Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Forest disturbances are sensitive to climate. However, our understanding of disturbance dynamics in response to climatic changes remains incomplete, particularly regarding large-scale patterns, interaction effects and dampening feedbacks. Here we provide a global synthesis of climate change effects on important abiotic (fire, drought, wind, snow and ice) and biotic (insects and pathogens) disturbance agents. Warmer and drier conditions particularly facilitate fire, drought and insect disturbances, while warmer and wetter conditions increase disturbances from wind and pathogens. Widespread interactions between agents are likely to amplify disturbances, while indirect climate effects such as vegetation changes can dampen long-term disturbance sensitivities to climate. Future changes in disturbance are likely to be most pronounced in coniferous forests and the boreal biome. We conclude that both ecosystems and society should be prepared for an increasingly disturbed future of forests.

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Forest disturbances under climate change

Time is divided by geologists according to marked shifts in Earth's state. Recent global environmental changes suggest that Earth may have entered a new human-dominated geological epoch, the Anthropocene. Here we review the historical genesis of the idea and assess anthropogenic signatures in the geological record against the formal requirements for the recognition of a new epoch. The evidence suggests that of the various proposed dates two do appear to conform to the criteria to mark the beginning of the Anthropocene: 1610 and 1964. The formal establishment of an Anthropocene Epoch would mark a fundamental change in the relationship between humans and the Earth system.

Defining the Anthropocene

Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.

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Quantifying Community Assembly Processes and Identifying Features that Impose Them

Climate-driven vegetation mortality is occurring globally and is predicted to increase in the near future. The expected climate feedbacks of regional-scale mortality events have intensified the need to improve the simple mortality algorithms used for future predictions, but uncertainty regarding mortality processes precludes mechanistic modeling. By integrating new evidence from a wide range of fields, we conclude that hydraulic function and carbohydrate and defense metabolism have numerous potential failure points, and that these processes are strongly interdependent, both with each other and with destructive pathogen and insect populations. Crucially, most of these mechanisms and their interdependencies are likely to become amplified under a warmer, drier climate. Here, we outline the observations and experiments needed to test this interdependence and to improve simulations of this emergent global phenomenon.

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The interdependence of mechanisms underlying climate-driven vegetation mortality

Most methods of multivariate analysis, in particular ordination and clustering techniques, are explicitly or implicitly based on the comparison of all possible pairs of objects or descriptors The comparisons take the form of association measures (often called coefficients or indices), which are assembled in a square and symmetric association matrix, of dimensions n × n when objects are compared, or p × p when variables are compared Since the subsequent analyses are done on association matrices, the choice of an appropriate measure is crucial In this Chapter you will quickly revise the main categories of association coefficients, learn how to compute, examine and visually compare dissimilarity matrices (Q mode) and dependence matrices (R mode), apply these techniques to a classical dataset and learn or revise some basics of programming functions with the R language

Association Measures and Matrices

The heterogeneity of the subfossil chironomid deposition (in terms of assemblages and paleo-diet) has to be studied to assess the reliability of paleolimnological interpretations (i.e., spatial representativeness). We collected 31 cores in the deepest part of Lake Grand Maclu (Jura, France) with the aim of assessing the spatial structures at two spatial scales: a sediment core surface (31.7 cm2) and 4 m2 in the deepest zone of the lake. The results showed that chironomid assemblages exhibited a uniform distribution at the two spatial scales studied. Moreover, a sediment core surface was very reliable for assessing the biodiversity (Simpson’s index) of the deepest part with more than 95% of the overall diversity sampled on average. However, δ
 13C values of Chironomus anthracinus-type remains revealed a spatial pattern in the contribution of carbon sources to its biomass. We suggest that a heterogeneous distribution of microbial biomass (such as methane-oxidizing bacteria) could induce a spatial pattern (patch) in food availability for chironomid larvae. We recommend increasing the number of head capsules analyzed in spectrometry to reduce this potential bias due to patterns and to improve upscaling results from individual downcore records to the entire deepwater basin.

Assemblages and paleo-diet variability of subfossil Chironomidae (Diptera) from a deep lake (Lake Grand Maclu, France)

We investigated the role of fire and other potential biotic and abiotic determinants for the occurrence of an obligate seeder and active pyrophyte, Cistus salviifolius, a vulnerable species in the Swiss Red List. Populations of this species are threatened by the change of fire regime that has occurred during the last ten years. Fires and burnt areas are today less frequent and it is not clear whether other factors can compensate for such fire-free periods should this trend continue. We used a stratified random design to collect data on the cover of three growth stages, i.e., juvenile, chamaephytic and nanophanerophytic (oldest), of C. salviifolius, on plant communities, and on environmental factors. A tree-based discriminant analysis showed that the time elapsed since last fire was the best predictor of Cistus occurrence, but plants could survive on rocky and sunny sites if no fire had occurred for more than 32 years. Contrary to our expectations, the number of fires and time elapsed since the last event was correlated with the oldest stages only, and not with that of seedlings or juveniles. Rank correlations showed that bare soil was a good predictor of young stages, whereas rocky outcrops and shallow soils were important for the chamaephytic stage. Our results confirm the role of disturbances and competition-free habitats as determinants of the survival of this vulnerable pyrophyte during long periods without fires and the existence of ontogenetic niche segregation of this species. In order to maintain viable C. salviifolius populations in the Alps, managers should undertake conservation actions according to the requirements of the different growth stages of this species.

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Determinants for the conservation of a vulnerable fire-dependent species at its marginal range

The traditional Braun-Blanquet approach and its modern variants are mainly restricted to the classification of phytocoenoses, i.e. assemblages that include all plants (or at least all vascular plants) of the community. How- ever, phytosociologists may also focus on the classification of synusiae – one-layered, ecologically homoge- neous assemblages (e.g., epiphytic or epilithic bryolichenic communities, herbaceous or shrubby fringe com- munities) – using similar class definition procedures. The integrated synusial approach (ISA), developed in Switzerland and France, is an extension of the synusial approaches to the description and classification of phytocoenoses conceived as assemblages of synusiae. Separate plot records are used to build separate consistent classification sections (CCSs) for each category of synusiae, i.e. tree, shrub, herb and moss synusiae. Lower- level synusial vegetation types are called ‘synusial elementary syntaxa’ (SESs). A type-based CCS can eventu- ally be created for the classification of complete phytocoenoses, based on their synusial composition, i.e. lists of SESs. Lower-level phytocoenotic vegetation types are called ‘elementary coenotaxa’.

The integrated synusial approach to vegetation classification and analysis

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This modular structure is likely to play a key role in the response of grassland ecosystems to future changes by limiting the impact of changes in agricultural practices such as intensification to some modules leaving species from other modules poorly impacted. The next step is to understand the importance of this modular structure for the long-term maintenance of grassland ecosystem structure and functions as well as to develop tools to integrate network structure into models to improve their capacity to predict future changes.

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Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches.

François Gillet

Papers

Association Measures and Matrices

Assemblages and paleo-diet variability of subfossil Chironomidae (Diptera) from a deep lake (Lake Grand Maclu, France)

Determinants for the conservation of a vulnerable fire-dependent species at its marginal range

The integrated synusial approach to vegetation classification and analysis

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches.