Molecular Phylogenetics and Evolution 166 (2022) 107328

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Molecular Phylogenetics and Evolution

journal homepage: www.elsevier.com/locate/ympev

Short Communication

The value of updating GenBank accessions for supermatrix phylogeny: The

case of the New Guinean marsupial carnivore genus Myoictis
Matthew J. Phillips a, *, Michael Westerman b, Manuela Cascini a
a
School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia
b
Department of Ecology, Environment and Evolution, La Trobe University, Melbourne 3086, VIC, Australia

A R T I C L E I N F O A B S T R A C T

Keywords: Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be
GenBank widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the
Marsupials phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae)
Myoictis
that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on
Phylogeny
dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with
Taxonomic misattribution
M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent
marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is
discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ
randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated
taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with
randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue
that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous
results. This would serve both as a caution for future supermatrix construction and to highlight accessions of
potentially significant biological interest for further study.

1. Introduction mammalian phylogenetics was substantially influenced by topological

GenBank houses DNA sequences from more than 478,000 formally
described taxa (Sayers et al., 2018). How many of the millions of ac­
cessions have obsolete or erroneous taxonomic attributions is poorly
known, although increasing recent attention suggests >99% fidelity for
generic and higher-level attributions (Leray et al., 2019), but often far
more (>5% errors) at the species level (e.g. Locatelli et al., 2020; van
den Burg et al., 2020). The extent to which these taxonomic mis­
attributions mislead phylogeny reconstruction is little studied. Such
errors may be perceived to be rare and overwhelmed by signal among
the correctly attributed majority of loci in multi-locus matrices. Our
recent work on mammal phylogeny leads us to suspect that erroneous
taxonomic attributions may often mislead phylogeny reconstruction.
This may involve minor errors within genera, as occurred with mis­
attributed wallaby sequences (see Celik et al., 2019). In other cases the
errors may have substantial downstream ramifications. We recently re­
ported (Phillips and Shazwani Zakaria, 2021) that Morgan et al.’s
(2014) conclusion that mitochondrial DNA is unreliable for ordinal-level
artefacts stemming from a Canis sequence (Q35873) that is mislabelled
in GenBank as a bat (Sturnia).
Taxonomic misattributions are rarely reported in the published
literature and standard GenBank policy is not to update accessions
without written agreement from the original authors/submitters.
Furthermore, the onus is on researchers to seek out and persuade the
original authors (who may no longer be contactable). We believe that
GenBank processes should be more conducive to correcting obsolete or
incorrect taxonomic attributions. This is increasingly important with
taxonomically broad supermatrix analyses becoming commonplace and
the authors being further removed from the data acquisition and taxo­
nomic history of the included accessions. Indeed, blame for erroneous
taxonomic attributions should not be assumed to lie with end users or
sequence submitters – they are just the last links along a chain of
possible falliblity from collectors to museum curators and various
intermediary researchers.
Here we consider the case of the New Guinean marsupial genus
Myoictis. These rat-sized, apparently largely terrestrial carnivores are

* Corresponding author.
E-mail address: m9.phillips@qut.edu.au (M.J. Phillips).

https://doi.org/10.1016/j.ympev.2021.107328
Received 18 June 2021; Accepted 12 October 2021
Available online 16 October 2021
1055-7903/© 2021 Elsevier Inc. All rights reserved.
M.J. Phillips et al.
widely distributed across forested habitats in New Guinea and sur­
rounding islands (Woolley, 2005). Within the family Dasyuridae they
are most closely related to small Australian carnivores (Parantechinus,
Dasycercus, Dasykaluta, Dasyuroides) from more open, even arid habitats
(see Westerman et al., 2016; García-Navas et al., 2020).
