Data from: Central Asian radiation of modern large-mammal faunas in mid-Miocene
Data files
Sep 23, 2025 version files 263.65 KB
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Data_S1_Taxa_name_and_age.xlsx
97.22 KB
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Data_S2_taxatree.tre
21.65 KB
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Data_S3_timetree.tre
26.36 KB
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Data_S4_binarytree.tre
26.74 KB
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Data_S5_upgreaded_timetree.tre
5.42 KB
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Data_S6_mammals_R-analysis.xlsx
77.62 KB
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Data_S7_Small_mammal_CA.csv
3.78 KB
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README.md
4.86 KB
Abstract
Elucidating how modern faunas were established is crucial for understanding mammalian evolution in response to the Cenozoic global climatic and tectonic changes. However, complicated exchanges of faunas between continents in the Late Cenozoic have made it challenging to identify general patterns of faunal evolution and migration. Here, we developed a new method, Faunal Phylogenetic Contribution, to quantify faunal relationships based on taxon distances in a supertree. Our results suggest Central Asia faunas exhibited two significant expansion phases: 19–16 Ma (pre-Tunggurian surge) and 11–9 Ma (Bahean surge). The latter phase was directly correlated with the formation of the modern large-mammalian faunas, driven by the ecomorphological revolution of local mammalian communities following a regional mass extinction, “the Central Asian Tortonian Crisis”. We propose that the rapid uplift of the Tibetan Plateau altered Central Asia’s hydrological system, promoting aridification and earlier development of open habitats, which in turn drove the adaptation of large mammals to prolonged environmental shifts.
https://doi.org/10.5061/dryad.31zcrjdwz
Description of the data and file structure
A supertree was constructed for large terrestrial mammals of the Late Cenozoic (Data S1–S5). The supertree includes 1246 genera from nine orders: Primates, Pholidota, Carnivora, Creodonta, Perissodactyla, Artiodactyla, Proboscidea, Hyracoidea, and Tubulidentata. These taxa spanned Eurasia, Africa, and North America, and dated back to the beginning of the Miocene (~23 Ma). The data were sourced from the NOW and Deepbone databases.
For quantifying the relationships between any two faunas of which all taxa were included on the supertree, we developed a new method: Faunal Phylogenetic Contribution (FPC). For details, please see the paper. The FPCs were calculated using MATLAB R2023b (Code S1) with detailed descriptions, including sensitive tests of FPC.
Generation and extinction rates based on the supertree were estimated using the fossilized birth-death model in BEAST 2.7.6 (Code S2–S5), and superficial faunal turnover rates were inferred with the R package paleotree (Code S6, S7). The average hypsodonty Index of Primates, Perissodactyla, Artiodactyla, Proboscidea, and Hyracoidea was also derived from the NOW and Deepbone databases.
Data S1. Large terrestrial mammalian genera (Primates, Pholidota, Carnivora, Creodonta, Perissodactyla, Artiodactyla, Proboscidea, Hyracoidea and Tubulidentata) of the Late Cenozoic form northern continents (NC), and their living ranges in NC, EU (Europe, Caucasus region, Iran, and Türkyie), NA (north America), AF (Africa and Arabia), SA (South Asia, Southeast Asia, southern China, China coastal region, and Japan), and CA (Central Asia, northern China, Mongolia, Asian part of Russia), as well as the tooth crown hypsodonty index of Primates, Perissodactyla, Artiodactyla, Proboscidea, and Hyracoidea. Empty cells represent data not available.
Data S2. Taxa tree topology without node age information.
Data S3. Time tree with topology and node age information.
Data S4. A binary tree is used in a tree topology sensitive test.
Data S5. Tree of “Upgrade analysis” with topology and node age information.
Data S6. Large mammalian genera of NC, EU, NA, AF, SA, and CA, for superficial faunal turnover rates calculation using code S6. Before calculation, export each sheet of Excel into a separate .csv file, using the filename: “NAME.csv.”
Data S7. Small mammalian genera of the Neogene of northern China and their living ranges, or superficial faunal turnover rates calculation using code S6. Before calculation, save it as a .csv file, using the filename: “NAME.csv.”
Code/Software
Code S1. Compact file for Matlab R2023b. Explanation: The code file S1 is a .zip archive that contains all the code compiled using MATLAB. After unzipping the package in any location, you will find two folders: MAIN, TEST1, and TEST2.
MAIN folder: there are three .m files: I_presetting, II_resultcalculation, and III_resultshow. Please run these files under the Matlab program in the order of I, II, and III.
TEST1 folder: Firstly, please run bitreegeneration.m, resulting in a binary tree.tre (in the fold TREE) for topology change tests. Sensitive test file, including ST1_bootstrap.m, ST2_topology.m, ST3_nodeage.m, ST4_rarefaction.m, ST5_rarefaction_CN.m, ST6_rareCN_topology.m, ST7_ taxonliving.m, and ST8_ taxonrange.m. These tests correspond to 1.4 Bootstrap test, 1.5.1 Sensitive to the tree topology, 1.5.2 Sensitive to the node ages, 1.5.3.1 Rarefaction tests for all taxa pool, 1.5.3.2 Rarefaction tests for CN taxa pool, 1.5.3.3 Rarefaction tests for CN taxa pool with change of family-level topology, 1.5.5 Sensitive to the taxa living duration, and 1.5.6 Sensitive to the fossil ages, respectively. Please see these sections in the Supplementary Methods. Furthermore, if you want to change the topology of any nodes, please run nodeselection.m first to get the node number and then revise these numbers in STtopology.m.
TEST2 folder: this folder contains the “Upgrade test”. All files are the same as those in the MAIN folder, only the tree has been replaced with the upgraded tree that collapses tips into family/subfamily/tribe level.
Code S2. Generation and extinction rates calculation with the skyline fossilized birth-death (SFBD) model, using BEAST 2.7.6.
Code S3. Sensitive tests of generation and extinction rates, MBL = 0.316.
Code S4. Sensitive tests of generation and extinction rates, MBL = 1.
Code S5. Sensitive tests of generation and extinction rates, MBL = 3.16.
Code S6. Superficial faunal turnover rates, using the R package paleotree. Data sources: Data S6 and S7.