scholarly journals An Implementation Approach for the Humboldt Extension to Darwin Core

2021 ◽  
Vol 5 ◽  
Author(s):  
Peter Brenton
Keyword(s):  
Species Abundance ◽  
Practical Implementation ◽  
Sampling Effort ◽  
Darwin Core ◽  
Implementation Approach ◽  
Sampling Protocols ◽  
Field Data Collection ◽  
Event Based ◽  
Temporal Coverage ◽  
Occurrence Records

The Humboldt extension to the Darwin Core Standard Event Core has been proposed in order to provide a standard framework to capture important information about the context in which biodiversity occurrence observations and samples are recorded. This information includes methods and effort, which are critical for determining species abundance and other measures of population dynamics, as well as completeness of survey coverage. As this set of terms is being developed, we are using real-world use cases to ensure that these terms can address all known situations. We are also considering approaches to implementation of the new standard to maximise opportunities for uptake and adoption. In this presentation I provide an example of how the Humboldt extension will be implemented in the Atlas of Living Australia’s (ALA) BioCollect application. BioCollect is a cloud-based multi-project platform for all types of biodiversity and ecological field data collection and is particularly suited for capturing fully described complex protocol-based systematic surveys. For example, BioCollect supports a wide array of customised survey event-based data schemas, which can be configured for different kinds of stratified (and other) sampling protocols. These schemas can record sampling effort at the event level and event effort can be aggregated across a dataset to provide a calculated measure of effort based on the whole dataset. Such data-driven approaches to providing useful dataset-level metadata can also be applied to measures of taxonomic completeness as well as spatial and temporal coverage. In addition, BioCollect automatically parses biodiversity occurrence records from event records for harvest by the ALA. In this process, the semantic relationship between the occurrence records and their respective event records is also preserved and linkages between them enable cross-navigation for improved contextual interpretation. The BioCollect application demonstrates one approach to a practical implementation of the Humboldt extension.

scholarly journals Ecological studies of mayflies (Insecta, Ephemeroptera): Can sampling effort be reduced without losing essential taxonomic and ecological information?

2018 ◽  
Vol 48 (2) ◽  
pp. 137-145 ◽  
Author(s):  
Yulie SHIMANO ◽  
Mylena CARDOSO ◽  
Leandro JUEN
Keyword(s):  
Species Composition ◽  
Species Abundance ◽  
Taxonomic Resolution ◽  
Sampling Effort ◽  
Ecological Information ◽  
Genus Level ◽  
Level Data ◽  
Group A ◽  
Species Richness And Abundance ◽  
Laboratory Time

ABSTRACT The present study evaluated the potential for the reduction of sampling effort in studies of ephemeropteran nymphs in Brazilian Amazon streams, Pará State, Brazil, without the loss of ecological information (species composition, abundance, and richness), and the congruence of different levels of taxonomic resolution (morphospecies, genus, family and functional group). Test groups of 15, 10 and five subsamples were selected from the 20 subsamples collected per stream (40 streams sampled), and were compared in terms of their species richness and abundance (ANOVA), and composition (Procrustes). Taxonomic resolution was also analyzed in Procrustes. Species abundance (F(3, 156) = 25.426; p < 0.001) and richness (F(3, 156) = 13.866, p < 0.001) varied significantly among sample groups, while the results of the 15-S group were statistically similar, in both cases, to those of the 20-S group. A similar pattern was found for species composition. The genus-level taxonomic resolution produced results 99% similar to those found for the species-level data. The results indicate that the reduction in sampling effort from 20 to 15 subsamples per site and a genus-level taxonomic resolution would not affect the reliability of analyses significantly. A reduction of five samples per site would result in a decrease of effort in the field and the amount of material to be processed, reducing laboratory time. In addition to a reduction in the time and resources needed to identify specimens, the adoption of a genus-level taxonomic resolution could help minimize errors of under- or over-estimation in the processing of the results.

Practical Implementation of a Test of Event-Based Corpuscular Model as an Alternative to Quantum Mechanics

2013 ◽  
Vol 43 (8) ◽  
pp. 913-922 ◽  
Author(s):  
Sergey V. Polyakov ◽  
Fabrizio Piacentini ◽  
Paolo Traina ◽  
Ivo P. Degiovanni ◽  
Alan Migdall ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Practical Implementation ◽  
Event Based

scholarly journals An audit of some processing effects in aggregated occurrence records

ZooKeys ◽  
2018 ◽  
Vol 751 ◽  
pp. 129-146 ◽  
Author(s):  
Robert Mesibov
Keyword(s):  
Data Loss ◽  
Global Biodiversity Information Facility ◽  
Australian Museum ◽  
Darwin Core ◽  
Species Groups ◽  
Processing Effects ◽  
Global Biodiversity ◽  
Name Changes ◽  
Biodiversity Information ◽  
Occurrence Records

