Content uploaded by Steen Wilhelm Knudsen
Author content
All content in this area was uploaded by Steen Wilhelm Knudsen on Aug 11, 2016
Content may be subject to copyright.
Data Article
Molecular, morphological and fossil input
data for inferring relationship among viviparous
brotulas (Bythitidae) –Resulting in a family
status change for Dinematichthyidae
Steen Wilhelm Knudsen
n
,1
, Peter Rask Møller
1
,
Werner Schwarzhans, Jørgen G. Nielsen
Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15,
DK-2100 Copenhagen Ø, Denmark
article info
Article history:
Received 13 April 2016
Received in revised form
17 Ma y 20 16
Accepted 24 May 2016
Available online 30 May 2016
Keywords:
Bythitinae
Aphyonidae
pedomorphism
Coral reef fishes
Deepsea fishes
Cave fishes
abstract
This article comprise the data related to the research article
(Møller et al., 2016) [1], and makes it possible to explore and
reproduce the topologies that allowed [1] to infer the relationship
between the families Bythitidae and Dinematichthyidae. The sup-
plementary data holds nexus-input files for the Bayesian analysis
and the ‘.xml’-input files –with and without nucleotide data –that
are used in the fossil-calibrated phylogenetic analysis with a
relaxed clock model. The resulting topologies are provided as ‘.
new’-files together with a characters matrix file for traits to trace
across the inferred phylogenies.
&2016 The Authors. Published by Elsevier Inc. This is an open
access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).
Specifications Table
Subject area Biology, Genetics and Genomics
More specific sub-
ject area
Phylogenetics and Phylogenomics
Contents lists available at ScienceDirect
journal homepage: www.elsevier.com/locate/dib
Data in Brief
http://dx.doi.org/10.1016/j.dib.2016.05.055
2352-3409/&2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).
DOI of original article: http://dx.doi.org/10.1016/j.ympev.2016.04.008
n
Corresponding author.
E-mail address: SWKnudsen@snm.ku.dk (S.W. Knudsen).
1
These authors contributed equally to this work
Data in Brief 8 (2016) 461–464
Type of data Phylogenetic.tre,.nex and.xml files
How data was
acquired
The sequence reads were examined using Sequencher v. 4.0 (sequence analysis
software, Gene Codes Corporation, Ann Arbor, MI USA http://www.genecodes.
com) and Geneious v. R7 [2], as described in the materials and methods section.
Alignment was performed with MAFFT [3], and optimal partitioning and sub-
stitution models was inferred using PartitionFinder [4]. The level of nucleotide
substitution saturation was inferred with DAMBE [5]. The resulting data matrix
was analyzed in MrBayes v.3.2.[6] and BEAST v.1.8.0 [7], with log-files examined
in Tracer [8] and resulting topologies examined in FigTree v. 1.4.2 [9] and
Mesquite v.3.04 [10].
Data format Analyzed
Experimental
factors
Sequence reads were visually inspected in Sequencher and Geneious. Aligne-
ments prepared in MAFFT [3] were inspected for nucleotide saturation in DAMBE
[5]. Third codon positions in the mtDNA-nd4 fragment was removed from the
alignment, as there appeared to be substantial saturation on these nucleotide
positions –see [1] for additional details. The phylogenies inferred was found
using the substitution models inferred in PartionFinder, and can also be found in
the ‘.nex’- and ‘.xml’-files provided. The fossil-calibrations applied can be found
in both the ‘.xml’-files provided, the supplied BEAuti-file and in Table 3 in [1].
Experimental
features
Tissue samples was obtained from 30 species of Ophidiiformes and used for DNA
extractions, PCR amplification and Sanger Sequencing. Sequence reads from
mitochondrial DNA and nuclear DNA was visually inspected and assembled in
alignments that subsequently could be used for preparing nexus-input files for
analysis in MrBayes and BEAST to infer the evolutionary relationship among
Ophidiiformes. Nucleotide sequences from extant outgroup representative spe-
cies from Beryciformes, Cetomimiformes, Gadiformes, Gasterosteiformes, Lam-
priformes and Perciformes (listed in Table 3 [1]) allowed nodes in the topology
to be time-calibrated using similar settings as described by [11]. The calibrations
applied are also listed in Table 3 by [1].
