Fitting individual-based models of spatial population dynamics to long-term monitoring data DOI Creative Commons
Anne‐Kathleen Malchow, Guillermo Fandós, Urs G. Kormann

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 27, 2022

Abstract Generating spatial predictions of species distribution is a central task for research and policy. Currently, correlative models (cSDMs) are among the most widely used tools this purpose. However, cSDMs fundamental assumption distributions in equilibrium with their environment rarely met real data limits applicability dynamic projections. Process-based, SDMs (dSDMs) promise to overcome these limitations as they explicitly represent transient dynamics enhance spatio-temporal transferability. Software implementing dSDMs become increasingly available, yet parameter estimation can be complex. Here, we test feasibility calibrating validating dSDM using long-term monitoring Swiss red kites ( Milvus milvus ). This population has shown strong increases abundance progressive range expansion over last decades, indicating non-equilibrium situation. We construct an individual-based model RangeShiftR modelling platform use Bayesian inference calibration. allows integration heterogeneous sources, such estimates from published literature well observational schemes, coherent assessment uncertainty. Our encompass counts breeding pairs at 267 sites across Switzerland 22 years. validate our spatial-block cross-validation scheme assess predictive performance rank-correlation coefficient. showed very good accuracy projections represented observed two decades. Results suggest that reproductive success was key factor driving expansion. According model, kite fills large parts its current but potential further density. demonstrate practicality validation RangeShifteR. approach improve compared cSDMs. The workflow presented here adopted any which some prior knowledge on demographic dispersal parameters observations or presence/absence available. fitted provides improved quantitative insights into ecology species, may greatly help conservation management actions. Open Research statement submission uses novel code provided external repository. All required replicate analyses private-for-peer review via public GitHub repository under following link: https://github.com/UP-macroecology/Malchow_IBMcalibration_2023 Upon acceptance, will archived versioned Zenodo DOI provided. For study, tagged development version R package available at: https://github.com/RangeShifter/RangeShiftR-package/releases/tag/v.1.1-beta.0

Language: Английский

rangr: An R package for mechanistic, spatially explicit simulation of species range dynamics DOI Creative Commons
Katarzyna Markowska, Katarzyna Malinowska, Lechosław Kuczyński

et al.

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Abstract Global change driven by human activities is causing profound shifts in species distributions. Understanding the mechanisms that influence these dynamics crucial for biodiversity management. Several mechanistic, spatially explicit models have been proposed to address this issue, but they do not cover full range of potential functionalities. We present a new open‐source R package called rangr , which integrates population and dispersal into mechanistic virtual simulator. The can be used study effects environmental on growth shifts. It extends capabilities previously available simulators allowing simple straightforward definition (including positive density dependence), extensive possibilities defining kernels ability generate ecologist data. showcased functionality simulating invasion collared dove ( Streptopelia decaocto ). First, we demonstrated how set up simulation with different investigating role long‐distance events colonisation outcome. Second, showed use assess an Allee effect impede biological invasion. Finally, framework determine timeframe required detect spread invasive species. package, comes documentation vignettes, easy up, flexible, fast, fully configurable capable emulating observation process. These features make particularly well suited generating data replicate existing wildlife monitoring programmes.

Language: Английский

Citations

1
Range and climate niche shifts in European and North American breeding birds DOI Creative Commons
Damaris Zurell, Katrin Schifferle, Sergi Herrando

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1902)

Published: April 7, 2024

Species respond dynamically to climate change and exhibit time lags. Consequently, species may not occupy their full climatic niche during range shifting. Here, we assessed tracking recent shifts of European United States (US) birds. Using data from two bird atlases the North American Breeding Bird Survey between 1980s 2010s, analysed overlap based on kernel density estimation. Phylogenetic multiple regression was used assess effect morphological, ecological biogeographic traits metrics. birds shifted ranges north north-eastwards, US westwards. Range unfilling lower than expected by null models, expansion more common unfilling. Also, generally in poorly explained traits. Overall, our results suggest that dispersal limitations were minor shifting Europe USA while delayed extinctions unfavourable areas seem important. Regional differences could be related land use history monitoring schemes. Comparative analyses provide a useful screening approach for identifying importance transient dynamics time-lagged responses change. This article is part theme issue 'Ecological novelty planetary stewardship: biodiversity transforming biosphere'.

Language: Английский

Citations

8
Detecting and attributing the causes of biodiversity change: needs, gaps and solutions DOI Creative Commons
Edward W. Tekwa, Andrew Gonzalez, Damaris Zurell

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 378(1881)

Published: May 29, 2023

This issue addresses the multifaceted problems of understanding biodiversity change to meet emerging international development and conservation goals, national economic accounting diverse community needs. Recent agreements highlight need establish monitoring assessment programmes at regional levels. We identify an opportunity for research develop methods robust detection attribution that will contribute assessments guide action. The 16 contributions this address six major aspects assessment: connecting policy science, establishing observation, improving statistical estimation, detecting change, attributing causes projecting future. These studies are led by experts in Indigenous studies, economics, ecology, conservation, statistics, computer with representations from Asia, Africa, South America, North America Europe. results place science context needs provide updated roadmap how observe a way supports action via science. article is part theme ‘Detecting change: needs, gaps solutions’

Language: Английский

Citations

15
Fitting individual‐based models of spatial population dynamics to long‐term monitoring data DOI Creative Commons
Anne‐Kathleen Malchow, Guillermo Fandós, Urs G. Kormann

et al.

