Brad Boyle

University of Arizona | UA · Department of Ecology and Evolutionary Biology

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here, we conduct a literature review estimating temporal trends in code sharing in ecology and evolution publications since 2010, and test for an inf...

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here we conduct a literature review examining temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influ...

Governments and society increasingly are demanding that industrial projects result in a net positive impact (NPI) on biodiversity. Impacts are commonly measured in terms of losses and gains of area and quality of vegetation, where quality refers to how closely a site matches the condition of native vegetation in its undisturbed state. Existing vege...

Biologists increasingly rely on computer code, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here we conduct a literature review examining temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation r...

Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This...

Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This...

Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This...

Aim Addressing global environmental challenges requires access to biodiversity data across wide spatial, temporal and taxonomic scales. Availability of such data has increased exponentially recently with the proliferation of biodiversity databases. However, heterogeneous coverage, protocols, and standards have hampered integration among these datab...

To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed...

Biodiversity contributes to the ecological and climatic stability of the Amazon Basin1,2, but is increasingly threatened by deforestation and fire3,4. Here we quantify these impacts over the past two decades using remote-sensing estimates of fire and deforestation and comprehensive range estimates of 11,514 plant species and 3,079 vertebrate specie...

Aim: Addressing global environmental challenges requires access to biodiversity data across wide spatial, temporal and biological scales. Recent decades have witnessed an exponential increase of biodiversity information aggregated by biodiversity databases (hereafter ‘databases’). However, heterogeneous coverage, protocols, and standards of databas...

paragraph To meet the ambitious objectives of biodiversity and climate conventions, countries and the international community require clarity on how these objectives can be operationalized spatially, and multiple targets be pursued concurrently ¹ . To support governments and political conventions, spatial guidance is needed to identify which areas...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Limiting climate change to less than 2°C is the focus of international policy under the climate convention (UNFCCC), and is essential to preventing extinctions, a focus of the Convention on Biological Diversity (CBD). The post-2020 biodiversity framework drafted by the CBD proposes conserving 30% of both land and oceans by 2030. However, the combin...

Limiting climate change to less than 2°C is the focus of international policy under the climate convention (UNFCCC), and is essential to preventing extinctions, a focus of the Convention on Biological Diversity (CBD). The post‐2020 biodiversity framework drafted by the CBD proposes conserving 30% of both land and oceans by 2030. However, the combin...

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress t...

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36...

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant species observation data in order to quantify the fraction of Earth’s extant land plant biodiversity...

Synthesising trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Despite the well-recognised importance of traits for addressing ecological and evolutionary questions, trait-based approaches still struggle with several basic data requirements to deliver openly accessible, reproducible, and tr...

Questions: Vegetation-plot records provide information on presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers, and thus, are rarely accessible at continental or global scales. Here we present the sPlot database,...

Ecosystem processes are driven by both environmental variables and the attributes of component species. The extent to which these effects are independent and/or dependent upon each other has remained unclear. We assess the extent to which climate affects net primary productivity (NPP) both directly and indirectly via its effect on plant size and le...

Much ecological research aims to explain how climate impacts biodiversity and ecosystem-level processes through functional traits that link environment with individual performance. However, the specific climatic drivers of functional diversity across space and time remain unclear due largely to limitations in the availability of paired trait and cl...

The concept of the biome has a long history dating back to Carl Ludwig Willdenow and Alexander von Humboldt. However, while the association between climate and the structure and diversity of vegetation has a long history, scientists have only recently begun to develop a more synthetic understanding of biomes based on the evolution of plant diversit...

The prediction of vegetation responses to climate requires a knowledge of how climate‐sensitive plant traits mediate not only the responses of individual plants, but also shifts in the species and functional compositions of whole communities. The emission of isoprene gas – a trait shared by one‐third of tree species – is known to protect leaf bioch...