Molecular phylogenetic studies that have focused on dasyurids and
were undertaken by experts on Australo-Papuan marsupials have
consistently resolved the interrelationships of the four Myoictis species,
grouping M. leucura with M. wavicus and placing M. wallacei and
M. melas as successively deeper divergences from these (e.g. Westerman
et al., 2006; Westerman et al., 2016; Kealy and Beck, 2017; see Fig. 1,
Tree 1). In contrast, recent, taxonomically broad supermatrix phylog­
enies across marsupials (May-Collado et al., 2015) and across all
mammals (Upham et al., 2019) reconstruct a Myoictis topology that is
discordant with both of the expected internal groupings (Fig. 1, Tree 2).
These supermatrix analyses include M. wavicus sequences that are mis­
attributed to M. melas on GenBank. Identifying and filtering out such
errors is less likely in supermatrix analyses, because they typically
include only one exemplar of each species per gene, which in turn are
often obtained from different specimens.
We investigate the basis for Myoictis misattributions and test
whether, despite being only a small minority of accessions, they may
mislead phylogeny reconstruction. This could be facilitated by errors
being taxonomically consistent rather than randomly distributed. Upon
correcting erroneous GenBank accessions and adding additional se­
quences to fill nuclear and mitochondrial sampling gaps we clarify the
phylogenetic relationships among Myoictis.
2. Materials and methods
2.1. Taxonomic attribution and provenance of Myoictis GenBank
accessions
Each GenBank accession for Myoictis was cross-checked against (1)
sample records in the original published study, (2) extraction and
sample donation notes made by one of us (MW) and sample provenance
data available in both Woolley (2005) and within the online zoological
collections of Australian museums (OzCam). This enabled us to assign
museum specimen numbers and reference numbers from Woolley
(2005) to each accession. Nine of 79 accessions were found to have
obsolete or otherwise erroneous taxonomic attributions. Phylogenies
were then reconstructed for each gene and this confirmed the species-
level taxonomic attributions expected from our cross-checking. One
possible exception is M. melas from the Arfak Mountains of New
2
Molecular Phylogenetics and Evolution 166 (2022) 107328
Guinea’s Bird’s Head Peninsula (UPNG3273), which was nested within
M. leucura, and will be discussed below.
2.2. Novel Myoictis DNA sequences
Additional DNA sequences for two nuclear genes, interphotoreceptor
binding protein (IRBP) and von Willebrand factor (vWF), and for mito­
chondrial cytochrome b (Cytb) and 12S rRNA-coding genes were
generated from tissue samples provided by the South Australian
Museum. These include Myoictis melas from the Torrecelli Mountains of
Papua New Guinea (ABTC1336), Myoictis wallacei from the Aru Islands
of Indonesia (ABTC50574) and the outgroup taxon, Parantechinus api­
calis from Western Australia (ABTC7518).
DNA was extracted using QIAGEN’s DNeasy Blood & Tissue Kits. PCR
reactions contained 9.5 µL of autoclaved H2O, 12.5 µL of Bioline MyFi
mix, forward and reverse primers (10 pmol/µL) at 1 µL each, 0.25 µL of
Taq polymerase, 1 µL of DNA template, for a total volume of 25 µL. PCR
products were checked by electrophoresis in 1% TBE agarose gel stained
with Gel Red (Biotium) alongside the BioLine HyperladderTM molecular
weight marker for comparison. PCR products were purified for
sequencing using an UltraCleanTM PCR clean up kit (Bioline). PCR
primers and cycle conditions are provided in the supplementary mate­
rial (Table S1). Amplicons were Sanger sequenced using ABI, BigDye
chemistry at Macrogen (Korea). Base-calling ambiguities were visually
inspected and corrected as appropriate. GenBank accession numbers are
provided in Tables S2 and S3.
