 200 in increments of 10. The MRC
of the results of all twenty analyses pooled together was
presented in Daza et al. (2020: g. S14); numbers of
optimal trees, tree lengths or indices were not published.
Although most nodes occur in 100% of the trees (a
number that may, however, result from rounding up to the
nearest unit in some cases), and although the analysis at
k = 200 was practically unweighted (the lower the value
of k, the more strongly are homoplastic characters down-
weighted), we ran our single analysis (c) unweighted to be
sure which trees the matrix supports at face value. Keating
et al. (2020) demonstrated that unweighted parsimony is
more accurate than implied-weights parsimony under
certain realistic conditions; in addition, a basic assump-
tion of implied weighting—an exponential distribution in
which homoplasy-free characters are more common than
those with any other number of extra steps—is not likely
to be met for this matrix, and the performance of implied
weights when that assumption is not met has not been
studied (Marjanović and Laurin 2019).
Instead of publishing matrix les, Daza et al. (2020)
published only the scores of the albanerpetid OTUs they
revised in, or added to, the previously published matrix
les they used. They confused the scores they added to
the matrix of Pardo et al. (2017a; their reference 22) with
the scores of Albanerpetidae they revised in the matrix
of Pardo et al. (2017b; their reference 21) and presented
these scores for the wrong matrix on pp. 16 and 17 of their
supplementary text. The matrix of Pardo et al. (2017a)
has 345 characters whereas that of Pardo et al. (2017b)
has 370. Unable to add a string of 370 scores to a matrix
of 345 characters, we added the string of 345 scores to
the matrix of Pardo et al. (2017a) without any changes.
The resulting NEXUS le, including a PAUP block that
repeats analysis c when executed, is published here as
Suppl. material 3. The search settings were as above.
Ordering continuous characters
In the analyses of both matrices performed by Pardo
et al. (2017a), as well as that by Daza et al. (2020), all
multistate characters were unordered, even though some
represent continuous or meristic morphoclines, which are
more appropriately treated as ordered characters (Grand
et al. 2013; Rineau et al. 2015, 2018; Marjanović and
Laurin 2019; and references therein). Many characters
used for phylogenetic analysis represent discretizations
of intrinsically continuous variables that represent sizes,
shapes and ratios, and the rationale for lumping similar
values into a single state to produce discrete states follows
the same logic as ordering the resulting states linearly
(Wiens 2001). Simulations showed that ordering such
states increases resolving power (the ability to recover
clades) and reduces the occurrence of erroneous topolo-
gies (Grand et al. 2013; Rineau et al. 2015, 2018).
In the process of ordering all such clines in the unmod-
ied published matrix, we discovered (like Kligman et
al. 2023: supp. inf. part 4) that state 2 of character 9 is
missing from the character list of Pardo et al. (2017a:
part C of the supplementary text). In the “charstatela-
bels” block of the NEXUS le published as part D of
the supplementary text, state 2 does occur, but in the
matrix it is scored exclusively for Ichthyophis. J. Pardo
(pers. comm. 2021) explained that state 2, absent from
Schoch’s (2013) matrix, was intended to be introduced
into the matrix, but this was implemented incompletely
and accidentally omitted from the published character
list. The states of character 9 (“preorbital region length”)
originally were: 0, “less than twice the length of posterior
skull table”; 1, “more” (than twice the length); 2, “equal
in length”, so that state 2 is a subset of state 0. Gee (2022)
and Kligman et al. (2023) noted this, but overlooked the
fact that state 2 is scored correctly for Ichthyophis; they
changed the name of state 2 to “twice as long” but did not
rescore Ichthyophis or score state 2 for any other taxon.
We have instead rescored Ichthyophis back to 0 for our
ordered analyses, making the character binary.
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For characters 3, 26 and 201, the implementation
of state 2 as published in part D seems complete even
though it is likewise missing from part C in all three cases.
Conversely, character 292 has three states in part C, of
which state 1 does not occur in the matrix. Characters 301
and 318 have three states in part C as well, of which the
matrix lacks state 2.
We performed two parsimony and two bootstrap anal-
yses—without (d1) and with (d2) Albanerpetidae as in
analyses b and c—ordering the following clinal charac-
ters of the published matrix: 67, 75, 110, 143, 145, 158,
163, 170, 182, 187, 191, 201, 205, 209, 213, 214, 221,
226, 229, 242, 243, 262, 264, 266, 269, 271, 273, 279,
298, 300, 302, 304, 327, 328, and 334 (35 ordered out
of 345 total characters; 10.1%). We rst reordered the
states of characters 205, 221, 327 and 328 to allow linear
ordering because the original order did not follow the
cline: states 0 and 1 of characters 205 and 221 had to be
exchanged, as well as states 1 and 2 of characters 327
and 328. The resulting data matrix (and PAUP block) is
available as Suppl. material 4.
The search settings were as above. 200 bootstrap repli-
cates were performed, each using 500 random addition
sequences. Instead of presenting the bootstrap values on
consensus trees, we present the bootstrap trees (including
the clades with greater frequencies than their alternatives)
with their bootstrap values.
Evaluation of potential synapomorphies and
revisions to the published matrix
Pardo et al. (2017a) suggested various features as synapo-
morphies of caecilians with either Chinlestegophis alone
or Chinlestegophis and other stereospondyls. Many
correspond to characters in the published matrix. Here
we evaluate all proposed synapomorphies and explain,
where applicable, our revisions of scores in the matrix.
We quote and discuss them below in the order in which
they appeared in Pardo et al. (2017a). Our intention is not
to fully revise the matrix (see Gee 2022), but to demon-
strate the strong inuence exerted by incorrect scores and
compounding errors.
The resulting modied matrix is presented in
Suppl. materials 5, 6 and was analyzed (analyses e1–
e4: Table 1) using the same parameters applied in our
analyses b–d, both without ordering characters (e1, e3;
Suppl. material 5) and with the same character ordering
used in analysis d (e2, e4; Suppl. material 6), and both
without (e1, e2) and with Albanerpetidae as in analyses
c and d2 (e3, e4). Analysis e4 was bootstrapped using
the same parameters as for the bootstraps of analyses b,
d1 and d2.
The diagnosis of Chinlestegophis states on p. E5389:
“A shared feature with stereospondyls and caeci-
lians is opisthotics fused to exoccipitals.” As pointed
out by Santos et al. (2020), that feature is universal
among lissamphibians except larval and some neotenic
salamanders (e.g., Duellman and Trueb 1994; Jones et
al. 2022). It further occurs in the amphibamiform temno-
spondyl Doleserpeton (Sigurdsen and Bolt 2010), a few
lepospondyls (e.g., Pardo et al. 2015) and some (Maddin
et al. 2013; Daza et al. 2020) though apparently not all
albanerpetids (Matsumoto and Evans 2018). Among
stereospondyls, conversely, it seems to be limited to
extremely large and correspondingly unusually highly
ossied adults of Mastodonsaurus giganteus (Jaeger,
1828) (Kligman et al. 2023: supp. inf. part 3). There is no
corresponding character in the published matrix of Pardo
et al. (2017a).
“Shared features with brachyopoids and caecilians”
were proposed to (p. E5389) “include lacrimal fused
to maxilla”. This hypothesis is dicult to evaluate.
The maxillopalatine of Funcusvermis does not contain
the nasolacrimal duct, so there is no evidence that it
contains the lacrimal bone (Kligman et al. 2023). In
Chinlestegophis, a separate lacrimal is absent, and the
nasolacrimal duct lies entirely in what would otherwise
be called the maxilla (Pardo et al. 2017a); however, the
maxilla is dorsoventrally much narrower than expected
for a fusion product. (The maxilla is slightly taller in the
closely related Rileymillerus [Bolt and Chatterjee 2000:
g. 1.3]; however, Kligman et al. [2023: supp. inf. part 3]
suggested quite plausibly that the fragmentary supposed
nasal of Rileymillerus is actually a separate lacrimal.)
As a result, fusion of the lacrimal to the maxilla cannot
be distinguished from wholesale absence of the lacrimal
in the currently known material of Chinlestegophis.
Similarly, the cause of the absence of a separate lacrimal
(loss or fusion) in most brachyopoids and a few other
stereospondyls is unknown; even the nasolacrimal canal
has not been traced in any of them (see Kligman et al.
2023: supp. inf. part 3 for details). Only in a few gymno-
phionans, as pointed out by Santos et al. (2020) and
discussed by Theska et al. (2018), is ontogenetic fusion
of the lacrimal to the maxilla documented (Hypogeophis
rostratus [Cuvier, 1829]: Müller 2006; Gegeneophis
ramaswamii Taylor, 1964: Müller et al. 2005; probably
Idiocranium russeli Parker, 1936: Theska et al. 2018;
possibly the “prefrontal” of Dermophis mexicanus
[Duméril & Bibron, 1841]: Wake and Hanken 1982),
although it has generally been hard in gymnophionans to
tell the prefrontal, the lacrimal, and even the septomaxilla
apart, and it is not clear whether the lacrimal ever forms
in most gymnophionans (Theska et al. 2018). It is unclear
if the two extant species scored in the matrix, Epicrionops
bicolor Boulenger, 1883, and Ichthyophis bannanicus
Yang, 1984, let alone the Early Jurassic Eocaecilia,
possess(ed) a discrete lacrimal bone during development
or not. However, character 21 of the published matrix
only describes the presence or absence of the lacrimal,
without mentioning the causes of such absence (such as
fusion to the maxilla). We interpret this as describing the
observed presence or absence of a separate bone in adults
and have therefore not changed the scores of these taxa
(all “absent”, state 1).
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The sentence quoted above continues: “and two small
posterior processes (‘horns’) on the occipital exposure of
the tabular, just posterior to the otic notch (as in chigut-
isaurids).” Part B of the supplementary text of Pardo et
al. (2017a) expressed some uncertainty about this: “two
modest protuberances project from the occipital face of
the tabular [of Chinlestegophis]. These processes may
correspond to a rudimentary tabular horn, but their size
and unusual topological relationship to the otic notch
makes this homology uncertain. However, it is similar
in position to the ‘tabular horn’ of some brachyopoids,
particularly Batrachosuchus and Vigilius” (both of
which are brachyopids, not chigutisaurids). Intriguingly,
Batrachosuchus was scored as lacking “tabular horns”
(pointed out by Gee 2022: app. 2.4.2), and see Kligman et
al. (2023: supp. inf. part 3) for the doubtful homology of
the “tabular horns” of Chinlestegophis and any brachyo-
poids. Later on p. E5390, Pardo et al. (2017a) made clear
that tabular “horns” are not known in any caecilians.
