DOI: 10.5061/dryad.xksn02vd0
title: Data from: ‘In 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

description: Encompassing some of the major hotspots of biodiversity on Earth, large
 mountain systems have long held the attention of evolutionary biologists.
 The region of the Qinghai-Tibet Plateau (QTP) is considered a
 biogeographic source for multiple colonization events into adjacent areas
 including the northern Palearctic. The faunal exchange between the QTP and
 adjacent regions could thus represent a one-way street (‘out of’ the QTP).
 However, immigration into the QTP region has so far received only little
 attention, despite its potential to shape faunal and floral communities of
 the QTP. In this study, we investigated centers of origin and dispersal
 routes between the QTP, its forested margins and adjacent regions for five
 clades of alpine and montane birds of the passerine superfamily
 Passeroidea (Johansson et al., 2008; Selvatti et al., 2015). We performed
 an ancestral area reconstruction using BioGeoBEARS and inferred a
 time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest
 endemic species of the QTP was dated to the early Miocene (ca. 18 Ma).
 Several additional QTP endemics evolved in the mid to late Miocene (12–7
 Ma). The inferred centers of origin and diversification for some of our
 target clades matched the ‘out of Tibet hypothesis’ or the ‘out of
 Himalayas hypothesis’ for others they matched the ‘into Tibet hypothesis’.
 Three radiations included multiple independent Pleistocene colonization
 events to regions as distant as the Western Palearctic and the Nearctic.
 We conclude that faunal exchange between the QTP and adjacent regions was
 bidirectional through time, and the QTP region has thus harbored both
 centers of diversification and centers of immigration.
description: Our sequence data set included four loci: the mitochondrial
 cytochrome-<i>b </i>(cyt<i>b</i>) and NADH
 dehydrogenase subunit 2 (ND2), as well as the nuclear introns ornithine
 decarboxylase (ODC) intron 7, and myoglobin (myo) intron 2. Sequences for
 target taxa were compiled from previous studies. We added missing species
 and filled gaps in sequence coverage with newly generated sequences. To
 have all families of Passeroidea represented by at least one species, we
 included further sequences from GenBank. Newly generated sequences were
 joined with sequences obtained from studies and sorted using the R package
 ‘ape’. Sequences were aligned with the stand-alone version of MAFFT 7.273
 with automatic selection of the appropriate alignment strategy, the
 scoring matrix set to '200PAM / κ=2', and the gap opening
 penalty set to 1.53 (with a gap extension penalty of 0.123). The obtained
 sequence alignments were manually checked for errors. The final data set
 included 281 taxa. Phylogenetic inference and
 divergence-time estimation were performed with BEAST v1.8.2. We
 partitioned our dataset in accordance with the best-fitting partitioning
 scheme that resulted from PartitionFinder v1.1.1 with all site models
 unlinked and one clock model for each gene resulting in a total of eight
 sites and four clock models. We linked all tree models to one tree model
 and a birth-death tree prior was applied. As initial condition for the
 BEAST run, we supplied a starting tree calculated with RAxML v8.2.0 .
 Search for the best-known likelihood tree was performed with 100
 replicates, bootstrap values obtained from a thorough bootstrap run using
 the autoMRE option were annotated onto the best-known likelihood tree. All
 analyses were performed using the same partitioning scheme as applied for
 BEAST analyses with the GTRGAMMA model applied to all partitions. 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. Trees were summarized with TreeAnnotator v1.8.2, where median
 heights were annotated to the maximum clade credibility (MCC) tree. We
 used eight calibration points in order to obtain estimates for node ages.
 Additionally, we applied a normal prior to the root age to avoid the
 occurrence of implausibly old root ages. We used R
 package BioGeoBEARS for ancestral range reconstruction. The maximum clade
 credibility tree obtained from BEAST was used as input tree (we kept the
 waxwing, <i>Bombycilla garrulus</i>, as the closest outgroup
 of Passeroidea and pruned all further outgroups used for fossil
 calibration from the input tree). We fitted the dispersal, extinction and
 cladogenesis (DEC) model to the time-calibrated Passeroidea tree (for
 further details, see Appendix S5). We used a “dispersal multipliers”
 matrix, allowing dispersal between all areas, favoring adjacent ones
 (1.0), but penalizing slightly (0.5) dispersal between non-adjacent areas
 interconnected by a third one (in a land continuum), and penalizing
 strongly (0.01) long distance dispersal between very distant continents
 (e.g. Europe and the New World).
description: This dataset includes: 4 sequence
 alignments of cytochrome-b, NADH dehydrogenase subunit 2, ornithine
 decarboxylase (ODC) intron 7 and myoglobin (myo) intron 2
 the list of taxa included in the study including information on
 origin of samples and GenBank accession numbers the
 time-calibrated maximum clade credibility tree of Passeroidea derived from
 Bayesian phylogenetic inference with BEAST the area
 matrices for 279 taxa used for biogeographic analyses with BioGeoBEARS
 (with 8 and 9 areas, respectively) the dispersal
 multiplier matrices used for biogeographic analyses with BioGeoBEARS (with
 8 and 9 areas, respectively)