Research applications of primary biodiversity databases in the digital age.

Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment

Research applications of primary biodiversity databases in the digital age

Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed

23 Things Physical Samples

Physical samples are a basic element for reference, study, and experimentation in research. The 23 Things for Physical Samples aims to provide a reference overview of resources centered on the management and sharing of data on material samples. The output focuses on existing work, recent developments, recommended practices, and community initiatives. The 23 resources are related to the following categories: 1) a general introduction, 2) persistent identifiers, 3) metadata, 4) citing samples, 5) data licensing and ownership, 6) tools, 7) repositories and 8) communities of practice

Diversity and Distribution of California Dragonflies and Other Aquatic Taxa Over the Past Century

Climate and land-use change have altered and continue to affect the diversity, composition, and distribution of freshwater organisms throughout the world. This is particularly true in arid and semi-arid regions, where aquatic organisms may experience more pronounced reductions in available habitat with declines in precipitation, increases in water demand, and habitat degradation through human land-use. However, documentation of changes in taxonomic assemblages over long-time periods has been rare because of the difficulty in obtaining historical occurrence data. This dissertation used data from previously published literature, a resurvey study, museum specimens, and enthusiast sightings to document changes in the occurrence rates and distribution of freshwater organisms throughout California over the past century.Summary information regarding freshwater taxa known to occur in California did not previously exist in a central publication. I therefore conducted a review of several primary groups of stream organisms found in the Mediterranean region of California and statewide. For this work, I gathered data from a variety of literature sources and museum specimens to summarize species composition and endemism in the region, and to identify data gaps and conservation priorities for the examined groups. The remainder of this dissertation focuses largely on changes in Odonata species diversity, composition, and occurrence rates over time in California. This charismatic group was ideal for study of change over time because of their relatively low diversity, well-known taxonomy, and the existence of sufficient historical and current specimen records and more recent enthusiast sightings of odonates.I conducted a resurvey of sites originally sampled for Odonata by Clarence H. Kennedy 1914-1915. This work involved surveys of odonates at 81 sites throughout central California and northwestern Nevada, 45 of which were directly comparable to Kennedy's original sites. I found that while site-level species richness has not changed significantly, assemblages have become more homogeneous across sites. Habitat generalists have generally expanded in the extent of their distribution while habitat specialists have declined. In examining current local and regional factors influencing the occurrence of Odonata species in this region, I found that species occurrence was higher during site visits with higher degree-days, especially for highly mobile groups, including dragonflies and migratory species. The probability of presence across species was lower in highly urban sites, particularly for habitat specialists. Overall, both regional and local factors influenced the occurrence of odonates in the study with implications for conservation.A large component of this dissertation included development and analysis of a database of over 33,000 Odonata occurrence records throughout California over the past century. This database included specimen records from museums in California and large odonate collections elsewhere, as well as statewide enthusiast sightings from recent years. I noted that these unstandardized data contain biases with regards to uneven sampling effort, which must be addressed in analysis. Subsequent analyses of occurrence records before and after 1975 indicated that Odonata distribution may have generally shifted northwards with temperature warming and to lower minimum elevations in response to increased summer water-availability in low-elevation agricultural regions. Similar to results from the resurvey study, the museum specimen data indicated that highly mobile migratory species have increased while habitat specialists have declined. I concluded that a combination of sampling biases, species traits, and climate that have influenced the probability of detection of Odonata species over the last century

Diversity and Distribution of California Dragonflies and Other Aquatic Taxa Over the Past Century