Indeed, for character 65—“Tabular (horn). Present in
some form (0), or entirely absent (1)”—Eocaecilia was
scored as unknown (?), and Epicrionops and Ichthyophis
were scored as inapplicable (-) because they unambig-
uously lack tabulars (presence/absence of tabulars is
coded by character 239). This means that this character
does not hold Chinlestegophis and caecilians together
in the published matrix. We have kept the scores for the
caecilians and only changed the scores of the extant sala-
manders Cryptobranchus and Hynobius from unknown
to inapplicable because they clearly lack tabulars; this
change has no impact on any calculations of relationships.
On the same page, “[s]hared features with Rileymillerus
and caecilians include the following: orbits small and later-
ally directed.” Orbit size, not coded in the published matrix,
should be quantied before it can be evaluated, but is expected
to be convergent among animals that live in darkness. Indeed,
the orbits of Funcusvermis appear to have been consider-
ably larger than those of other caecilians, Chinlestegophis
or Rileymillerus (Kligman et al. 2023). Orbit location was
included as character 26: “Orbit location. Medial, framed by
wide jugals laterally (0), or lateral emplacement, framed by
very slender jugals (1).” Dilkes (2015) revised the denition
of character 26, but focused on the width of the jugal in his
modications. We, instead, interpret the intention of char-
acter 26 to be the location of the orbit and suggest rewording
this character. Additionally, although three states are scored
in the original matrix, only two are given in the character
denition. The third state refers to particularly large orbits
framed by relatively slender jugals and slender frontals (J.
Pardo pers. comm. 2021; Kligman et al. 2023: supp. inf. part
4), but it is scored for batrachians that lack jugals. In order to
keep the scores, we have reinterpreted it as referring to the
size of the orbit or orbitotemporal fenestra rather than the
jugal explicitly. Therefore, like Kligman et al. (2023), we
have only changed the score of Eocaecilia from 2 to 1. We
have further followed Kligman et al. (2023) in changing the
scores of two amphibamiforms: Platyrhinops from 2 to 1,
Apateon from 0 to 2.
“Shared features with caecilians include double tooth
row on mandible” is stated in the next sentence of Pardo
et al. (2017a). This feature is represented in the published
matrix as no less than seven characters: 146, 147, 148,
272, 273, 322 and 344.
Character 146 reads: “Symphyseal teeth. No accessory
teeth posterior to symphyseal tusks (0), or a transverse
row of such teeth (1).” State 1 is found in some stereo-
spondyl taxa. Despite the absence of symphysial tusks,
state 1 also was scored for Chinlestegophis, Eocaecilia
and the two extant caecilians (Pardo et al. 2017a). We
changed the score of Chinlestegophis to 0 because the
lingual toothrow of the holotype and the referred spec-
imens is restricted to the coronoids, and the coronoids
do not participate in the symphysial region of this
animal (Pardo et al. 2017a: g. S3, movies S4 and S7).
The lingual toothrow of Eocaecilia, Epicrionops and
Ichthyophis does reach all the way to the symphysis, so
we retained a score of 1 for those, but caution that this
likely duplicates scores for the coronoid dentition char-
acters. (As discussed in Marjanović et al. [2023], we
provisionally disagree with Kligman et al. [2023] that this
toothrow is borne on the adsymphysial bone.)
Characters 147 and 148 describe presence/absence of
teeth on specic coronoids and are thus redundant with
character 272, which describes presence/absence of coro-
noid teeth in general (Pardo et al. 2017a). Characters
147 and 148 contain potentially important, non-overlap-
ping variation, so we opted to keep that variation over
retaining the more general variation captured by character
272, which we have excluded from our analyses. Because
it is dicult to identify which coronoid is tooth-bearing
in some taxa (i.e., when fewer than three distinguishable
coronoids are present), Doleserpeton and caecilians in
particular, we have, unlike Kligman et al. (2023: supp.
inf. part 4), modied the denition of characters 147 and
148 as follows, which allowed us to keep all of the orig-
inal scores:
147. Dentition lingual to distal half of labial
toothrow. Present (0), or absent (1).
148. Dentition lingual to mesial half of labial
toothrow. Present (0), or absent (1).
Character 322, “Splenial teeth. Present (0), absent (1)”,
was scored 0 exclusively for Ichthyophis, Epicrionops
and the dvinosaurian temnospondyl Trimerorhachis
insignis Cope, 1878. The scores for the former two
refer to the fact that the lingual toothrow of caecilians
has historically been thought to be borne on the splenial
(references in Müller 2006; “splenial” was still used in
quotation marks by Wilkinson et al. 2021). However,
the bone that bears this toothrow is not in the ventral
position of a splenial, but the dorsolingual one of a
coronoid, in the three extant caecilians whose devel-
opment is well enough understood to tell (Müller et al.
2005; Müller 2006; Theska et al. 2018); a splenial has
never been positively identied in any caecilian—or
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any other lissamphibian. In other words, the scores of
1 for Triadobatrachus, Cryptobranchus, Hynobius,
Ambystoma and Leptodactylus are not correct either; we
have followed Gee (2022) in changing the scores of all
lissamphibians that were not already scored as unknown
to inapplicable (-). Moreover, the existence of teeth
(including “denticles”: Gee et al. 2017) on the splenial
of any species of Trimerorhachis has never been claimed
or illustrated in the literature (most recently Milner and
Schoch 2013), and D. M. found teeth to be absent there in
personal observation of AMNH FARB 4565 (type spec-
imen of T. insignis) and AMNH FARB 4572 (referred to
the same species). This is not surprising. Only one certain
and one possible case of tooth-bearing splenials are
known in all of Tetrapodomorpha, if not Gnathostomata,
and neither is sampled in any of the matrices we mention
here: Caerorhachis, in which a “denticle” eld extends
from the coronoids and the prearticular onto the splenial
(Ruta et al. 2002), and the unnamed “Parrsboro jaw”,
where the same may or may not be the case (Sookias et al.
2014). In short, we changed the score of Trimerorhachis
to 1, so that state 0 does not occur in the revised matrix at
all; the character is constant and therefore uninformative
in a parsimony analysis. Finally, Chinlestegophis was
scored as unknown; we have corrected this to 1 because
Pardo et al. (2017a: g. S3) depicted the absence of teeth
on the splenial.
It is worth mentioning that all three caecilians were
correctly scored as lacking splenials in the published
matrix of Pardo et al. (2017a: state 2 of character 264).
This is contrary to the main text, which erroneously
described the pseudodentary as “comprising the dentary,
coronoid, splenial, and anterior Meckel’s cartilage”
(p. E5391).
Character 344 also appears to target the presence of
a lingual row of dentition on the mandible as seen in
gymnophionans and taxa like Chinlestegophis. The char-
acter is dened as: “Dentary marginal dentition. Single
row (0), multiple rows (1).” The three caecilian OTUs
and Chinlestegophis, and no other OTUs, were scored as
having multiple rows (1); however, Chinlestegophis has
only one dentary toothrow as described and illustrated
by Pardo et al. (2017a), and in caecilians, as discussed
above, the lingual row of teeth is borne on a coronoid
rather than on the dentary. Thus, we rescored those taxa
as having a single row of dentary teeth (0), meaning that
state 1 does not occur in the revised matrix and this char-
acter, too, is uninformative.
Additionally, character 273 is: “Coronoid teeth. Larger
than marginal (0), equal to marginal (1), smaller than
marginal (2).” State 1 was scored exclusively for the
three caecilians, Chinlestegophis and the stereospondyl
Benthosuchus. We rescored Chinlestegophis as possessing
state 2 because Pardo et al. (2017a: g. S3) showed that
the coronoid teeth are smaller than the marginal teeth.
The next feature listed as shared between
Chinlestegophis and caecilians is “quadrate completely
anterior to ear”, possibly meaning the otic capsules. If so,
this character state—which is not coded in the matrix—is
standard among brachystelechid and lysorophian lepo-
spondyls (Maddin et al. 2011; Glienke 2013, 2015; Pardo
et al. 2015; Pardo and Anderson 2016) and widespread
among lissamphibians as well. For present purposes it is
only interesting if caecilians are temnospondyls, which
this matrix cannot test.
Next is “broad, parallel-sided parasphenoid cultri-
form process >20% skull width”. Three characters in
the published matrix (112, 114, 343) attempt to capture
variation in parasphenoid shape, particularly that of the
cultriform process, but “broad” and “parallel-sided” have
dierent distributions. Although the cultriform process of
Chinlestegophis is even broader than that of Eocaecilia,
this condition is more or less universal among lissam-
phibians (references in Marjanović and Laurin 2008:
185–189), occurs prominently in lysorophians (Pardo
and Anderson 2016), and also is found in the morpholog-
ically most immature dissorophoid temnospondyls (e.g.,
Nyranerpeton: Werneburg 2012).
Character 112 is presented in the character list as
having two states: “Cultriform process (width). Base
not wider than rest, clearly set o from basal plate (0),
or merging continuously into plate (1)” (Pardo et al.
2017a: part C of the supplementary text). In the matrix,
however, three states are scored; the rst two are as given
in the list, and the third (state 2) is called “aring anteri-
orly” in the “charstatelabels” block, as in Schoch (2013).
We followed Gee (2022) and Kligman et al. (2023) in
transferring state 2 to character 343, which originally
described whether the cultriform process is “[n]arrow,
tapering anteriorly (0)” or “spatulate and parallel-sided
(1)”. In other words, character 112 now describes the
shape of the caudal end of the cultriform process in two
states, and character 343 now describes the shape of
the rostral end in three states that form a continuum of
widths; character 343 is therefore ordered in our analyses
with ordered characters (e2, e4). Our scores for both char-
acters follow those of Gee (2022), which represents an
update on Kligman et al. (2023). In addition, we scored
Chinlestegophis as unknown for character 343; it was
reconstructed as having state 1 (Pardo et al. 2017a: g.
1H) and scored accordingly, but the entire rostral half of
the cultriform process appears to be unknown (Pardo et
al. 2017a: g. 1B).
Character 114 is: “Cultriform process (outline). Of
similar width throughout (0), or posteriorly expanding
abruptly to about twice the width (1).” State 1 was scored
only for the two extant caecilian OTUs and for the temno-
spondyls Rileymillerus, Eryops and Onchiodon. We are
not sure if the conditions of those taxa should be consid-
ered primarily homologous: the two eryopids have a
bulbous expansion near the base of the cultriform process,
followed caudally by a constriction and then the basal
plate along with its contacts to the pterygoids (Sawin
1941; Boy 1990); Rileymillerus has a strongly biconcave
cultriform process that gradually expands caudally until
it reaches ve times its narrowest width where it merges
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into the basal plate (Bolt and Chatterjee 2000: g. 1.2,
2.2); Epicrionops and Ichthyophis have rostrally pointed
cultriform processes that widen rather suddenly at the
caudal ends of their contacts with the (maxillo)pala-
tines (Jenkins et al. 2007: g. 6B, D). But, in any case,
Chinlestegophis and Eocaecilia were correctly scored 0,
so (like Gee 2022 and Kligman et al. 2023) we have not
modied this character or its scores.