Ecological Applications, Journal Year: 2024, Volume and Issue: 34(4)

Published: April 17, 2024

Abstract Generating spatial predictions of species distribution is a central task for research and policy. Currently, correlative models (cSDMs) are among the most widely used tools this purpose. However, fundamental assumption cSDMs, that distributions in equilibrium with their environment, rarely fulfilled real data limits applicability cSDMs dynamic projections. Process‐based, SDMs (dSDMs) promise to overcome these limitations as they explicitly represent transient dynamics enhance spatiotemporal transferability. Software implementing dSDMs becoming increasingly available, but parameter estimation can be complex. Here, we test feasibility calibrating validating dSDM using long‐term monitoring Swiss red kites ( Milvus milvus ). This population has shown strong increases abundance progressive range expansion over last decades, indicating nonequilibrium situation. We construct an individual‐based model RangeShiftR modeling platform use Bayesian inference calibration. allows integration heterogeneous sources, such estimates from published literature observational schemes, coherent assessment uncertainty. Our encompass counts breeding pairs at 267 sites across Switzerland 22 years. validate our spatial‐block cross‐validation scheme assess predictive performance rank‐correlation coefficient. showed very good accuracy projections represented well observed two decades. Results suggest reproductive success was key factor driving expansion. According model, kite fills large parts its current potential further density. demonstrate practicality validation RangeShiftR. approach improve compared cSDMs. The workflow presented here adopted any which some prior knowledge on demographic dispersal parameters observations or presence/absence available. fitted provides improved quantitative insights into ecology species, greatly aid conservation management efforts.

Language: Английский

Citations

3
Demography–environment relationships improve mechanistic understanding of range dynamics under climate change DOI Creative Commons
Anne‐Kathleen Malchow, Florian Härtig, Jette Reeg

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 378(1881)

Published: May 29, 2023

Species respond to climate change with range and abundance dynamics. To better explain predict them, we need a mechanistic understanding of how the underlying demographic processes are shaped by climatic conditions. Here, aim infer demography–climate relationships from distribution data. For this, developed spatially explicit, process-based models for eight Swiss breeding bird populations. These jointly consider dispersal, population dynamics climate-dependence three processes—juvenile survival, adult survival fecundity. The were calibrated 267 nationwide time series in Bayesian framework. fitted showed moderate excellent goodness-of-fit discriminatory power. most influential predictors performance mean breeding-season temperature total winter precipitation. Contemporary benefitted trends typical mountain birds leading lower losses or even slight increases, whereas lowland adversely affected. Our results emphasize that generic embedded robust statistical framework can improve our predictions may allow disentangling processes. future research, advocate stronger integration experimental empirical studies order gain more precise insights into mechanisms which affects This article is part theme issue ‘Detecting attributing causes biodiversity change: needs, gaps solutions’.

Language: Английский

Citations

6
Fitting individual-based models of spatial population dynamics to long-term monitoring data DOI Creative Commons
Anne‐Kathleen Malchow, Guillermo Fandós, Urs G. Kormann

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 27, 2022

Abstract Generating spatial predictions of species distribution is a central task for research and policy. Currently, correlative models (cSDMs) are among the most widely used tools this purpose. However, cSDMs fundamental assumption distributions in equilibrium with their environment rarely met real data limits applicability dynamic projections. Process-based, SDMs (dSDMs) promise to overcome these limitations as they explicitly represent transient dynamics enhance spatio-temporal transferability. Software implementing dSDMs become increasingly available, yet parameter estimation can be complex. Here, we test feasibility calibrating validating dSDM using long-term monitoring Swiss red kites ( Milvus milvus ). This population has shown strong increases abundance progressive range expansion over last decades, indicating non-equilibrium situation. We construct an individual-based model RangeShiftR modelling platform use Bayesian inference calibration. allows integration heterogeneous sources, such estimates from published literature well observational schemes, coherent assessment uncertainty. Our encompass counts breeding pairs at 267 sites across Switzerland 22 years. validate our spatial-block cross-validation scheme assess predictive performance rank-correlation coefficient. showed very good accuracy projections represented observed two decades. Results suggest that reproductive success was key factor driving expansion. According model, kite fills large parts its current but potential further density. demonstrate practicality validation RangeShifteR. approach improve compared cSDMs. The workflow presented here adopted any which some prior knowledge on demographic dispersal parameters observations or presence/absence available. fitted provides improved quantitative insights into ecology species, may greatly help conservation management actions. Open Research statement submission uses novel code provided external repository. All required replicate analyses private-for-peer review via public GitHub repository under following link: https://github.com/UP-macroecology/Malchow_IBMcalibration_2023 Upon acceptance, will archived versioned Zenodo DOI provided. For study, tagged development version R package available at: https://github.com/RangeShifter/RangeShiftR-package/releases/tag/v.1.1-beta.0

Language: Английский

Citations

1