Data integration enables global biodiversity synthesis

Heberling, J. Mason; Miller, Joe; Noesgaard, Daniel; Weingart, Scott; Schigel, Dmitry

doi:10.1073/pnas.2018093118

Cited by 186 publications

(175 citation statements)

References 60 publications

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“…Large-scale meta-analyses offer a promising strategy to understand the broad-scale effects of geography, geology, and climate change on species distributions (Guralnick & Hill 2009) and hold immense potential for insight (Dawson 2014;Heberling et al 2021). However, the considerable variation in study design and statistical analyses used across studies render meta-analysis in population genetics and phylogeography difficult (Garrick et al 2015).…”

Section: Introductionmentioning

confidence: 99%

phylogatR: Phylogeographic data aggregation and repurposing

Pelletier

Parsons

Decker

et al. 2021

Preprint

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Patterns of genetic diversity within species contain information about the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyze sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR, large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalyzed and increase accessibility to big data for research labs and classroom instructors with limited computational expertise and resources.

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Section: Introductionmentioning

confidence: 99%

phylogatR: Phylogeographic data aggregation and repurposing

Pelletier

Parsons

Decker

et al. 2021

Preprint

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“…In the past, researchers had to visit herbaria in person to examine large numbers of herbarium specimens covering broad regions. Now, tens of millions of herbarium specimens, collected from all around the world, have been imaged and are available online (Blagoderov et al ., 2012; Soltis, 2017), including through the Global Biodiversity Information Facility (Heberling et al ., 2021). This facilitates the combining of detailed observations and experiments from botanical gardens with the broad geographical perspectives supplied by herbarium specimens collected across regions, continents, and the world.…”

Section: New Methods and Resourcesmentioning

confidence: 99%

The growing and vital role of botanical gardens in climate change research

et al. 2021

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Botanical gardens make unique contributions to climate change research, conservation, and public engagement. They host unique resources, including diverse collections of plant species growing in natural conditions, historical records, and expert staff, and attract large numbers of visitors and volunteers. Networks of botanical gardens spanning biomes and continents can expand the value of these resources. Over the past decade, research at botanical gardens has advanced our understanding of climate change impacts on plant phenology, physiology, anatomy, and conservation. For example, researchers have utilized botanical garden networks to assess anatomical and functional traits associated with phenological responses to climate change. New methods have enhanced the pace and impact of this research, including phylogenetic and comparative methods, and online databases of herbarium specimens and photographs that allow studies to expand geographically, temporally, and taxonomically in scope. Botanical gardens have grown their community and citizen science programs, informing the public about climate change and monitoring plants more intensively than is possible with garden staff alone. Despite these advances, botanical gardens are still underutilized in climate change research. To address this, we review recent progress and describe promising future directions for research and public engagement at botanical gardens.

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“…Finally, aside from research applications, a positive future trend is a broadening of global participation in biodiversity research, shifting the main centers of impactful publications away from the Global North. Freely available data are increasingly enabling high impact research in the biodiversity field (Heberling et al, 2021), increasing access for scientists from countries or institutions with fewer financial resources and for whom generating new large data sets is not always feasible. Broadening access to data repositories is one necessary step (though insufficient in isolation) in the path to decolonize biodiversity science, which had its origins in colonialist practices that are still reflected in the current dynamics of the field (Das and Lowe, 2018; Eichhorn et al, 2020).…”

Section: The Future Of Plant Biodiversity Datamentioning

confidence: 99%

“…Aside from phylodiversity, spatial plant data have seen many other applications (for details, see Heberling et al, 2019Heberling et al, , 2021). As an excellent example of taking new approaches to old ideas (below), researchers have applied quantitative ordination and network-based approaches to delimiting phytogeographic regions for applications in biogeography and conservation (González-Orozco et al, 2014;Vilhena and Antonelli, 2015), a revival of the classical ideas of Takhtajan, Croizat, and other early biogeographers.…”

Section: Toward a Map Of Lifementioning

confidence: 99%

Biodiversity at the global scale: the synthesis continues

Folk

Siniscalchi

2021

American J of Botany

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Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever‐widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad‐scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.

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Data integration enables global biodiversity synthesis

Cited by 186 publications

References 60 publications

phylogatR: Phylogeographic data aggregation and repurposing

phylogatR: Phylogeographic data aggregation and repurposing

The growing and vital role of botanical gardens in climate change research

Biodiversity at the global scale: the synthesis continues

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