“[O]ccipital condyles extend far beyond posterior
edge of skull roof” is the next character state proposed
to be shared by Chinlestegophis and caecilians (Pardo et
al. 2017a: E5390). It is coded in the published matrix as
character 137: “Exoccipital condyles. Short and broad
base, projecting only with their posterior half behind the
rim of the skull table (0), or almost the complete element
posterior to level of occipital ange (1)”. State 1 was
scored exclusively for most trematosauroids and brachy-
opoids, Rileymillerus, Chinlestegophis, Eocaecilia,
Cryptobranchus and Ambystoma. However, that state
(which appears to be more widespread among stereo-
spondyl and dvinosaurian temnospondyls: Kligman et
al. 2023: supp. inf. part 3) can be reached by elongating
the condyles, reducing the caudal extent of the skull roof,
extending the braincase caudally, or a combination of
two or all three factors. The stalked occipital condyles of
Chinlestegophis (and Rileymillerus: Bolt and Chatterjee
2000) are standard for stereospondyls, but are not found
in any caecilians; this was beautifully illustrated by Pardo
et al. (2017a: g. 3). Rather, lissamphibians (and albaner-
petids: Daza et al. 2020) generally expose large parts of the
otic capsules in dorsal view, resulting in the entire occip-
ital condyles lying far beyond the posterior edge of the
skull roof. The condyles themselves are weakly elongated
in some caecilians and not at all in others, as again shown
by Pardo et al. (2017a: g. 3) and described and illus-
trated by Jenkins et al. (2007: g. 1–4, 6). This includes
Eocaecilia, despite its retention of postparietal and prob-
able tabular bones (Pardo et al. 2017a: g. 3; Jenkins et
al. 2007). Conversely, milder examples of the stereo-
spondyl condition exist in various lepospondyls (Santos
et al. 2020, and references therein). Therefore, Eocaecilia
should not receive the same score as Chinlestegophis; we
reinterpreted the character as referring to condyle elonga-
tion instead of the skull table, limiting state 1 to condyles
with a stalked base, and consequently revised the scores
of Eocaecilia, Cryptobranchus and Ambystoma to 0.
The last character state proposed to be shared by
Chinlestegophis and caecilians (Pardo et al. 2017a: E5390)
is presence of a “pterygoquadrate”, referring to fusion of
the pterygoid and the quadrate bones, as observed in the
ontogeny of some extant caecilians (Wake and Hanken
1982; Müller et al. 2005; Müller 2006; Theska et al. 2018:
g. 1c). On the next page, however, Chinlestegophis is
more cautiously stated to possess, “perhaps, an incipient
pterygoquadrate based on the structure of the suspenso-
rium and apparent absence of the quadratojugal.” The
full description of the skull (Pardo et al. 2017a: part B
of the supplementary text) states the matter in a simi-
larly limited way: “A separate quadrate is not evident in
either side of the skull, but it is likely that the saddle-
shaped posterolateral face of the pterygoid represents the
articular glenoid, and we hypothesize that this therefore
represents a fused pterygoid-quadrate element (pterygo-
quadrate).” Thus, a pterygoquadrate is not observed in
Chinlestegophis, and cannot be used to link it to caeci-
lians. The issue is further complicated by Eocaecilia, in
which the quadrate appears to be fused to the stapes and
not to the pterygoid (Jenkins et al. 2007). Additionally, a
pterygoquadrate is not universal in Gymnophiona, being
absent in non-teresomatans like Ichthyophis, Epicrionops
and Amazops (Jenkins et al. 2007: g. 6B, D; Wilkinson et
al. 2021: g. 3) and the teresomatan Chikila (“pterygoid
process of the quadrate”, separated from the quadrate by
a suture and meeting the maxillopalatine, in Kamei et al.
2012: g. S2(b)). If the fused pterygoquadrate is not only
real in Chinlestegophis, but also homologous between
Chinlestegophis and Teresomata or a subset thereof, it
must have been independently lost three successive times
in Eocaecilia, Rhinatrematidae and Ichthyophiidae, and
at least once more in Chikila.
The pterygoquadrate may be coded as state 2 of char-
acter 318: “Quadrate-maxilla separated by. [sic] Pterygoid
(0), small pterygoid and pterygoid process of quadrate (1),
by pterygoid process of quadrate only (pterygoid absent)
(2).” In agreement with the discussion above, state 2 does
not occur in the matrix, which lacks teresomatans.
Pardo et al. (2017a: E5390) also stressed that “[i]n the
temporal region, there is a small, round supratemporal
that is only loosely articulated to its surrounding calvarial
elements. This bone is morphologically and topolog-
ically identical to an element identied as the ‘tabular’
in Eocaecilia”. As pointed out by Marjanović and Laurin
(2019: 151, app. S1: 35), the statement of identity rests
entirely on the reconstruction drawing published by
Jenkins et al. (2007: g. 1), which shows almost no
uncertainty (by dashed lines, dierential shading or any
other means), but rather depicts a preferred hypothesis
of what an undamaged skull looked like. The text, spec-
imen drawings and photos in Jenkins et al. (2007), further
supported by the μCT rendering in Maddin et al. (2012a:
g. 1A), make clear that the morphology and topology
of the “?tabular” in the reconstruction are guesses—the
presence and independence of the bone are evident, but
not its shape or size. In the crushed holotype (Jenkins et
al. 2007: g. 2; Maddin et al. 2012a: g. 1A), the left
“?tabular” is caudally broken, but the right one may well
have reached the caudal edge of the skull table (pers. obs.
H. M. and D. M.), reopening the possibility that it is, in
fact, a tabular and not homologous to the supratemporal of
Chinlestegophis. Pardo et al. (2017a) actually scored the
tabular as present in Eocaecilia (state 0 of character 239).
However, given the uncertainty surrounding the element,
we changed this score to unknown (?), and retained the
scores of “unknown” in the tabular-related characters 62,
63 and 65–67. We also followed Gee (2022) and Kligman
et al. (2023) in changing the scores of all salamanders
to not applicable (-) for the tabular-related character 63,
because they clearly lack tabulars, and changed the scores
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67
of all lissamphibians (including Eocaecilia) to inappli-
cable for character 71, which references tabular horns.
The implication later in the same paragraph (Pardo et
al. 2017a: E5390) that the real tabular could be part of the
os basale in Eocaecilia is unfounded: there is no reason
to think, from their shapes or topological relationships,
that the dorsal sides of the ossa basalia contain tabulars
or any other dermal bones of the skull roof (Jenkins et al.
2007: g. 2, showing the holotype; compare extant caeci-
lians and their ontogeny: Wake and Hanken 1982; Müller
et al. 2005; Müller 2006; Theska et al. 2018).
In their Discussion section, Pardo et al. (2017a:
E5393) made a far-reaching claim: “a sulcus associated
with the opening of the nasolacrimal duct in the orbit
is present in both Chinlestegophis and Eocaecilia in a
similar position to the tentacular sulcus of the basal caeci-
lian Epicrionops petersi”, citing Jenkins et al. (2007: g.
10), which indeed shows the tentacular foramen inside
the orbit of the extant Epicrionops and a “tentacular
sulcus” on the orbital margin of the maxilla of Eocaecilia.
Evidence of the caecilian tentacle, a body part composed
mostly of the nasolacrimal duct and eye musculature
and associated with chemosensation in extant caeci-
lians, has not been reported from any vertebrates other
than Gymnophiona and Eocaecilia. In Chinlestegophis,
the maxilla does not reach the orbit, being excluded by
a contact of the prefrontal and the lateral exposure of the
palatine (Pardo et al. 2017a: g. 1, S4). The nasolacrimal
duct is housed in the maxilla and meets the orbit in two
pores well medial of the skull surface (Pardo et al. 2017a:
g. S4C). Although the sulcus is stated to be in the orbit
margin in part F of the supplementary material, it was
not reconstructed in g. 1J, which instead shows an ellip-
tical orbit devoid of any corners; the reconstruction in g.
1I shows a more angular orbit, tting the μCT images in
g. 1E–G, but these corners are very wide, obtuse and
rounded, oering no evidence of a tentacular sulcus. A
nasolacrimal duct that is separated from the surface of
the head would not function in sensory reception, and
seems unlikely to explain the evolution of the caecilian
tentacle. Funcusvermis also lacked a tentacular sulcus
unless the sulcus had an unusually far dorsal position, i.e.,
at the dorsoventral midpoint of the rostral orbit margin at
minimum (Kligman et al. 2023: g. 1a, g–i). In any case,
no feature relating to the nasolacrimal duct or the shape
of the orbit is coded in the published matrix.
Results
See Table 1 for a brief overview of our analyses and their
results.
Analyses of the unpublished matrix of Pardo et
al. (2017a)
Our unconstrained analysis (a1; Fig. 2) found 12 MPTs
of 1450 steps, as reported in Part G of the supplementary
information of Pardo et al. (2017a); their previously
unreported indices are: CI excluding uninformative char-
acters = 0.2668, RI = 0.6532, RC = 0.1815. The resulting
strict consensus is identical to that of Pardo et al. (2017a:
g. S6B), with Chinlestegophis and Rileymillerus posi-
tioned as the sister-group to all other amphibamiform
temnospondyls including Lissamphibia, which in turn
contains Eocaecilia and Gymnophiona. Of the 319 char-
acters, 292 are parsimony-informative.
The MPTs form two islands that dier in their resolution
of Lissamphibia: (1) Gerobatrachus as the sister-group of
Lissamphibia, within which “frogs” + Triadobatrachus is
the sister-group of a clade formed by “salamanders” +
Karaurus on one side and Albanerpetidae + Eocaecilia
and crown caecilians on the other; (2) crown caecilians
+ Eocaecilia as the sister-group of the other lissamphib-
ians, within which Gerobatrachus is the sister-group of a
clade formed by “frogs” + Triadobatrachus on one side
and Albanerpetidae + (“salamanders” + Karaurus) on the
other. Note that only (2) is compatible with phylogenies
of extant amphibians based on molecular data (Hime et
al. 2020, and references therein).
Constraining Eocaecilia to be closer to the lepo-
spondyl Carrolla (analysis a2; Fig. 3) than to the
temnospondyl Doleserpeton produced 48 MPTs of
a very similar length (1454 steps) and very similar
indices (CI excluding uninformative characters
= 0.2661, RI = 0.6519, RC = 0.1807). The positions of
Chinlestegophis and Rileymillerus remain unchanged
compared to Pardo et al. (2017a: g. S6). Although the
“lepospondyl hypothesis” is supported in this exper-
iment, Lissamphibia contains Gerobatrachus, and it
nests far from Carrolla, indeed on the other side of
the lepospondyl tree—next to the limbless aïstopods,
followed by the limb-reduced Brachydectes, much as
in Marjanović and Laurin (2009; Fig. 1) whose matrix
has a common ancestor with this one (Anderson et al.