2.3. Phylogenetic analysis
The pre-existing and novel DNA sequences for all loci that were
attributed to at least three Myoictis species (thus, with potential to be
directly phylogenetically informative) were concatenated for individual
specimens. These loci include nuclear IRBP, vWF, ε-globin, bfib7 and
mitochondrial tPhe-12S-tVal-16S, Cytb. Relevant dasyurine outgroup
taxa were added (Parantechinus apicalis, Dasykaluta rosamondae, Dasy­
cercus cristicauda, Dasyuroides byrnei, Sarcophilus harrisii, Dasyurus hal­
lucatus, Neophascogale lorentzii, Phascolosorex dorsalis). All sequences
were visually inspected and manually aligned in Se-Al 2.0a (Rambaut,
1996).
We inferred tree topologies using maximum likelihood (IQ-TREE,
Nguyen et al., 2015) and Bayesian inference (MrBayes 3.2.7, Ronquist
et al., 2012). Alternative partitioning schemes were considered for the
nuclear data, either modelling genes separately or modelling codon
positions separately. In each case the mtDNA was partitioned into RNA
Fig. 1. The affect of updating GenBank ac­
cessions on Myoictis phylogeny reconstruc­
tion. A. Myoictis phylogenies including Tree
1, the expected topology as inferred in mo­
lecular phylogenetic analyses focusing on
dasyurid marsupials, Tree 2, the topology
reconstructed in recent mammal and
marsupial-wide molecular supermatrix
studies, and Trees 3 & 4, which are two
alternative topologies. B. Percentage of trees
supported from among 100 maximum likeli­
hood analyses in which one of the available
GenGank accessions for each nuclear and
mitochondrial gene was randomly sampled
for each species, initially with the original
GenBank taxonomic attributions and then
with our updated taxonomic attributions.
M.J. Phillips et al.
stem and loop positions and into codon positions for Cytb, following
Celik et al. (2019). Models for each partition were selected by Model­
Finder within IQ-TREE (see Table S4). Maximum likelihood analyses
were performed with branch lengths estimated independently (-sp op­
tion) and with proportional branch lengths among partitions (-spp op­
tion). Both corrected AIC and BIC favoured the codon-wise and -spp
partitioning options. Ultrafast bootstrap approximation (1000 repli­
cates) was employed for assessing confidence in the resulting topologies.
For Bayesian inference in MrBayes, two independent analyses were
each run with three Markov Chain Monte Carlo (MCMC) chains for five
million generations. The same gene-wise and codon-wise partitions were
used as described above for ML. Models were unlinked across all parti­
tions for the substitution matrix, state frequencies (empirical), invariant
sites and the shape parameter of the rates-across-sites gamma distribu­
tion. Branch lengths were unlinked between the nuclear and mtDNA
data, but were proportionally scaled across partitions within each of
these genomes. Trees were sampled every 5000 generations, with the
first 25% discarded as burn-in. Clade frequencies across the two inde­
pendent runs reached convergence (clade frequency standard de­
viations < 0.01) and estimated sample sizes for likelihood, prior and
substitution parameter estimates were all above 200 (Tracer v1.7.1,
Rambaut et al., 2018).
To examine the affinities of the Arfak Myoictis specimen (UPNG3273)
additional 12S rRNA ML and Bayesian inference trees were recon­
structed, based on the above methods. These analyses included all
available Myoictis 12S rRNA accessions. We added two previously un­
published 12S rRNA sequences that were obtained as part of Westerman
et al.’s (2006) study. These were M. melas (ANWC M35780) and
M. leucura (QM J672), respectively from the Frieda River and Vanapa
River Valley, both in Papua New Guinea. Several of the sequences are
short (390–500 bp), so to ensure the appropriate phylogenetic context
the relationships among the outgroup and monohyly of each species
were enforced in accordance with the multi-gene tree (Fig. 2), but with
relationships within species unconstrained and the Arfak and new se­
quences allowed to float unconstrained across the tree.
