Biodiversity indicators using

GBIF data

Introduction to the hands-on exercise

Vânia Proença

vania.proenca@técnico.ulisboa.pt

MARETEC, IST, University of Lisbon

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Genetic

Species

Ecosystems

Individual species or taxa (i.e., species groups)

Species communities (i.e., interacting popul.)

Biodiversity indicators are measures of biodiversity. Indicators respond to drivers of change and are used to assess and monitor the state and trends of biodiversity in all its dimensions.

Trends in conservation status

Red List Index (e.g., pollinators)

Living Planet Index

Trends in invasive species

(…)

Protected Area Coverage

% forest under certified management

(…)

Species diversity & evenness

% Endemics, or rare species

Trends in similarity

% declining or increasing spcs.

(…)

Breed and cultivar diversity

Crop origin

(…)

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Cultivated species

Non-cultivated species

Support/Regulation Threats Cultural value Indicators

Biological control

Pollinators

Decomposers

Soil fertility

Nutrient cycling

etc.

Invasive sp.

Pathogens

Herbivores

etc.

Mushrooms

Medicinal plants

Charismatic sp.

etc.

Habitat specialists

Rare/threatened sp.

Lichens

etc.

Agrobiodiversity

Genetic

Species

Ecosystems

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Adapted from Hortal et al. 2007 Conservation Biology Volume 21, No. 3, 853–863; DOI: 10.1111/j.1523-1739.2007.00686.x

Extract biodiversitydata from GBIF

Check quality of records- Taxonomic accuracy- Geographic accuracy- Temporal accuracy Assess sampling effort

(survey completeness)

Identify well-sampledcells

Use in biodiversityassessment andmodelling

Discard records with errors

Revise extraction filtersand / or

add new data to GBIF

if few

or

none

Protocol to obtain reliable species community data from GBIF

Alternative: model the distribution of individual species and assemble comunities with

overlapping distribution

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Hortal et al. 2007 Conservation Biology Volume 21, No. 3, 853–863; DOI: 10.1111/j.1523-1739.2007.00686.x

Relationship between sampling effort and observed species in grid cells

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Gotelli, Nicholas J., and Robert K. Colwell. "Estimating species richness." Biological diversity: frontiers in measurement

and assessment 12 (2011): 39-54.

Species accumulation curves and rarefaction curves

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Williams, N. M., R. L. Minckley, and F. A. Silveira. 2001. Variation in native bee faunas and its implications for detecting community changes. Conservation Ecology 5(1): 7. [online] URL: http://www.consecol.org/vol5/iss1/art7/

Rarefaction curves for bee communities from different surveys around the world

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Coddington, Jonathan A., et al. "Undersampling bias: the null hypothesis for singleton species in tropical

arthropod surveys." Journal of animal ecology 78.3 (2009): 573-584.; DOI: 10.1111/j.1365-2656.2009.01525.x

Survey completeness = (observed/estimated) * 100

If completeness > 75% accept as well-surveyed

Singletons

Doubletons

Estimated

352 species

443 species

(352/443)* 100 = 79% OK!

Estimation of species richness & Assessment of survey completeness

Observed

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Bird data: 80 well-surveyed cells for 2010 in Alentejo

GBIF Search query

• Scientific name: (several bird orders)

• Basis of Record: Human Observations

• Location: Including coordinates and with

no known issues

• Month: from April to June

• Country: Portugal

• License: CC0 1.0

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Bird data: 35 well-surveyed cells for 2005 in Alentejo

GBIF Search query

• Scientific name: (several bird orders)

• Basis of Record: Human Observations

• Location: Including coordinates and with

no known issues

• Month: from April to June

• Country: Portugal

• License: CC0 1.0

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Free software packages with tools for estimating species richness from

sample data:

EstimateS (Colwell 2009): http://purl.oclc.org/estimates

EcoSim (Gotelli & Entsminger 2009): http://garyentsminger.com/ecosim/index.htm

SPADE: http://chao.stat.nthu.edu.tw/softwareCE.html

VEGAN (for R): http://cc.oulu.fi/∼jarioksa/softhelp/vegan.html

Gotelli, Nicholas J., and Robert K. Colwell. "Estimating species richness." Biological diversity: frontiers in

measurement and assessment 12 (2011): 39-54.

TRAINING COURSE: USE OF AGROBIODIVERSITY INFORMATION IN GBIF AND OTHER DATABASES

28, 29 AND 30 JUNE '17

Adapted from Hortal et al. 2007 Conservation Biology Volume 21, No. 3, 853–863; DOI: 10.1111/j.1523-1739.2007.00686.x

Extract biodiversitydata from GBIF

Check quality of records- Taxonomic accuracy- Geographic accuracy- Temporal accuracy Assess sampling effort

(survey completeness)

Identify well-sampledcells

Use in biodiversityassessment andmodelling

Discard records with errors

Revise extraction filtersand / or

add new data to GBIF

if few

or

none

Protocol to obtain reliable species community data from GBIF