2008a). The strict consensus shows a less well resolved
version of the abovementioned topology (2).
The dierences in t to the matrix between the uncon-
strained and the constrained trees are not signicant
(Kishino/Hasegawa test: p = 0.6284; Templeton test:
p = 0.6276; winning-sites test: p = 0.7160).
Analyses of the unmodied previously
published matrix
Reanalysis of the published matrix (analysis b) yielded
identical results to those of Pardo et al. (2017a),
Marjanović and Laurin (2019: g. 30I–K), Serra Silva
and Wilkinson (2021) and Gee (2022), returning 882
MPTs with a length of 1,514 steps, CI excluding uninfor-
mative characters = 0.2548, RI = 0.6858, RC = 0.1812.
Of the 345 characters, 322 are parsimony-informative.
The MPTs are spread across the ve islands found and
described by Serra Silva and Wilkinson (2021) and above
(Matrices, Methodologies, and Missteps: Phylogeny
inferred from parsimony).
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68
Acanthostega
Greererpeton
Balanerpeton
Dendrerpetidae
Eryops
Tambachia
Ecolsonia
Acheloma
Chinlestegophis
Rileymillerus
Branchiosauridae
Micromelerpetidae
Tersomius
Micropholis
Eoscopus
Platyrhinops
Amphibamus
Doleserpeton
Gerobatrachus
frogs
Triadobatrachus
salamanders
Karaurus
Albanerpetidae
Eocaecilia
Rhinatrematidae
Ichthyophiidae
Scolecomorphidae
Herpelidae
Indotyphlidae
Caeciliidae
Typhlonectidae
Dermophidae
Siphonopidae
Proterogyrinus
Seymouria baylorensis
Limnoscelis
Utaherpeton
Microbrachis
Adelogyrinus
Scincosaurus
Sauropleura scalaris
Ptyonius
Urocordylus
Brachydectes
Oestocephalus
Phlegethontia
Keraterpeton galvani
Batrachiderpeton
Diceratosaurus
Diplocaulus magnicornis
Diploceraspis
“Asaphestera” (chimeric)
Tuditanus
Hapsidopareion
Saxonerpeton
Pantylus
Stegotretus
Rhynchonkos
Batropetes
Carrolla
Nannaroter
Pelodosotis
Micraroter
Huskerpeton
Tambaroter
Pariotichus
Cardiocephalus sternbergi
Cardiocephalus peabodyi
Euryodus primus
Euryodus dalyae
Gerobatrachus
frogs
Triadobatrachus
Albanerpetidae
salamanders
Karaurus
Eocaecilia
Gymnophiona
Tetrapoda
(wrong)
Amphibia (Temnospondyli)
Liss-
amphibia
Lissamphibia
Dissorophoidea
Amphibamiformes?
Rhachitomi?
Lepospondyli “microsaurs”
Gymno-
phiona
Figure 2. Strict consensus of the 12 MPTs obtained from our analysis a1 (see Table 1), using the unpublished matrix used by Pardo et
al. (2017a: g. S6B). The two islands are represented by the duplication of Lissamphibia and its sister-group (on one island) or member
(on the other island) Gerobatrachus. The branch marked “(wrong)” contradicts the molecular consensus (Hime et al. 2020). Question
marks indicate names with uncertain application given the taxon sample. Colored rectangles and boldface, as well as “Asaphestera” and
Dendrerpetidae, as in Fig. 1; red rectangle for Chinlestegophis, brown rectangle for crown-group caecilians (Gymnophiona).
Fossil Record 27 (1) 2024, 55–94
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69
Acanthostega
Greererpeton
Balanerpeton
Dendrerpetidae
Eryops
Tambachia
Ecolsonia
Acheloma
Chinlestegophis
Rileymillerus
Branchiosauridae
Micromelerpetidae
Tersomius
Micropholis
Eoscopus
Doleserpeton
Amphibamus
Platyrhinops
Proterogyrinus
Seymouria baylorensis
Limnoscelis
Utaherpeton
“Asaphestera” (chimeric)
Tuditanus
Hapsidopareion
Saxonerpeton
Pantylus
Stegotretus
Rhynchonkos
Batropetes
Carrolla
Nannaroter
Pelodosotis
Micraroter
Huskerpeton
Tambaroter
Pariotichus
Cardiocephalus sternbergi
Cardiocephalus peabodyi
Euryodus primus
Euryodus dalyae
Microbrachis
Adelogyrinus
Scincosaurus
Sauropleura scalaris
Ptyonius
Urocordylus
Keraterpeton galvani
Batrachiderpeton
Diceratosaurus
Diplocaulus magnicornis
Diploceraspis
Brachydectes
Oestocephalus
Phlegethontia
Albanerpetidae
salamanders
Karaurus
frogs
Triadobatrachus
Gerobatrachus
Eocaecilia
Rhinatrematidae
Ichthyophiidae
Scolecomorphidae
Herpelidae
Indotyphlidae
Caeciliidae
Typhlonectidae
Dermophidae
Siphonopidae
Tetrapoda
Temnospondyli
Lissamphibia
Batrachia
Gymno-
phiona
Dissorophoidea
Amphibamiformes?
Rhachitomi?
Amphibia
(Lepospondyli)
“microsaurs”
“nectrideans”
Aïstopoda
Figure 3. Strict consensus of the 48 MPTs obtained from the unpublished matrix used by Pardo et al. (2017a) in an analysis (a2;
see Table 1) constrained against the “temnospondyl hypothesis” of lissamphibian origins; a version of the “lepospondyl hypothesis”
results. Colors, boldface, “Asaphestera” and Dendrerpetidae as in Fig. 2.
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The bootstrap tree of analysis b (Fig. 4) shows moderate
support for the diphyly of modern amphibians as presented
by Pardo et al. (2017a): the three caecilians form the sister-
group of the stereospondyl Chinlestegophis in 52% of the
bootstrap replicates, while the batrachians are found as
amphibamiform dissorophoids closest to Gerobatrachus in
only 43%, and adding any further dissorophoids depresses
this value to a maximum of 35%. This latter value is the
highest that separates caecilians and batrachians + karau-
rids; even Rileymillerus occurs as the sister-group of
Chinlestegophis and the caecilians together in only 32%.
Most bootstrap values in the rest of the tree, except for the
majority of the most highly nested nodes, are even lower.
Inspection of the list of bipartitions in the output of PAUP*
(Suppl. material 2: table S1), including those that are incom-
patible with the bootstrap tree, shows that Lissamphibia was
found in 37% of the bootstrap replicates—support compa-
rable to that for Dissorophoidea including Batrachia (35%),
which is shown in the bootstrap tree (Fig. 4). An exclusive
clade of all lissamphibians and Chinlestegophis occurs in
21% of the replicates and combines with Rileymillerus in
20%; all lissamphibians and any or all dissorophoids form
an exclusive clade in no more than 16% of the replicates.
Stereospondyli excluding Chinlestegophis and option-
ally Rileymillerus appears in only 9%, as often as, e.g., an
improbable clade of all lissamphibians except Eocaecilia.
Only 8% group all lissamphibians, Chinlestegophis and
Gerobatrachus exclusively.
Addition of Albanerpetidae to the previously
published matrix
The matrix of Daza et al. (2020: g. 4E, S14), i.e.,
the published matrix of Pardo et al. (2017a) with
Albanerpetidae added, yielded a single island of 45
MPTs (analysis c; length = 1565 steps, CI excluding
uninformative characters = 0.2510, RI = 0.6795, RC =
0.1741). Their strict consensus (Fig. 5) is topologically
identical to that of Daza et al. (2020: g. S14), except for
slightly lower resolution: Dissorophidae, Trematopidae,
and a node supporting Edingerella, Benthosuchus,
Capitosauroidea and Trematosauroidea + Brachyopoidea
are unresolved. Interestingly, all nodes marked “95” in
the MRC of Daza et al. (2020: g. S14) are present in the
strict consensus of our analysis, whereas a few of those
marked “100” are not. Amphibamiformes, including
Lissamphibia, is resolved exactly as in Daza et al. (2020:
g. 4E, S14): there is a clade (Apateon (Albanerpetidae
(Karauridae, Lissamphibia))) which is the sister-group of
(Micropholis (Platyrhinops (Amphibamus (Doleserpeton,
Gerobatrachus)))) within Dissorophoidea. Likewise,
Chinlestegophis and Rileymillerus are positioned as
in Daza et al. (2020: g. S14), as the sister-group to
Brachyopoidea within Stereospondyli.
The addition of Albanerpetidae renders seven charac-
ters parsimony-informative, so that 329 of the total of 345
now have this status.
Ordering continuous characters
Ordering of clinal characters (analysis d1) in the other-
wise unmodied published matrix of Pardo et al. (2017a)
rendered two characters parsimony-informative (for
a total of 324 of the 345 characters in the matrix) and
resulted in three islands of 270 MPTs in total (length
= 1554 steps, CI excluding uninformative characters =
0.2508, RI = 0.6885, RC = 0.1777). The strict consensus
is well resolved (Fig. 6) and shows Lissamphibia as the
sister-group of the clade formed by Chinlestegophis
and Rileymillerus, nested within the brachyopoid
stereospondyls.
The bootstrap tree of analysis d1 (Fig. 7) recovers a
rather weakly supported (46% frequency) Lissamphibia
with the same sister-group, and the Chinlestegophis-
Rileymillerus clade is again less supported (40%).
Anities between the Chinlestegophis-Rileymillerus
clade and Lissamphibia are slightly better supported
than with unordered states, but at 29%, this clade is still
weak. The position of Chinlestegophis as a stem-cae-
cilian, incompatible with the bootstrap tree, occurs
with a frequency of 44% (Suppl. material 2: table
S2). Lissamphibia is separated from Doleserpeton or
Gerobatrachus by bootstrap values no higher than 30%;
an exclusive clade of frogs, salamanders, karaurids
and Gerobatrachus has 36% support (less if any other
dissorophoids are added) and an exclusive Lissamphibia-
Gerobatrachus clade only 15% (likewise less if other
dissorophoids are added; Suppl. material 2: table S2).
When the clinal characters are ordered and
Albanerpetidae is added (analysis d2), 329 charac-
ters are parsimony-informative, and the published
matrix yields a single island of 30 MPTs (1605 steps,
CI excluding uninformative characters = 0.2453, RI
= 0.6830, RC = 0.1711). The strict consensus (Fig.
8) shows (Apateon (Albanerpetidae (Karauridae,
Lissamphibia))) in Amphibamiformes—next to a clade
that contains Doleserpeton and Gerobatrachus—while
the Chinlestegophis-Rileymillerus clade forms the sister-
group of the brachyopoid stereospondyls.
