Data from: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution

Khang TF, Soo OYM, Tan WB, Lim LHS

Date Published: February 4, 2016

DOI: http://dx.doi.org/10.5061/dryad.50sg7

 

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Title Ligophorus image data
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Description Images of ventral and dorsal anchors of 530 specimens from 13 Ligophorus species.
Download Ligophorus image data.zip (82.32 Mb)
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Title Landmark coordinate data of ventral and dorsal anchors of 13 Ligophorus species
Downloaded 29 times
Description The file contains landmark coordinate data of ventral and dorsal anchors of 530 specimens from 13 Ligophorus species. Data generated from Ligophorus Image Data using TPSDIG2.
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Title R scripts and associated data files
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Description This file contains R scripts and associated data files for reproducing the analyses in Khang et al. (2016). Note: The authors of the geomorph package has recently informed me (21 January 2016) that changes to the latest version (3.0.0) have rendered some arguments in the gpagen function obsolete. To ensure smooth running of the script, please install geomorph version 2.1.1. as in Khang et al. (2016). Updates to monogeneaGM are forthcoming and will be announced in the PeerJ reader comment section.
Download monogeneaGM R script.zip (295.8 Kb)
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Title Concatenation of MAFFT-aligned DNA sequences for 13 Ligophorus species
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Description This file contains concatenated multiple sequence alignments of 18S rRNA, ITS-1 and 28S rRNA sequences (in this order) for 13 Ligophorus species. Multiple sequence alignment was performed using MAFFT (version 7). Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53. The sequences were manually concatenated from trimmed MAFFT-alignments.
Download MSA_18S_ITS1_28S.fas (34.06 Kb)
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Title Trimmed multiple sequence alignments
Downloaded 15 times
Description This file contains MAFFT-aligned (Version 7) 28S rRNA, 18S rRNA, and ITS-1 sequences of 13 Ligophorus species which have been manually trimmed at the left and right ends. Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53.
Download MAFFT aligned trimmed.zip (6.914 Kb)
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Title Untrimmed multiple sequence alignments
Downloaded 17 times
Description This file contains MAFFT-aligned (Version 7) 28S rRNA, 18S rRNA, and ITS-1 sequences of 13 Ligophorus species as they were at the end of running MAFFT. Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53.
Download MAFFT aligned untrimmed.zip (7.609 Kb)
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Title Maximum likelihood tree of 13 Ligophorus species
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Description This file contains the inferred maximum likelihood tree of 13 Ligophorus species (Figure 3 in Khang et al. (2016)). The tree was inferred using the IQ-tree pipeline. Parameters: DNA substitution model: GTR + G; 10 000 bootstrap replicates; mid-point rooting.
Download ligophorus_MLtree.nwk (450 bytes)
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When using this data, please cite the original publication:

Khang TF, Soo OYM, Tan WB, Lim LHS (2016) Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4: e1668. http://dx.doi.org/10.7717/peerj.1668

Additionally, please cite the Dryad data package:

Khang TF, Soo OYM, Tan WB, Lim LHS (2016) Data from: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.50sg7
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