Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon

This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon" by Stervander et al. 

For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript.  

Phylogenetic analyses

Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa

BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml

BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log

BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees

TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk

Species delimitation

Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk

mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt

mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt

mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg