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This submission contains data and R-code that enable to reproduce the data manipulations and analyses in the paper “Why are population growth rate estimates of past and present hunter-gatherers so different?” by Miikka Tallavaara and Erlend Kirkeng Jørgensen (Philosophical transactions of the Royal Society B). Please, cite the paper and this Zenodo repository if you use the files included in this Zenodo record in your work. The submission includes a html-file titled “Why are population growth rate estimates of past and present hunter-gatherers so different? - Data analyses” (TJ2020.html) that contains R-code and instructions and comments for running the code (open this file in your browser). In addition, the submission includes Rdata-file (dataTJ2020.Rdata) containing all the data that are not created within the code and pure R-code (TJ2020.R).

A public participatory GIS -survey dataset detailing public understandings of and attitudes towards carbon-smart urban green infrastructure in Kumpula, Helsinki, Finland. This dataset was funded by the Strategic Research Council, Academy of Finland through the CO-CARBON project (project number: 335203).

• Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. • PROTAX-fungi outperformed the SINTAX and RDB classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. • With empirical data on root- and wood-associated fungi, PROTAX-fungi identified reliably (with at least 90% identification probability) the majority of sequences to the order level but only ca. one fifth of them to the species level, reflecting the current limited coverage of the databases. • When applied to examine the internal consistencies of the Index Fungorum and UNITE databases, PROTAX-fungi revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. • PROTAX-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships. Root-associated fungi from GreenlandFungal ITS2 sequence data of root-associated fungi from Greenland in fasta format. DNA extracted from different plant species roots collected along the altitudinal gradient of Aucella mountain in the Zackenberg valley.root-associated fungi from Greenland.fas

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32–5.23 million years ago, a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia. 'SNP_data_for_H.annectans' is the SNP data for Hyla annectans in vcf formats. Which is used for the phylogeney tree, genetic structure, genetic differentiation, demographic analyses. 'Morphological_data_info' are the statistic data of snout-vent length (SVL), weight and spots numbers used for morphological analyses and QST-FST comparison. 'SDM_input_ascii' are the SDM ascii files used for SDMs. 'SDM_locality_info' are the occurrence data points of five genetic clusters for the H. annectans.

Supplementary Tables in excel-format describing the detailed results of GLM models for each measurand.

Supplementary Tables in excel-format describing the AIC model selection process for each measurand in GLM analyses.

This dataset merges nitrogen data from the Yedoma domain. It includes numerous fieldwork campaigns, which take place since 1998. In total 467 samples from the active layer (seasonally thawed layer), 175 samples from perennially frozen Holocene cover deposits, 479 samples from thermokarst deposits in drained thermokarst, 175 in-situ thawed, diagenetically (anaerobic microbial decomposition possible during unfrozen phase) altered Yedoma deposits (called Taberite), and 917 samples from frozen Yedoma deposits are included. Moreover it includes a NH4+ and NO3- quantification basing on of 658 samples, including 378 data points for NH4+ (active layer, 93; Holocene cover, 108; thermokarst sediment, 138; Taberite, 0; Yedoma deposit, 39) and 542 data points for NO3- (active layer, 94; Holocene cover, 137; thermokarst sediment, 119; Taberite, 6; Yedoma deposit, 186). The bootstrapping code we adjusted for this study is available from Zenodo (Jongejans & Strauss, 2020, doi:10.5281/zenodo.3734247). The code is published under a GNU General Public License v3.0. The included areal estimation of the Yedoma domain was used from the IRYP database (Strauss et al., 2022, doi:10.1594/PANGAEA.940078).

Fine-root biomass production, sedge root, sedge leaf, and Sphagnum moss shoot mass loss data, along with environmental data (soil water-table level, air temperature, soil temperature at 5 cm, and soil temperature at 15 cm) from two sedge fens located in southern Finland (Lakkasuo, Orivesi, 61°48' N 24°19'E) and northern Finland (Lompolojänkkä, Kittilä, 68°N 24°12'E). Data are from a climate change experiment, where warming was induced with open top chambers (OTCs) and drying with shallow ditching. Data are from years 2011-2013.