Bootstrapping analysis d2 (Fig. 9) shows moderate
support for Lissamphibia (52%). Lissamphibia and a
clade formed by Chinlestegophis and Rileymillerus
are found as sister groups with low support (27%).
Interestingly, both clades together form the sister-group of
Dissorophoidea; the support for exclusion from a position
close to Gerobatrachus or Doleserpeton is compar-
atively high (62%), but the support for exclusion from
Trematosauria within Stereospondyli is very low (12%).
Noteworthy, on the other hand, is the support (75%) for
excluding Karauridae (Karaurus and Kokartus), univer-
sally considered a clade of stem-salamanders (Jones et
al. 2022, and references therein), from Batrachia (frogs
+ salamanders). An exclusive clade of Albanerpetidae,
Karauridae and Batrachia has 58% support, moderately
contradicting Matsumoto and Evans (2018) and Daza et
al. (2020); this may be due to character sampling.
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Figure 4. Bootstrap tree obtained from the published matrix used by Pardo et al. (2017a) when all characters are unordered (analysis
b). The bootstrap tree shows moderate support (52%) for the diphyly of extant amphibians. Colors and boldface as in Fig. 3, boot-
strap values ≥ 50% also in boldface; darker brown rectangle for Lapillopsis, a small temnospondyl thought to be a stereospondyl
convergent to dissorophoids. The blue rectangle for Temnospondyli is omitted because all OTUs except Greererpeton and Protero-
gyrinus are (inferred to be) temnospondyls; the cyan rectangle for Lissamphibia is omitted because the name Lissamphibia does not
apply on this tree. Tr.-oidea = Trematosauroidea. The Dendrerpetidae OTU was called “Dendrerpeton acadianum” by Pardo et al.
(2017a) but is mostly based on its apparently close relative Dendrysekos. In this and the following gures we have also corrected
spelling mistakes in taxon names compared to the matrix and the gures of Pardo et al. (2017a).
Proterogyrinus scheelei
Greererpeton burkemorani
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Lapillopsis nana
Acanthostomatops vorax
Zatrachys serratus
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Ecolsonia cutlerensis
Acheloma cumminsi
Phonerpeton pricei
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Apateon pedestris
Gerobatrachus hottoni
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Sclerocephalus haeuseri
Australerpeton cosgriffi
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Lydekkerina huxleyi
Chomatobatrachus halei
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Sangaia lavina
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
(Eryopiformes)
Dissorophoidea
Euskelia
Amphibamiformes
Stereospondylomorpha
= Limnarchia
Stereospondyli
Trematosauria
Tr.-oidea
Brachy-
opoidea
Capitosauria
Batrachia
91
14
67
29
97
46
41 48
22
22
68
66
100
13
9
28 100
14
21
100
35
92
86 52
95 52
21
82
29
10
23 14
18
43
87
72
54
95 91
80 41
11
41
20
35 88
23
23
47
84 57
23
15
32
52
83 100
21
38
32
41 100
15
72
100
40
44
75
15
31
91
80 53
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Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Rhineceps nyasaensis
Uranocentrodon senekalensis
Broomistega putterilli
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Tr.-oidea
Brachyopoidea
Capitosauria
Lissamphibia
Figure 5. Strict consensus of the 45 MPTs obtained from the published matrix of Pardo et al. (2017a) with addition of Albanerpeti-
dae from Daza et al. (2020); all characters are unordered (analysis c). The resolution diers slightly from Daza et al. (2020: g. S14)
because we used parsimony with equal rather than implied weights. Colors, boldface and Dendrerpetidae as in Fig. 3 and 4 here and
in all following gures; Tr.-oidea = Trematosauroidea.
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Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Rhineceps nyasaensis
Uranocentrodon senekalensis
Broomistega putterilli
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Laidleria gracilis
Siderops kehli
Batrachosuchus watsoni
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Trematosaurus brauni
Trematolestes hagdorni
Peltostega erici
Lyrocephaliscus euri
Callistomordax kugleri
Metoposaurus diagnosticus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Tr.-oidea
Brachyopoidea
(Trematosauria)
Capito-
sauria
Lissamphibia
Figure 6. Strict consensus of the 270 MPTs obtained from the published matrix of Pardo et al. (2017a) with clinal characters ordered
(analysis d1). Tr.-oidea = Trematosauroidea.
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Proterogyrinus scheelei
Greererpeton burkemorani
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Apateon pedestris
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Australerpeton cosgriffi
Sclerocephalus haeuseri
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Lydekkerina huxleyi
Chomatobatrachus halei
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Benthosuchus sushkini
Edingerella madagascariensis
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Hynobius japonicus
Cryptobranchus alleganiensis
Ambystoma opacum
92
16
19
21
5
16
25
49
30
20
92
36
56
40
26
87
93
34
84
39
79
50
95
71
98
21
9
16
46
29
14
13
12
13
14
15
9
99
48
28
37
87
72
82
40
21
72
14
23
39
94
48
70
99
100
78
17
100
31
69
29
49
43
89
59
42
71
53
100
100
91
42
66
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
(Eryopiformes)
Dissorophoidea
Amphibamiformes
Eu-
skelia
Stereospondylomorpha
Stereospondyli
Trematosauria
Trematosauroidea
Brachyop-
oidea
Capito-
sauria
Lissamphibia
Figure 7. Bootstrap tree obtained from the published matrix of Pardo et al. (2017a) with clinal characters ordered (analysis d1).
Bootstrap values ≥ 50% in boldface.
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Figure 8. Strict consensus of the 30 MPTs obtained from the published matrix of Pardo et al. (2017a) with clinal characters ordered
and Albanerpetidae added (analysis d2).
Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Rhineceps nyasaensis
Uranocentrodon senekalensis
Broomistega putterilli
Lydekkerina huxleyi
Chomatobatrachus halei
Benthosuchus sushkini
Edingerella madagascariensis
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria Tr.-oidea
Brachyopoidea
Capito-
sauria
Lissamphibia
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Figure 9. Bootstrap tree obtained from the published matrix of Pardo et al. (2017a) with clinal characters ordered and Albanerpeti-
dae added (analysis d2). Bootstrap values ≥ 50% in boldface. Tr.-oidea = Trematosauroidea.
Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Acanthostomatops vorax
Zatrachys serratus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Hynobius japonicus
Cryptobranchus alleganiensis
Ambystoma opacum
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Lapillopsis nana
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Ecolsonia cutlerensis
Acheloma cumminsi
Phonerpeton pricei
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Australerpeton cosgriffi
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Lydekkerina huxleyi
Chomatobatrachus halei
Benthosuchus sushkini
Edingerella madagascariensis
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
92
26
15
14
65
99
48
100
90
48
16
83
51
42
45
100
88
55
50
100
78
47
99
54
74
35
95
77
36
87
36
45
61
75
19
62
91
34
46
30
38
79
97
23
58
52
12
16
80
47
36
20
27
47
100
54
12
10
19
21
13
7
36
13
29
49
65
90
70
9
14
77
97
6
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Tr.-oidea
Brachyopoidea
Capito-
sauria
Lissamphibia
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The list of bipartitions not compatible with the bootstrap
tree (Suppl. material 2: table S3) reveals 40% bootstrap
support for a clade of Chinlestegophis and the three
caecilians (slightly more than the 38% without ordering
and without Albanerpetidae) and 30% for a clade that
includes these four and Rileymillerus. Chinlestegophis
and Rileymillerus are excluded from Dissorophoidea +
Lissamphibia in 21% of the bootstrap replicates. The
support for exclusion of Albanerpetidae from Lissamphibia
(17%) is lower than it could be given the 58% for a specic
placement in Lissamphibia mentioned above; 12% of the
replicates group the caecilians with Albanerpetidae, 6%
nd all dissorophoids, all batrachians, the karaurids and
Albanerpetidae in an exclusive clade.
Revised published matrix
The matrix including the changes we propose was run
both with all characters unordered, as they were in Pardo
et al. (2017a), and with the herein proposed characters
that form morphological clines ordered; both of these
options were used both without and with the addition
of Albanerpetidae from Daza et al. (2020). The anal-
ysis with all characters unordered and Albanerpetidae
excluded (e1) resulted in 1341 MPTs, each with a length
of 1514 steps (CI excluding uninformative characters
= 0.2535, RI = 0.6849, RC = 0.1801), distributed over
seven islands of optimal trees. Of the 344 characters,
only 319 are parsimony-informative. In all seven islands,
Lissamphibia is recovered and excludes Chinlestegophis
(as well as Rileymillerus). One island (Fig. 10) places
(Brachyopoidea (Lissamphibia (Chinlestegophis,
Rileymillerus))) in Stereospondyli, and Karauridae on
the batrachian stem; the others recover Lissamphibia
next to Gerobatrachus in Amphibamiformes while the
Chinlestegophis-Rileymillerus clade remains nested in
Stereospondyli next to or inside Brachyopoidea, and
Lissamphibia is resolved either as (frogs (karaurids
(caecilians, salamanders))) (Fig. 11), contradicting the
molecular consensus (Hime et al. 2020), or as (caecilians
(frogs (karaurids, salamanders))) (Fig. 12).
The second analysis, using ordered characters (e2),
resulted in three islands of 99 MPTs in total (1558 steps; CI
excluding parsimony-uninformative characters = 0.2489,
RI = 0.6870, RC = 0.1759). 321 characters were parsi-
mony-informative. The well-resolved strict consensus
is shown in Figs 13, 14. Lissamphibia is recovered and
placed next to a Rileymillerus + Chinlestegophis clade,
which lies next to Plagiosauridae within the brachyopoid
stereospondyls; Karauridae lies on the batrachian stem.
Gerobatrachus remains next to Doleserpeton inside a
variably resolved Dissorophoidea.
The third and fourth analyses dier from the rst
and second by the addition of Albanerpetidae (from
Daza et al. 2020) as in analysis c. In both, 326 of the
344 characters were parsimony-informative. The unor-
dered analysis e3 yielded 297 MPTs (1564 steps, CI
excluding uninformative characters = 0.2498, RI =
0.6790, RC = 0.1732); PAUP* groups them as two
islands, but these are similar enough that we present
the overall strict consensus in Fig. 15. Dissorophoidea
including Lissamphibia is resolved as in analysis c; the
Rileymillerus + Chinlestegophis clade is grouped with the
poorly resolved brachyopoid stereospondyls.
In the ordered analysis e4, 81 MPTs are recovered
(1609 steps, CI without uninformative characters =
0.2434, RI = 0.6817, RC = 0.1695). They all group
the Rileymillerus + Chinlestegophis clade with
Brachyopoidea as in analysis e3, while Lissamphibia is
nested among the amphibamiform dissorophoids, closer
to Apateon than to Gerobatrachus or Doleserpeton.