Climate and land-use change have altered and continue to affect the diversity, composition, and distribution of freshwater organisms throughout the world. This is particularly true in arid and semi-arid regions, where aquatic organisms may experience more pronounced reductions in available habitat with declines in precipitation, increases in water demand, and habitat degradation through human land-use. However, documentation of changes in taxonomic assemblages over long-time periods has been rare because of the difficulty in obtaining historical occurrence data. This dissertation used data from previously published literature, a resurvey study, museum specimens, and enthusiast sightings to document changes in the occurrence rates and distribution of freshwater organisms throughout California over the past century.Summary information regarding freshwater taxa known to occur in California did not previously exist in a central publication. I therefore conducted a review of several primary groups of stream organisms found in the Mediterranean region of California and statewide. For this work, I gathered data from a variety of literature sources and museum specimens to summarize species composition and endemism in the region, and to identify data gaps and conservation priorities for the examined groups. The remainder of this dissertation focuses largely on changes in Odonata species diversity, composition, and occurrence rates over time in California. This charismatic group was ideal for study of change over time because of their relatively low diversity, well-known taxonomy, and the existence of sufficient historical and current specimen records and more recent enthusiast sightings of odonates.I conducted a resurvey of sites originally sampled for Odonata by Clarence H. Kennedy 1914-1915. This work involved surveys of odonates at 81 sites throughout central California and northwestern Nevada, 45 of which were directly comparable to Kennedy's original sites. I found that while site-level species richness has not changed significantly, assemblages have become more homogeneous across sites. Habitat generalists have generally expanded in the extent of their distribution while habitat specialists have declined. In examining current local and regional factors influencing the occurrence of Odonata species in this region, I found that species occurrence was higher during site visits with higher degree-days, especially for highly mobile groups, including dragonflies and migratory species. The probability of presence across species was lower in highly urban sites, particularly for habitat specialists. Overall, both regional and local factors influenced the occurrence of odonates in the study with implications for conservation.A large component of this dissertation included development and analysis of a database of over 33,000 Odonata occurrence records throughout California over the past century. This database included specimen records from museums in California and large odonate collections elsewhere, as well as statewide enthusiast sightings from recent years. I noted that these unstandardized data contain biases with regards to uneven sampling effort, which must be addressed in analysis. Subsequent analyses of occurrence records before and after 1975 indicated that Odonata distribution may have generally shifted northwards with temperature warming and to lower minimum elevations in response to increased summer water-availability in low-elevation agricultural regions. Similar to results from the resurvey study, the museum specimen data indicated that highly mobile migratory species have increased while habitat specialists have declined. I concluded that a combination of sampling biases, species traits, and climate that have influenced the probability of detection of Odonata species over the last century

California dragonfly and damselfly (Odonata) database: temporal and spatial distribution of species records collected over the past century

The recently completed Odonata database for California consists of specimen records from the major entomology collections of the state, large Odonata collections outside of the state, previous literature, historical and recent field surveys, and from enthusiast group observations. The database includes 32,025 total records and 19,000 unique records for 106 species of dragonflies and damselflies, with records spanning 1879–2013. Records have been geographically referenced using the point-radius method to assign coordinates and an uncertainty radius to specimen locations. In addition to describing techniques used in data acquisition, georeferencing, and quality control, we present assessments of the temporal, spatial, and taxonomic distribution of records. We use this information to identify biases in the data, and to determine changes in species prevalence, latitudinal ranges, and elevation ranges when comparing records before 1976 and after 1979. The average latitude of where records occurred increased by 78 km over these time periods. While average elevation did not change significantly, the average minimum elevation across species declined by 108 m. Odonata distribution may be generally shifting northwards as temperature warms and to lower minimum elevations in response to increased summer water availability in low-elevation agricultural regions. The unexpected decline in elevation may also be partially the result of bias in recent collections towards centers of human population, which tend to occur at lower elevations. This study emphasizes the need to address temporal, spatial, and taxonomic biases in museum and observational records in order to produce reliable conclusions from such data

California dragonfly and damselfly (Odonata) database: temporal and spatial distribution of species records collected over the past century.

The recently completed Odonata database for California consists of specimen records from the major entomology collections of the state, large Odonata collections outside of the state, previous literature, historical and recent field surveys, and from enthusiast group observations. The database includes 32,025 total records and 19,000 unique records for 106 species of dragonflies and damselflies, with records spanning 1879-2013. Records have been geographically referenced using the point-radius method to assign coordinates and an uncertainty radius to specimen locations. In addition to describing techniques used in data acquisition, georeferencing, and quality control, we present assessments of the temporal, spatial, and taxonomic distribution of records. We use this information to identify biases in the data, and to determine changes in species prevalence, latitudinal ranges, and elevation ranges when comparing records before 1976 and after 1979. The average latitude of where records occurred increased by 78 km over these time periods. While average elevation did not change significantly, the average minimum elevation across species declined by 108 m. Odonata distribution may be generally shifting northwards as temperature warms and to lower minimum elevations in response to increased summer water availability in low-elevation agricultural regions. The unexpected decline in elevation may also be partially the result of bias in recent collections towards centers of human population, which tend to occur at lower elevations. This study emphasizes the need to address temporal, spatial, and taxonomic biases in museum and observational records in order to produce reliable conclusions from such data