Data source
location
n/a
Data accessibility Data are with this article
Value of the data
●The provided nexus-files holds sequence data and alignments and can be directly utilized in future
studies in the evolution of perciform fishes
●The nexus file with traits can be used to reconstruct and trace ancestral characters states across
inferred phylogenies.
●The provided ‘.xml’-files and the BEAuti-file holds information on the settings applied in the fossil-
calibrated analysis, which can facilitate similar fossil-calibrated studies on perciform fishes.
1. Data
Sequence alignments are provided in ‘.nex’-files and ‘.xml’-files for fossil calibrated analysis in
BEAST [7]. Resulting topologies can be found in ‘.new’-file formats. A list of specimens and sam-
ples together with sampling time and locality is provided in Table 1 in [1].A‘.nex’-file [Dinema-
tichthyidae_map_morph_05.nex] that holds 15 traits and morphological characters for the 30 species
of Ophidiiformes is also included and can be opened in Mesquite v.3.04 [10].
S.W. Knudsen et al. / Data in Brief 8 (2016) 461–464462
2. Experimental design, materials and methods
2.1. Input files for inferring phylogenetic relationship in Bythitidae and Dinematichthyidae
Detailed descriptions of how DNA sequences were obtained and analyzed can be found in the
main material and methods section by [1], associated with this article. The data used for inferring the
relationship between Bythitidae and Dinematichthyidae [1] comprise one nexus-file, one BEAUti-file
and two ‘.xml’-files with sequence alignments of mtDNA and nDNA markers inferred from 30 tissue
samples, together with the sequences from the 23 outgroup representatives [mb_ophidiiform.nex]
(see Tables 1 and 2 by [1]) and resulting topologies in ‘.new’-file format. The input-data matrix
provided in [mb_ophidiiform.nex] was used in MrBayes [6], the settings (i.e. data partitioning and
nucleotide substitution models used for this analysis) is implemented in this input-file [mb_ophi-
diiform.nex]. The phylogeny inferred from the MrBayes analysis is presented in Fig. 2 by [1] and can
also be explored as a ‘.new’-file [mb_ophidiiform.nex.con.new] provided in this zipped supplemen-
tary material. The MrBayes inferred topology was made completely bifurcating in Mesquite v. 3.04
[10] and used as a starting tree in the ‘.xml’-files prepared in BEAUti v.1.8.0 [7]. Both the BEAUti-file
[beast_ophidiiform_input.beautiv180] and the input-‘.xml’-files [beast_ophidiiform.xml] and
[beast_ophidiiformE.xml] for BEAST are provided in the zipped supplementary data file. The taxon
sets and fossil calibrations applied in the ‘.xml’-files are listed in Table 3 by [1] and can also be found
in both the ‘.xml’-file [beast_ophidiiform_v04.xml] and in the BEAUti-file [beast_ophid-
iiform_input_04.beautiv180]. These input-files also hold information on the partitioning schemes and
the substitution models applied in the fossil-calibrated analysis. The resulting time-calibrated
topology is presented in Fig. 3 by [1] and can also be explored in the ‘.new-file’[beast_-
ophidiiform_v04_02.tre.new] provided.
All supplied supplementary data files for MrBayes [6] and BEAST [7] can be analyzed directly in the
appropriate software following the methods described in the material and methods section provided
by [1].
2.2. Input files for reconstructing ancestral states in Bythitidae and Dinematichthyidae
The file with traits and morphological characters [Dinematichthyidae_map_morph_05.nex] can be
opened in Mesquite 3.04 [10] and the used for mapping traits on the consensus tree derived from the
BEAST analysis of the ‘.xml’-input file for BEAST v.1.8.0 [beast_ophidiiform_v04.xml]. The likelihood
for each character and trait can be reconstructed by using all the 9000 trees obtained from the BEAST
analysis after burnin, and tracing reconstructed states across all 9000 trees as described by [1].
Acknowledgements
We are grateful for all loans, donated tissue samples and specimens from the following institu-
tions: AMS, CAS, CSIRO, IFREMER, IMR, Indonesian Institute of Science, KU, MCZ, MNHN, MNNH,
NMNZ, NMV, NT, SAMA, SIO, SMNS, Texas A&M Galveston, University of Hawaii, UW, and ZMUB –
institutional abbreviations follow [12], and for all help with collection of material from the partici-
pants of the MAR-ECO and Galathea 3 expeditions.
