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

https://www.whoi.edu/cms/files/Ecological_Modelling_2002_Boyce_53558.pdf

Evaluating resource selection functions

The use of recommender systems is an emerging trend today, when user behavior information is abundant. There are many large datasets available for analysis because many businesses are interested in future user opinions. Sophisticated algorithms that predict such opinions can simplify decision-making, improve customer satisfaction, and increase sales. However, modern datasets contain millions of records, which represent only a small fraction of all possible data. Furthermore, much of the information in such sparse datasets may be considered irrelevant for making individual recommendations. As a result, there is a demand for a way to make personalized suggestions from large amounts of noisy data.
Current recommender systems are usually all-in-one applications that provide one type of recommendation. Their inflexible architectures prevent detailed examination of recommendation accuracy and its causes. We introduce a novel architecture model that supports scalable, distributed suggestions from multiple independent nodes. Our model consists of two components, the input matrix generation algorithm and multiple platform-independent combination algorithms. A dedicated input generation component provides the necessary data for combination algorithms, reduces their size, and eliminates redundant data processing. Likewise, simple combination algorithms can produce recommendations from the same input, so we can more easily distinguish between the benefits of a particular combination algorithm and the quality of the data it receives. Such flexible architecture is more conducive for a comprehensive examination of our system.
We believe that a user's future opinion may be inferred from a small amount of data, provided that this data is most relevant. We propose a novel algorithm that generates a more optimal recommender input. Unlike existing approaches, our method sorts the relevant data twice. Doing this is slower, but the quality of the resulting input is considerably better. Furthermore, the modular nature of our approach may improve its performance, especially in the cloud computing context. We implement and validate our proposed model via mathematical modeling, by appealing to statistical theories, and through extensive experiments, data analysis, and empirical studies.
Our empirical study examines the effectiveness of accuracy improvement techniques for collaborative filtering recommender systems. We evaluate our proposed architecture model on the Netflix dataset, a popular (over 130,000 solutions), large (over 100,000,000 records), and extremely sparse (1.1%) collection of movie ratings. The results show that combination algorithm tuning has little effect on recommendation accuracy. However, all algorithms produce better results when supplied with a more relevant input. Our input generation algorithm is the reason for a considerable accuracy improvement.

/pdf/a-distributed-architecture-centric-approach-to-computing-31zmh6iinx.pdf

A distributed, architecture-centric approach to computing accurate recommendations from very large and sparse datasets

Community ecology is often perceived as a mess, given the seemingly vast number of processes that can underlie the many patterns of interest, and the apparent uniqueness of each study system. However, at the most general level, patterns in the composition and diversity of speciesthe subject matter of community ecologyare influenced by only four classes of process: selection, drift, speciation, and dispersal. Selection represents deterministic fitness differences among species, drift represents stochastic changes in species abundance, speciation creates new species, and dispersal is the movement of organisms across space. All theoretical and conceptual models in community ecology can be understood with respect to their emphasis on these four processes. Empirical evidence exists for all of these processes and many of their interactions, with a predominance of studies on selection. Organizing the material of community ecology according to this framework can clarify the essential similarities and dif...

/pdf/conceptual-synthesis-in-community-ecology-52geaid7wu.pdf

Conceptual Synthesis in Community Ecology

.P ]redator-prey interactions have long captured the attention of ecologists, and with good reason. Predation leads inevitably to the removal of prey individuals from ecological systems, which can have major impacts on prey population dynamics and on entire ecosystems. Interest in predator-prey interactions can be traced to the foundations of modern ecology, from early work on predator-prey population dynamics by historical figures such as Lotka, Volterra, and Gause (Taylor 1984) to classic work on the role of predation in regulating species diversity (e.g., Paine 1966). Ecologists continue to be greatly interested in predation and its effects on populations, communities, and ecosystems (Crawley 1992, Carpenter and Kitchell 1993). A perusal of any recent textbook on ecology will not only confirm the importance of predation in modern ecology, but also illustrate the preeminence of the "lethal" perspective on predation-that is, predation is seen as important only insofar as it results in the death of prey and their removal from the system. However, the obvious and sometimes dramatic lethal aspects of predation can obscure the nonlethal effects of the mere presence of predators in an ecological system. In the presence of predators, prey may alter their behavior so that they are more difficult

Nonlethal Effects in the Ecology of Predator-Prey Interactions What are the ecological effects of anti-predator decision-making?

