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

http://aerg.canberra.edu.au/library/sex_general/2002_Devlin_Nagahama_sex_determination_in_fish_review.pdf

Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences

Communities of microscopic plant life, or phytoplankton, dominate the Earth's aquatic ecosystems. This important new book by Colin Reynolds covers the adaptations, physiology and population dynamics of phytoplankton communities in lakes and rivers and oceans. It provides basic information on composition, morphology and physiology of the main phyletic groups represented in marine and freshwater systems and in addition reviews recent advances in community ecology, developing an appreciation of assembly processes, co-existence and competition, disturbance and diversity. Although focussed on one group of organisms, the book develops many concepts relevant to ecology in the broadest sense, and as such will appeal to graduate students and researchers in ecology, limnology and oceanography.

/pdf/the-ecology-of-phytoplankton-4ev70n3jsq.pdf

The Ecology of Phytoplankton

Introduction to freshwater invertebrates, J.H.Thorp and A.P.Covich freshwater communities, A.P.Covich and J.H.Thorp protozoa, W.D.Taylor and R.W.Sanders porifera, T.M.Frost the freshwater cnidaria - or coelenterates, L.E.Slobodkin and P.E.Bossert flatworms - turbellaria and nemertea, J.Kolasa gastrotricha, D.L.Strayer and W.D.Hummon rotifera, R.L.Wallace and T.W.Snell nematoda and nematomorpha, G.O.Poinar mollusca - gastropoda, K.M.Brown mollusca - bivalvia, R.F.McMahon annelida - oligochaeta and branchiobdellida, R.O.Brinkhurst and S.R.Gelder annelida - leeches, polychaetes, and acanthobdellids, R.W.Davies bryozoans, T.W.Wood tardigrada, D.R.Nelson water mites, I.M.Smith and D.R.Cook diversity and classification of insects and collembola, W.L.Hilsenhoff crustacea - introduction and peracarida, A.P.Covich and J.H Thorp ostracoda, L.D.Delorme cladocera and other branchiopoda, S.I.Dodson and D.G.Frey copepoda, C.E.Williamson decapoda, H.H.Hobbs III.

Ecology and classification of North American freshwater invertebrates

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

1. Many freshwater systems receive substantial inputs of terrestrial organic matter. Terrestrially derived dissolved organic carbon (t-DOC) inputs can modify light availability, the spatial distrib ...

https://onlinelibrary.wiley.com/doi/pdf/10.1111/fwb.12909

James H. Thorp

Papers

Ecology and classification of North American freshwater invertebrates

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

How important are terrestrial organic carbon inputs for secondary production in freshwater ecosystems