• Energy Research

This repository contains the `R` code and some example data (for 7 unique niche samples) to run the steppe bison model `paleopop` simulations. In order to run the example simulations, `paleopop v 2.0.0` or later must be installed. It is available on CRAN. The code has a number of package dependencies listed below: "poems" "paleopop" "raster" "purrr" "stringr" "dplyr" "furrr" "data.table" "fs" "readxl" "rgdal" The scripts are designed to run in parallel across *n* sessions - please set *n* accordingly. There are two scripts contained in the repository. They need to be run in the following order: bison_simulations.R bison_summary_metrics.R The first script builds, runs, and saves the output from a multi-simulation manager (see `paleopop` documentation for details). The second script calculates summary metrics for the simulation outputs. These summary metrics can be compared against observed patterns for model selection by Approximate Bayesian Computation, as described in the main manuscript. All outputs are saved in the `results/` directory. Additional niche samples are available on reasonable request. Directory structure: steppe-bison/ - Data/ # data necessary to build the models - k_cuts/ # niche samples required for the models - results/ # output directory for simulation results

AbstractPathways to extinction start long before the death of the last individual. However, causes of early-stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.

AbstractAimTo determine the ecological processes and drivers of range collapse, population decline and eventual extinction of the steppe bison in Eurasia.LocationSiberia.Time periodPleistocene and Holocene.Major taxa studiedSteppe bison (Bison priscus).MethodsWe configured 110,000 spatially explicit population models (SEPMs) of climate–human–steppe bison interactions in Siberia, which we ran at generational time steps from 50,000 years before present. We used pattern‐oriented modelling (POM) and fossil‐based inferences of distribution and demographic change of steppe bison to identify which SEPMs adequately simulated important interactions between ecological processes and biological threats. These “best models” were then used to disentangle the mechanisms that were integral in the population decline and later extinction of the steppe bison in its last stronghold in Eurasia.ResultsOur continuous reconstructions of the range and extinction dynamics of steppe bison were able to reconcile inferences of spatio‐temporal occurrence and the timing and location of extinction in Siberia based on hundreds of radiocarbon‐dated steppe bison fossils. We showed that simulating the ecological pathway to extinction for steppe bison in Siberia in the early Holocene required very specific ecological niche constraints, demographic processes and a constrained synergy of climate and human hunting dynamics during the Pleistocene–Holocene transition.Main conclusionsEcological processes and drivers that caused ancient population declines of species can be reconstructed at high spatio‐temporal resolutions using SEPMs and POM. Using this approach, we found that climatic change and hunting by humans are likely to have interacted with key ecological processes to cause the extinction of the steppe bison in its last refuge in Eurasia.

European bison ( Bison bonasus ) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene–Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.