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

We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

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

▪ Abstract Local habitat and biological diversity of streams and rivers are strongly influenced by landform and land use within the surrounding valley at multiple scales. However, empirical associations between land use and stream response only varyingly succeed in implicating pathways of influence. This is the case for a number of reasons, including (a) covariation of anthropogenic and natural gradients in the landscape; (b) the existence of multiple, scale-dependent mechanisms; (c) nonlinear responses; and (d) the difficulties of separating present-day from historical influences. Further research is needed that examines responses to land use under different management strategies and that employs response variables that have greater diagnostic value than many of the aggregated measures in current use. In every respect, the valley rules the stream.      H.B.N. Hynes (1975)

http://deq.idaho.gov/media/525804-Landscapes_Riverscapes_Influence_landuse_stream_ecosystems_Allan_2004.pdf

Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems

It is widely agreed that fecundity selection and sexual selection are the major evolutionary forces that select for larger body size in most organisms. The general, equilibrium view is that selection for large body size is eventually counterbalanced by opposing selective forces. While the evidence for selection favoring larger body size is overwhelming, counterbalancing selection favoring small body size is often masked by the good condition of the larger organism and is therefore less obvious. The suggested costs of large size are: (1) viability costs in juveniles due to long development and/or fast growth; (2) viability costs in adults and juveniles due to predation, parasitism, or starvation because of reduced agility, increased detectability, higher energy requirements, heat stress, and/or intrinsic costs of reproduction; (3) decreased mating success of large males due to reduced agility and/or high energy requirements; and (4) decreased reproductive success of large females and males due to late reproduction. A review of the literature indicates a substantial lack of empirical evidence for these various mechanisms and highlights the need for experimental studies that specifically address the fitness costs of being large at the ecological, physiological, and genetic levels. Specifically, theoretical investigations and comprehensive case studies of particular model species are needed to elucidate whether sporadic selection in time and space is sufficient to counterbalance perpetual and strong selection for large body size.

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The evolution of body size: what keeps organisms small?

We propose an integrated, heuristic model of lotic biocomplexity across spatiotemporal scales from headwaters to large rivers. This riverine ecosystem synthesis (RES) provides a framework for understanding both broad, often discontinuous patterns along longitudinal and lateral dimensions of river networks and local ecological patterns across various temporal and smaller spatial scales. Rather than posing a completely new model, we arrange a conceptual marriage of eco-geomorphology (ecological aspects of fluvial geomorphology) with a terrestrial landscape model describing hierarchical patch dynamics. We modify five components of this terrestrial model for lotic ecosystems: (1) nested, discontinuous hierarchies of patch mosaics; (2) ecosystem dynamics as a composite of intra- and inter-patch dynamics; (3) linked patterns and processes; (4) dominance of non-equilibrial and stochastic processes; and (5) formation of a quasi-equilibrial, metastable state. Our conceptual model blends our perspectives on biocomplexity with aspects of aquatic models proposed from 1980–2004.

Contrasting with a common view of rivers as continuous, longitudinal gradients in physical conditions, the RES portrays rivers as downstream arrays of large hydrogeomorphic patches (e.g. constricted, braided and floodplain channel areas) formed by catchment geomorphology and climate. The longitudinal distribution of these patches, which are identifiable using standard geomorphic techniques, varies amongst rivers and is difficult to forecast above ecoregional scales. Some types of hydrogeomorphic patches may reoccur along this downstream passage. Unique ecological ‘functional process zones’ are formed by individual types of hydrogeomorphic patches because of physiochemical habitat differences which affect ecosystem structure and function.

The RES currently includes 14 tenets predicting how patterns of individual species distributions, community regulation, lotic ecosystem processes, and floodplain interactions will vary over spatiotemporal scales, especially as they relate to the functional process zones formed by hydrogeomorphic differences in the river network. Copyright © 2006 John Wiley & Sons, Ltd.

The riverine ecosystem synthesis : Biocomplexity in river networks across space and time

Our current views of the structure and function of large river ecosystems are based primarily on three influential and still valuable riverine models: (1) the river continuum concept, or RCC (e.g., Vannote et al. 1980); (2) the serial discontinuity concept (Ward and Stanford 1983), which integrated the effects of large dams and reservoirs on the RCC; and (3) the flood pulse concept in river-floodplain systems (Junk et al. 1989) and its relationship to the RCC (Sedell et al. 1989). With regard to food webs in large rivers, these models accentuated the importance of nutrients derived from either headwater streams or seasonal floodplain pulses and downplayed or virtually ignored the role of local instream primary production and riparian litterfall. We believe that the general portrayal of ecosystem function within large rivers needs substantial revision because previous models relied too heavily on data from either lower-order streams, floodplain rivers (thereby exluding large rivers with constricted channels), or main channel habitats with their dominant collector feeding guild (thus de-emphasizing nearshore areas where species in many feeding guilds congregate). We propose an alternative hypothesis the riverine productivity model (RPM) which stresses the varying importance to large river food webs of local autochthonous production and direct organic inputs from the riparian zone. The RPM's portrayal of ecosystem function differs most significantly from that of previous models for rivers characterized by constricted channels, such as the upper two-thirds of the Ohio River.

The riverine productivity model: an heuristic view of carbon sources and organic processing in large river ecosystems

This paper addresses the river heterotrophy paradox, “How can animal biomass within riverine food webs be fueled primarily by autochthonous autotrophic production if the ecosystem as a whole is heterotrophic?”. Reviewed, stable isotope data from tropical, temperate, and arctic rivers provide evidence consistent with the revised riverine productivity model (RPM): “The primary, annual energy source supporting overall metazoan production and species diversity in mid- to higher-trophic levels of most rivers (≥4th order) is autochthonous primary production entering food webs via algal-grazer and decomposer pathways”. The revised RPM does not conflict with the heterotrophy paradox because: (a) the decomposer (microbial loop) food pathway processes most of the transported, allochthonous and autochthonous carbon and, with algal respiration in some cases, is primarily responsible for a river's heterotrophic state (P/R<1); but (b) biomass production of mid- to higher-trophic levels is principally supported by an algal-grazer (phytoplankton and benthic microalgae) pathway that is only weakly linked to the decomposer pathway. The reason the algal-grazer pathway supports the majority of metazoan biomass is that allochthonous carbon is mostly recalcitrant, whereas carbon from autochthonous primary production, though much less plentiful, is commonly more labile (easier to assimilate), contains more energy per unit mass, and is typically preferred by metazoa.

Dominance of autochthonous autotrophic carbon in food webs of heterotrophic rivers