3
Molecular Phylogenetics and Evolution 166 (2022) 107328
2.4. Simulated supermatrix phylogeny with randomized sampling of
GenBank accessions
To investigate the effect of taxonomic misattributions on super­
matrix reconstruction of Myoictis phylogeny we simulated supermatrices
by randomly sampling one exemplar from each species for each of the
seven nuclear and mitochondrial genes (for consistency among acces­
sions, partial tPhe and tVal sequences were excluded, and 12S and 16S
rRNA were sampled separately). Outgroup sampling was retained from
the primary phylogenetic analyses and held constant. In this way 100
supermatrices with randomized accessions for Myoictis were built. Six of
the 51 relevant Myoictis accessions were originally misattributed. The
maximum likelihood tree was inferred for each matrix, using IQ-TREE
(modelled as above) for two sets of analyses, one with the original
taxonomic misattributions and another with the updated taxonomic
attributions.
3. Results and discussion
3.1. Myoictis phylogeny
We identified nine of the 79 Myoictis GenBank accessions as being
attributed to the incorrect species. Our investigation was guided by the
gene trees we reconstructed, but these alone cannot distinguish between
misattribution, hemiplasy, erroneous taxonomy and sometimes phylo­
genetic uncertainty for the less informative nuclear loci. Confident
attribution of accessions to Myoictis species was further facilitated by a
combination of sample numbers being included in accessions or asso­
ciated publications (e.g., Krajewski et al., 2004; Westerman et al., 2006)
and record keeping by the original authors. The majority (6) of the
erroneous attributions were for older accessions that retained obsolete
taxonomy, with M. wavicus specimens listed as M. melas before the
former taxon was erected as a full species from among the formerly
paraphyletic M. melas. Three more recent M. wallacei accessions were
mistakenly labelled as M. wavicus. All nine accessions have subsequently
been updated in GenBank.
Upon updating the taxonomic attributions our phylogenetic analyses
Fig. 2. Myoictis phylogeny inferred from the
combined nuclear (IRBP, vWF, ε-globin, bfib7) and
mitochondrial (tPhe-12S-tVal-16S, Cytb) dataset.
Individual specimens are denoted with collection
numbers (and W-reference numbers from Wool­
ley, 2005). Node support values are Bayesian
inference posterior probability (MrBayes, above)
and ML bootstrap (IQ-TREE, below). Asterisks
indicate full support for both analyses. These re­
sults are with codon-wise partitioning. Gene-wise
partitioning favoured the same topology. The
placement of the Arfak mountains Myoictis was
inferred in a separate analysis that included only
12S rRNA (Fig. S1).
M.J. Phillips et al.
reconstructed each Myoictis species as monophyletic, except one spec­
imen attributed to M. melas from the Arfak Mountains (from only 392 bp
partial 12S rRNA sequence, AY730705) falls within M. leucura, and is
discussed below. Otherwise, the monophyly of each species and inter-
specific relationships are all resolved with strong ML bootstrap and
Bayesian posterior probability (Fig. 2) and in agreement with Wester­
man et al. (2006, 2016). One caution here is that the signal for the
placement of M. leucura is dominated by mtDNA, since only the poorly
informative ε-globin is included for this species from among the nuclear
loci. The dibbler (Parantechinus apicalis) from Western Australia is fav­
oured as sister to Myoictis (Fig. 2) in agreement with most recent studies
(e.g., Mitchell et al., 2014; Kealy and Beck, 2017).
3.2. Taxonomic misattributions mislead randomized accession
supermatrix phylogeny
Supermatrices were built by randomly sampling one accession per
species for each gene, to investigate whether being unaware of the small
proportion (12%) of misattributed sequences was likely to mislead
phylogeny reconstruction. Remarkably, a Myoictis topology that is
incongruent with the expected tree (see Fig. 1) was recovered from 71%
of the randomised accession supermatrices. Almost all of these were the
putatively incorrect topology inferred by the recent supermatrix studies
(May-Collado et al., 2015; Upham et al., 2019). Upon updating the
taxonomic accessions the expected tree was recovered for all rando­
mised accession supermatrices.
