BioGeomancer: Automated Georeferencing to Map the World's Biodiversity Data

The BioGeomancer Project provides a toolkit to georeference data and specimens collected for natural history collections, a crucial task if the potential of these specimens is to be fully realized

The Big Questions For Biodiversity Informatics

This is the publisher's version, which the author has permission to share. The original version may be found at http://dx.doi.org/10.1080/14772001003739369Science is a sequence of generating new ideas, detailed explorations, incorporation of the results into a toolbox for understanding data, and turning them into useful knowledge. One recent development has been large-scale, computer-aided management of biodiversity information. This emerging field of biodiversity informatics has been growing quickly, but without overarching scientific questions to guide its development; the result has been developments that have no connection to genuine insight and forward progress. We outline what biodiversity informatics should be, a link between diverse dimensions of organismal biology – genomics, phylogenetics, taxonomy, distributional biology, ecology, interactions, and conservation status – and describe the science progress that would result. These steps will enable a transition from ‘gee-whiz’ to fundamental science infrastructure

Grasshopper Community Response to Climatic Change: Variation Along an Elevational Gradient

The impacts of climate change on phenological responses of species and communities are well-documented; however, many such studies are correlational and so less effective at assessing the causal links between changes in climate and changes in phenology. Using grasshopper communities found along an elevational gradient, we present an ideal system along the Front Range of Colorado USA that provides a mechanistic link between climate and phenology.This study utilizes past (1959-1960) and present (2006-2008) surveys of grasshopper communities and daily temperature records to quantify the relationship between amount and timing of warming across years and elevations, and grasshopper timing to adulthood. Grasshopper communities were surveyed at four sites, Chautauqua Mesa (1752 m), A1 (2195 m), B1 (2591 m), and C1 (3048 m), located in prairie, lower montane, upper montane, and subalpine life zones, respectively. Changes to earlier first appearance of adults depended on the degree to which a site warmed. The lowest site showed little warming and little phenological advancement. The next highest site (A1) warmed a small, but significant, amount and grasshopper species there showed inconsistent phenological advancements. The two highest sites warmed the most, and at these sites grasshoppers showed significant phenological advancements. At these sites, late-developing species showed the greatest advancements, a pattern that correlated with an increase in rate of late-season warming. The number of growing degree days (GDDs) associated with the time to adulthood for a species was unchanged across the past and present surveys, suggesting that phenological advancement depended on when a set number of GDDs is reached during a season.Our analyses provide clear evidence that variation in amount and timing of warming over the growing season explains the vast majority of phenological variation in this system. Our results move past simple correlation and provide a stronger process-oriented and predictive framework for understanding community level phenological responses to climate change

Towards global data products of Essential Biodiversity Variables on species traits

Essential Biodiversity Variables (EBVs) allow observation and reporting of global biodiversity change, but a detailed framework for the empirical derivation of specific EBVs has yet to be developed. Here, we re-examine and refine the previous candidate set of species traits EBVs and show how traits related to phenology, morphology, reproduction, physiology and movement can contribute to EBV operationalization. The selected EBVs express intra-specific trait variation and allow monitoring of how organisms respond to global change. We evaluate the societal relevance of species traits EBVs for policy targets and demonstrate how open, interoperable and machine-readable trait data enable the building of EBV data products. We outline collection methods, meta(data) standardization, reproducible workflows, semantic tools and licence requirements for producing species traits EBVs. An operationalization is critical for assessing progress towards biodiversity conservation and sustainable development goals and has wide implications for data-intensive science in ecology, biogeography, conservation and Earth observation

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided

OBIS-USA: A Data-Sharing Legacy of the Census of Marine Life

This is the publisher's version, also available electronically from http://www.tos.org/oceanography.The United States Geological Survey's Biological Informatics Program hosts OBIS-USA, the US node of the Ocean Biogeographic Information System (OBIS). OBIS-USA gathers, coordinates, applies standard formats to, and makes widely available data on biological collections in marine waters of the United States and other areas where US investigators have collected data and, in some instances, specimens. OBIS-USA delivers its data to OBIS international, which then delivers its data to the Global Biodiversity Information Facility (GBIF) and other Web portals for marine biodiversity data. OBIS-USA currently has 145 data sets from 36 participants, representing over 6.5 million occurrence records of over 83,000 taxa from more than 888,000 locations. OBIS-USA, a legacy of the decade-long (2001–2010) international collaborative Census of Marine Life enterprise, continues to add data, including those from ongoing Census projects. Among the many challenges in creating OBIS, including OBIS-USA, were developing a community of trust and shared value among data providers, and demonstrating to providers the value of making their data accessible to others. Challenges also posed by the diversity of data sets relevant to marine biodiversity stored on thousands of computers, in a variety of formats, not all widely accessible, have been met in OBIS-USA by implementing a uniform standard and publishing platform that is easily accessible to a broad range of users

Commonly collected thermal performance data can inform species distributions in a data‑limited invader

Predicting potential distributions of species in new areas is challenging. Physiological data can improve interpretation of predicted distributions and can be used in directed distribution models. Nonnative species provide useful case studies. Panther chameleons (Furcifer pardalis) are native to Madagascar and have established populations in Florida, USA, but standard correlative distribution modeling predicts no suitable habitat for F. pardalis there. We evaluated commonly collected thermal traits– thermal performance, tolerance, and preference—of F. pardalis and the acclimatization potential of these traits during exposure to naturally-occurring environmental conditions in North Central Florida. Though we observed temperature-dependent thermal performance, chameleons maintained similar thermal limits, performance, and preferences across seasons, despite long-term exposure to cool temperatures. Using the physiological data collected, we developed distribution models that varied in restriction: time-dependent exposure near and below critical thermal minima, predicted activity windows, and predicted performance thresholds. Our application of commonly collected physiological data improved interpretations on potential distributions of F. pardalis, compared with correlative distribution modeling approaches that predicted no suitable area in Florida. These straightforward approaches can be applied to other species with existing physiological data or after brief experiments on a limited number of individuals, as demonstrated here

Colour scales with climate in North American ratsnakes: a test of the thermal melanism hypothesis using community science images

Animal colour is a complex trait shaped by multiple selection pressures that can vary across geography. The thermal melanism hypothesis predicts that darker coloration is beneficial to animals in colder regions because it allows for more rapid solar absorption. Here, we use community science images of three closely related species of North American ratsnakes (genus Pantherophis) to examine if climate predicts colour variation across range-wide scales. We predicted that darker individuals are found in colder regions and higher elevations, in accordance with the thermal melanism hypothesis. Using an unprecedented dataset of over 8000 images, we found strong support for temperature as a key predictor of darker colour, supporting thermal melanism. We also found that elevation and precipitation are predictive of colour, but the direction and magnitude of these effects were more variable across species. Our study is the first to quantify colour variation in Pantherophis ratsnakes, highlighting the value of community science images for studying range-wide colour variation