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1 PrefaceFigure P.1. Representation of the number of publications according to different ...

2 Chapter 1Figure 1.1. Zimmermann’s Tabula mundi geographico zoologica sistems quadrupedes ...Figure 1.2. The biogeographic regions of Morrone (2015). Areas in yellow are par...Figure 1.3. Carte Botanique de France, pour la 3e Edition de la Flore française ...Figure 1.4. Humboldt’s Tableau physique showing a cross-section of Mount Chimbor...Figure 1.5. “Representation of the distribution of mammals according to their zo...Figure 1.6. “Map of the World, showing the Zoo-Geographical Regions and the cont...Figure 1.7. “The six major biogeographical divisions are highlighted in the dend...Figure 1.8. Vertebrate zoogeographical regions and subregions (Proches and Ramdh...Figure 1.9. “Map of the terrestrial zoogeographic realms and regions of the worl...

3 Chapter 2Figure 2.1. Biogeographic processes. Four types of biogeographic processes are c...Figure 2.2. Event-based biogeography. a) An organism phylogeny with six species ...Figure 2.3. TreeFitter reconstruction among areas of endemism in Mexico based on...Figure 2.4. Accounting for phylogenetic uncertainty: the Bayes-DIVA approach. Tr...Figure 2.5. Parametric models in biogeographic inference. Top: a continuous-time...Figure 2.6. Parametric biogeographic reconstruction of the spatio-temporal evolu...Figure 2.7. Effect of decoupling biogeographic inference from time in DEC+J. Two...

4 Chapter 3Figure 3.1. Number of publications with the word “phylogeography” in the “topic”...Figure 3.2. Schematic representation of the five categories of phylogeographic p...Figure 3.3. Schematic drawing explaining how ecological niche modeling (ENM) can...Figure 3.4. Six potential patterns of phylogeographic structure and phenotypic d...

5 Chapter 4Figure 4.1. Terrestrial realms and biomes (left), and ecoregions (right), reflec...Figure 4.2. Geographical distribution of species richness for mammals (top, data...Figure 4.3. Continental drift, oceanic rifting, mountain building over the last ...Figure 4.4. Global temperature of the deep ocean, estimated from 18O measured on...Figure 4.5. Speciation mechanisms. All start from an identical condition with a ...Figure 4.6. Cartoon showing the relationships between geodynamics, climate and t...Figure 4.7. Alexander von Humboldt’s views on the relationships between latitude...Figure 4.8. From elevation to landscape connectivity (Salles et al. 2019). Left ...Figure 4.9. Quaternary climate indicators relative to present day (Bintanja and ...

6 Chapter 5Figure 5.1. The theory of island biogeography predicts that species richness on ...Figure 5.2. Panel (a) illustrates how island isolation (i.e. distance to the mai...Figure 5.3. The theory of island biogeography as first proposed by MacArthur and...Figure 5.4. The general dynamic model of island biogeography as derived by Whitt...

7 Chapter 6Figure 6.1. Map of world hotspots of subterranean biodiversity. This includes th...Figure 6.2. Distribution patterns of some beetle groups with cave species: (a) P...Figure 6.3. An example of amphi-Atlantic distribution, the family Metacrangonyct...

8 Chapter 7Figure 7.1. Molecular tools used to characterize the abundance and diversity of ...Figure 7.2. a) Soil sampling strategy at the worldwide scale (Delgado-Baquerizo ...Figure 7.3. a) Distribution of land uses in France. b) Heterogeneity of the Fren...Figure 7.4. a) Mapping of soil bacterial richness at the French national scale p...Figure 7.5. Relation between the turnover rate of the bacterial community struct...Figure 7.6. National mapping of the variation in relative abundance of the diffe...Figure 7.7. Soil bacterial co-occurrence networks for the four main land uses in...Figure 7.8. Regression tree defining the 16 bacterial habitats of French soils. ...Figure 7.9. Mapping of the bacterial habitats of French soils (modified from Kar...Figure 7.10. Diagnostic of the microbiological quality of the soils of an agricu...

9 Chapter 8Figure 8.1. Schematic diagram exploring the potential filters driving the contra...

10 Chapter 9Figure 9.1. Conceptual diagram representing freshwater fish community assembly m...

11 Chapter 10Figure 10.1. a) The USS Vincennes during the U.S. Exploring Expedition sailing t...Figure 10.2. Characteristics of terrestrial, marine and freshwater realms in ter...Figure 10.3. Diversification patterns in marine and terrestrial organisms over g...Figure 10.4. Examples of the variability in historical, current and future patte...

12 Chapter 11Figure 11.1. Ebola-virus disease (EVD) outbreaks (events of zoonotic transmissio...Figure 11.2. Empirical modeling of transmission risk of a mosquito-borne disease...