modeling the biosphere: the natural historian's perspective
TRANSCRIPT
MODELING THE BIOSPHERE: THE NATURAL HISTORIAN'S PERSPECTIVE
Rutger Vos @rvosa
Characterizing the spatial and temporal patterns of biodiversity
Global latitudinal gradients
Distributions modulated by biotic and abiotic conditions
Trends and cycles in "ecological time"
Patterns of speciation, adaptation and extinction
Spatial patterns Temporal patterns
Understanding the processes that generate patterns of biodiversity
Dispersal and migration Evolution Species interactions
Competition Predation Parisitism Mutualism
What can modeling the biosphere contribute to global challenges?
Climate change - Better understanding of implications of scenarios
Food security - Identification of useful traits in crop wild relatives
Emerging diseases - Understanding and controlling dispersal of pathogens and vectors
Conservation - Why species are at risk and how they might be saved
The natural historian's toolkit
Species identification
Phylogenetic analysis
Species distribution modeling Diversity analysis
Species identification
Natural historians (almost) never work with "model organisms"
90% (?) of all species are new species that still need to be described
Described species need to be identified correctly, for example using: Taxonomic expertise DNA barcoding Image recognition
Phylogenetic analysis
Phylogenetics attempts to reconstruct the "tree of life" by reconciling observed species' properties with hypothetical evolutionary histories
Phylogenetic trees are used in: Systematics/taxonomy Testing evolutionary hypotheses Disentangling the effects of shared ancestry from
those of adaptation
Species distribution modeling
Given distribution data and GIS overlays of abiotic conditions, SDM constructs correlative models of species' tolerance ranges
Based on SDM models: Species' potential distributions can be predicted Species' past distributions can be hindcasted
Diversity analysis
Biodiversity can be expressed in terms of: Species diversity Functional diversity Phylogenetic diversity
Patterns of biodiversity are often structured as: αdiversity at local scale βdiversity between
areas (turnover) γdiversity: cumulative
The role of natural history collections
Natural history collections can provide the data to: Establish diagnostic
characters for species descriptions
Calibrate the time scale of phylogenesis using fossils
Compare traits within and among species
Establish (past and current) species occurrences
Data mining collection specimens
A large variety of data can be mined from collection specimens: Phenotype/character/trait values from direct
observation, image analysis, scanning (e.g. microCT) Molecular data from (ancient) DNA sequencing,
proteomics, isotope analysis Occurrence data from OCR and text mining specimen
labels
Challenges
Collection data has huge taxonomic and geographic biases
Taxonomic and geographic names are fluid
In 200 years, we've described 10% (?) of all species
The 4th paradigm: eScience for natural history
"Big Data": -omics data billions of occurrences 2D/3D digitizations
Computationally intensive
Reproducibility concerns
Three take-home facts
1. Old natural history collections can generate new insights to address global challenges
2. Natural history collection data is very multimodal, very multidimensional, and very dirty
3. New tech must be employed to speed up discovery
THANK YOU!
@rvosa on GitHub/Twitter/SlideShare