Data Requirements for Biodiversity Indicators

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Data Requirements for Biodiversity Indicators

• Carlo Heip
• Centre for Estuarine and Marine Ecology
• Netherlands Institute of Ecology
• Ghent University, Belgium
• State University of Groningen, The Netherlands
• c.heip_at_nioo.knaw.nl
•  

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Biodiversity what is it?

• The variability among living organisms from all
  sources, including inter alia, terrestrial,
  marine and other aquatic ecosystems and the
  ecological complexes of which they are part this
  includes diversity within species, between
  species and of ecosystems.
• The totality of genes, species and ecosystems in
  a region.
• Biological variation

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Why marine biodiversity matters

• Species are disappearing at a rate never observed
  since life began on earth. The extinction
  crisis ranks with global climate change as the
  greatest threat to the integrity of the biosphere
  in the 21st century
• Species extinction is not just an aesthetic or
  moral problem. Marine organisms play a crucial
  role in almost all biogeochemical processes that
  sustain the biosphere, and provide a variety of
  products (goods) and functions (services) which
  are essential to mankinds well-being

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• The rate and efficiency of any of the processes
  that marine organisms mediate, as well as the
  range of goods and services that they provide,
  are determined by interactions, between
  organisms, and between organisms and their
  environment, and therefore by biodiversity.
• These relationships have not yet been quantified,
  and we are at present unable to predict the
  consequences of loss of biodiversity resulting
  from environmental change in ecological, economic
  or social terms.

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Marine Biodiversity what are the threats?

• Overexploitation of resources
• Physical alteration of the coastline
• Pollution and eutrophication
• Introduction of exotic species
• Global climate change

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What is at stake?

• Marine resources (goods)
• Genetic resources
• Example Pompei worm
• Species
• Fisheries, aquaculture 100 MT of food
• Habitat
• Tourism
• Functioning of marine ecosystems (services)
• Relationship between species and biogeochemical
  processes

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A better understanding of marine biodiversity
requires

• Knowledge of existing biodiversity inventories
• Understanding of how biodiversity changes in
  space and through time, both now and in the past
• Ergo surveys and monitoring
• Interpreting these changes in terms of a theory
• Experiments and modelling

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Genes and Genomics
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• FUNDAMENTAL QUESTIONS
• For a targeted range of environments and field
  sites, environmental genomics can address
• Which genes are turned on, and what do they do?
• Is there intraspecific variation in gene
  expression in response to environmental change,
  and is this variation adaptive?
• What are the ecosystem-, community-, and
  population-level consequences of the molecular
  transformations performed by these genes?
• Which taxa are involved?
• What happens if the system is experimentally
  perturbed

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NSF Press Release November 2001

• Scientists funded in part by the National Science
  Foundation (NSF) and affiliated from the
  University of Delaware and Amersham Biosciences,
  Inc., in Piscataway, New Jersey, have succeeded
  in conducting the first-ever DNA sequencing
  experiments at sea. Using the research vessel
  Atlantis and submersible Alvin, the team carried
  out a pioneering environmental genomic study of
  the strange life that inhabits super-hot
  hydrothermal vents almost two miles deep in the
  Pacific Ocean

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Pompei worm (Alvinella pompejana)
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Genome Science and Bioinformatics

• One of the core activities in genomics is to
  establish integrated Web-based databases and
  research interfaces.
• Bioinformatics deals with the computational
  management of all kinds of biological
  information. It develops the mathematical tools
  required for analysing and processing the
  information in those databases
• At some stage as the data obtained in genomics
  research will be linked to information on
  species, including geographical and environmental
  information and using methods developed in
  bioinformatics

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Inventorying and Monitoring of Species Diversity

• The rational use and conservation of marine
  biodiversity requires programmes of inventorying
  and monitoring that allow understanding the past
  and present states of biodiversity and the causes
  of its change.
• Inventories establish a baseline distribution of
  biodiversity for a particular place at a
  particular time.
• Monitoring addresses the issue of change or lack
  of change of biodiversity through time at
  particular places.
• Ideally, modelling should allow for predicting
  future states of biodiversity

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Why surveys and monitoring are required.

• Inventories and monitoring serve to set the
  baseline against which changes can be evaluated.
• Monitoring is the only way to keep track of the
  state of the system, which is necessary because
• Much change is triggered by random events.
• Accidents will happen.
• Monitoring is required to evaluate effects of
  policy measures.
• Time series data become more valuable when they
  are longer. Much variation is in the longer time
  periods
• Validation and calibration of ecological models
  can only be done on the basis of real data. The
  longer the time series the better the models
  perform.

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Inventorying and Monitoring How?

• The goal of an inventorying and monitoring
  program of biodiversity is to document patterns
  of change in order to understand the impact of
  natural or anthropogenic disturbance on species
  composition and abundance in communities and
  ecosystems.
• An inventory establishes a baseline for the
  distribution of biodiversity at a particular
  place and a particular time.
• Monitoring addresses the issue of change or lack
  of change of biodiversity through time at
  particular places, against the baseline

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Setting up a baseline by a network of sites

• A network of sites can survey and monitor
  biodiversity in space and in time simultaneously
• An ideal network of sites would cover a selection
  of critical ecosystems and cover
• Areas with marginal or undetectable impact versus
  (heavily) impacted areas
• Transition zones between biogeographical regions
  and sites which are aligned along gradients such
  as longitude, latitude, salinity
• Sites which have been intensively studied and
  have well established species lists, coupled with
  meteorological and ecological data sets.

