scholarly journals BDcleaner: A workflow for cleaning taxonomic and geographic errors in occurrence data archived in biodiversity databases

2020 ◽  
Vol 21 ◽  
pp. e00852 ◽  
Author(s):  
Jing Jin ◽  
Jun Yang
Keyword(s):  
Occurrence Data ◽  
Biodiversity Databases

scholarly journals Research applications of primary biodiversity databases in the digital age

2019 ◽  
Author(s):  
Joan E. Ball-Damerow ◽  
Laura Brenskelle ◽  
Narayani Barve ◽  
Pamela S. Soltis ◽  
Petra Sierwald ◽  
...  
Keyword(s):  
Data Quality ◽  
Habitat Degradation ◽  
Data Types ◽  
Species Occurrence ◽  
Online Systems ◽  
Occurrence Data ◽  
Data Compilation ◽  
Taxonomic Groups ◽  
Extinction Events ◽  
Biodiversity Databases

ABSTRACTWe are 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 and genetic barcodes. 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 world.

Species occurrence data from the Range-Wide Bull Trout eDNA Project

2017 ◽  
Author(s):  
Michael K. Young ◽  
Daniel J. Isaak ◽  
Kevin S. McKelvey ◽  
Michael K. Schwartz ◽  
Kellie J. Carim ◽  
...  
Keyword(s):  
Bull Trout ◽  
Species Occurrence ◽  
Occurrence Data

scholarly journals Metapopulation Patterns of Iberian Butterflies Revealed by Fuzzy Logic

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 392
Author(s):  
Antonio Pulido-Pastor ◽  
Ana Luz Márquez ◽  
José Carlos Guerrero ◽  
Enrique García-Barros ◽  
Raimundo Real
Keyword(s):  
Fuzzy Logic ◽  
Set Theory ◽  
Fuzzy Set Theory ◽  
Metapopulation Dynamics ◽  
Butterfly Species ◽  
Dynamics Analysis ◽  
Metapopulation Structure ◽  
Occurrence Data ◽  
Metapopulation Theory ◽  
The Cost

Metapopulation theory considers that the populations of many species are fragmented into patches connected by the migration of individuals through an interterritorial matrix. We applied fuzzy set theory and environmental favorability (F) functions to reveal the metapopulational structure of the 222 butterfly species in the Iberian Peninsula. We used the sets of contiguous grid cells with high favorability (F ≥ 0.8), to identify the favorable patches for each species. We superimposed the known occurrence data to reveal the occupied and empty favorable patches, as unoccupied patches are functional in a metapopulation dynamics analysis. We analyzed the connectivity between patches of each metapopulation by focusing on the territory of intermediate and low favorability for the species (F < 0.8). The friction that each cell opposes to the passage of individuals was computed as 1-F. We used the r.cost function of QGIS to calculate the cost of reaching each cell from a favorable patch. The inverse of the cost was computed as connectivity. Only 126 species can be considered to have a metapopulation structure. These metapopulation structures are part of the dark biodiversity of butterflies because their identification is not evident from the observation of the occurrence data but was revealed using favorability functions.

Inferring temporal patterns of preservation, origination, and extinction from taxonomic survivorship analysis

Paleobiology ◽  
2001 ◽  
Vol 27 (4) ◽  
pp. 602-630 ◽  
Author(s):  
Michael Foote
Keyword(s):  
Simulated Data ◽  
Temporal Patterns ◽  
Marine Animals ◽  
Survivorship Analysis ◽  
Occurrence Data ◽  
Apparent Variation ◽  
Stratigraphic Ranges ◽  
Extinction Events ◽  
Preliminary Application ◽  
Preservation Rate