A total of ca 800,000 occurrence records from the Australian Museum (AM), Museums Victoria (MV) and the New Zealand Arthropod Collection (NZAC) were audited for changes in selected Darwin Core fields after processing by the Atlas of Living Australia (ALA; for AM and MV records) and the Global Biodiversity Information Facility (GBIF; for AM, MV and NZAC records). Formal taxon names in the genus- and species-groups were changed in 13–21% of AM and MV records, depending on dataset and aggregator. There was little agreement between the two aggregators on processed names, with names changed in two to three times as many records by one aggregator alone compared to records with names changed by both aggregators. The type status of specimen records did not change with name changes, resulting in confusion as to the name with which a type was associated. Data losses of up to 100% were found after processing in some fields, apparently due to programming errors. The taxonomic usefulness of occurrence records could be improved if aggregators included both original and the processed taxonomic data items for each record. It is recommended that end-users check original and processed records for data loss and name replacements after processing by aggregators.

scholarly journals Sampling networks of ecological interactions

2015 ◽  
Author(s):  
Pedro Jordano
Keyword(s):  
Sampling Effort ◽  
Ecological Interactions ◽  
Formal Approach ◽  
Sampling Protocols ◽  
Biodiversity Inventories ◽  
Adequate Sampling ◽  
Potential Interactions ◽  
Sizable Fraction ◽  
Interspecific Encounter

1. Sampling ecological interactions presents similar challenges, problems, potential biases, and constraints as sampling individuals and species in biodiversity inventories. Interactions are just pairwise relationships among individuals of two different species, such as those among plants and their seed dispersers in frugivory interactions or those among plants and their pollinators. Sampling interactions is a fundamental step to build robustly estimated interaction networks, yet few analyses have attempted a formal approach to their sampling protocols. 2. Robust estimates of the actual number of interactions (links) within diversified ecological networks require adequate sampling effort that needs to be explicitly gauged. Yet we still lack a sampling theory explicitly focusing on ecological interactions. 3. While the complete inventory of interactions is likely impossible, a robust characterization of its main patterns and metrics is probably realistic. We must acknowledge that a sizable fraction of the maximum number of interactions I_{max among, say, A animal species and P plant species (i.e., I_max= AP) is impossible to record due to forbidden links, i.e., life-history restrictions. Thus, the number of observed interactions I in robustly sampled networks is typically I<<I_{max}, resulting in extremely sparse interaction matrices with low connectance. 4. Reasons for forbidden links are multiple but mainly stem from spatial and temporal uncoupling, size mismatches, and intrinsically low probabilities of interspecific encounter for most potential interactions of partner species. Adequately assessing the completeness of a network of ecological interactions thus needs knowledge of the natural history details embedded, so that forbidden links can be "discounted'' when addressing sampling effort. 5. Here I provide a review and outline a conceptual framework for interaction sampling by building an explicit analogue to individuals and species sampling, thus extending diversity-monitoring approaches to the characterization of complex networks of ecological interactions. This is crucial to assess the fast-paced and devastating effects of defaunation-driven loss of key ecological interactions and the services they provide and the analogous losses related to interaction gains due to invasive species and biotic homogenization.

scholarly journals Unlocking Inventory Data Capture, Sharing and Reuse: The Humboldt Extension to Darwin Core

2021 ◽  
Vol 5 ◽  
Author(s):  
Yanina Sica ◽  
Paula Zermoglio
Keyword(s):  
Relevant Information ◽  
Task Group ◽  
Quality Data ◽  
Systematic Sampling ◽  
Sampling Effort ◽  
Inventory Data ◽  
Biodiversity Data ◽  
Darwin Core ◽  
Rich Data ◽  
Key Aspects