Analyses of stable isotope (δ13C and δ15N) and C:N ratios of food webs within a floodplain and a constricted-channel region of the Ohio River during October 1993 and July 1994 indicate that the increasingly influential flood pulse concept (FPC) does not, for either location, adequately address food web structure for this very large river Furthermore, results of this study suggest that the riverine productivity model (RPM) is more appropriate than the widely known river continuum concept (RCC) for the constricted region of this river These␣conclusions are based on stable isotope analyses of potential sources of organic matter (riparian C3 trees, riparian C4 grasses and agricultural crops, submerged macrophytes, benthic filamentous algae, benthic particulate organic matter, and transported organic matter containing detritus and phytoplankton) and various functional feeding groups of invertebrate and fish consumers The FPC, which stresses the key contribution of organic matter, particularly terrestrial organic matter, originating from the floodplain to riverine food webs, was judged inappropriate for the floodplain region of the Ohio River for hydrodynamic and biotic reasons The rising limb and peak period of discharge typically occur in November through March when temperatures are low (generally much less than 10°C) and greater than bank-full conditions are relatively unpredictable and short-lived The major food potentially available to riverine organisms migrating into the floodplain would be decaying vegetation because autotrophic production is temperature and light limited and terrestrial insect production is minimal at that time It is clear from our data that terrestrial C4 plants contribute little, if anything, to the consumer food web (based on δ13C values), and δ15N values for C3 plants, coarse benthic organic matter, and fine benthic organic matter were too depleted (∼7-12‰ lower than most invertebrate consumer values) for this organic matter to be supporting the food web The RPM, which emphasizes the primary role of autotrophic production in large rivers, is the most viable of the remaining two ecosystem models for the constricted-channel region of the Ohio based on stable isotope linkage between sources and consumers of organic matter in the food web The most important form of food web organic matter is apparently transported (suspended) fine (FTOM) and ultra-fine particulate organic matter We propose that phytoplankton and detritus of an autochthonous origin in the seston would represent a more usable energy source for benthic (bivalve molluscs, hydropsychid caddisflies) and planktonic (microcrustaceans) suspension feeders than the more refractory allochthonous materials derived from upstream processing of terrestrial organic matter Benthic grazers depend heavily on nonfilamentous benthic algae (based on gut analysis from a separate study), but filamentous benthic algae have no apparent connection to invertebrate consumers (based on δ13C values) Amphipod and crayfish show a strong relationship to aquatic macrophytes (possibly through detrital organic matter rather than living plant tissue) These observations contrast with the prediction of the RCC that food webs in large rivers are based principally on refractory FTOM and dissolved organic matter from upstream inefficiencies in organic-matter processing and the bacteria growing upon these suspended or dissolved detrital compounds The conclusions drawn here for the Ohio River cannot yet be extended to other floodplain and constricted-channel rivers in temperate and tropical latitudes until more comparable data are available on relatively pristine and moderately regulated rivers

Isotopic analysis of three food web theories in constricted and floodplain regions of a large river

/ Lapwai Creek, an agriculturally impacted stream in northern Idaho, was sampled seasonally over a two-year period to determine if macroinvertebrate community composition changed along the longitudinal gradient and if changes followed predictions of the river continuum concept. Possible relationships between changes in food resource availability and community structure were also examined. Benthic invertebrates were collected at eight locations along the longitudinal gradient of Lapwai Creek using a Hess sampler. Random skewer analysis suggested there was no longitudinal gradient for either number of individuals or functional feeding group composition. Cluster analysis revealed that all locations, excluding a site receiving outflow from a small, eutrophic reservoir, had a similar community structure, further suggesting that invertebrate community composition remained consistent along the longitudinal gradient of the stream. The community was dominated at all sites, excluding the site below the reservoir, by functionalgrazers. Shredders were rare throughout Lapwai Creek, even in areas where healthy riparian vegetation still remained. Studies of other streams within the drainage basin show that many species found in the upper reaches of these streams, where agricultural impacts are low, were absent throughout the length of Lapwai Creek. Data collected concurrently with macroinvertebrates indicated that the input, storage, and transport of particulate organic matter was low throughout the stream, whereas periphyton abundance was high. The absence of longitudinal changes, despite flowing through three distinct geomorphological regions, and the grouping of all sites except one by cluster analysis for both dominant taxa and functional feeding groups suggest that agricultural alteration has influenced community structure of Lapwai Creek, resulting in a relatively homogeneous assemblage of macroinvertebrates capable of tolerating agricultural nonpoint source pollution. Additional support for this hypothesis is the high abundance of one food source, periphyton, and the small quantities of terrestrially derived organic matter. The abundance of the former and the rarity of the latter can be attributed to alteration of the drainage basin resulting from agricultural activities through inputs of fertilizers that generated high nutrient concentrations and the removal of riparian vegetation to clear more land for agriculture and provide increase access to the stream.KEY WORDS: Agriculture; Longitudinal patterns; Macroinvertebrates; Nonpoint source; River continuum

Michael D. Delong

Papers

The riverine ecosystem synthesis : Biocomplexity in river networks across space and time

The riverine productivity model: an heuristic view of carbon sources and organic processing in large river ecosystems

Dominance of autochthonous autotrophic carbon in food webs of heterotrophic rivers

Isotopic analysis of three food web theories in constricted and floodplain regions of a large river

Macroinvertebrate Community Structure Along the Longitudinal Gradient of an Agriculturally Impacted Stream