Preprints

Filtering by Subject: Physical Sciences and Mathematics

ausplotsR: An R package for rapid extraction and analysis of vegetation and soil data collected by Australia’s Terrestrial Ecosystem Research Network

Samantha Munroe, Greg Guerin, Tom Saleeba, et al.

Published: 2020-12-15
Subjects: Biostatistics, Botany, Life Sciences, Other Plant Sciences, Physical Sciences and Mathematics, Plant Biology, Plant Sciences, Statistics and Probability

The Terrestrial Ecosystem Research Network (TERN), Australia’s national land ecosystem monitoring program, measures critical environmental attributes from local to continental scale and generates quality data for research and land management. Since 2011, TERN has performed standardised field surveys and sampling across a national plot network. At each plot, TERN records vegetation structure, [...]

Phylogenetic multilevel meta-analysis: A simulation study on the importance of modeling the phylogeny

Ozan Cinar, Shinichi Nakagawa, Wolfgang Viechtbauer

Published: 2020-11-23
Subjects: Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Statistical Models, Statistics and Probability

1. Meta-analyses in ecology and evolution require special attention due to certain study characteristics in these fields. First, the primary articles in these fields usually report results that are observed from studies conducted with different species, and the phylogeny among the species violates the independence assumption. Second, articles frequently allow the computation of multiple effect [...]

Motif: an open-source R tool for pattern-based spatial analysis

Jakub Nowosad

Published: 2020-10-17
Subjects: Categorical Data Analysis, Earth Sciences, Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics, Statistics and Probability, Terrestrial and Aquatic Ecology

*Context* Pattern-based spatial analysis provides methods to describe and quantitatively compare spatial patterns for categorical raster datasets. It allows for spatial search, change detection, and clustering of areas with similar patterns. *Objectives* We developed an R package **motif** as a set of open-source tools for pattern-based spatial analysis. *Methods* This package provides [...]

Synergistic impacts of anthropogenic fires and aridity on plant diversity in the Western Ghats: Implications for management of ancient social-ecological systems

Charuta Kulkarni, Walter Finsinger, Pallavi Anand, et al.

Published: 2020-10-01
Subjects: Biodiversity, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics, Sustainability

Identifying the impacts of anthropogenic fires on biodiversity is imperative for human-influenced tropical rainforests because: i) these ecosystems have been transformed by human-induced fires for millennia; and ii) their effective management is essential for protecting the world’s terrestrial biodiversity in the face of global environmental change. While several short-term studies elucidate the [...]

Recent advances of quantitative modeling to support invasive species eradication on islands

Christopher Baker, Michael Bode

Published: 2020-09-08
Subjects: Biodiversity, Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Natural Resources and Conservation, Physical Sciences and Mathematics

The eradication of invasive species from islands is an important part of managing these ecologically unique and at-risk regions. Island eradications are complex projects and mathematical models play an important role in supporting efficient and transparent decision-making. In this review we cover the past applications of modelling to island eradications, which range from large-scale [...]

Indigenous Conservation Practices Are Not a Monolith: Western cultural biases and a lack of engagement with Indigenous experts undermine studies of land stewardship

Kelsey Leonard, Jared Dahl Aldern, Amy Christianson, et al.

Published: 2020-07-24
Subjects: Environmental Sciences, Forest Sciences, Life Sciences, Natural Resources and Conservation, Other Social and Behavioral Sciences, Physical Sciences and Mathematics, Plant Sciences, Social and Behavioral Sciences

Commentary On: Oswald, W. W., Foster, D. R., Shuman, B. N., Chilton, E. S., Doucette, D. L., Duranleau, D. L. Conservation implications of limited Native American impacts in pre-contact New England. Nature Sustainability https://doi.org/10.1038/s41893-019-0466-0

FIRED (Fire Events Delineation): An open, flexible algorithm & database of US fire events derived from the MODIS burned area product (2001-19)

Jennifer Balch, Lise A. St. Denis, Adam Lee Mahood, et al.

Published: 2020-06-27
Subjects: Ecology and Evolutionary Biology, Environmental Monitoring, Environmental Sciences, Life Sciences, Other Ecology and Evolutionary Biology, Physical Sciences and Mathematics

Harnessing the fire data revolution, i.e., the abundance of information from satellites, government records, social media, and human health sources, now requires complex and challenging data integration approaches. Defining fire events is key to that effort. In order to understand the spatial and temporal characteristics of fire, or the classic fire regime concept, we need to critically define [...]

