DOI: 10.5061/dryad.pk0p2ngmj
title: Data from: Geological and climatic histories likely shaped the origins of terrestrial vertebrates endemic to the Tibetan Plateau

description: Aim The Tibetan Plateau (TP) hosts many endemic species, but questions
 regarding when and from where these species originated have not been
 comprehensively answered. Here, we provide a synthesis of the
 biogeographical history of terrestrial vertebrates endemic to the TP and
 investigate the potential drivers of their spatio-temporal origins.
 Location Tibetan Plateau and its surrounding regions Time period Cenozoic
 Major taxa studied Terrestrial vertebrates Methods We used
 dispersal–extinction–cladogenesis models based on time-calibrated
 phylogenies to reconstruct the ancestral ranges of 174 endemic TP species
 and compiled the ancestral ranges and age estimates of their dispersal
 events. We generated a possibility map of source areas for endemic TP
 species by counting the incidence of non-TP sister clades in 110 km × 110
 km grid cells. We used generalized linear mixed models to assess the
 relative importance of historical processes and environmental factors in
 explaining the geographical variations in the source areas. We created
 subsets based on four vertebrate classes to test whether the dispersal
 events varied spatially and temporally among taxonomic groups. Results We
 found that the endemic species colonised the TP as early as 55 Ma, and
 that the main colonisation phase started to increase around 15 Ma and
 peaked after 6 Ma. The major source areas of endemic TP species include
 the Hengduan Mountains, the Himalayas, and Central Asia. Elevation
 difference had the strongest effect on the source areas, followed by
 geographical distance. The spatio-temporal origins of species endemic to
 the TP and the potential drivers showed significant differences among
 vertebrate classes. Main conclusions Our study supports the hypothesis
 that endemic TP species originated from various zoogeographical regions at
 different times and highlights the important roles of the TP uplift and
 past climatic changes for determining the spatio-temporal origins of
 endemic TP species.
description: We compiled a checklist of
 terrestrial vertebrates endemic to the TP according to the species
 distribution data against the TP’s geographical range. The species
 geographical ranges were obtained from the IUCN Red List database (http://www.iucnredlist.org) for mammals and amphibians, BirdLife International and NatureServe (http://www.birdlife.org) for birds, and Roll et al. (2017) for reptiles. We combined the geographical range data with the Global Biodiversity Information Facility (GBIF; http://www.gbif.org) and Fauna of China to validate the checklist of endemic TP species. Finally, we identified 178 terrestrial vertebrates endemic to the TP, including 68 mammals, 57 birds, 23 reptiles, and 30 amphibians. We obtained dated phylogenies from Upham, Esselstyn, & Jetz (2019) for mammals, Jetz et al. (2014) for birds, Tonini, Beard, Ferreira, Jetz, & Pyron (2016) for reptiles, and Jetz & Pyron (2018) for amphibians. These phylogenies are available online (http://vertlife.org/phylosubsets) as the posterior distribution of trees (<i>n</i> = 1,000), and we built maximum clade credibility phylogenies using the ‘phangorn’ package (Schliep, 2011) in R version 3.6.0 (R Development Core Team, 2019). The number of endemic TP species that could be matched to the tips in the phylogenies was 174 (out of the 178 species).
description: This zip package contains the data and R code supporting the
 findings of the following paper: He et al. Geological and climatic
 histories likely shaped the origins of terrestrial vertebrates endemic to
 the Tibetan Plateau