Taxonomic Impediments & Species Discovery

Taxonomic Impediment

• Knowledge gaps in a taxonomic system are a taxonomic impediment.
• Inability to identify species is caused by:
  • Inadequate taxonomic guides that are rare, only available for a few taxonomic groups and geographic areas, and made for taxonomists and not non-taxonomists.
  • Inaccessible taxonomic information caused by language barriers, specimen locations in industrialized nations, biodiversity-rich but economically poorer countries, and geographical disparities of taxonomists.
  • Concerns about experts from foreign countries taking resources (biopiracy).
  • A high species count, low taxonomist count, and limited resources are contributing factors.

Species Discovery

• New species are primarily derived from field work in emergent countries instead of being found in museum collections of developed countries.
• Technological and methodological restrictions on data analysis and publication norms hinder rapid species delineation and description.
• Most new species are rare and represented by singletons when first collected, causing taxonomists to wait for more specimens before formal description.

Information for Taxonomists

• The following information is helpful for taxonomists:
  • Taxonomic, morphological, geographical, and ecological information.
  • Genetic information (DNA sequences, DNA barcodes, genomic data)
  • Life history/natural history information (reproductive behavior, life cycle, population size, fecundity)
  • Behavioral information (mating, nesting, foraging, territorial behavior)
• Behavioral and ecological information often overlap.
• Geographical/spatial information includes habitat (ecosystem) data.

Obtaining Habitat Information

• Habitat information may be obtained through basic observation, dynamic observation, interactions with other species, and movements.
• Genetic information can be derived from a dead body cross-section.
• Behavioral information is equal to ecological information.
• Interactions with other species include data about predators, hunting, and mating.
• Morphological information can be learned from a dead body or during a life cycle.
• Tricky cases are from species that outlive the researcher, or display variations in behavior between juveniles and adults
• Life history information includes reproductive behavior.
• Impact of species on the environment can be observed through defecation habits, hunting/feeding behavior, and food.

Online Resources

• General species information is organized online into species pages and species records in databases.
• Species pages such as Wikipedia are global.
• There exists species records in databases such as iNaturalist that can show species range based on real data points
• Static web pages are unchanging and dynamic web interfaces as being constantly updated in species pages.

Species Databases

• iNaturalist and GBIF (Global Biodiversity Information Facility)
• BHL (Biodiversity Heritage Library) is another resource to locate species.
• National Library of Medicine also provides biological information.
• Genetic information for Sundasciurus tenuis can be found at NIH National Library of Medicine.
• Each link provided is a genetic fragment.

Biodiversity Data Mobilization

• Biodiversity data mobilization is the process of making biodiversity datasets publicly accessible and discoverable through standardized formats and online platforms, thus facilitating research, conservation, and policy development.
• Most newly collected specimens are archived in museums and herbaria (collections act as a reservoir of potential new species).
• Taxonomists will likely increasingly describe species from museum collections as species go extinct.

Reasons for Time Lag

• Shortage of specialists (taxonomists).
• Identification is easy for large organisms and hard for small ones.
• Expert skills are needed for correct identification of plants, insects, fungi and microorganisms.
• Most organisms are uncategorized or lack formal scientific names.
• An inability to identify species causes taxonomic impediment.

Factors that Influence Time Lag

• Sociological factors, such as tenured researchers having less incentive to publish, influence time lag.
• Socio-geopolitical factors, such as hyperdiverse countries having less scientific infrastructure, influence time lag.

Digitization vs. Data Mobilization

• There is a difference between digitization and data mobilization.
• Data mobilization is the overall process of moving information from the real world to the digital world.
• Digitization is a step in moving data to the digital world.
• Georeferencing involves adding GPS coordinates and mapping on a global scale, particularly useful for butterflies.
• Butterflies are essentially 2D when wings are open Digitization includes having two pictures of every specimen with data.

Mobilizing Biodiversity Data

• To be accessible, shareable, and usable for critical purposes.
• To promote conservation and research.
• To aid policy and management and sustainable development.
• Online data standards facilitates tracking species distribution such as GBIF.
• Identification of threatened species and support for ecosystem management.
• Public awareness is increased and helps to solve the taxonomic impediment.

Mobilizing Biodiversity Data

• Mobilization involves digitization.
• It also entails using online platforms for uploading data to open-access repositories.
• Incorporating data standards like Darwin Core.
• Promoting partnerships among museums, researchers, and citizen scientists.
• Institutions publish datasets in repositories, leveraging tools for georeferencing and quality control.