Ten simple rules for building an anti-racist lab

Bala Chaudhary, Asmeret Asefaw Berhe

Published: 2020-06-18
Subjects: Life Sciences, Physical Sciences and Mathematics

Demographics of the Science, Technology, Engineering, and Mathematics (STEM) workforce and student body in the U.S. and Europe continue to show severe underrepresentation of Black, Indigenous, and people of color (BIPOC). Among the documented causes of the persistent lack of diversity in STEM include bias, discrimination, and harassment of members of underrepresented minority groups (URMs). These [...]

[Final version available] Explainable Artificial Intelligence enhances the ecological interpretability of black-box species distribution models

Masahiro Ryo, Boyan Angelov, Stefano Mammola, et al.

Published: 2020-04-17
Subjects: Artificial Intelligence and Robotics, Biodiversity, Computer Sciences, Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Research Methods in Life Sciences, Terrestrial and Aquatic Ecology

Species distribution models (SDMs) are widely used in ecology, biogeography and conservation biology to estimate relationships between environmental variables and species occurrence data and make predictions of how their distributions vary in space and time. During the past two decades, the field has increasingly made use of machine learning approaches for constructing and validating SDMs. Model [...]

What we can learn from the parallels between the COVID-19 and the future climate change crises

Rubén D. Manzanedo, Peter Manning

Published: 2020-04-11
Subjects: Environmental Sciences, Life Sciences, Physical Sciences and Mathematics

The ongoing COVID-19 outbreak pandemic is now a global crisis. It has caused 1.6+ million confirmed cases and 100 000+ deaths at the time of writing and triggered unprecedented preventative measures that have put a substantial portion of the global population under confinement, imposed isolation, and established ‘social distancing’ as a new global behavioral norm. The COVID-19 crisis has affected [...]

Understanding the tripartite approach to Bayesian divergence time estimation

Rachel Warnock, April Marie Wright

Published: 2020-04-07
Subjects: Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics

Placing evolutionary events in the context of geological time is a fundamental goal in paleobiology and macroevolution. In this article we describe the tripartite model used for Bayesian estimation of time calibrated phylogenetic trees. The model can be readily separated into its component models: the substitution model, the clock model and the tree model. We provide an overview of the most [...]

StableClim, continuous projections of climate stability from 21000 BP to 2100 CE at multiple spatial scales

Stuart C Brown, Tom M. L. Wigley, Bette L. Otto-Bliesner, et al.

Published: 2020-02-22
Subjects: Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Other Ecology and Evolutionary Biology, Other Environmental Sciences, Physical Sciences and Mathematics

Paleoclimatic data are used in eco-evolutionary models to improve knowledge of biogeographical processes that drive patterns of biodiversity through time, opening windows into past climate–biodiversity dynamics. Applying these models to harmonised simulations of past and future climatic change can strengthen forecasts of biodiversity change. StableClim provides continuous estimates of climate [...]

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

Shinichi Nakagawa, Malgorzata Lagisz, Rose E O'Dea, et al.

Published: 2019-12-29
Subjects: Applied Mathematics, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Physical Sciences and Mathematics

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, [...]

Experimenting with the past to improve environmental monitoring programs

Easton R White, Christie A. Bahlai

Published: 2019-10-13
Subjects: Agriculture, Biodiversity, Ecology and Evolutionary Biology, Environmental Monitoring, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics, Research Methods in Life Sciences

Long-term monitoring programs are a fundamental part of both understanding system dynamics and informing management decisions. However, monitoring programs not always designed to consider statistical power, site selection, or the full costs and benefits of monitoring. Further, data from monitoring programs with different goals and protocols are now being combined for comparative analyses. Key [...]

Toward a Pluralistic Conception of Resilience

Matteo Convertino, James Valverde

Published: 2019-06-29
Subjects: Applied Mathematics, Computer Sciences, Dynamic Systems, Ecology and Evolutionary Biology, Environmental Health and Protection, Environmental Indicators and Impact Assessment, Environmental Monitoring, Environmental Sciences, Life Sciences, Medicine and Health Sciences, Natural Resources and Conservation, Numerical Analysis and Computation, Other Medicine and Health Sciences, Other Physical Sciences and Mathematics, Physical Sciences and Mathematics, Social and Behavioral Sciences, Sustainability, Systems Biology

The concept of resilience occupies an increasingly prominent position within contemporary efforts to confront many of modernitys most pressing challenges, including global environmental change, famine, infrastructure, poverty, and terrorism, to name but a few. Received views of resilience span a broad conceptual and theoretical terrain, with a diverse range of application domains and settings. In [...]

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