Readme data files for Päckert et al. ‘Into and Out of’ the Qinghai-Tibet Plateau and the Himalayas: centers of origin and diversification compared across five clades of Eurasian montane and alpine passerine birds

File: ‘QTP_Material_Table279taxa’
Samples and sequences included in this data set used for phylogenetic reconstruction; taxon names according to two taxonomic standards (Clements et al., 2015 and Gill & Donsker, 2018); sequences newly generated for this study marked in bold; collections who donated samples for this study: MTD = Senckenberg Natural History Collections Dresden, Museum of Zoology, Germany; ZMB = Museum für Naturkunde Berlin; ZFMK = Zoologisches Forschungsmuseum Alexander Koenig Bonn, Germany; NME = Naturkundemuseum Erfurt, Germany; BMNH = Natural History Museum at Tring, Bird Group, UK; ZMUC = Zoological Museum of the University of Copenhagen, Denmark (NHMD = Natural History Museum of Denmark); NHMC = Natural History Museum of Crete, Greece; UWBM = Burke Museum of Natural History and Culture, Seattle, USA – further collection acronyms (GenBank sequences): NRM = Natural History Museum of Stockholn, Sweden; AJN = Ajtte Swedish Mountain and Sami Museum, Jokkmokk, Sweden; ZMA = Zoological Museum of Amsterdam, The Netherlands; RMNH = Naturalis Biodiversity Center, Leiden, The Netherlands; MRSNT = Museo di Storia Naturale, Torino, Italy; AMNH = American Museum of Natural History, NY, USA; USNM = National Museum of Natural History, Smithsonian Institution, Washington D.C., USA; FMNH = The Field Museum of Natural History, Chicago, USA; LSUMZ = Lousiana Museum of Natural History, Baton Rouge, USA; MVZ = Museum of Vertebrate Zoology, University of California, Berkley, USA; BMNH# = Bell Museum of Natural History, Minneapolis, USA; KU = Kansas University, USA; CAS/IOZ = Chinese Academy of Sciences, Institute of Zoology, Beijing, China; NMNS = National Museum of Natural Science, Taipei, Taiwan.

File: ‘QTP_cytb279taxa’
Alignment of cytochrome-b sequences (1041 bp, n= 279) used for phylogenetic reconstruction of the Passeroidea tree.

File: ‘QTP_ND2279taxa’
Alignment of ND2 sequences (1041 bp, n= 279) used for phylogenetic reconstruction of the Passeroidea tree.

File: ‘QTP_myo279taxa’
Alignment of myoglobin intron 2 sequences (750 bp, n= 279) used for phylogenetic reconstruction of the Passeroidea tree.

File: ‘QTP_ODC279taxa’
Alignment of ODC intron 7 sequences (1594 bp, n= 279) used for phylogenetic reconstruction of the Passeroidea tree.

File: ‘QTP_MCCtree279taxa’
Maximum clade credibility tree for 279 taxa of Passeroidea (Aves: Passeriformes) based on 4 genetic markers (cytochrome-b: 1041 bp; ND2: 1041 bp; myoglobin: 750 bp; ODC: 1594 bp); the best-fitting partitioning scheme was estimated using PartitionFinder v1.1.1, accordingly we partitioned the data set in eight sites and four clock models; The BEAST run was performed using the BEAGLE v2.3 library with a chain length of 1.1 x 108 generations with trees being sampled every 10,000 generations; we used eight calibration points in order to obtain estimates for node ages (modified from Päckert et al., 2016: Ibis, 158:530-540).

File: ‘QTP_BirdDistFinal4’
Area matrix of species distributions for 279 taxa of Passeroidea as used for analysis with BioGeoBEARS; 0= absence, 1= presence; eight areas distinguished: A= New World (Nearctic + Neotropics), B= Western Palearctic (including North Africa), C= Afrotropics, D= Central Asia + Middle East, E= Qinghai-Tibet Plateau, F= Sinohimalayas, G= Eastern Palearctic, H= Oriental Region

File: ‘QTP_BirdDistFinal5’
Area matrix of species distributions for 279 taxa of Passeroidea as used for analysis with BioGeoBEARS; 0= absence, 1= presence; nine areas distinguished: A= New World (Nearctic + Neotropics), B= Western Palearctic (including North Africa), C= Afrotropics, D= Central Asia + Middle East, E= Qinghai-Tibet Plateau, F1= Himalayas, F2= Hengduanshan, G= Eastern Palearctic, H= Oriental Region

File: ‘QTP_DMmatrix8areas’
Dispersal multiplier matrix as applied to BioGeoBEARS analysis in ARR1; eight areas: A= New World (Nearctic + Neotropics), B= Western Palearctic (including North Africa), C= Afrotropics, D= Central Asia + Middle East, E= Qinghai-Tibet Plateau, F= Sinohimalayas, G= Eastern Palearctic, H= Oriental Region.

File: ‘QTP_DMmatrix9areas’
Dispersal multiplier matrix as applied to BioGeoBEARS analysis in ARR2; nine areas: same area coding as in ARR1 only Sinohimalayas treated as two separate areas F1 (Himalayas) F2 (Hengduanshan).