Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM

Date Published: March 22, 2013

DOI: http://dx.doi.org/10.5061/dryad.m0n61

 

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Title BPP control file
Downloaded 23 times
Description control file for one set of priors and 1/11 topologies tested
Download varanus_1.bpp.ctl (1.221 Kb)
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Title BPP sequence file
Downloaded 21 times
Description phased sequence input file; for specimen IDs please refer to manuscript appendix
Download varanus1_V1.txt (189.4 Kb)
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Title BPP lineage assignments
Downloaded 11 times
Description lineage assignment for each sample in the sequence file
Download varanus1.Imap.txt (1.085 Kb)
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Title STRUCTURE data file
Downloaded 9 times
Description input data file for STRUCTURE analysis, with individual coded by haplotype assignment per locus
Download INFILE (7.967 Kb)
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Title STRUCTURE control file
Downloaded 8 times
Description control file for all parameters run in STRUCTURE analyses, for 1/20 population (K) inferences
Download mainparams.txt (2.577 Kb)
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Title RAxML alignment
Downloaded 23 times
Description concatenated, 5 locus alignment including all Varanus data and relevant outgroup samples
Download Varanus_all_concatenated.phy (626.2 Kb)
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Title RAxML partitions
Downloaded 15 times
Description locus and codon partitions for phylogenetic analyses
Download Varanus_partitions (389 bytes)
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Title DGL-alpha
Downloaded 11 times
Description DGL-alpha fasta alignment for *BEAST analyses
Download glor44.fasta (104.2 Kb)
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Title L52
Downloaded 10 times
Description L52 fasta alignment for *BEAST analyses
Download glor52.fasta (85.65 Kb)
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Title L74
Downloaded 10 times
Description L74 fasta alignment for *BEAST analyses
Download glor74.fasta (32.24 Kb)
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Title PRLR
Downloaded 8 times
Description PRLR fasta alignment for *BEAST analyses
Download prlr.fasta (75.41 Kb)
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Title mtDNA
Downloaded 11 times
Description ND1, ND2, and flanking tRNAs fasta alignment for *BEAST analyses
Download mt.fasta (187.4 Kb)
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Title *BEAST xml 1
Downloaded 11 times
Description 1 of 6 xml files for *BEAST analysis
Download varanus_sptree_1q_2rr_1strictclock.xml (583.5 Kb)
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Title *BEAST xml 2
Downloaded 8 times
Description 2 of 6 xml files for *BEAST analyses
Download varanus_sptree_1q_2rr_1ucldclock0.05.xml (593.8 Kb)
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Title *BEAST xml 3
Downloaded 10 times
Description 3 of 6 xml files for *BEAST analyses
Download varanus_sptree_2q_0rr_2strictclock.xml (586.8 Kb)
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Title *BEAST xml 4
Downloaded 8 times
Description 4 of 6 xml files for *BEAST analyses
Download varanus_sptree_2q_0rr_2ucldclock0.05.xml (597.9 Kb)
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Title *BEAST xml 5
Downloaded 12 times
Description 5 of 6 xml files for *BEAST analyses
Download varanus_sptree_2q_2rr_1strictclock.xml (586.4 Kb)
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Title *BEAST xml 6
Downloaded 10 times
Description 6 of 6 xml files for *BEAST analyses
Download varanus_sptree_2q_2rr_1ucldclock0.05.xml (596.7 Kb)
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When using this data, please cite the original publication:

Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM (2013) Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Molecular Ecology 22(13): 3495–3510. http://dx.doi.org/10.1111/mec.12324

Additionally, please cite the Dryad data package:

Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM (2013) Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.m0n61
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