Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)

Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS

Date Published: February 4, 2016

DOI: http://dx.doi.org/10.5061/dryad.s630c

 

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Title Fasta alignment files for all genetic loci used
Downloaded 81 times
Description FASTA alignment files of the sequences for each molecular marker used in the current study. The number of individuals is indicated in the file name (e.g. N=122). Information concerning choice of loci, primers used and alignment optimisation is described in section 2.2 of the paper (2.2 DNA extraction & PCR), in Table S2 and section 2.3 Sequencing & alignments. The alignment files provided (and used in the paper) are the optimised alignments (i.e. sites in the alignment which consisted of one or a few individuals having a 1bp insertion were typically highlighted a bad following T-COFFEE analysis and were removed). The original sequences are available on GenBank (see Table S1).
Download 1_Fasta_alignment_files.zip (59.38 Kb)
Download README.pdf (394.6 Kb)
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Title Maximum likelihood tree files
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Description Maximum likelihood tree files generated using RAXML for each nuclear intron and mtDNA and 6-nuclear intron partition. Please see the ReadME file for the full data package for further information.
Download 3_ML_tree_files.zip (1.055 Mb)
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Title PAML MCMCTREE dated phylogeny
Downloaded 25 times
Description PAML MCMCTREE dated phylogeny based on the Bayesian 6-nuclear topology generated in BEAST. Please see the ReadME file for the full data package for further information.
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Title Bayesian tree files - Gene Trees
Downloaded 36 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 1_Individual_gene_LogC_TAn_files.zip (406.6 Mb)
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Title Bayesian tree files - 6-intron partitioned tree
Downloaded 49 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 2_6NucIntronTopology_LogC_TAn_files.zip (58.68 Mb)
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Title Bayesian tree files - 5-intron partitioned topologies
Downloaded 13 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 3_5NucTopologies_LogC_TAn_files.zip (352.0 Mb)
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Title Bayesian tree files - Combinations-of-two-introns topologies
Downloaded 19 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 4_Intron_combinations_LogC_TAn_files.zip (334.1 Mb)
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Title Bayesian tree files - Combinations-of-mtDNA+each intron in turn
Downloaded 15 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 5_mtDNA_with_each_intron_LogC_TAn_files.zip (395.0 Mb)
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Title Bayesian tree files - Subsets of the mtDNA locus topologies
Downloaded 17 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 6_parts_of_mtDNA_LogC_TAn_files.zip (223.7 Mb)
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Title Bayesian tree files - 6-intron+mtDNA partitioned topology
Downloaded 14 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 7_6NucIntronPlusMtDNATopology_LogC_TAn_files.zip (58.00 Mb)
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Title Bayesian tree files - Rhinolophus capensis clade, mtDNA topology
Downloaded 15 times
Description Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
Download 8_CapensisCladeOnly_mtDNA_LogC_TAn_files.zip (19.54 Mb)
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Title Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format).
Downloaded 37 times
Description Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format). This analysis is described in section 2.5 of the paper, Species delimitation & divergence time estimation, and was conducted in BEAST v. 1.8. The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.5. The LogCombiner files contain all trees generated from 5 independent runs with burn-in removed for each analysis (i.e. 180,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 180,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files.
Download 4_StarBEAST.zip (709.4 Mb)
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When using this data, please cite the original publication:

Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS (2016) Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Molecular Phylogenetics and Evolution 97: 196-212. http://dx.doi.org/10.1016/j.ympev.2016.01.003

Additionally, please cite the Dryad data package:

Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS (2016) Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.s630c
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