PAUP* groups the MPTs into three islands depending on
how they resolve amphibamiform phylogeny: one island
(Fig. 16) has (Doleserpeton (Gerobatrachus (Apateon,
Lissamphibia))) inside Amphibamidae, Albanerpetidae on
the caecilian stem and Karauridae on the batrachian stem;
the other two (Fig. 17) have (Apateon (Albanerpetidae
(Karauridae, Lissamphibia))) close to but outside
Amphibamidae, which contains Gerobatrachus; the
Early Triassic amphibamiform Micropholis is either on
the amphibamid or on the lissamphibian side.
Bootstrapping analysis e4 reveals (Fig. 18) consid-
erable support for Lissamphibia (77%), within which
Albanerpetidae (43%) and Karauridae (64%) lie on the
batrachian stem but not in Batrachia (75%). Lissamphibia
is, with limited support, placed next to Apateon (22%)
in Dissorophoidea (35%); similar support is recov-
ered for placing Chinlestegophis (and Rileymillerus)
close to brachyopoids including plagiosaurids (27%) in
Stereospondyli (34%).
Groupings not compatible with the bootstrap tree
(Suppl. material 2: table S4) include Chinlestegophis +
Rileymillerus as gymnophionomorphs (15%) or in an
exclusive clade with Lissamphibia (29%); comparable
support exists for Lissamphibia without Albanerpetidae
(30%) or Lissamphibia without Karauridae or
Albanerpetidae (20%), both of which are also incom-
patible with the bootstrap tree. An exclusive clade of
lissamphibians and stereospondyls occurs in only 10% of
the bootstrap replicates.
Discussion
Support for alternative topologies
Our work corroborates some of the results of the analyses
performed by Pardo et al. (2017a), but also highlights
weaknesses in the phylogenetic signal that was claimed
to support caecilian anities of Chinlestegophis. Indeed,
Pardo et al. (2017a: abstract) claimed: “Our results place
the taxon condently within lissamphibians.” On the
contrary, our results demonstrate that the anities of
Chinlestegophis cannot be ascertained with condence
based on either of the two matrices of Pardo et al. (2017a).
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Figure 10. Strict consensus tree of some of the 1341 MPTs recovered in analysis e1 (published matrix of Pardo et al. [2017a] after
revision, all characters unordered). For the other MPTs, see Figs. 11 and 12. Br.-oidea = Brachyopoidea.
Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Rhineceps nyasaensis
Uranocentrodon senekalensis
Broomistega putterilli
Lydekkerina huxleyi
Chomatobatrachus halei
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Edingerella madagascariensis
Benthosuchus sushkini
Sangaia lavina
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Tremato-
sauroidea
Br.-
oidea
Capitosauria
Lissamphibia
one island
see Figures 11 and 12
for the other six islands
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Figure 11. Strict consensus of each of two further islands of MPTs from analysis e1. For space reasons, one of the two resolutions of
Trematosauria is mirrored and presented without species names. For the other MPTs, see Figs 10, 12. Tr.-oidea = Trematosauroidea.
The branch marked “(wrong)” contradicts the molecular consensus (Hime et al. 2020).
Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Australerpeton cosgriffi
Sclerocephalus haeuseri
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Trematosaurus brauni
Trematolestes hagdorni
Peltostega erici
Lyrocephaliscus euri
Callistomordax kugleri
Metoposaurus diagnosticus
Sangaia lavina
Laidleria gracilis
Siderops kehli
Batrachosuchus watsoni
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Ambystoma opacum
Cryptobranchus alleganiensis
Hynobius japonicus
Sangaia
Peltostega
Lyrocephaliscus
Trematosaurus
Trematolestes
Callistomordax
Metoposaurus
Rileymillerus
Chinlestegophis
Siderops
Batrachosuchus
Laidleria
Plagiosuchus
Gerrothorax
Amphibia (Temnospondyli, Rhachitomi, Eryopiformes)
Dvinosauria
Edopoidea = Euskelia
Amphibamiformes
Stereospondylomorpha
= Limnarchia
Stereospondyli
Tremato-
sauria
Tr.-
oidea
Tr.-oidea
Brachyo-
poidea
Brachyopoidea
Capito-
sauria
Lissamphibia
(wrong)
two islands
differing only in Trematosauria
see Figures 10 and 12
for the other five islands
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Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Karaurus sharovi
Kokartus honorarius
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissoro-
phoidea
Amphiba-
miformes
Eryopiformes
Stereospondylomorpha
Stereospondyli as in Fig. 11
Lissamphibia
either as shown
or as in Fig. 11
four islands
(both combinations of both
resolutions of Lissamphibia
and Stereospondyli occur)
see Figures 10 and 11
for the other three islands
Figure 12. Strict consensus of each of the remaining four islands of MPTs from analysis e1. Except for Lissamphibia, the part de-
picted here is identical in all four islands; Lissamphibia is resolved either as shown or as in Fig. 11, Stereospondyli is resolved as in
Fig. 11 (with both options shown there for Trematosauria). For the other MPTs, see Figs 10, 11.
First, we stress that the unpublished matrix (our analysis
a1, see Table 1; Fig. 2; Pardo et al. 2017a: g. S6) yielded a
commonly recovered Lissamphibia, nested within dissoro-
phoids and optionally containing Gerobatrachus but never
Chinlestegophis. This is important because it suggests that
when a broader sample of extinct tetrapods is included, a
more mainstream hypothesis of both lissamphibian ancestry
and Paleozoic tetrapod relationships is produced, and the
stereospondyls represented in this matrix, Rileymillerus
and Chinlestegophis, are distanced from lissamphibian
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Proterogyrinus scheelei
Greererpeton burkemorani
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Iberospondylus schultzei
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Sclerocephalus haeuseri
Glanochthon latirostris
Australerpeton cosgriffi
Archegosaurus decheni
Platyoposaurus stuckenbergi
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Trematosaurus brauni
Trematolestes hagdorni
Peltostega erici
Lyrocephaliscus euri
Callistomordax kugleri
Metoposaurus diagnosticus
Sangaia lavina
Laidleria gracilis
Siderops kehli
Batrachosuchus watsoni
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Trematosauroidea
Brachyopoidea
Capitosauria
Lissamphibia
strict consensus
one island
see Figure 14
for the other two islands
Figure 13. Strict consensus of all (to the right and below the dashed line) or some (to the left and above the stippled line) of the 99
MPTs recovered in analysis e2 (published matrix of Pardo et al. [2017a] after revision, clinal characters ordered). See Fig. 14 for
the remaining MPTs.
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82
origins. Constraining Eocaecilia to nest among lepospon-
dyls (analysis a2; Fig. 3) results in only slightly longer trees
(4 steps added to the 1450 of the unconstrained trees) that
are not signicantly dierent from the unconstrained trees
(p between 0.62 and 0.72 according to the three usual tests)
despite conforming to the “lepospondyl hypothesis” of
amphibian origins.
All of our remaining analyses focused on the
published matrix of Pardo et al. (2017a). Unsurprisingly,
we conrmed (analysis b) the results of Marjanović and
Laurin (2019: g. 30I–K), Serra Silva and Wilkinson
(2021) and Gee (2022) that Pardo et al. (2017a) found
all MPTs that t this matrix, that the MRC tree they
reported is accurate as such, and that the MRC tree is
a highly incomplete representation of the MPTs: it is
equally parsimonious for Batrachia and Gymnophiona
to lie in Stereospondyli or Amphibamiformes, and for
them to form Lissamphibia or not, which may or may
not contain Chinlestegophis. We further contribute the
rst fully published bootstrap analysis of this matrix
(Fig. 4, Suppl. material 2: table S1); contrary to Pardo
et al. (2017a: g. S7B), it supports diphyly of extant
amphibians, although the support is not strong (52% for
grouping Chinlestegophis with the caecilians; 43% for
grouping Gerobatrachus with the batrachians; only 35%
for grouping all dissorophoids with the batrachians to the
exclusion of any caecilians).
Pardo et al. (2017a: g. S7B) found no bootstrap
values of 50% or higher on any node that separates caeci-
lians and batrachians. Dierences in bootstrap settings
may explain why our results dier somewhat from those
of Pardo et al (2017a); we used 200 bootstrap replicates
of 500 addition-sequence replicates each, whereas Pardo
et al. (2017a) used 1000 bootstrap replicates of 100 addi-
tion-sequence replicates each (J. Pardo pers. comm. 2023;
the settings were not published).
However, adding Albanerpetidae to the matrix (anal-
ysis c; Fig. 5) conrms the result of Daza et al. (2020):
Lissamphibia is found in Amphibamiformes in all
MPTs, while Chinlestegophis is always a stereospondyl.
The omission of albanerpetids from the original matrix
was clearly a suboptimal choice, given that all studies
published since their discovery over half a century
ago support close anities between albanerpetids and
lissamphibians, if not a position among lissamphibians
(e.g., Estes 1969; Estes and Hostetter 1976; Fox and
Naylor 1982; McGowan and Evans 1995; Maddin et al.
2013; Daza et al. 2020; Kligman et al. 2023). Even the
most unorthodox analysis of albanerpetid anities that
we know of suggested close anities to batrachians
(McGowan 2002).
The eect of ordering characters within the orig-
inal published matrix (i.e., without Albanerpetidae and
without corrections other than renumbering the states
of some ordered characters) (analysis d1; Fig. 6) was
to decrease the number of islands from ve to one:
Lissamphibia (which has 46% bootstrap support) forms
the sister group of the stereospondyls Chinlestegophis and
Rileymillerus. This arrangement only occurs in 29% of
the bootstrap replicates, however (Fig. 7; Suppl. material
2: table S2). Adding Albanerpetidae (analysis d2) moved
Lissamphibia into the amphibamiform dissorophoids;
Chinlestegophis and Rileymillerus remained brachyo-
poid stereospondyls (Fig. 8). Bootstrapping this analysis
(Fig. 9; Suppl. material 2: table S3) revealed increased, if
still modest, support for Lissamphibia (52%) and weak
support for any position of that clade, but comparatively
strong support against a position close to Gerobatrachus
or Doleserpeton (62%).
A modest revision of the published matrix, without
Albanerpetidae, replicated the basic results of analyses c
and d1 as equally parsimonious when all characters were
unordered (analysis e1; Figs 10–12). Ordering (analysis
e2; Figs 13, 14) restricted Lissamphibia to Stereospondyli
as in analysis d1 (unmodied matrix, likewise ordered,
likewise without Albanerpetidae). Adding Albanerpetidae
without ordering (analysis e3; Fig. 15) essentially repli-
cated analysis c; ordering (analysis e4; Figs 16, 17)
introduced variation within Lissamphibia but kept it in the
same place as in analysis c—with strong bootstrap support:
a lissamphibian-stereospondyl clade is not compatible
with the bootstrap tree (Fig. 18) and only occurs in 10%
of the replicates (Suppl. material 2: table S4). The 77%
support for Lissamphibia (with Albanerpetidae) excluding
Chinlestegophis (or Rileymillerus, Gerobatrachus or any
other traditional non-member) is worth highlighting.