The apparent paradox that a small proportion of misattributed se­
quences can mislead a substantial majority of the random accession
supermatrices may largely be explained by the misattributions being
non-randomly distributed among species. Five of the six misattributed
accessions from which the supermatrices were assembled involve
M. wavicus sequences that were attributed to M. melas. Moreover, three
mtDNA loci (Cytb, 12S and 16S rRNA) disproportionately contribute
phylogenetic signal due to their rapid evolution and coverage across all
Myoictis species. Prior to our updates one of the three ‘M. melas’ acces­
sions for each of these three loci was in fact M. wavicus – giving a 70.4%
probability of at least one of these misattributed mtDNA accessions
being randomly included. Another factor in propagating error that de­
serves further consideration with simulations is that alternative topo­
logical hypotheses are often distinguished by short internal branches.
The concern here is that near-identical sequences between conspecifics
that are incorrectly assumed to be different species for one gene may
outweigh the sum of weaker signals for the true sister grouping across
several correctly attributed genes.
Not only can a small proportion of erroneous (or obsolete) taxonomic
attributions mislead phylogeny reconstruction, but subsequent down­
stream inferences may also be mislead, such as tracing ancestral states
and molecular dating. We have not estimated divergence dates because
there are no reliable fossil calibrations among Myoictis or its close out­
groups. However, we note that randomized accession supertrees with
misattributions that mislead the phylogeny have average tip to Myoictis
crown lengths / stem length far lower (0.65) than the average for trees
with correctly attributed accessions (1.07). This suggests that substan­
tial divergence estimation error is likely.
3.3. Flagging anomalous accessions
Little attention has been paid in the literature to erroneous or sur­
prising sequences, except in human and ancient DNA research, where
identifying contamination is fundamental (Llamas et al., 2017). NCBI do
provide a range of tools to assist taxomnomic assignment and to help
identify rogue sequence taxonomy (e.g. Ciufo et al., 2018; Schoch et al.,
2020). However, the requirement of GenBank to seek and receive
agreement from original authors/submitters in order to correct or place
notes of caution on accessions is clearly a source of inertia. A more
flexible system is needed to make users aware of potential errors in
4
Molecular Phylogenetics and Evolution 166 (2022) 107328
sequences and to encourage authors to check and update their acces­
sions. Any such system should also limit the potential for identifiers to be
stigmatized and for vexatious bullying of original authors in the already
competitive and often adversarial field of systematics. Linking acces­
sions to collection specimen numbers is one potential solution (Kealy
et al., 2019), but may be precluded by funding shortfalls at many
institutions.
We propose that accession anomalies could be brought to GenBank’s
attention privately, by identified individuals. The evidence provided
would be considered for veracity and worthiness for passing on to the
original authors, who would either agree to alter the accession, decline
or alternatively, flag the accession. Flagging would not distinguish be­
tween errors and biological anomalies. Any counter evidence provided
by the original authors would be considered by GenBank upon deciding
whether or not to flag the accession. Other changes would not be made
without permission from the author(s). This process would be separate
from the standard review process in which GenBank staff may label
sequences as ‘UNVERIFIED’ until submitters can verify queries.
‘UNVERIFIED’ sequences do not appear in BLAST searches, whereas
flagged sequences would, given their highlighted potential biological
interest. NCBI intend to discuss this and other models for sequence
flagging (C. Schoch, pers. comm.).
We believe that the “Arfak Myoictis (W130)” partial 12S rRNA
accession (AY730705) is a candidate for flagging. It remains the only
sequence generated to date from a specimen collected from Nenei in the
Arfak mountains of New Guinea. Although attributed to M. melas, our
12S rRNA ML and Bayesian analyses nest the sequence within M. leucura
(Fig. S1). Despite its short length (392 bp) there is enough signal for KH
testing (in IQ-TREE) to reject placing the Arfak sequence within M. melas
at P = 0.0621. Notably, Menzies (1991) who collected the sample ap­
pears to have considered all Myoictis to belong to M. melas, which might
help to explain propagation of obsolete taxonomy. However, if the
sample is indeed M. leucura, it was collected more than 1000 km from its
nearest conspecific records on the other side of New Guinea and would
provide a considerable range extension for this species. Flagging sam­
ples such as this should serve both as a caution for supermatrix inclusion
and to encourage and target further biological research; in the present
case, into the systematics and biogeography of Myoictis.
