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Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early-Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution, have included an over reliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Using process-explicit macroecological models that integrate modern and fossil occurrence records, spatiotemporal reconstructions of past climatic change, speciesspecific population ecology and the growth and spread of anatomically modern humans, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia, and in its expansion in North America. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years requires high dispersal abilities, large maximum densities, and a small Allee effect. Climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses reveal that the range collapse and extinction of the muskox in Europe (~ 13 thousand years ago) was caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By disentangling the ecological processes that shaped the distribution of the muskox through space and time, process-explicit models have important applications for the future conservation and management of this iconic species in a warming Arctic. We built process-explicit macroecological models of muskox that simulate interactions between metapopulation dynamics, climate variability, and hunting by humans. We used calibrated fossils and modern occurrence records obtained from publicly available databases and published literature. Records were intersected with paleoclimate reconstructions accessed using PaleoView, and modern climate data from CRU TS v4. Niche hypervolumes and spatiotemporal projections of habitat suitability were built in R using the 'hypervolume' package. Process-explicit macroecological models were built in R using the 'poems' and 'paleopop' package. Human abundance was modelled using a Climate Informed Spatial Genetics Model (CISGeM). Funding provided by: Australian Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000923Award Number: DP180102392Funding provided by: Australian Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000923Award Number: FT140101192Funding provided by: Danish Research Foundation*Crossref Funder Registry ID: Award Number: DNRF96