Biodiversity Data Standards

• Structure/format data fields and ensure consistency.
• Agreed-upon protocols/frameworks such as the Darwin Core must be in place.
• They also enable interoperability across datasets, making aggregation, analysis, and sharing feasible.
• Interoperability is when data collected by different organizations or individuals can be combined and analyzed seamlessly.

Biological Data Standards

• Consistency.
• To ensure compatibility and streamline data integration.
• To ensure data is interpretable across different platforms.
• Interoperability allows different systems to exchange and analyze data without technical issues.
• Facilitate data sharing between organizations and countries.
• Support tool development and reduce errors
• Quality assurance, accuracy and reliability

Reproducibility

• Enhance reproducibility in studies like meta-analyses or large-scale conservation planning.
• Allows repeating studies and verify results.
• The importance of digitizing type specimens.
• Importance of type specimen: Generally difficult on a whole to do scanning.
• Takes time and resources to digitize.
• The next questions involve are which and who?
• Which species to prioritize.
• Who is going to do and fund it?
• Digitizing an entire collection takes way more time and resources.
• Hence the need for collaboration with computer scientists etc.

Darwin Core Standards

• Darwin Core's can be found at https://dwc.tdwg.org/terms/#dwc:basisOfRecord
• A TDWG-developed set of terms/specifications for sharing species occurrence data.
• Examples include scientificName, decimalLatitude, eventDate
• Standardizes how biodiversity data is recorded, collected, shared, and exchanged.
• Facilitates exchange through platforms like GBIF and is widely used for datasets like occurrence records and specimen information.

Metadata

• Metadata provides information about other data
• Authorship, methodology, and geographic scope of data.
• Contextual data.
• How/when the data was collected as well as who collected it.
• Ensures transparency, reproducibility, and proper citation.
• It also helps users assess data quality and relevance, aid understanding and interpretability.

GBIF

• GBIF stands for Global Biodiversity Information Facility.
• It is an international network aggregating open-access biodiversity data.
• GBIF provides (free and open) access to a lot of biodiversity data collected from around the world.
• GBIF allows researchers, policymakers, and public to use for various purposes.
• Occurrence records from museums, surveys, and citizen science.
• They support research, policy, and conservation.

Occurrence Dataset

• Collection of records documenting a species' presence at specific times and locations.
• Each occurrence includes data like species name, coordinates (latitude & longitude), collector, and date of observation, and additional metadata to identify context of observation.

Natural History Collections

• Serves as biodiversity data sources/repositories.
• Contain physical specimens (vouchers) with associated data, digital records, and photographs.
• Digitized collections help track species shifts, validate identifications, and inform conservation, often serving as authoritative references.
• Provides historical baselines for biodiversity; providing invaluable reference material for taxonomists, conservationists, and researchers.
• Source of primary data for studies on species distribution, morphology, and genetic diversity.

Georeferencing

• Georeferencing specimen locality information converts textual locality descriptions into precise coordinates.
• (+) enables spatial analysis (on environmental data), modelling habitats
• (+) understand species distribution; mapping species ranges; mapping biodiversity patterns
• (+) assessing climate impacts

Observations

• Allow researchers to precisely locate where species have been observed, which is essential for ecological studies and conservation efforts.
• EX: understanding life cycle and behavior and assessing whether or not, an area should be repopulated

Museum Label Transcription Complexities

• Accuracy of transcription can be affected by illegible handwriting/faded text/ambiguous terms.
• May require interpretation of the labels and locality descriptions that were verbatim (rivers etc)
• Taxonomic changes in species names leads to missing data.
• Consistency is needed because of varied formats of unit.
• Validation ensures correct data entry and preserving original context.
• Historic and scientific context of label can influence interpretation of data.
• Scientific accuracy must be ensured when checking all scientific names (taxa/ family).
• It is vital to confirm compliance with DarwinCore standards, includes all required fields?, and data cleaning efficacy.
• Data must be organized.

Museum Visit w7c1

• Original specimen.
• Used for wet type specimens.
• Must go back to check to if the specimen is this species.
• Red means holotype, yellow is paratype, orange is replacement of type specimen that is lost
• Is lost and a new most representative type neotype is found
• Types of chips are placed inside to tell ethanol concentration and to show how much it's been diluted
• Maggots that survive in 50–60% ethanol are an issue.
• Jars should have internal seals etc.
• Need to top up ethanol/inert gas after a while depending on specimens in inert gases.
• Old preservatives like beeswax and other organic materials have been improved.
• Must innovate to supply and specimens last longer.