CRediT authorship contribution statement
Matthew J. Phillips: Conceptualization, Methodology, Formal
analysis, Writing – original draft, Writing – review & editing, Visuali­
zation, Supervision. Michael Westerman: Data curation, Investigation,
Writing – review & editing. Manuela Cascini: Data curation, Investi­
gation, Writing – review & editing.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Acknowledgements
We thank Jim Menzies, Stephen Donnellan and the late Ken Aplin for
making Myoictis material available. Conrad Schoch at NCBI provided
valuable comments on the manuscript and additional guidance on
GenBank processes. Two anonymous reviewers provided valuable
feedback on the manuscript.
Funding
This work was supported by a Discovery Project grant to MJP from
the Australian Research Council (DP190103636).
M.J. Phillips et al.
Appendix A. Supplementary material
Supplementary data to this article can be found online at https://doi.
org/10.1016/j.ympev.2021.107328.
References
Celik, M., Cascini, M., Haouchar, D., Van Der Burg, C., Dodt, W., Evans, A.R., Prentis, P.,
Bunce, M., Fruciano, C., Phillips, M.J., 2019. A molecular and morphometric
assessment of the systematics of the Macropus complex clarifies the tempo and mode
of kangaroo evolution. Zool. J. Linn. Soc. 186, 793–812. https://doi.org/10.1093/
zoolinnean/zlz005.
Ciufo, S., Kannan, S., Sharma, S., Badretdin, A., Clark, K., Turner, S., Brover, S.,
Schoch, C.L., Kimchi, A., DiCuccio, M., 2018. Using average nucleotide identity to
improve taxonomic assignments in prokaryotic genomes at the NCBI. Int. J. Syst.
Evol. Microbiol. 68, 2386–2392.
García-Navas, V., Kear, B.P., Westerman, M., 2020. The geography of speciation in
dasyurid marsupials. J. Biogeog. 47, 2042–2053.
Kealy, S., Beck, R., 2017. Total evidence phylogeny and evolutionary timescale for
Australian faunivorous marsupials (Dasyuromorphia). BMC Evol. Biol. 17, 240.
https://doi.org/10.1186/s12862-017-1090-0.
Kealy, S., Donnellan, S.C., Mitchell, K.J., Herrera, M., Aplin, K., O’Connor, S., Louys, J.,
2019. Phylogenetic relationships of the cuscuses (Diprotodontia: Phalangeridae) of
island Southeast Asia and Melanesia based on mitochondrial ND2 gene. Australian
Mammalogy 42, 266–276. https://doi.org/10.1071/AM18050.
Krajewski, C., Moyer, G.R., Sipiorski, J.T., Fain, M.G., Westerman, M., 2004. Molecular
systematics of the enigmatic “Phascolosoricine” marsupials of New Guinea. Aust. J.
Zool.. 52 (4), 389. https://doi.org/10.1071/ZO04020.
Leray, M., Knowlton, N., Ho, S.-L., Nguyen, B.N., Machida, R.J., 2019. GenBank is a
reliable resource for 21st century biodiversity research. PNAS 116, 22651–22656.
https://doi.org/10.1073/pnas.1911714116.
Llamas, B., Valverde, G., Fehren-Schmitz, L., Weyrich, L.S., Cooper, A., Haak, W., 2017.
From the field to the laboratory: controlling DNA contamination in human ancient
DNA research in the high-throughput sequencing era. Sci. Technol. Arcaeol. Res. 3
(1), 1–14.
Locatelli, N.S., McIntyre, P.B., Therkildsen, N.O., Baetscher, D.S., 2020. GenBank’s
reliability is uncertain for biodiversity researchers seeking species-level assignment
for eDNA. PNAS 117 (51), 32211–32212. https://doi.org/10.1073/
pnas.2007421117.