In all four cases, ordering increased the resolution of
the results. We interpret this as an example of ordering
bringing out phylogenetic signal in data, congruent with
results from simulations and some empirical examples;
note that ordering does not automatically increase the net
resolution (Marjanović and Laurin 2008, 2019; Grand et
al. 2013; Rineau et al. 2015, 2018; and references therein).
Strikingly, none of the trees from analyses c, d or
e (most parsimonious or bootstrap) support anities
between Chinlestegophis and caecilians to the exclusion of
other lissamphibians. The bootstrap analysis of the original
matrix under original conditions (analysis b; Fig. 4, Suppl.
material 2: table S1) only weakly supports diphyly of extant
amphibians and an exclusive clade of Chinlestegophis
and the three caecilians (bootstrap frequency of 52%) or
an exclusive clade of frogs, salamanders, karaurids and
Gerobatrachus (frequency of 43%). Our highly restricted
revisions to the published matrix (analyses e1, e2; see Gee
2022 for a generally much more thorough revision), as
well as the addition of Albanerpetidae to the taxon sample
(analysis c) or the combination of both (analyses e3, e4),
resulted in an exclusive clade comprising lissamphibians
being nested among dissorophoids (analyses c, e1, e3, e4
and its bootstrap analysis), or Lissamphibia as sister to
Chinlestegophis + Rileymillerus within Stereospondyli
(analyses e1, e2). The former is the currently most wide-
spread hypothesis on the origin of the extant amphibian
clades; the latter is new, but considerably less novel
than extant amphibian diphyly as proposed by Pardo
et al. (2017a).
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Proterogyrinus scheelei
Greererpeton burkemorani
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Iberospondylus schultzei
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Apateon pedestris
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Australerpeton cosgriffi
Sclerocephalus haeuseri
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Apateon pedestris
Micropholis stowi
Lapillopsis nana
Acanthostomatops vorax
Zatrachys serratus
Micromelerpeton credneri
Limnogyrinus elegans
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Limnarchia = Stereospondylomorpha Stereospondyli as in Fig. 13
Amphibia (Temnospondyli, Rhachitomi, Eryopiformes)
Dvinosauria as in Fig. 13
“Edopoidea” as in Fig. 13
Dissorophoidea
Edopoidea
= Euskelia
Amphibamiformes
Dissorophoidea
Amphibamiformes
one island
one island
both islands
see Figure 13
for the third island
Figure 14. Strict consensus of the remaining MPTs recovered in analysis e2 (published matrix of Pardo et al. [2017a] after revision,
clinal characters ordered). See Fig. 13 for the MPTs not represented here and for the clades shown collapsed here.
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Figure 15. Strict consensus of the 297 MPTs recovered in analysis e3 (published matrix of Pardo et al. [2017a] after revision, Alba-
nerpetidae added from Daza et al. [2020], all characters unordered). Capito. = Capitosauria; Tr.-oidea = Trematosauroidea.
Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Acanthostomatops vorax
Zatrachys serratus
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Onchiodon labyrinthicus
Eryops megacephalus
Sclerocephalus haeuseri
Archegosaurus decheni
Platyoposaurus stuckenbergi
Glanochthon latirostris
Australerpeton cosgriffi
Rhineceps nyasaensis
Uranocentrodon senekalensis
Broomistega putterilli
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Trematosaurus brauni
Trematolestes hagdorni
Peltostega erici
Lyrocephaliscus euri
Callistomordax kugleri
Metoposaurus diagnosticus
Laidleria gracilis
Siderops kehli
Batrachosuchus watsoni
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Amphiba-
miformes
Dissoro-
phoidea
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Tr.-oi-
dea
Brachyopoidea
Capito.
Lissamphibia
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Proterogyrinus scheelei
Greererpeton burkemorani
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Australerpeton cosgriffi
Sclerocephalus haeuseri
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Sangaia lavina
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Laidleria gracilis
Siderops kehli
Batrachosuchus watsoni
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Lapillopsis nana
Acanthostomatops vorax
Zatrachys serratus
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Albanerpetidae
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Amphibia (Temnospondyli, Rhachitomi, Eryopiformes)
Dvinosauria
Edopoidea = Euskelia
Dissorophoidea
Amphibamifomres
Limnarchia =
Stereo-
spondylo-
morpha
Stereospondyli
Trematosauria
Trematosauroidea
Brachyopoidea
Capitosauria
Lissamphibia
strict consensus one island
see Figure 17
for the other two islands
Figure 16. Strict consensus of all (to the left and above the stippled line) or some (to the right and below the stippled line) of the
81 MPTs recovered in analysis e4 (published matrix of Pardo et al. [2017a] after revision, Albanerpetidae added from Daza et al.
[2020], clinal characters ordered). For the other MPTs, see Fig. 17.
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86
The published matrix of Pardo et al. (2017a) contains
some data that suggest anities between Lissamphibia and
the Chinlestegophis + Rileymillerus clade, always within
Stereospondyli, as recovered in analyses b (as one of several
equal options), d1 (if only with 29% bootstrap support), e1
(as one of two options) and e2. Although weakly supported,
the fact that this result occurred in the original (analyses b,
d1) and the revised matrix (analyses e1, 2) suggests that
Chinlestegophis may contribute important information about
amphibian evolution in the context of the “temnospondyl
hypothesis”, even if it cannot be supported specically as
a stem-caecilian. More likely, however, it may highlight
convergence between the Chinlestegophis + Rileymillerus
clade and lissamphibians in general or caecilians in particular;
this is supported to an extent by our bootstrap of analysis e4
(Fig. 18; Suppl. material 2: table S4), where Chinlestegophis
+ Rileymillerus were recovered next to Lissamphibia in only
29% and as gymnophionomorphs in only 15% of the boot-
strap replicates while a lissamphibian-stereospondyl clade
only has 10% bootstrap support (all three groupings are
incompatible with the bootstrap tree: Fig. 18), as well as by
the bootstrap analysis conducted by Kligman et al. (2023:
extended data gure 6), where Lissamphibia excluding
Chinlestegophis and Rileymillerus occurred in 55% of the
replicates and Stereospondyli including a Chinlestegophis +
Rileymillerus clade in 57%. Minimally, our results highlight
the importance of albanerpetids—sampled in analyses c, d2,
e3 and e4—for understanding lissamphibian relationships.
Pardo et al. (2017a) emphasized that the topology
they presented was supported by Bayesian inference. As
discussed above (Matrices, Methodologies, and Missteps:
Bayesian inference of phylogeny), missing data have unpre-
dictable, sometimes very strong, eects on parametric
methods of phylogenetics such as Bayesian inference, while
the non-parametric method called parsimony is unaected
by this particular issue and therefore safer for paleontolog-
ical data. Matrix quality remains more important than the
method of analysis (Simões et al. 2017; Marjanović and
Laurin 2019; Gee 2021, 2022; and references therein).
Assessment of qualitative arguments
As further support for a close relationship between
Chinlestegophis and caecilians, Pardo et al. (2017a)
proposed a number of features supposedly shared
between both taxa, and in some cases with other stereo-
spondyls. Most of them are coded in the matrix in some
form. However, our review of these features (Materials
and Methods: Evaluation of potential synapomorphies
and revisions to the published matrix) nds serious prob-
lems in all of them; none supports placing caecilians as
the sister taxon of Chinlestegophis (or Chinlestegophis +
Rileymillerus), or in stereospondyls in general.
We note several other features, not discussed by Pardo
et al. (2017a), by which Chinlestegophis resembles other
stereospondyls but diers starkly from caecilians. The
basicranial articulation in Chinlestegophis supercially
resembles that of Eocaecilia and Gymnophiona. However,
in Chinlestegophis, the basicranial joint forms a strong
girder, tightly sutured (Pardo et al. 2017a), similar to the
condition seen in other stereospondyls. In caecilians,
the basicranial joint is instead loosely constructed, with
thick cartilage covering the bony joint surfaces of both
the os basale and the (epi)pterygoid or pterygoquadrate
(Maddin et al. 2012b). Furthermore, Chinlestegophis has
well-developed posttemporal fenestrae, as in brachyopoid
stereospondyls, while in lissamphibians and albaner-
petids these fenestrae are absent.
What little is known and described of the postcranial
skeleton of Chinlestegophis (Pardo et al. 2017a: g. S5)
also resembles other stereospondyls but starkly diers from
caecilians. The interclavicle of Chinlestegophis is a large
plate, as usual for stereospondyls; in lissamphibians and
albanerpetids, no interclavicle is known. Similarly, the clav-
icles consist mostly of a large plate and look unremarkable
for a stereospondyl in all details of their shape; clavicles are
absent in albanerpetids, caecilians (including Eocaecilia)
and salamanders, and those of frogs are robust curved struts
more similar to those of extant amniotes. A few neural arches
are preserved in Chinlestegophis, but centra are not; this is
standard for morphologically immature temnospondyls, but
only observable (as presence or absence of ossication) in a
very short phase in the ontogeny of frogs and hynobiid sala-
manders, and not known in caecilians—in Gegeneophis and
in Caecilia orientalis Taylor, 1968, the centra ossify before
the neural arches (Müller 2006; Pérez et al. 2009). Indeed,
early ossication of the centra (earlier than the neural arches
or not long after them), quickly followed by suturing or even
fusion to the neural arches, is a synapomorphy of lissam-
phibians and probably a few amphibamiforms (notably
Doleserpeton and Gerobatrachus) under the “temnospondyl
hypothesis”, or of Seymouriamorpha, Chroniosuchia and
Tetrapoda under the “lepospondyl hypothesis” (Laurin and
Reisz 1997; Danto et al. 2019). Full neurocentral fusion is
not found outside these clades (and Albanerpetidae), but
is found in all known vertebrae of Eocaecilia (Jenkins et
al. 2007) and the lone vertebra referred to Funcusvermis
(Kligman et al. 2023). The ribs of Chinlestegophis are,
plesiomorphically, longer than three successive vertebrae;
they are shorter in amphibamiforms and a few select lepo-
spondyls (Marjanović and Laurin 2008, 2019), and much
shorter, about as long as one vertebra, in albanerpetids and
all lissamphibians except a few peramorphic salamandrids
(Marjanović and Witzmann 2015, and references therein).
The only known postcranial similarity to caecilians is body
elongation; the massive dermal shoulder girdle does not
suggest limb reduction, and indeed the presumed ulna has
an unremarkable size.
