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Table of contents
Thanks
Index
Introduction
What is Biodiversity? Why it matters? How to study it?
Biodiversity: a multi-faceted concept
Species richness, the golden standard of biodiversity measures
Why studying biodiversity?
Systematics and ecology: two complementary approaches to study biodiversity
Species occurrences, biologists’ raw material
Primary biodiversity data
Datasets: From cabinet of curiosities to databases
“Big data”: a change in scale and practices
Ecoinformatics, the “big data” of biodiversity
Global Biodiversity Information Facility
Data quality and bias
A global pattern of biodiversity: the latitudinal diversity gradient
Species richness varies with latitude
The multiple hypotheses behind the LDG
Questions addressed in this thesis dissertation
Can biological diversity be investigated in its entirety?
How is the practice of biodiversity data gathering evolving?
Latitudinal Diversity Gradient at large taxonomic scale: which factors shape it?
Chapter 1: Material and Methods
Using the GBIF mediated data
Datasets from the GBIF portal
The Darwin Core format
Big data in practice
Workflow architecture
Reading and filtering occurrences
Indexing the table to get a functioning database
Characterizing a biodiversity dataset: biases and trends
Species names from the GBIF Backbone Taxonomy and multimedia files
Public interest and taxonomic research quantity
Putting the GBIF database into numbers
Statistical tools
Working on biodiversity patterns: delving into ecoinformatics
Cleaning data
Estimating species richness
Using our results to understand the LDG
The species richness covariates
Statistical analysis of species richness and its covariates
Chapter 2: The increasing disconnection of primary biodiversity data from specimens: How does it happen and how to handle it? (Troudet et al. Systematic Biology, submitted as a Point of View)
Abstract
Keywords
Introduction
Material and Methods
Data Set
Data Quantity
Data Origin
Supporting Files
Evolution of Data Completeness
Evolution of Taxonomic and Spatial Precision
Results and Discussion
A Shift in the Recording of Primary Biodiversity Data
Primary Biodiversity Data for systematics and evolutionary studies in the 21st
Century: Are We There Yet?
Acknowledgments
Chapter 3: Taxonomic bias in biodiversity data and societal preferences (Troudet et al. Scientific reports, published 22-08-2017)
Abstract
Introduction
Results
Discussion
Methods
Acknowledgements
Author Contributions
Chapter 4: Latitudinal Diversity Gradient: Geometric hypotheses revisited using massive biodiversity occurrences in plants and animals of the New World (article in preparation)
Introduction
Materiel and Methods
Species richness estimates
Explanatory Variables
Statistical analyses
Results
Basic statistics
Latitudinal diversity gradient
Environmental hypotheses
Discussion
Acknowledgement
Chapter 5: DwCSP a fast biodiversity occurrence curator (article in preparation)
Introduction
Software
Data Enrichment
Searching for outliers
Results
Discussion
Discussion
Big-data and biodiversity
The big-data paradigm
The genesis of Biodiversity big-data
A new way of doing science
Primary Biodiversity data, a proxy to assess the state of the study of biodiversity
Biodiversity data are disconnected from specimens
Taxonomic bias while aiming at investigating the whole biodiversity
Using biodiversity data to decipher the origin of global biodiversity patterns .
Estimating global species richness from a large and geographically widespread
taxonomic sample
Further into the Latitudinal Diversity Gradient
The GBIF-mediated data: a fascinating tool for biodiversity analyses
References
Appendixes
Appendix 1: List of used Java Libraries and Dependencies
Appendix 2: List of indexes of the OCCURRENCES table
Appendix 3: List of additional database tables
Appendix 4: VBA script for Web Search Results
Appendix 5: R script for spatial outlier detection
Appendix 6: Worldwide species richness maps and plots