Apparent variation in rates of origination and extinction reflects the true temporal pattern of taxonomic rates as well as the distorting effects of incomplete and variable preservation, effects that are themselves exacerbated by true variation in taxonomic rates. Here I present an approach that can undo these distortions and thus permit estimates of true taxonomic rates, while providing estimates of preservation in the process. Standard survivorship probabilities are modified to incorporate variable taxonomic rates and rates of fossil recovery. Time series of these rates are explored by numerical optimization until the set of rates that best explains the observed data is found. If internal occurrences within stratigraphic ranges are available, or if temporal patterns of fossil recovery can otherwise be assumed, these constraints can be exploited, but they are by no means necessary. In its most general form, the approach requires no data other than first and last appearances. When tested against simulated data, the method is able to recover temporal patterns in rates of origination, extinction, and preservation. With empirical data, it yields estimates of preservation rate that agree with those obtained independently by tabulating internal occurrences within stratigraphic ranges. Moreover, when empirical occurrence data are artificially degraded, the method detects the resulting gaps in sampling and corrects taxonomic rates. Preliminary application to data on Paleozoic marine animals suggests that some features of the apparent record, such as the forward smearing of true origination events and the backward smearing of true extinction events, can be detected and corrected. Other features, such as the end-Ordovician extinction, may be fairly accurate at face value.

scholarly journals Habitat Characteristics Coincidence of Dead and Living Long-Tailed Gorals (Naemorhedus caudatus) According to Extreme Snowfall

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 997
Author(s):  
Hee-Bok Park ◽  
Sungwon Hong
Keyword(s):  
Species Distribution Modeling ◽  
Habitat Characteristics ◽  
Heavy Snowfall ◽  
Field Surveys ◽  
Location Data ◽  
Pregnant Females ◽  
Occurrence Data ◽  
Animal Remains ◽  
Extensive Field ◽  
Lower Mobility

The long-tailed goral (Naemorhedus caudatus) is a critically endangered herbivore in South Korea. Despite government efforts to recover the population through reintroduction programs, the animal remains vulnerable to heavy snowfall. From March to June 2010, 24 animals were found dead due to heavy snowfall in the Wangpi Stream basin. In this study, we hypothesized that gorals that died due to snowfall are low-status individuals that lived in the sub-optimal or non-suitable areas. Using the occurrence data from extensive field surveys from 2008 to 2010 in the Wangpi Stream and the carcass location data, we (1) defined the goral habitat characteristics and (2) compared the habitat characteristics between dead and living gorals using ensemble species distribution modeling. The results suggested that the sites where dead gorals were found were highly related to typical goral habitats. These results implied that the optimal goral habitats could become uninhabitable following heavy snowfall. Most of the dead animals were pregnant females or were young, implying that they could not escape their primary habitats due to lower mobility. Thus, when there is a climate catastrophe, the optimal goral habitats should be considered for rescue and artificial feeding.

scholarly journals Application Natura 2000 Data For The Invasive Plants Spread Prediction

2015 ◽  
Vol 46 (4) ◽  
pp. 159-166 ◽  
Author(s):  
J. Pěknicová ◽  
D. Petrus ◽  
K. Berchová-Bímová
Keyword(s):  
Environmental Factors ◽  
Invasive Plants ◽  
Species Distribution ◽  
Natura 2000 ◽  
Distribution Model ◽  
Distribution Data ◽  
Habitat Types ◽  
Distribution Models ◽  
Occurrence Data ◽  
Heracleum Mantegazzianum

AbstractThe distribution of invasive plants depends on several environmental factors, e.g. on the distance from the vector of spreading, invaded community composition, land-use, etc. The species distribution models, a research tool for invasive plants spread prediction, involve the combination of environmental factors, occurrence data, and statistical approach. For the construction of the presented distribution model, the occurrence data on invasive plants (Solidagosp.,Fallopiasp.,Robinia pseudoaccacia,andHeracleum mantegazzianum) and Natura 2000 habitat types from the Protected Landscape Area Kokořínsko have been intersected in ArcGIS and statistically analyzed. The data analysis was focused on (1) verification of the accuracy of the Natura 2000 habitat map layer, and the accordance with the habitats occupied by invasive species and (2) identification of a suitable scale of intersection between the habitat and species distribution. Data suitability was evaluated for the construction of the model on local scale. Based on the data, the invaded habitat types were described and the optimal scale grid was evaluated. The results show the suitability of Natura 2000 habitat types for modelling, however more input data (e.g. on soil types, elevation) are needed.

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