Biodiversity inventories, i.e., recording multiple species at a specific place and time, are routinely performed and offer high-quality data for characterizing biodiversity and its change. Digitization, sharing and reuse of incidental point records (i.e., records that are not readily associated with systematic sampling or monitoring, typically museum specimens and many observations from citizen science projects) has been the focus for many years in the biodiversity data community. Only more recently, attention has been directed towards mobilizing data from both new and longstanding inventories and monitoring efforts. These kinds of studies provide very rich data that can enable inferences about species absence, but their reliability depends on the methodology implemented, the survey effort and completeness. The information about these elements has often been regarded as metadata and captured in an unstructured manner, thus making their full use very challenging. Unlocking and integrating inventory data requires data standards that can facilitate capture and sharing of data with the appropriate depth. The Darwin Core standard (Wieczorek et al. 2012) currently enables reporting some of the information contained in inventories, particularly using Darwin Core Event terms such as samplingProtocol, sampleSizeValue, sampleSizeUnit, samplingEffort. However, it is limited in its ability to accommodate spatial, temporal, and taxonomic scopes, and other key aspects of the inventory sampling process, such as direct or inferred measures of sampling effort and completeness. The lack of a standardized way to share inventory data has hindered their mobilization, integration, and broad reuse. In an effort to overcome these limitations, a framework was developed to standardize inventory data reporting: Humboldt Core (Guralnick et al. 2018). Humboldt Core identified three types of inventories (single, elementary, and summary inventories) and proposed a series of terms to report their content. These terms were organized in six categories: dataset and identification; geospatial and habitat scope; temporal scope; taxonomic scope; methodology description; and completeness and effort. While originally planned as a new TDWG standard and being currently implemented in Map of Life (https://mol.org/humboldtcore/), ratification was not pursued at the time, thus limiting broader community adoption. In 2021 the TDWG Humboldt Core Task Group was established to review how to best integrate the terms proposed in the original publication with existing standards and implementation schemas. The first goal of the task group was to determine whether a new, separate standard was needed or if an extension to Darwin Core could accommodate the terms necessary to describe the relevant information elements. Since the different types of inventories can be thought of as Events with different nesting levels (events within events, e.g., plots within sites), and after an initial mapping to existing Darwin Core terms, it was deemed appropriate to start from a Darwin Core Event Core and build an extension to include Humboldt Core terms. The task group members are currently revising all original Humboldt Core terms, reformulating definitions, comments, and examples, and discarding or adding new terms where needed. We are also gathering real datasets to test the use of the extension once an initial list of revised terms is ready, before undergoing a public review period as established by the TDWG process. Through the ratification of Humboldt Core as a TDWG extension, we expect to provide the community with a solution to share and use inventory data, which improves biodiversity data discoverability, interoperability and reuse while lowering the reporting burden at different levels (data collection, integration and sharing).

scholarly journals Disentangling metacommunity processes using multiple metrics in space and time

2020 ◽  
Author(s):  
Laura Melissa Guzman ◽  
Patrick L. Thompson ◽  
Duarte S Viana ◽  
Bram Vanschoenwinkel ◽  
Zsófia Horváth ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Dynamics ◽  
Variation Partitioning ◽  
Species Abundance ◽  
Emergent Properties ◽  
Sampling Effort ◽  
Summary Statistics ◽  
Space And Time ◽  
Metacommunity Dynamics ◽  
Analytical Approaches

AbstractMetacommunity ecology has focused on using observational and analytical approaches to disentangle the role of critical assembly processes, such as dispersal limitation and environmental filtering. Many methods have been proposed for this purpose, most notably multivariate analyses of species abundance and its association with variation in spatial and environmental conditions. These approaches tend to focus on few emergent properties of metacommunities and have largely ignored temporal community dynamics. By doing so, these are limited in their ability to differentiate metacommunity dynamics. Here, we develop a Virtual ecologist’ approach to evaluate critical metacommunity assembly processes based on a number of summary statistics of community structure across space and time. Specifically, we first simulate metacommunities emphasizing three main processes that underlie metacommunity dynamics (density-independent responses to abiotic conditions, density-dependent biotic interactions, and dispersal). We then calculate a number of commonly used summary statistics of community structure in space and time, and use random forests to evaluate their utility for understanding the strength of these three processes. We found that: (i) time series are necessary to disentangle metacommunity processes, (ii) each of the three studied processes is distinguished with different descriptors, (iii) each summary statistic is differently sensitive to temporal and spatial sampling effort. Some of the most useful statistics include the coefficient of variation of abundances through time and metrics that incorporate variation in the relative abundances (evenness) of species. Surprisingly, we found that when we only used a single snapshot of community variation in space, the most commonly used approaches based on variation partitioning were largely uninformative regarding assembly processes, particularly, variation in dispersal. We conclude that a combination of methods and summary statistics will be necessary to understand the processes that underlie metacommunity assembly through space and time.

scholarly journals Does the size of the butterfly enhance detection? Factors influencing butterfly detection in species inventory surveys

2021 ◽  
Vol 13 (3) ◽  
pp. 17950-17962
Author(s):  
Anju Velayudhan ◽  
Mohanarangan Ashokkumar ◽  
George Chandy ◽  
Biju Sreedharan
Keyword(s):  
Multiple Regression ◽  
Linear Relation ◽  
Species Abundance ◽  
Abundance Estimation ◽  
Sampling Effort ◽  
Butterfly Species ◽  
Wildlife Sanctuary ◽  
Species Inventory ◽  
Factors Influencing

