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

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

The Environmental Protection Agency (EPA) provides access to information on a variety of topics related to the environment and strives to inform citizens of health risks. The EPA also has an extensive library network that consists of 26 libraries throughout the United States, which provide access to a plethora of information to EPA employees, scientists, and researchers. The EPA implemented a reorganization project to digitize their materials so they would be more accessible to a wider range of users, but this plan was drastically accelerated when the EPA was threatened with a budget cut. It chose to close and reduce the hours and services of some of their libraries. As a result, the agency was accused of denying users the “right to know” by making information unavailable, not providing an adequate strategic plan, and discarding vital materials. This case study explores the background of the digitization project, the practices implemented, and the critiques of the project.

/pdf/the-environmental-protection-agency-3gx4opzrjm.pdf

The Environmental Protection Agency

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

/pdf/global-effects-of-land-use-on-local-terrestrial-biodiversity-31yzxze5ly.pdf

Global effects of land use on local terrestrial biodiversity

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Iconography : An arboreal spider protects its offspring by diving into the water of tank bromeliads

Niche divergence resulting from coevolution is commonly believed to favour coexistence among competing species; however, recent investigations have demonstrated that an unexpected niche convergence...

Stable isotope niche convergence in coexisting native and non-native salmonids across age classes

Artificial neural networks were used to pattern the use and partition of riverbed mesohabitats by four coexisting mayflies (Ephemera danica, Rhithrogena semicolorata, Caenis sp., and Serratella ignita), in a fast-flowing stream. Sixty-six samples were taken from the various mesohabitat types throughout a one-year period. Water depth, current velocity, substratum composition, and particulate organic matter were used to describe the mesohabitats within each sample unit. The species and abiotic data were computed separately with the self-organizing map (SOM) algorithm. Then, using the k-means algorithm, clusters were detected on the maps and the sampling units were classified separately for each variable and for species densities. Four clusters could be identified on the SOM according to nine environmental variables, and this classification was related to the morphodynamic conditions, chiefly with respect to substrate composition and current velocity. Similarly, three subsets were derived from the SOM according to gradients of species densities. The coincidence between ‘abiotic’ and ‘mayfly’ clusters showed that: (1) E. danica, Caenis sp. and S. ignita used similar mesohabitats, but E. danica was temporally segregated; (2) competition for space was likely to occur between Caenis sp. and S. ignita; and (3) R. semicolorata was spatially segregated from the three other mayflies. The method is discussed with reference to two alternative techniques: habitat preference curves, and multivariate analyses. The former implies a greater computation effort and is rather convenient under applied perspectives. The second approach faces the basic assumption that non-linear modelling methods should be preferred for dealing with ecological data which vary and covary in non-linear fashions. By combining ordering and clustering abilities (and other advantages such as gradient analysis and detection of outliers), SOM provides a visual and efficient way to bring out structures in the distribution of co-occurring species within multivariate microenvironments. Copyright © 2005 John Wiley & Sons, Ltd.

Assessment of an artificial intelligence technique in investigating habitat partitioning by coexisting benthic invertebrates in gravel‐bed rivers

While future climate scenarios predict declines in precipitations in many regions of the world, little is known of the mechanisms underlying community resilience to prolonged dry seasons, especially in ‘naive’ Neotropical rainforests. Predictions of community resilience to intensifying drought are complicated by the fact that the underlying mechanisms are mediated by species' tolerance and resistance traits, as well as rescue through dispersal from source patches.
We examined the contribution of in situ tolerance‐resistance and immigration to community resilience, following drought events that ranged from the ambient norm to IPCC scenarios and extreme events.
 We used rainshelters above rainwater‐filled bromeliads of French Guiana to emulate a gradient of drought intensity (from 1 to 3.6 times the current number of consecutive days without rainfall), and we analysed the post‐drought dynamics of the taxonomic and functional community structure of aquatic invertebrates to these treatments when immigration is excluded (by netting bromeliads) or permitted (no nets).
 Drought intensity negatively affected invertebrate community resistance, but had a positive influence on community recovery during the post‐drought phase. After droughts of 1 to 1.4 times the current intensities, the overall invertebrate abundance recovered within invertebrate life cycle durations (up to 2 months). Shifts in taxonomic composition were more important after longer droughts, but overall, community composition showed recovery towards baseline states. The non‐random patterns of changes in functional community structure indicated that deterministic processes like environmental filtering of traits drive community re‐assembly patterns after a drought event. Community resilience mostly relied on in situ tolerance‐resistance traits. A rescue effect of immigration after a drought event was weak and mostly apparent under extreme droughts.
Under climate change scenarios of drought intensification in Neotropical regions, community and ecosystem resilience could primarily depend on the persistence of suitable habitats and on the resistance traits of species, while metacommunity dynamics could make a minor contribution to ecosystem recovery. Climate change adaptation should thus aim at identifying and preserving local conditions that foster in situ resistance and the buffering effects of habitat features.

In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a Neotropical ecosystem

Abstract Photosynthetic microbes are omnipresent in land and water. While they critically influence primary productivity in aquatic systems, their importance in terrestrial ecosystems remains largely overlooked. In terrestrial systems, photoautotrophs occur in a variety of habitats, such as sub-surface soils, exposed rocks, and bryophytes. Here, we study photosynthetic microbial communities associated with bryophytes from a boreal peatland and a tropical rainforest. We interrogate their contribution to bryophyte C uptake and identify the main drivers of that contribution. We found that photosynthetic microbes take up twice more C in the boreal peatland (~4.4 mg CO 2 .h −1 .m −2 ) than in the tropical rainforest (~2.4 mg CO 2 .h −1 .m −2 ), which corresponded to an average contribution of 4% and 2% of the bryophyte C uptake, respectively. Our findings revealed that such patterns were driven by the proportion of photosynthetic protists in the moss microbiomes. Low moss water content and light conditions were not favourable to the development of photosynthetic protists in the tropical rainforest, which indirectly reduced the overall photosynthetic microbial C uptake. Our investigations clearly show that photosynthetic microbes associated with bryophyte effectively contribute to moss C uptake despite species turnover. Terrestrial photosynthetic microbes clearly have the capacity to take up atmospheric C in bryophytes living under various environmental conditions, and therefore potentially support rates of ecosystem-level net C exchanges with the atmosphere. 

/pdf/photosynthetic-microorganisms-effectively-contribute-to-c0ukerkc.pdf

Régis Céréghino

Papers

Iconography : An arboreal spider protects its offspring by diving into the water of tank bromeliads

Stable isotope niche convergence in coexisting native and non-native salmonids across age classes

Assessment of an artificial intelligence technique in investigating habitat partitioning by coexisting benthic invertebrates in gravel‐bed rivers

In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a Neotropical ecosystem

Photosynthetic microorganisms effectively contribute to bryophyte CO2 fixation in boreal and tropical regions