DOI: 10.5061/dryad.16mg6
title: Data from: Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae)

description: The avian genus Calandrella (larks) was recently suggested to be
 non-monophyletic, and was divided into two genera, of which Calandrella
 sensu stricto comprises 4–5 species in Eurasia and Africa. We analysed
 mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated
 DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22
 recognised subspecies, with the aim to clarify the phylogenetic
 relationships within the genus and to compare large-scale nuclear sequence
 patterns with a widely used mitochondrial marker. Cytb indicated deep
 splits among the currently recognised species, although it failed to
 support the interrelationships among most of these. It also revealed
 unexpected deep divergences within C. brachydactyla, C. blanfordi/C.
 erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C.
 brachydactyla and C. blanfordi, as presently circumscribed, are
 paraphyletic. In contrast, most of the many subspecies of C. brachydactyla
 and C. cinerea were unsupported by cytb, although two populations of C.
 cinerea were found to be genetically distinct. The RAD data corroborated
 the cytb tree (for the smaller number of taxa analysed) and recovered
 strongly supported interspecific relationships. However, coalescence
 analyses of the RAD data, analysed in SNAPP both with and without an
 outgroup, received equally strong support for two conflicting topologies.
 We suggest that the tree rooted with an outgroup – which is not
 recommended for SNAPP – is more trustworthy, and suggest that the
 reliability of analyses performed without any outgroup species should be
 thoroughly evaluated. We also demonstrate that degraded museum samples can
 be phylogenetically informative in RAD analyses following careful
 bioinformatic treatment. We note that the genus Calandrella is in need of
 taxonomic revision.
description: Sanger_alignment_LONGSanger sequence alignment_LONG.nex is the “alignment LONG”, which comprises full (or partial but long) cytb sequences, including outgroups.alignment_LONG.nexSanger_alignment_FULLSanger 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 &lt;200 bp long are included here, which are not deposited at GenBank, due to their policy on sequence length.alignment_FULL.nexRAD_all_datasets_vcf_baseRAD_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.RAD_all_datasets_vcf_thinnedRAD_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.RAD_datasetFRESH_nex_subsets_ingroupRAD_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.RAD_datasetFRESH_nex_subsetsRAD_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.RAD_datasetDAAROODENSIS_nex_subsetsRAD_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.RAD_datasetMUSEUM_nex_subsetsRAD_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.RAD_datasetERLANGERI_nex_subsetsRAD_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.RAD_datasetFRESH_xml_SNAPP_ingroupRAD_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.RAD_datasetFRESH_xml_SNAPPRAD_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.RAD_datasetDAAROODENSIS_xml_SNAPPRAD_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.RAD_datasetMUSEUM_xml_SNAPPRAD_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.RAD_datasetERLANGERI_xml_SNAPPRAD_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.ReadMeThis general ReadMe file details the contents of each archive and provides further details.