Data from: Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW

Date Published: April 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.cd711

 

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Title Ancestral mitogenome reconstruction
Downloaded 9 times
Description As interspecific comparisons featured heavily in our analyses, it was important to choose a reference sequence that would limit the introduction of a bias during the mapping of sequences (“mapping bias”). Mapping algorithms become less effective when the reference is very dissimilar (Prüfer et al. 2010; Schubert et al. 2012) impacting the number of sequences identified as ‘on-target’. As some of the species in this study currently do not have a reference sequence available from GenBank (Table 1), we reconstructed an ancestral mitogenome of all Felidae (Appendix S1; Supporting Table S2) to be used as reference. To reconstruct the ancestral sequence, the most appropriate model of substitution for the alignment of the felid mitogenomes was estimated using jModeltest 2.1.4 under the Bayesian Information Criterion (Posada 2008), which was then implemented in PhyML (Guindon et al. 2010) to infer the topology of the phylogeny (as shown in Fig. 1A). Reconstruction of the ancestral sequence was performed using the webserver of Ancestors v1.1 (Diallo et al. 2007, 2010). For additional information, please refer to the manuscript and its supplements.
Download felids_ancestral_29.11.2013.fasta (17.34 Kb)
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Title Perl script 1
Downloaded 12 times
Description Perl script written by Kanchon Dasmahapatra (University of York; kanchon.dasmahapatra@york.ac.uk). This script uses a variant file (VCF) generated by GATK to call the individual bases per position for a haploid genome. After this script, run "convert_callsfile_to_one_line_fasta.pl" script to covert the base calls to a fasta file.
Download filter_multiple_sample_gatk1.5_vcf_mtDNA_indels.pl (17.86 Kb)
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Title Perl script 2
Downloaded 4 times
Description Perl script written by Kanchon Dasmahapatra (University of York; kanchon.dasmahapatra@york.ac.uk). This script uses the output from "filter_multiple_sample_gatk1.5_vcf_mtDNA_indels.pl" and writes the base calls to a fasta file.
Download convert_callsfile_to_one_line_fasta.pl (1.463 Kb)
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Title Tree files
Downloaded 42 times
Description Tree files for the phylogenies displayed in Supporting Figure 5. Phylogenies were generated using PhyML.
Download Tree-files.zip (4.703 Kb)
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Title Incomplete mitogenomes for Neofelis Nebulosa and Leptailurus serval
Downloaded 34 times
Description This zip file contains two fasta files with the incomplete mitogenomes for Neofelis Nebulosa ("NNE_Fell") and Leptailurus serval ("LSE_Togo"). These mitogenomes were too low quality for upload on GenBank: LSE_Togo is 44.5% complete and NNE_Fell is 51.0% complete. The length of stretches of N's are estimated based on a closely related individual. For more information regarding these sequences, feel free to contact the authors.
Download LSE-NNE_incomplete-mitogenomes.zip (6.602 Kb)
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When using this data, please cite the original publication:

Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW (2015) Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Molecular Ecology Resources 16(1):42-55. http://dx.doi.org/10.1111/1755-0998.12420

Additionally, please cite the Dryad data package:

Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW (2015) Data from: Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cd711
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