Matthew J. Smith

Agrimetrics

The illegal trade in endangered plants damages both the environment and local communities by threatening and destroying numerous species and important natural resources. There is very little research which systematically addresses this issue by identifying specific opportunities for crime. This article presents the results of an interdisciplinary s...

An enduring challenge in ecology is to characterise and understand species richness patterns in tropical regions. Species richness maps produced by stacking species distribution model (SDM) range maps could prove useful in this regard, but little attention has been given to this approach. Here we generate a species richness map by stacking the rang...

With the volume of Earth observation data expanding rapidly, cloud computing is quickly changing the way these data are processed, analyzed, and visualized. Collocating freely available Earth observation data on a cloud computing infrastructure may create opportunities unforeseen by the original data provider for innovation and value-added data re-...

Artificial intelligence (AI) is beginning to live up to its promise of delivering real value, driven by recent advances in the availability of relevant data, computation and algorithms. In the present paper, I discuss the value to agriculture from AI over the next decade. The more immediate applications will be to improve precision information about...

Ensemble techniques, common in many disciplines, have yet to be fully exploited with spatially explicit projections from land-change models. We trial a land-change model ensemble to assess the impact of policies designed to conserve tropical rainforest at the municipality scale in Brazil, noting the achievements made and challenges ahead. Four spat...

Improving international food security under a changing climate and increasing human population will be greatly aided by improving our ability to modify, understand and predict crop growth. What we predominantly have at our disposal are either process-based models of crop physiology or statistical analyses of yield datasets, both of which suffer fro...

Monitoring internet trade to inform species conservation actions Valentina Vaglica, Maurizio Sajeva, H. Noel McGough, Dylan Hutchison, Claudio Russo, Andrew D. Gordon, Aro Vonjy Ramarosandratana, Wolfgang Stuppy, Matthew J. Smith* *Email: matthew.smith@microsoft.com ABSTRACT: Specimens, parts and products of threatened species are commonly traded...

Terrestrial ecosystems have absorbed roughly 30 % of anthropogenic CO2 emissions over the past decades, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling and experimental and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under global change is st...

We develop a theory for transit times and mean ages for nonautonomous compartmental systems. Using the McKendrick-von Förster equation, we show that the mean ages of mass in a compartmental system satisfy a linear nonautonomous ordinary differential equation that is exponentially stable. We then define a nonautonomous version of transit time as the...

Invasive species are a serious threat to biodiversity worldwide and predicting whether an introduced species will first establish and then become invasive can be useful to preserve ecosystem services. Establishment is influenced by multiple factors, such as the interactions between the introduced individuals and the resident community, and demograp...

Ecology studies the interactions between individuals, species and the environment. The ability to predict the dynamics of ecological systems would support the design and monitoring of control strategies and would help to address pressing global environmental issues. It is also important to plan for efficient use of natural resources and maintenance...

Improving international food security under a changing climate and increasing human population will be greatly aided by improving our ability to modify, understand and predict crop growth. What we predominantly have at our disposal are either process based models of crop physiology or statistical analyses of yield datasets, both of which suffer fro...

Terrestrial ecosystems absorb roughly 30 % of anthropogenic CO2 emissions since preindustrial era, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling, experimental, and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under climate change is still no...

Document S1. Figures S1–S4, Tables S1 and S2, and Supplemental Experimental Procedures

Tropical deforestation has caused a significant share of carbon emissions and species losses, but historical patterns have rarely been explicitly considered when estimating these impacts [1]. A deforestation event today leads to a time-delayed future release of carbon, from the eventual decay either of forest products or of slash left at the site [...

Geotemporal information, information associated with geographical space and time, has always been critical to climate and environmental science. However, this information is certainly not universally or easily accessible. In fact, obtaining and using geotemporal information often comes with a considerable technical overheads, impeding research prog...

A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. Therefore a thorough analysis of their key differences will be very useful for the future development of these models. Here we compare...

Soil carbon (C) is a critical component of Earth system models (ESMs) and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the 3rd to 5th assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system model...