Sample collection Samples of FWW were collected from 16 locations across its distribution range in China; 14 of these have previously been used for population genetics analysis using microsatellite markers (Cao et al., 2016). The other two newly collected populations were obtained from the expansion fronts of FWW in 2017-2018. Larvae of FWW were each sampled from different silk webs at each sampling location to reduce the chances of collecting siblings. In total, 306 larvae of FWW were obtained and used for DNA extraction, library construction, and genotyping, with 13-20 individuals per population. Library construction, SNP calling, and filtering Genomic DNA was isolated from larvae individually using a DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany). We used the ddRAD method to develop genome-wide SNPs for FWW (Peterson et al., 2012). Genomic DNA from each individual was digested by the restriction enzymes NlaIII and AciI for 3 hours at 37 °C (Aguilar et al., 1979; Li et al., 2018). Then we used 67.5 µl (1.5×) SpeedBeads (GE) to purify the digested DNA. A pair of uniquely modified Illumina P1 (5 bp) and P2 adapters (4 bp) were ligated to the digested DNA at 16 °C overnight. A heat-deactivation step was used to end the ligating reaction under conditions of 65 °C for 10 min and 22 cycles at 20 °C for 1 min. We pooled ligated products with a unique adapter into one library, followed by a purifying step using (1.5×) SpeedBeads (GE). Fragments of 420 - 540 bp were selected using BluePippin on a 2% gel cassette (Sage Sciences, Beverly, MA, USA) and then amplified using 12 PCR (polymerase chain reaction) amplification cycles. We used 64 µl 0.8× SpeedBeads to purify the amplified libraries. The quantity and quality of each library were evaluated using Qubit 3.0 and Agilent Bioanalyses 2100. The Illumina NovaSeq 6000 platform was used for sequencing to obtain 150-bp paired-end reads. We used Stacks version 2.52 to filter the low-quality sequencing data and call SNPs (Catchen et al., 2013). Raw sequencing reads were demultiplexed and trimmed using the process_radtags. Reads for each individual were mapped to the reference genome of FWW with a size of 510.5 Mb from NCBI (Assembly: GCA_003709505.1 ASM370950v1) (Wu et al., 2018) using Bowtie version 2.3.5.1 (Langmead et al., 2012). SNPs were called using a maximum likelihood framework and filtered with populations implemented in Stacks, VCFtools version 0.1.16 (Danecek et al., 2011), and the R package vcfR (Knaus et al., 2017) based on the following criteria: (a) samples with a mapping rate less than 80% were removed; (b) SNPs with a sequencing depth higher than eight and less than 500 were removed; (c) samples and SNPs with a missing rate higher than 10% in the corresponding dataset were removed; (d) SNPs with a minor allele count lower than 10 were removed; (e) SNPs with observed heterozygosity of > 0.75 across all populations were removed; (f) SNPs with a p-value of Hardy-Weinberg equilibrium (HWE) lower than 10-7 in all populations were removed to generate dataset of neutral SNPs. In order to reduce the influence of linkage on population structure inferences, we retained only SNPs separated by at least 1000 bp (Lowry et al., 2017). References Aguilar, J. D., & Riom, J. (1979). Nemoraea pellucida (Meigen), A new parasite of Hyphantria cunea (Drury) [France; fall webworm]. Bulletin De La Société Entomologique De France, 84, 204-207. Cao, L. J., Wei, S. J., Hoffmann, A. A., Wen, J. B., & Chen, M. (2016). Rapid genetic structuring of populations of the invasive fall webworm in relation to spatial expansion and control campaigns. Diversity and Distributions, 22, 1276-1287. Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., anks, E. B., Depristo, M. A., . . . Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27, 2156-2158. Knaus, B. J., & Grünwald, N. J. (2017). VCFR: A package to manipulate and visualize variant call format data in R. Molecular Ecology Resources, 17, 44-53. Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359. Li, B. Y., Gao, Q., Cao, L. J., Hoffmann, A. A., Yang, Q., Zhu, J. Y., & Wei, S. J. (2018). Conserved profiles of digestion by double restriction endonucleases in insect genomes facilitate the design of ddRAD. Zoological Systematics, 43, 341-355. Lowry, D. B., Hoban, S., Kelley, J. L., Lotterhos, K. E., Reed, L. K., Antolin, M. F., & Storfer, A. (2017). Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Molecular Ecology Resources, 17, 142-152. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS ONE, 7, e37135. Wu, N., Zhang, S., Li, X., Cao, Y., Liu, X., Wang, Q., . . . Zhan, S. (2018). Fall webworm genomes yield insights into rapid adaptation of invasive species. Nature Ecology and Evolution, 3, 105-115. Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographic factors explained a similar proportion of the genetic variation across all populations compared to climatic factors. However, when the two population groups were analyzed separately, environmental factors explained more of the variation than geographic factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile. Here we provided VCF files generated and its population map generated in this study. Three VCF files were included. 1.fww_invariant+SNP_miss20_DP3.GQ20.vcf.gz, includes SNPs and invariant sites of all populations; 2.fww.ddRAD.all.vcf.gz, includes SNPs of all populations; 3.fww.4fds.vcf.gz, includes four degenerated SNPs of all populations; 4.fww_265_popmap.txt, includes a population map of all individuals. The three VCF files and a population map file can be opened by VCFtools and used as input files for population genetic diversity, population genetic structure, demographic inference, and outlier scanning analysis.Funding provided by: National Key Research and Development Program of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100012166Award Number: 2021YFD1400300Funding provided by: Joint Laboratory of Pest Control Research Between China and Australia*Crossref Funder Registry ID: Award Number: Z201100008320013

All scripts and functions underpinning the Global Food System Intervention Meta-Regression Model (GFSI-MRM) used to derive the results and figures presented in the manuscript entitled 'Mitigating risk of exceeding environmental limits requires ambitious food system interventions' (see pre-print on EarthArXiv, DOI: https://doi.org/10.31223/X50H2B). Version 1.2 contains the following script and repository updates: Models refitted and all results checked Cosmetic updates to scripts and functions Added archives to .gitignore file

GERALDINE is a free-to-use resource that enables the detection and characterisation of mass movements onto glaciers. Tool available at: GERALDINE (v1.1) Citation: Smith, W. D., Dunning, S. A., Brough, S., Ross, N., and Telling, J.: GERALDINE (Google Earth Engine supRaglAciaL Debris INput dEtector): a new tool for identifying and monitoring supraglacial landslide inputs, Earth Surf. Dynam., 8, 1053–1065, https://doi.org/10.5194/esurf-8-1053-2020, 2020. Version 1.1 removes the NDWI mask from the GERALDINE processing flow following reviewer comments.