May-Collado, L.J., Kilpatrick, C.W., Agnarsson, I., 2015. Mammals from ‘down under’: a
multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria).
PeerJ. 3.
Molecular Phylogenetics and Evolution 166 (2022) 107328
Menzies, J.I., 1991. A Handbook of New Guinea Marsupials and Monotremes. Kristen
Press, Madang.
Mitchell, K.J., Pratt, R.C., Watson, L.N., Gibb, G.C., Llamas, B., Kasper, M., Edson, J.,
Hopwood, B., Male, D., Armstrong, K.N., et al., 2014. Molecular phylogeny,
biogeography, and habitat preference evolution of marsupials. Mol. Biol. Evol. 31,
2322–2330. https://doi.org/10.1093/molbev/msu176.
Morgan, C.C., Creevey, C.J., O’Connell, M.J., 2014. Mitochondrial data are not suitable
for resolving placental mammal phylogeny. Mammal. Genome 25 (11-12), 636–647.
Nguyen, L.-T., Schmidt, H.A., von Haeseler, A., Minh, B.Q., 2014. IQ-TREE: a fast and
effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol.
Biol. Evol. 32, 268–274.
Phillips, M.J., Shazwani Zakaria, S., 2021. Enhancing mitogenomic phylogeny and
resolving the relationships of extinct megafaunal placental mammals. Mol.
Phylogenet. Evol. 158, 107082. https://doi.org/10.1016/j.ympev.2021.107082.
Rambaut, A., 1996. Sequence alignment editor. Available at: http://tree.bio.ed.ac.
uk/software/seal.
Rambaut, A., Drummond, A.J., Xie, D., Baele, G., Suchard, M.A., 2018. Posterior
summarisation in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S.,
Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient
Bayesian phylogenetic inference and model choice across a large model space. Syst.
Biol. 61, 539–542.
Sayers, E.W., Cavanaugh, M., Clark, K., Pruitt, K.D., Schoch, C.L., Sherry, S.T., Karsch-
Mizrachi, I., 2018. GenBank. Nucleic Acids Res. 49, D92–D96. https://doi.org/
10.1093/nar/gkaa1023.
Schoch, C.L., Ciufo, S., Domrachev, M., Hotton, C.L., Kannan, S., Khovanskaya, R.,
Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B., et al., 2020. NCBI Taxonomy: a
comprehensive update on curation, resources and tools. Database 2020, baaa062.
https://doi.org/10.1093/database/baaa062.
Upham, N.S., Esselstyn, J.A., Jetz, W., Tanentzap, A.J., 2019. Inferring the mammal tree:
species-level sets of phylogenies for questions in ecology, evolution, and
conservation. PLoS Biol. 17 (12), e3000494. https://doi.org/10.1371/journal.
pbio.3000494.
van den Burg, M.P., Herrando-Pérez, S., Vieites, D.R., 2020. ACDC, a global database of
amphibian cytochrome-b sequences using reproducible curation for GenBank
records. Sci. Data 7, 268. https://doi.org/10.1038/s41597-020-00598-9.
Westerman, M., Krajewski, C., Kear, B.P., Meehan, L., Meredith, R.W., Emerling, C.A.,
Springer, M.S., 2016. Phylogenetic relationships of dasyuromorphian marsupials
revisited. Zool. J. Linn. Soc. 176 (3), 686–701.
Westerman, M., Young, J., Donnellan, S., Woolley, P.A., Krajewski, C., 2006. Molecular
relationships of New Guinean three-striped dasyures, (Myoictis, Marsupialia:
Dasyuridae). J. Mammal Evol. 13 (3-4), 211–222.
Woolley, P.A., 2005. Revision of the Three-striped Dasyures, Genus Myoictis
(Marsupialia: Dasyuridae), of New Guinea, with a description of a new species. Rec.
Aust. Mus. 57, 321–340.