We are grateful for all help with laboratory work provided by Terry Bertozzi (SAMA), Steve
Donnellan (SAMA), Peter Gravlund (ZMUC), Charlotte Hansen (ZMUC), Anders Illum (ZMUC), Jan Yde
Poulsen (AMS), Kathy Saint (SAMA) and Leanne Wheaton (SAMA).
Financial support for this project was provided by the Johannes Schmidt Foundation, the Carlsberg
foundation grant ANS-0620/20, Danish council for independent research and the visiting Collection
Fellowship grant from the Australian Museum, Sydney. We also want to thank Stephan Nylinder
(Swedish Museum of Natural History) for advice on the BEAST setup. We also want to thank The New
Zealand e-Science Infrastructure and the staff at the Centre for e-Research at the University of
Auckland, URL http://www.nesi.org.nz for providing help and access to high-performance computing
facilities.
S.W. Knudsen et al. / Data in Brief 8 (2016) 461–464 463
Transparency document. Supplementary material
Transparency data associated with this article can be found in the online version at http://dx.doi.
org/10.1016/j.dib.2016.05.055
Appendix A. Supplementary material
Supplementary data associated with this article can be found in the online version at http://dx.doi.
org/10.1016/j.dib.2016.05.055.
References
[1] P.R. Møller, S.W. Knudsen, W. Schwarzhans, J.G. Nielsen, A new classification of viviparous brotulas (Bythitidae) –with
family status for Dinematichthyidae –based on molecular, morphological and fossil data, Mol. Phylogenet. Evol. 100 (2016)
391–408.
[2] A.J. Drummond,B. Ashton,S. Buxton,M. Cheung,A. Cooper,J. Heled,M. Kearse,R. Moir,S. Stones-Havas,S. Sturrock,T.
Thierer,A. Wilson,Geneious v5.1, Available from 〈http://www.geneious.com〉,2010.
[3] K. Katoh, K. Toh, Parallelization of the MAFFT multiple sequence alignment program, Bioinformatics 26 (2010) 1899–1900 .
[4] R. Lanfear, B. Calcott, S.Y.W. Ho, S. Guindon, Partitionfinder: combined selection of partitioning schemes and substitution
models for phylogenetic analyses, Mol. Biol. Evol. 29 (2012) 1695–1701 .
[5] X. Xia, Z. Xie, DAMBE: data analysis in molecular biology and evolution, J. Hered. 92 (2001) 371–373.
[6] F. Ronquist, M. Teslenko, P. van der Mark, D.L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M.A. Suchard, J.P. Huelsenbeck,
MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space, Syst. Biol. 61 (2012)
1–4.
[7] A.J. Drummond, M.A. Suchard, D. Xie, A. Rambaut, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol. 29
(2012) 1969–1973 .
[8] A. Rambaut,A.J. Drummond,Tracer v1.5: MCMC Trace Analyses Tool. Available: 〈http://beast.bio.ed.ac.uk/Tracer〉, 2007.
[9] A. Rambaut, FigTree v1.4.2, A Graphical Viewer of Phylogenetic Trees. Available from 〈http://tree.bio.ed.ac.uk/software/
figtree/〉,2014.
[10] W.P. Maddison, D.R. Maddison, 2015. Mesquite: A Modular System for Evolutionary Analysis. Version 3.04. 〈http://mes
quiteproject.org〉,2015.
[11] T.J. Near, R.I. Eytan, A. Dornburg, K.L. Kuhn, J.A. Moore, M.P. Davis, P.C. Wainwright, M. Friedman, W.L. Smith, Resolution of
ray-finned fish phylogeny and timing of diversification, Proc. Natl. Acad. Sci. USA 109 (2012) 13698–1370 3.
[12] R. Fricke, W.N. Eschmeyer, Guide to Fish Collections.〈http://researcharchive.calacademy.org/research/ichthyology/catalog/
collections.asp〉,Electronic version, 2016 (accessed 17.05.16).
S.W. Knudsen et al. / Data in Brief 8 (2016) 461–464464