Homoplastic rather than stepwise evolution
Interpretations of functional biology and evolutionary
trends rely on our perspective of phylogenetic relation-
ships. In the original description of Chinlestegophis, once
Fossil Record 27 (1) 2024, 55–94
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87
Figure 17. Strict consensus of each of the remaining two islands of MPTs from analysis e4. The remainder of the tree is identical in
all three islands and not repeated here; see Fig. 16.
Lapillopsis nana
Dissorophus multicinctus
Cacops aspidephorus + C. morrisi
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Lapillopsis nana
Acanthostomatops vorax
Zatrachys serratus
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Micropholis stowi
Apateon pedestris
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Acanthostomatops vorax
Zatrachys serratus
Dissorophoidea
Amphibamiformes
Amphibamiformes
Lissamphibia
Dissorophoidea
Lissamphibia
rest of tree identical to overall strict consensus in Figure 16
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David Marjanović et al: Dataset quality, Chinlestegophis and origin of caecilians
88
Figure 18. Bootstrap tree of analysis e4 (published matrix of Pardo et al. [2017a] after revision, Albanerpetidae added from Daza et
al. [2020], clinal characters ordered). Bootstrap values ≥ 50% in boldface. Tr.-oidea = Trematosauroidea.
Proterogyrinus scheelei
Greererpeton burkemorani
Dendrerpetidae
Balanerpeton woodi
Capetus palustris
Edops craigi
Adamanterpeton ohioense
Nigerpeton ricqlesi
Cochleosaurus bohemicus
Chenoprosopus milleri
Iberospondylus schultzei
Trimerorhachis insignis
Neldasaurus wrightae
Isodectes obtusus
Acroplous vorax
Lapillopsis nana
Acanthostomatops vorax
Zatrachys serratus
Cacops aspidephorus + C. morrisi
Dissorophus multicinctus
Broiliellus texensis
Acheloma cumminsi
Phonerpeton pricei
Ecolsonia cutlerensis
Micromelerpeton credneri
Limnogyrinus elegans
Micropholis stowi
Platyrhinops lyelli
Amphibamus grandiceps
Doleserpeton annectens
Gerobatrachus hottoni
Apateon pedestris
Eocaecilia micropodia
Epicrionops bicolor
Ichthyophis bannanicus
Albanerpetidae
Karaurus sharovi
Kokartus honorarius
Triadobatrachus massinoti
Xenopus tropicalis
Leptodactylus mystacinus
Cryptobranchus alleganiensis
Hynobius japonicus
Ambystoma opacum
Peltobatrachus pustulatus
Onchiodon labyrinthicus
Eryops megacephalus
Australerpeton cosgriffi
Sclerocephalus haeuseri
Glanochthon latirostris
Archegosaurus decheni
Platyoposaurus stuckenbergi
Broomistega putterilli
Rhineceps nyasaensis
Uranocentrodon senekalensis
Lydekkerina huxleyi
Chomatobatrachus halei
Edingerella madagascariensis
Benthosuchus sushkini
Parotosuchus
Cyclotosaurus robustus
Paracyclotosaurus davidi
Mastodonsaurus giganteus
Peltostega erici
Lyrocephaliscus euri
Trematosaurus brauni
Trematolestes hagdorni
Callistomordax kugleri
Metoposaurus diagnosticus
Sangaia lavina
Rileymillerus cosgriffi
Chinlestegophis jenkinsi
Siderops kehli
Batrachosuchus watsoni
Laidleria gracilis
Plagiosuchus pustuliferus
Gerrothorax pulcherrimus
97
60
25
27
96
39
31 51
24
13
8
69
61
99
18
20
100
35
92
77 40
96 43
21
81
28
56
38 49
22
77
93 100
43
64
70
75
98 93
87 57
7
38 100
17
48
25
36 86
34
82 58
24
60
34
16
30
93
76 49
24
70
99
38
55
77
26
27
64
34
22
42 100
40
Amphibia (Temnospondyli)
Dvinosauria
Edopoidea
Rhachitomi
Dissorophoidea
Amphibamiformes
Eryopiformes
Stereospondylomorpha
Stereospondyli
Trematosauria
Tr.-oidea
Brachyopoidea
Capito-
sauria
Lissamphibia
Fossil Record 27 (1) 2024, 55–94
fr.pensoft.net
89
a consensus tree was selected and reported, a number of the
characteristics used in the matrices and discussed above
were used to infer a stepwise evolution of traits toward the
specialized fossorial and head-rst burrowing lifestyle of
caecilians. Those features include fusion of the lacrimal
+ maxilla and exoccipital + opisthotic (interpreted as
stages in the consolidation of the skull), repositioning of
the jaw suspension, small and laterally oriented eyes, etc.
However, as we demonstrate above, most of those features
have a wider distribution across Paleozoic tetrapods or
present confounding problems of homoplasy across many
disparate clades, extinct and extant.
In particular, we regard as unfortunate the aforemen-
tioned removal of all lepospondyls from the unpublished
matrix to create the published matrix after the initial
recovery of Chinlestegophis as a temnospondyl by Pardo
et al. (2017a). Potential anities between lepospondyls
and lissamphibians have been controversial for more than
two decades (Anderson 2001; Marjanović and Laurin
2008, 2009, 2013, 2019; Laurin et al. 2022; Jansen and
Marjanović 2022; Mann et al. 2022; and references
therein). Thus, including lepospondyls in tests of the
origins of extant amphibians is critical to represent the
full range of morphology during the Paleozoic and reveal
potential homoplasy. Removing those taxa from analyses
could make it more likely that any elongate, fossorial, or
burrowing taxa such as Chinlestegophis and caecilians be
placed together incorrectly in the phylogeny.
Schoch et al. (2020) added three lepospondyls to the
published matrix of Pardo et al. (2017a), but they did not add
any characters that would help resolve their phylogeny or
their relationship to lissamphibians. This was not changed
by Kligman et al. (2023), in whose results those three lepo-
spondyls form the sister-group of Greererpeton (Kligman
et al. 2023: extended data gs 5–7), an Early Carboniferous
colosteid that is a more appropriate outgroup than the
anthracosaur Proterogyrinus that was used as such.
Considering that alternative hypotheses of relation-
ships are equally supported by the published matrix, even
without broader taxonomic sampling to include lepospon-
dyls, the proposed stepwise evolution of caecilian features
falls apart. Rather than traits linking Chinlestegophis and
caecilians, those same characteristics appear to represent
homoplasy, as shown in trees that place Chinlestegophis
close to but outside Lissamphibia (our analyses a, d, e2
and some MPTs of b and e1 plus the bootstrap of b) or far
away (our analyses c, e3, e4 and some MPTs of b and e1).
Evolutionary ecology
The grooves for the lateral-line organ identied by Pardo
et al. (2017a) on the skull of Chinlestegophis indicate
an animal that was strictly aquatic for at least part of
its adult life. In contrast, there is no evidence of later-
al-line grooves or other aquatic features in Eocaecilia or
the admittedly fragmentary Funcusvermis, and among
extant caecilians aquatic lifestyles are restricted to larvae
(of those few taxa that have them) and the highly nested
clade Typhlonectidae. The inference of an aquatic life-
style in Chinlestegophis is further supported by its poorly
ossied vertebral column and probably also by its cranio-
caudally elongate plate-like clavicles. Perhaps aquatic
vs. terrestrial lifestyles explain why Chinlestegophis
was able to coexist with caecilians like the slightly older
Funcusvermis; the wide, at vertebra referred to the latter
lacks a neural spine, interpreted as a fossorial adaptation
by Kligman et al. (2023).
Matrix quality, taxon sampling and character
sampling
The discussion above takes at face value both the coding
and scoring of the two matrices, and their character
and taxon samples, apart from our limited modica-
tions in analyses c, d2 and e; but these issues deserve
comments. We have not scrutinized the matrices in full
(see Gee 2022 for a cautious but comprehensive treat-
ment of the published matrix of Pardo et al. 2017a), as
we wished only to test whether alternative topologies can
be equally (or better) supported by the original matrices,
and to show the impact of a few scoring changes that
were obviously needed. The absence of lepospondyls
in the matrix published by Pardo et al. (2017a) prevents
us from looking into how many extra steps an origin of
lissamphibians among them would imply, compared to
an origin among temnospondyls. Similarly, the removal
of characters that are variable only among lepospondyls
prevents using the published matrix as a starting point for
such comparisons; unfortunately, this was not changed by
Schoch et al. (2020) or Kligman et al. (2023) despite the
former’s addition of three lepospondyl OTUs which the
latter then retained. The heretofore unpublished precursor
matrix remains available for this purpose, but it would
need to be updated and greatly enlarged; in its present
form, only four extra steps need to be added to the orig-
inal 1450 to make an odd version of the lepospondyl
hypothesis possible.
Conclusions
Published in one of the most prestigious journals, the
description of Chinlestegophis (Pardo et al. 2017a)
resulted in a new hypothesis about the origins of the
extant amphibian clades and a new scenario for the origin
of caecilians and their fossorial lifestyle that has attracted
attention far beyond that of specialist researchers (Pough
et al. 2022). We show that these exciting proposals are
poorly supported by the original datasets and the original
methods of analysis, as well as by limited revisions to one
of the datasets aimed at eliminating the most conspicuous
cases of character redundancy and a few question-
able anatomical interpretations of Chinlestegophis
and other taxa. The question of lissamphibian origins
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David Marjanović et al: Dataset quality, Chinlestegophis and origin of caecilians
90
remains unsolved, although our revisions to the matrix
reveal further support for Lissamphibia excluding
Chinlestegophis and any Paleozoic taxa. In any case, we
join Kligman et al. (2023) in cautioning against calibrating
the divergence of caecilians and batrachians according to
the phylogenetic hypothesis of Pardo et al. (2017a), i.e.,
by using the Late Carboniferous age of certain dissoro-
phoid temnospondyls as the calibration date.
Concerning phylogenetics, we reiterate that the major-
ity-rule consensus is not a useful representation of the
result of a parsimony analysis, and that not all issues with
Bayesian analysis of matrices with missing data have been
solved; but most importantly, matrix quality remains para-
mount in phylogenetic analysis. This concerns typographic
errors, misinterpretations of published literature, redundant
characters (in the dataset we revised, the double toothrow
in the lower jaw of caecilians was coded as seven characters
that an analysis could only treat as independent), characters
that represent two or more independently varying features,
and inconsistencies in scoring. As previously pointed out
(e.g. Marjanović and Laurin 2019; Kligman et al. 2023;
and references in both), avoiding, detecting and mitigating
these issues is time-consuming but not dicult.
Acknowledgments
Jason Pardo and Adam Huttenlocker kindly sent us both
matrices, and J. Pardo and Ben Kligman discussed certain
characters with us. The reviewers Marvalee Wake and
Christian Sidor led us to improve the clarity of our writing.
D. M.’s understanding of current issues in phylogenetics
beneted from a course taught by Tiago Simões and
Oksana Vernygora and organized by Transmitting Science.
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