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.
Sanger_alignment_LONG
Sanger sequence alignment_LONG.nex is the “alignment LONG”, which comprises full (or partial but long) cytb sequences, including outgroups.
alignment_LONG.nex
Sanger_alignment_FULL
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.
alignment_FULL.nex
RAD_all_datasets_vcf_base
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.
RAD_all_datasets_vcf_thinned
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.
RAD_datasetFRESH_nex_subsets_ingroup
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.
RAD_datasetFRESH_nex_subsets
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.
RAD_datasetDAAROODENSIS_nex_subsets
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.
RAD_datasetMUSEUM_nex_subsets
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.
RAD_datasetERLANGERI_nex_subsets
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.
RAD_datasetFRESH_xml_SNAPP_ingroup
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.
RAD_datasetFRESH_xml_SNAPP
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.
RAD_datasetDAAROODENSIS_xml_SNAPP
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.
RAD_datasetMUSEUM_xml_SNAPP
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.
RAD_datasetERLANGERI_xml_SNAPP
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.
ReadMe
This general ReadMe file details the contents of each archive and provides further details.