Droughts are increasing in frequency and severity globally due to climate change, leading to changes in resource availability that may have cascading effects on animal ecology. Resource availability is a key driver of animal space use, which in turn influences interspecific interactions like intraguild competition. Understanding how climate-induced changes in resource availability influence animal space use, and how species-specific responses scale up to affect intraguild dynamics, is necessary for predicting broader community-level responses to climatic changes. Although several studies have demonstrated the ecological impacts of drought, the behavioral responses of individuals that scale up to these broader-scale effects are not well known, particularly among animals in top trophic levels like large carnivores. Furthermore, we currently lack understanding of how the impacts of climate variability on individual carnivore behavior are linked to intraguild dynamics, in part because multi-species datasets collected at timescales relevant to climatic changes are rare. Using 11 years of GPS data from four sympatric large carnivore species in southern Africa – lions (Panthera leo), leopards (Panthera pardus), African wild dogs (Lycaon pictus), and cheetahs (Acinonyx jubatus) – spanning 4 severe drought events, we test whether drought conditions impact 1) large carnivore space use, 2) broad-scale intraguild spatial overlap, and 3) fine-scale intraguild interactions. Drought conditions expanded space use across species, with carnivores increasing their monthly home range sizes by 35% (wild dogs) to 66% (leopards). Drought conditions increased the amount of spatial overlap between lions and subordinate felids (cheetahs and leopards) by up to 119%, but only lion-cheetah encounter rates were affected by these changes, declining in response to drought. Our findings reveal that drought has a clear signature on the space use of multiple sympatric large carnivore species, which can alter spatiotemporal partitioning between competing species. Our study thereby illuminates the links between environmental change, animal behavior, and intraguild dynamics. While fine-scale avoidance strategies may facilitate intraguild coexistence during periodic droughts, large carnivore conservation may require considerable expansion of protected areas or revised human-carnivore coexistence strategies to accommodate the likely long-term increased space demands of large carnivores under projected increases in drought intensity. Funding provided by: Royalty Research Fund*Crossref Funder Registry ID: Award Number: Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: Funding provided by: Alfred P. Sloan FoundationROR ID: https://ror.org/052csg198Award Number: The dataset was collected from GPS collars from four African carnivore species. Fix rates varied between 5 minutes and 3 hours, and were regularized to 3 hour intervals.

Kroon F, Barneche DR, Emslie M Fish predators control outbreaks of Crown-of-Thorns Starfish. Nature Communications (accepted).

The potential contribution of kelp forests to blue carbon sinks is currently of great interest but interspecific variance has received no attention. In the temperate Northeast Atlantic, kelp forest composition is changing due to climate-driven poleward range shifts of cold temperate Laminaria digitata and L. hyperborea and warm temperate L. ochroleuca. To understand how this might affect the carbon sequestration potential of this ecosystem, we quantified interspecific differences in carbon export and decomposition alongside changes in detrital photosynthesis and biochemistry. We found that while warm temperate kelp exports up to 71% more carbon per plant, it decomposes up to 155% faster than its boreal congeners. Elemental stoichiometry and polyphenolic content cannot fully explain faster carbon turnover, which may be attributable to contrasting tissue toughness or unknown biochemical and structural defences. Faster decomposition causes the detrital photosynthetic apparatus of L. ochroleuca to be overwhelmed 20 d after export and lose integrity after 36 d, while detritus of cold temperate species maintains carbon assimilation. Depending on the photoenvironment, detrital photosynthesis could further exacerbate interspecific differences in decomposition via a potential positive feedback loop. Through compositional change such as the predicted prevalence of L. ochroleuca, ocean warming may therefore reduce the carbon sequestration potential of such temperate marine forests. Data are deposited as CSV files and can be opened with any data software. The code accompanying these data is deposited at github.com/lukaseamus/CSP alongside further usage information. We place no restrictions on data usage.

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