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