Butterfly species’ abundance and factors influencing butterfly detection in Chimmony Wildlife Sanctuary, Kerala was studied from April to June 2018.  The survey was carried out on 15 tracks of 2-km lengths surveyed two times resulting in the sampling effort of 60km.  A total of 141 species of butterflies belonging to two orders, six families and 103 genera were observed during the study, of which 15 species were recorded as endemic.  The majority of butterfly species belonged to the families Nymphalidae and Lycanidae.  The size of butterflies varies significantly among families with the largest butterflies recorded in Papilionidae and Nymphalidae and the smallest butterflies from Hesperidae and Lycanidae.  The factors that determine butterfly detection during the count was determined using multiple regression.  The number of detections had a linear relation with abundance, size, and activities of the butterflies.  The model was highly significant and explained 86.9% of the variation in the detection of butterflies (F=407.8; df=3; p<0.000).  Abundance had a primary influence on detection followed by the size and activities of the butterflies.  Further studies on relative detectability of different species of butterflies in the diversity and abundance estimation would help in refining methods of assessment of butterflies.

scholarly journals Scaling of species distribution explains the vast potential marine prokaryote diversity

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Victor M. Eguíluz ◽  
Guillem Salazar ◽  
Juan Fernández-Gracia ◽  
John K. Pearman ◽  
Josep M. Gasol ◽  
...  
Keyword(s):  
Red Sea ◽  
Power Law ◽  
Species Distribution ◽  
Species Abundance ◽  
Global Ocean ◽  
Sampling Effort ◽  
Power Law Distribution ◽  
Rarefaction Curves ◽  
The Earth ◽  
Repeated Sampling

AbstractGlobal ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.

Optimising design and effort for environmental surveys using dung beetles (Coleoptera: Scarabaeidae)

2016 ◽  
Vol 149 (2) ◽  
pp. 214-226 ◽  
Author(s):  
Claudia Tocco ◽  
Danielle E.A. Quinn ◽  
John M. Midgley ◽  
Martin H. Villet
Keyword(s):  
Sampling Method ◽  
Ground Level ◽  
Dung Beetle ◽  
Pitfall Trap ◽  
Dung Beetles ◽  
Sampling Effort ◽  
Eastern Cape ◽  
Trap Design ◽  
Sampling Protocols ◽  
By Catch

AbstractIn biological monitoring, deploying an effective standardised quantitative sampling method, optimised by trap design and sampling effort, is an essential consideration. To exemplify this using dung beetle (Coleoptera: Scarabaeidae: Scarabaeinae and Aphodiinae) communities, three pitfall trap designs (un-baited (TN), baited at ground level (flat trap, TF), and baited above the trap (hanging trap, TH)), employed with varying levels of sampling effort (number of traps=1, 2, 3 … 10; number of days=1, 2, 3), were evaluated for sampling completeness and efficiency in the Eastern Cape, South Africa. Modelling and resampling simulation approaches were used to suggest optimal sampling protocols across environmentally diverse sites. Overall, TF recovered the greatest abundance and species richness of dung beetles, but behavioural guilds showed conflicting trends: endocoprids preferred TH while paracoprids and telocoprids preferred TF. Resampling simulation of trap type and the two components of sampling effort suggested that six TF traps left for three days was most efficient in obtaining a representative sample and allowed differentiation between trap types, allowing the improved efficiency to be recognised. The effect of trap type on non-target specimens, particularly ants, was also investigated. TF and TH caught almost no by-catch, which is ethically desirable.

An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii)

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Jarrett D. Phillips ◽  
Rodger A. Gwiazdowski ◽  
Daniel Ashlock ◽  
Robert Hanner
Keyword(s):  
Fundamental Problem ◽  
Dna Barcode ◽  
Haplotype Diversity ◽  
Species Abundance ◽  
Small Sample ◽  
Sampling Effort ◽  
Dna Barcodes ◽  
Sample Sizes ◽  
Sample Number ◽  
Starting Point

AbstractEstimating appropriate sample sizes to measure species abundance and richness is a fundamental problem for most biodiversity research. In this study, we explore a method to measure sampling sufficiency based on haplotype diversity in the ray-finned fishes (Animalia: Chordata: Actinopterygii). To do this, we use linear regression and hypothesis testing methods on haplotype accumulation curves from DNA barcodes for 18 species of fishes, in the statistics platform R. We use a simple mathematical model to estimate sampling sufficiency from a sample-number based prediction of intraspecific haplotype diversity, given an assumption of equal haplotype frequencies. Our model finds that haplotype diversity for most of the 18 fish species remains largely unsampled, and this appears to be a result of small sample sizes. Lastly, we discuss how our overly simple model may be a useful starting point to develop future estimators for intraspecific sampling sufficiency in studies using DNA barcodes.

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