Including a terrestrial nitrogen (N) cycle in Earth system models has led to substantial attenuation of predicted biosphere-climate feedbacks. However, the magnitude of this attenuation remains uncertain. A particularly important, but highly uncertain process is biological nitrogen fixation (BNF), which is the largest natural input of N to land eco...

Leaf seasonality impacts a variety of important biological, chemical and physical Earth system processes, which makes it essential to represent leaf phenology in ecosystem and climate models. However, we are still lacking a general, robust parametrisation of phenology at global scales. In this study, we use a simple process-based model, which descr...

Analyses of satellite-derived chlorophyll data indicate that the phase of rapid phytoplankton population growth in the North Atlantic (the ‘spring bloom') is actually initiated in the winter rather than the spring, contradicting Sverdrup's Critical Depth Hypothesis. An alternative disturbance-recovery hypothesis (DRH) has been proposed to explain t...

Microbes influence soil organic matter decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) will make more realistic global C cycle projections. Explicit representation o...

A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. Therefore a thorough analysis of their key differences will be very useful for the future development of these models. Here we compare...

Multi-component model engineering is described, for example, to model multi-component dynamical systems in which the true underlying processes are incompletely understood such as the Earth's biosphere, whole organisms, biological cells, the immune system, and anthropogenic systems such as agricultural systems, and economic systems. In an embodiment...

ISSUE • Soil organic carbon (SOC) is the largest terrestrial carbon pool, and can produce substantial feedbacks to changing climate in the form of CO₂ release • Currently, models don't represent SOC dynamics well (Todd-Brown et al., 2013) • Data-informed microbial models have been demonstrated to represent spatial distribution of SOC better than co...

Figure S1. The results of the classification and regression tree (CART) analysis (Ripley 2007) of the relative error of the estimates of activation energy. The number at the leaves of the tree indicates the mean percentage value of the relative error of the estimate (see expression 8) over all the simulated experiments, following partitioning of th...

Figure S2. Estimates of the logarithm of the growth rate (panel A) and carrying capacity (panel B) of Paramecium caudatum. The error bars show the 95% confidence interval of the estimates obtained at each temperature separately using the phenomenological likelihood 15. The red continuous line and shaded area represent the estimate of activation ene...

Data S1. Time series of the species Paramecium caudatum at different temperatures.

Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them...

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However major uncertainty remains in global soil responses to climate change, particularly uncertainty in ho...

Terrestrial ecosystems play a crucial role in the global carbon cycle and in the regulation of climate change. Anthropogenic CO2 emissions increased from 2.4 Pg C in 1960 to 8.7 Pg C per year in 2008 while terrestrial ecosystems absorbed roughly 30% during that period (Le Quere et al., 2009). If that absorption capacity were to change, in either di...

Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence–environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive m...

A new mode of development for Earth system models is needed to enable better targeted and more informative projections for both decision makers and scientists. A key step toward this is to enable models to be built that include much more robust estimates of uncertainty, which in turn guides where scientific and computational resources need to be di...

A process for the review of significant trade in species listed in CITES Appendix II was established to address problems with the application of CITES Article IV. Article IV states that international trade in Appendix II species requires a Scientific Authority of the state of export to determine that such trade will not be detrimental to the specie...

The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is extended here to slow-fast systems in which the fast variables exhibit metastable behaviour. The key paramete...

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and functi...

A number of nonlinear models have recently been proposed for simulating soil carbon decomposition. Their predictions of soil carbon responses to fresh litter input and warming differ significantly from conventional linear models. Using both stability analysis and numerical simulations, we showed that two of those nonlinear models (a two-pool model...

A number of nonlinear models have recently been proposed for simulating soil carbon decomposition. Their predictions of soil carbon responses to fresh litter input and warming differ significantly from conventional linear models. Using both stability analysis and numerical simulations, we showed that two of those nonlinear models (a two-pool model...

The MaxEnt software package is one of the most popular tools for species distribution and environmental niche modeling, with over 1000 published applications since 2006. Its popularity is likely for two reasons: 1) MaxEnt typically outperforms other methods based on predictive accuracy and 2) the software is particularly easy to use. MaxEnt users m...

Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable t...

There is burgeoning interest in predicting road development because of the wide ranging important socioeconomic and environmental issues that roads present, including the close links between road development, deforestation and biodiversity loss. This is especially the case in developing nations, which are high in natural resources, where road devel...

Aim Human impacts on the biosphere are a matter of urgent and growing concern, with ecologists increasingly being asked to project biodiversity futures. The Intergovernmental Platform on Biodiversity and Ecosystem Services ( IPBES ) is likely to comprehensively assess such projections, yet despite being widely used and potentially critical tools fo...

Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern p...

Methods for predicting the probability and timing of a species' extinction are typically based on single species population dynamics. Assessments of extinction risk often lack effects of interspecific interactions. We study a birth and death process in which the death rate includes an effect of predation. Predation is included via a general nonline...

International trade in species that are or may be endangered by collection from the wild is regulated under the Convention on International Trade in Endangered Species of wild fauna and flora (CITES) for 176 member States (Parties). Internet commerce is a relatively new route for such trade. In 2007, the CITES Secretariat asked Parties to collect i...

Average MaxEnt predictions from 40 runs of LQ models built using the herbarium and NVS datasets when geographical sampling bias is and is not corrected. Using the MaxEnt logistic output, blue colours indicate a higher “probability of occurrence” (suitability) while the orange colours indicate lower probabilities. (TIF)

Response plots showing the relationship between predicted probability of presence and environmental variables when all other variables are held at their empirical averages. Models were fitted using LQ features trained on herbarium data (a) and NVS data (c), and models were fitted using Auto features trained on herbarium data (b) and NVS data (d). G...

The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System (the thin layer that contains and supports life) over the coming decades and centuries. However, Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differ...

Spatiotemporal chaos in the complex Ginzburg-Landau equation is known to be associated with a rapid increase in the density of defects, which are isolated points at which the solution amplitude is zero and the phase is undefined. Recently there have been significant advances in understanding the details and interactions of defects and other coheren...

The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System over the coming decades and centuries. However Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differences in their carbon cycle models. A major goal i...

Background/Question/Methods Maxent is one of the most popular species distribution modeling methods, with over 400 published applications in the just the last six years. Maxent users are confronted with a wide variety of options when fitting their models, from the multiple options and settings available in the software to which input datasets to...

The rational design of synthetic cell populations with prescribed behaviours is a long-standing goal of synthetic biology, with the potential to greatly accelerate the development of biotechnological applications in areas ranging from medical research to energy production. Achieving this goal requires well-characterized components, modular implemen...

Some grass species mount a defensive response to grazing by increasing their rate of uptake of silica from the soil and depositing it as abrasive granules in their leaves. Increased plant silica levels reduce food quality for herbivores that feed on these grasses. Here we provide empirical evidence that a principal food species of an herbivorous ro...

The absence of clear quantification of the effects of different sources of uncertainty in earth system models (ESM) makes it practically impossible to understand why different ESMs make different, and sometimes widely diverging, predictions. We tackle this directly by developing a global terrestrial carbon model within a new model engineering frame...

Human societies urgently need more accurate predictions of how the biosphere is going to change under plausible future scenarios. The current major source of uncertainty in these predictions is how the biotic components will interact with a changing climate. Unfortunately, models of the terrestrial carbon-climate feedback make widely diverging pred...

We suggest a more straightforward improvement to CITES implementation: Scientists should consider choosing CITES-listed taxa as model taxa for their research.

The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) came into effect in 1975 to protect certain species of wild fauna and flora against over-exploitation through international trade. Determining which trade is detrimental to the survival of species in the wild can be a major difficulty in the implementation o...

The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) came into effect in 1975 to protect certain species of wild fauna and flora against over-exploitation through international trade. Determining which trade is detrimental to the survival of species in the wild can be a major difficulty in the implementation o...

1. We review our ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions. 2. New molecular approaches hold potential to increase our understanding of p...