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European Marine Biodiversity Research Sites
ATBI
Reference sites Non-impacted
Focal sites Impacted
LTBR
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European Marine Biodiversity Research Sites
148 research sites, of which 38 are reference
sites
WP1 Candidate Reference and Focal sites - ATBI
(red dots) - other sites (blue dots)
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Habitat diversity as measured by remote sensing,
acoustic or imaging methodsAll Taxon
Biodiversity InventoryDiversity indices e.g.
Hill or Renyi numbers (Species richness,
Shannon-Wiener etc) of selected taxonomic
groupsTaxonomic distinctnessBenthic community
analysisDiversity of ecosystem
engineersInvading SpeciesPopulation
structureGenetic diversity
Direct indicators of Biodiversity at Different
levels

• Within a research site
• Within a habitat or community
• Within a population

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Existing Data

• Taxonomic collections information on taxa with
  or without geographical information or reference
  to authors
• Local and Regional Faunas and Floras lists with
  geographical references
• Biogeographical research
• Paleo-ecology
• Environmental research and Monitoring
• Fisheries and aquaculture data
• Ecological research quantitative and qualitative
• Proxies

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Problems

• No systematic collection
• No reference to sites
• No standardization in collecting methods
• No quality control
• Not electronically available

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Requirements for new data

• A standard minimum set and sampling methodology
  of environmental variables
• Space (geographical location) and Time
• Temperature, light, nutrients (salinity) regime
• Substrate for benthic populations, water column
  structure for pelagic populations
• .
• Standard methodologies for biodiversity
  measurement
• Electronically available on the Web using
  adequate data-base structure
• Application and Development of Bioinformatics
  (data mining software, .)

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Socio-economics and Indicators
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Key features of indicators
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The Pressure-State-Response model
Statistical Office of the European Commission
(EUROSTAT).
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The Driving force-Pressure-State-Impact-Response
model
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Marine Biodiversity

1. Global
2. European
3. Regional
4. Local

1. Long term (10)
2. Ph.D. term (3-4)
3. Short term (lt1)

Biodiversity data
Socio-economic
Ecosystem data
DNA sequences Species abundances Benthic
mapping Remote Sensing
Socio-economic drivers
Chemical and Physical Processes
Primary production Mineralisation Nitrogen
fixation Etc.
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Can we do it?

• Need for handling massive data of very different
  nature, origin, quality,
• Bioinformatics a quantum jump in the level of
  expertise and sophistication required
• Best start with a number of Pilot projects
• Networking within Europe (6th framework
  programme) and globally (Census of Marine Life)

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ESF Research Objectives

• To characterise marine biodiversity at a range of
  biological, spatial and temporal scales.
• To quantify the role of marine biodiversity in
  providing goods and services in both relatively
  natural and more human-impacted environments.
• To determine the probable effects of natural and
  man-made changes in biodiversity on ecosystem
  goods and services.
• To provide a scientific rationale and tools for
  the proper management of living resources in
  European seas.

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MARBEF EoI Research Objectives

• 1. Exploring marine biodiversity in Europe.
• 2. Determining the relationship between
  ecosystem functioning and biodiversity.
• 3. Exploring the relationship between species
  and the stability of ecosystems, including
  functional groups and the role of rare species
• 4. What determines the success or failure of
  invasive species.
• 5. What are the large-scale gradients in species
  richness and how do they change in time.
• 6. What is the relationship between ecosystem
  functioning and the sustainable use of marine
  biodiversity across Europe and globally.

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Thank you for your attention
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Bioinformatics

• Bioinformatics is the study of the inherent
  structure of biological information and
  biological systems. It brings together the
  avalanche of systematic biological data (e.g.
  genomes, but going on to ecosystems) with the
  analytic theory and practical tools of
  mathematics and computer science

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• First, the data produced by the thousands of
  research teams all over the world are collected
  and organized in databases specialized for
  particular subjects. Well-known examples are GDB
  , SWISS-PROT , GenBank , and PDB. The latter -
  for example - deals with three-dimensional
  structures of biological molecules.

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• In the next step, computational tools are needed
  to analyse the collected data in the most
  efficient manner. For example, many
  bioinformaticists are working on the prediction
  of the biological functions of genes and proteins
  (or parts of them) based on structural data

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• Bioinformatics is a newly emerging
  interdisciplinary research area which may be
  defined as the interface between biological and
  computational sciences. Although the term
  'Bioinformatics' is not really well-defined, you
  could say that this scientific field deals with
  the computational management of all kinds of
  biological information, whether it may be about
  genes and their products, whole organisms or even
  ecological systems.

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Species diversity

•  Its structure life has originated in the sea
  and is much older in the sea than on land. As a
  consequence, the diversity of higher taxonomic
  levels is much greater in the sea where there are
  14 endemic (unique) animal phyla whereas only 1
  phylum is endemic to land
• Its function Marine organisms play crucial roles
  in many biogeochemical processes that sustain the
  biosphere, and provide a variety of products
  (goods) and functions (services) which are
  essential to mankinds well-being, including the
  production of food and natural substances, the
  assimilation of waste and regulation of the
  worlds climate