Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW

Date Published: September 23, 2016

DOI: http://dx.doi.org/10.5061/dryad.8br5c

 

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Title Sanger_sequence_data
Downloaded 12 times
Description Sequencher v4.7 (Gene Codes Corp., Ann Arbor, MI) was used to analyze data quality, trim primer sequences, produce alignments and call heterozygous sites to produce these fasta files, including alignments from Gottscho et al. (2014). See Appendix A for specimen information.
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Title PHASE
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Description PHASE v2.1 (Stephens et al. 2001) and seqPHASE (Flot 2010) were used to determine haplotypes; input and output files provided.
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Title Geneland
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Description Included are input files, R scripts and output files for an analysis of 10 Sanger loci in the R package Geneland v4.0.3 (Guillot 2008; Guillot et al. 2005, 2008).
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Title starBEAST
Downloaded 7 times
Description Included are input xml files and a summary of results for Bayes Factor Delimitation (BFD, Grummer et al. 2014) and *BEAST (Heled and Drummond 2010) analysis of species trees in BEAST v1.8.1 (Drummond et al. 2012).
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Title raw_HiSeq_data1
Downloaded 11 times
Description These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
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Title raw_HiSeq_data2
Downloaded 6 times
Description These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
Download raw_HiSeq_data2.zip (893.3 Mb)
Download README.txt (927 bytes)
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Title raw_HiSeq_data3
Downloaded 5 times
Description These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
Download raw_HiSeq_data3.zip (971.6 Mb)
Download README.txt (927 bytes)
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Title raw_HiSeq_data4
Downloaded 6 times
Description These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
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Download README.txt (927 bytes)
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Title pyRAD
Downloaded 9 times
Description We used pyRAD v2.1.2 (Eaton 2014) with muscle3.8.31 and usearch7.0.1090 to filter and process raw data files. Two example parameter files are provided. Please see “raw_HiSeq_data” to download the .fastq files.
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Title raxml
Downloaded 6 times
Description We used RAxML v8.1.1 (Stamatakis 2014) to created a maximum-likelihood phylogeny for our concatenated data. Input and output files provided.
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Title beast2
Downloaded 4 times
Description The folder BFD* contains .xml input files and output logs for Bayes Factor Delimitation with genomic data (Leache et al. 2014) implemented in SNAPP/BEAST 2.3.1 (Bryant et al. 2012, Bouckaert et al. 2014). The concatenated folder includes input and output for a concatenated analysis of RAD data in BEAST 2.1.2. The SNAPP folder contains species tree input and output for SNAPP 1.1.5 implemented in BEAST 2.1.2.
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Title smartPCA_Admixture
Downloaded 7 times
Description These two programs are grouped together because they share a common data format. Admixture was described by Alexander et al. (2009), smartPCA by Patterson et al. (2006). There is a folder with the R script used to create the input files, and separate folders for each analysis; R scripts for visualizing results are also provided.
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Title DAPC
Downloaded 25 times
Description We used Discriminant Analysis of Principal Components in the R package adegenet 2.0.0 (Jombart et al. 2010) using the structure (.str) file output from pyRAD. Input file and annotated R script are provided.
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Title gphocs
Downloaded 18 times
Description Included are data files, control files, log files and output files for G-PhoCS v1.2.3 (Gronau et al. 2011). Results summarized in G-PhoCs_results_120715.xlsx.
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When using this data, please cite the original publication:

Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow. Molecular Phylogenetics and Evolution 106: 103-117. http://dx.doi.org/10.1016/j.ympev.2016.09.008

Additionally, please cite the Dryad data package:

Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW (2016) Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8br5c
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