Robert P. Guralnick

Locating Pleistocene refugia: Comparing phylogeographic and ecological niche model predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.

Darwin Core: an evolving community-developed biodiversity data standard.

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.

Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform todays portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.

Biodiversity informatics

MOTIVATION Data about biodiversity have been scattered in different formats in natural history collections, survey reports and the literature. A central challenge for the biodiversity informatics community is to provide the means to share and rapidly synthesize these data and the knowledge they provide us to build an easily accessible, unified global map of biodiversity. Such a map would provide raw and summary data and information on biodiversity and its change across the world at multiple scales. RESULTS We discuss a series of steps required to create a unified global map of biodiversity. These steps include: building biodiversity repositories; creating scalable species distribution maps; creating flexible, user-programmable pipelines which enable biodiversity assessment; and integrating phylogenetic approaches into biodiversity assessment. We show two case studies that combine phyloinformatic and biodiversity informatic approaches to document large scale biodiversity patterns. The first case study uses data available from the Barcode of Life initiative in order to make species conservation assessment of North American birds taking into account evolutionary uniqueness. The second case study uses full genomes of influenza A available from Genbank to provide an auto-updating documentation of the evolution and geographic spread of these viruses. AVAILABILITY Both the website for tracking evolution and spread of influenza A and the website for applying phyloinformatics analysis to Barcode of Life data are available as outcomes of case studies (http://biodiversity.colorado.edu).

Evolutionary informatics: unifying knowledge about the diversity of life

The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwins ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.

Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity

The time is ripe for a comprehensive mission to explore and document Earths species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.

Global priorities for an effective information basis of biodiversity distributions

Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs.

Monitoring plant functional diversity from space

The world’s ecosystems are losing biodiversity fast. A satellite mission designed to track changes in plant functional diversity around the globe could deepen our understanding of the pace and consequences of this change and how to manage it.

VertNet: A New Model for Biodiversity Data Sharing

Responding to the urgent need to make biodiversity records broadly accessible, the natural history community turned to “the cloud.”

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.