Aim Despite several recent efforts to map plant traits and to identify their climatic drivers, there are still major gaps. Global trait patterns for major functional groups, in particular, the differences between woody and herbaceous plants, have yet to be identified. Here, we take advantage of big data efforts to compile plant species occurrence a...

Significance Identifying and explaining regional differences in tropical forest dynamics, structure, diversity, and composition are critical for anticipating region-specific responses to global environmental change. Floristic classifications are of fundamental importance for these efforts. Here we provide a global tropical forest classification tha...

There is an urgent need for large‐scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling human‐biodiversity interactions and global change dynamics such as food and energy sec...

This dataset provides growth form classifications for 67,413 vascular plant species from North, Central, and South America. The data used to determine growth form were compiled from five major integrated sources and two original publications: the Botanical Information and Ecology Network (BIEN), the Plant Trait Database (TRY), the SALVIAS database,...

Advances in both informatics and mobile technology are providing exciting new opportunities for generating, disseminating, and engaging with information in the biological sciences at unprecedented spatial scales, particularly in disentangling information on the distributions and natural history of hyperdiverse groups of organisms. We describe an ap...

During the Late Pleistocene and early Holocene 59 species of South American megafauna went extinct. Their extinction potentially triggered population declines of large-seeded tree species dispersed by the large-bodied frugivores with which they co-evolved, a theory first proposed by Janzen and Martin (1982). We tested this hypothesis using species...

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approx...

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approx...

Macro-scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as m...

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approx...

One of the key hypothesized drivers of gradients in species richness is environmental filtering, where environmental stress limits which species from a larger species pool gain membership in a local community owing to their traits. Whereas most studies focus on small-scale variation in functional traits along environmental gradient, the effect of l...

Significance We present a conceptual framework for testing theories for the latitudinal gradient of species richness in terms of variation in functional diversity at the alpha, beta, and gamma scales. We compared ecological community theory with large-scale observational data of tree species richness and functional diversity. We found that the patt...

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ~ 85 000 plant species across the New World. We assess promin...

Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack...

Example R script which uses the TNRS API to correct names on a phylogeny.

Taxonomic names used to compare performance of TNRS, Plantminer and GNResolver.

List of submitted names, expected targets, and descriptions of errors for names which failed matching by one or more name resolution applications.

Premise of the study: Leaf area is a key trait that links plant form, function, and environment. Measures of leaf area can be biased because leaf area is often estimated from dried or fossilized specimens that have shrunk by an unknown amount. We tested the common assumption that this shrinkage is negligible. Methods: We measured shrinkage by co...

Aim In recent years evidence has accumulated that plant species are differentially sorted from regional assemblages into local assemblages along local‐scale environmental gradients on the basis of their function and abiotic filtering. The favourability hypothesis in biogeography proposes that in climatically difficult regions abiotic filtering shou...

Aim To evaluate the strength of evidence for hypotheses explaining the relationship between climate and species richness in forest plots. We focused on the effect of energy availability which has been hypothesized to influence species richness: (1) via the effect of productivity on the total number of individuals (the more individuals hypothesis, M...

Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites (β diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in β diversity c...

Background/Question/Methods Taxonomic error is a major impediment to integrative research in organismal biology. Misspelled, outdated, or ambiguous names are common in ecological data, and can lead to mismatched observations, erroneous conclusions, and an inability to generalize results across space and time. Even databases such as GBIF (www.gbif...

Question: Collaborative research efforts and synthetic vegetation analyses are often limited by difficulties in sharing or combining datasets. Can we facilitate these activities by means of an exchange standard for plot-based vegetation data? Methods: In 2003, the Ecoinformatics Working Group and the Council of the International Association for Veg...

Question: Collaborative research efforts and synthetic vegetation analyses are often limited by difficulties in sharing or combining datasets. Can we facilitate these activities by means of an exchange standard for plot-based vegetation data? Methods: In 2003, the Ecoinformatics Working Group and the Council of the International Association for Veg...

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that...