Data from: Cryptic diversity within the endemic Prehensile-tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographic structure and isolation at the multilocus level

 

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Title urocotyledon_citb_haplotypes
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Description nexus file of haplotypes of cytochrome-b used to phylogenetic analysis (figure 2). Whole alignments of unphased sequences can be obtained from public genbank database (acession numbers given in the manuscript). Only further sequence alignment files used for analyses are provided here. All "specimen" codes in the files are as given in Appendix S1 of manuscript ("a" and "b" added when needed to represent the different haplotypes of the same individual.
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Title urocotyledon_cmos
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Description fasta file of haplotypes for the fragment of c-mos gene for all individuals (note that no heterozygous individuals were observed, so for this gene both haplotypes for each individual are identical). This is the alignment used for the MJ networks and all further analysis.
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Title urocotyledon_pdc_phased
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Description fasta file of haplotypes from the pdc fragment for all individuals (note that no multiple heterozigous were observed, so all haplotypes - phases - are determined with certainty)
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Title urocotyledon_rag2_phased08_network
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Description fasta file of haplotypes infered for the rag2 dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics, and IMa analysis.
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Title urocotyledon_rag2_phased08_ambiguities
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Description fasta file of haplotypes infered for rag2 dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.
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Title urocotyledon_mc1R_phased08_network
Downloaded 27 times
Description fasta file of haplotypes infered for the mc1r dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics and IMa analysis.
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Title urocotyledon_mc1R_phased08_ambiguities
Downloaded 28 times
Description fasta file of haplotypes infered for mc1r dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.
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Title urocotyledon_reln_phased08_network
Downloaded 25 times
Description fasta file of haplotypes infered for the reln dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3) and summary statistics.
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Title urocotyledon_reln_phases08_ambiguities
Downloaded 29 times
Description fasta file of haplotypes infered for reln dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP.
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Title urocotyledon_reln_phased08_bestguesses
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Description fasta file of haplotypes infered for reln dataset for all individuals, where positions whose phases were resolved with < 0.8 posterior probability are nevertheless coded with the respective best guesses for each base. (as in this dataset the different runs of PHASE (Stephens et al., 2001 - to be fund on manuscript references) were inconsistent at some positions we used results of the run with the highest likelihood score, whose seed (and command line) is given bellow. The known haplotypes used (uro_reln.known) were those read directly from sequences heterozigous for indels, and that can be found on genbank - accession numbers given in the paper). [phase comand line: ./PHASE -MS -p0.8 -q0.8 -d1 -s48993 -kuro_reln.known uro_reln.inp uro_reln.out 10000 1 100]
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Title urocotyledon_reln_imgc_Cw03
Downloaded 29 times
Description fasta file resulting from the trimming of the file "urocotyledon_reln_phased08_network.fas" to the maximum block free of evidence of recombination, using the program IMgc (Woerner et al., 2007 - reference to be found in the ms) with a chromosome copy weight of 0.3 (the value chosen as it maximized the sequence lenght keeping all needed populations represented). Used for IMa and species-tree analyses (that assume no recombination within each sequence fragment)
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Title urocotyledon_reln_bestguesses_imgc_Cw03
Downloaded 28 times
Description fasta file resulting from the trimming of the file "urocotyledon_reln_phased08_bestguesses.fas" to the maximum block free of evidence of recombination, using the program IMgc (Woerner et al., 2007 - reference to be found in the ms) with a chromosome copy weight of 0.3 (the value chosen as it maximized the sequence lenght keeping all needed populations represented). Used for IMa and species-tree analyses (that assume no recombination within each sequence fragment)
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When using this data, please cite the original publication:

Rocha S, Harris DJ, Posada D (2011) Cryptic diversity within the endemic Prehensile-tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographic structure and isolation at the multilocus level. Biological Journal of the Linnean Society 104(1): 177-191. http://dx.doi.org/10.1111/j.1095-8312.2011.01710.x

Additionally, please cite the Dryad data package:

Rocha S, Harris DJ, Posada D (2011) Data from: Cryptic diversity within the endemic Prehensile-tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographic structure and isolation at the multilocus level. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.989d0
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