Data from: Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae)

Stervander M, Alström P, Olsson U, Ottosson U, Hansson B, Bensch S

Date Published: June 17, 2016

DOI: http://dx.doi.org/10.5061/dryad.16mg6

 

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Title Sanger_alignment_LONG
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Description Sanger sequence alignment_LONG.nex is the “alignment LONG”, which comprises full (or partial but long) cytb sequences, including outgroups.
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Title Sanger_alignment_FULL
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Description Sanger sequence alignment_FULL.nex is the “alignment FULL”, which comprises all cytb sequences, including outgroups. The sequences in “alignment LONG” are included in this alignment. Note also that several sequences <200 bp long are included here, which are not deposited at GenBank, due to their policy on sequence length.
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Title RAD_all_datasets_vcf_base
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Description RAD_all_datasets_vcf_base.tar is an archive containing the basic SNP datasets FRESH, MUSEUM, DAAROODENSIS, and ERLANGERI (before genomic subsetting) in vcf format. See the ReadMe file for more information.
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Title RAD_all_datasets_vcf_thinned
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Description RAD_all_datasets_vcf_thinned.tar is an archive containing the genomically subsetted SNP datasets FRESH, MUSEUM, DAAROODENSIS, and ERLANGERI in vcf format. The dataset FRESH (with and without outgroup) has first been divided into three non-overlapping genomic subsets (every third SNP; pos1–3), which has then been thinned to retain SNPs at a minimum physical distance (according to the interspecific mapping) of 50 Kbp. The remaining datasets have only been thinned to retain SNPs at a minimum distance of 10 Kbp. See the ReadMe file for more information.
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Title RAD_datasetFRESH_nex_subsets_ingroup
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Description RAD_datasetFRESH_nex_subsets_ingroup.tar is an archive containing the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset FRESH, retaining the ingroup only, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetFRESH_nex_subsets
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Description RAD_datasetFRESH_nex_subsets.tar is an archive containing the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset FRESH, including the outgroup, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetDAAROODENSIS_nex_subsets
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Description RAD_datasetDAAROODENSIS_nex_subsets.tar is an archive containing the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset DAAROODENSIS, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetMUSEUM_nex_subsets
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Description RAD_datasetMUSEUM_nex_subsets.tar is an archive containing the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset MUSEUM, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetERLANGERI_nex_subsets
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Description RAD_datasetERLANGERI_nex_subsets.tar is an archive containing the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset ERLANGERI, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetFRESH_xml_SNAPP_ingroup
Description RAD_datasetFRESH_xml_SNAPP_ingroup.tar is an archive containing input xml files used for SNAPP analyses of the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset FRESH, retaining the ingroup only. See the ReadMe file for more information.
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Title RAD_datasetFRESH_xml_SNAPP
Description RAD_datasetFRESH_xml_SNAPP.tar is an archive containing input xml files used for SNAPP analyses of the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset FRESH, including the outgroup. See the ReadMe file for more information.
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Title RAD_datasetDAAROODENSIS_xml_SNAPP
Downloaded 3 times
Description RAD_datasetDAAROODENSIS_xml_SNAPP.tar is an archive containing input xml files used for SNAPP analyses of the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset DAAROODENSIS, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetMUSEUM_xml_SNAPP
Description RAD_datasetMUSEUM_xml_SNAPP.tar is an archive containing input xml files used for SNAPP analyses of the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset MUSEUM, in nexus format. See the ReadMe file for more information.
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Title RAD_datasetERLANGERI_xml_SNAPP
Description RAD_datasetERLANGERI_xml_SNAPP.tar is an archive containing input xml files used for SNAPP analyses of the replicates of random allele pairings of individual SNPs within the genomically subsetted SNP dataset ERLANGERI, in nexus format. See the ReadMe file for more information.
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Title ReadMe
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Description This general ReadMe file details the contents of each archive and provides further details.
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When using this data, please cite the original publication:

Stervander M, Alström P, Olsson U, Ottosson U, Hansson B, Bensch S (2016) Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae). Molecular Phylogenetics and Evolution 102: 233–245. http://dx.doi.org/10.1016/j.ympev.2016.05.032

Additionally, please cite the Dryad data package:

Stervander M, Alström P, Olsson U, Ottosson U, Hansson B, Bensch S (2016) Data from: Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.16mg6
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