119 Small invertebrates are functionally important in many terrestrial and aquatic ecosystems (Wilson 1992, Freckman et al. 1997, Palmer et al. 1997, Postel and Carpenter 1997). In freshwater sediments, benthic invertebrates are diverse and abundant, but they are often patchily distributed and relatively difficult to sample, especially when they live in deep subsurface sediments. Thus, the species richness and functional importance of freshwater benthic invertebrates generally go unnoticed until unexpected changes occur in ecosystems. Unanticipated changes in freshwater ecosystems are often due to alterations in the complex connections among sediment-dwelling species and associated food webs (e.g., Goedkoop and Johnson 1996, Lodge et al. 1998b, Stockley et al. 1998) or to disturbances, such as floods or drought (e.g., Covich 1993, Power 1995, Johnson et al. 1998), that alter the species composition of the benthos. In addition, benthic species can themselves constitute a disturbance, such as when they transmit diseases. For example, certain benthic invertebrate species (e.g., Tubifex tubifex) serve as parasite-transmitting vectors; if these invertebrates increase in abundance in stream sediments, they may spread a lethal disease to trout, causing trout populations to decline (Brinkhurst 1997). Fish kills may also occur because of increased accumulation of nutrients, which cause formation of toxic algal blooms, deoxygenation of deeper, density-stratified waters, and high concentrations of ammonia or hydrogen sulfide (Covich 1993). The bottom muds of lakes and streams may at first glance appear to be uniform and, therefore, unlikely habitats for high biodiversity. However, physical, chemical, and biological processes create significant horizontal and vertical heterogeneities in the substrata (Figure 1) that provide a physical template for distinct niches (Hutchinson 1993). These sedimentary processes include changes in direction and rates of flows, differential deposition of sediment grain sizes and dead organisms, growth and death of roots, burrowing and sediment reworking, and fecal production by benthic consumers. Microhabitats are also created by chemical gradients and microzonation in concentrations of dissolved oxygen, hydrogen sulfide, ammonia, phosphorus, and other critical chemicals (Groffman and Bohlen 1999). Colwell (1998) emphasizes that such “biocomplexity” of habitats and biological relationships is an important aspect of biodiversity. Bioturbation and other biotic interactions create extensive biocomplexity in freshwater sediments (Charbonneau and Hare 1998). These biocomplexities must be better understood if clean drinking water and recreational uses of fresh waters are to be maintained. Science-based policies require an ecosystem perspective on the multiple roles of many diverse benthic species. Previous studies have often dealt with the “goods” produced by benthic species, such as the quantity of prey items consumed by fish. These goods are clearly important components of food webs, but how their functional relationships respond to changes in species composition are also important. In this article, we highlight examples of how some species have a disproportionately large impact on food-web dynamics and how particular species provide essential ecosystem services. These ecosystem functions include sediment mixing, nutrient cycling, and energy flow through food webs. The Role of Benthic Invertebrate Species in Freshwater Ecosystems

https://www.jstor.org/stable/10.1525/bisi.1999.49.2.119

The Role of Benthic Invertebrate Species in Freshwater Ecosystems: Zoobenthic species influence energy flows and nutrient cycling

The snail Physella virgata virgata, a widely distributed freshwater pulmonate, was observed to change its life-history characteristics in the presence of the crayfish Orconectes virilis in spring-fed Oklahoma streams. These changes were apparently initiated by a water-borne cue released when crayfish fed on conspecific snails. In the presence of the cue, snails exhibited rapid growth rates and little reproduction until they reached a size of about 10 mm after 8 months. In the absence of the cue, snails typically grew to about 4 mm (3.5 months) and then began reproduction. The chemically inducible shift indicates that the life histories of these snails are phenotypically plastic. By increasing the variance associated with size and age of maturity, prey may increase the likelihood of coexisting with seasonal predators.

https://science.sciencemag.org/content/sci/247/4945/949.full.pdf

Predator-Induced Life-History Shifts in a Freshwater Snail

Invasive species, disease vectors, and pathogens affect biodiversity, ecosystem function and services, and human health. Climate change, land use, and transport vectors interact in complex ways to determine the spread of native and non-native invasive species, pathogens, and their effects on ecosystem dynamics. Early detection and in-depth understanding of invasive species and infectious diseases will require an integrated network of research platforms and information exchange to identify hotspots of invasion or disease emergence. Partnerships with state and federal agencies that monitor the spread and impacts of invasive species and pathogens will be critical in developing a national data and research network that can facilitate a full understanding of the resulting effects on ecosystems and society. Citizen science can also play a role; individuals can report new invasions, record phenological changes associated with invasions or disease outbreaks, and can participate in efforts such as the Breeding Bir...

https://esajournals.onlinelibrary.wiley.com/doi/epdf/10.1890/070151

The spread of invasive species and infectious disease as drivers of ecosystem change

We conducted a survey of 198 sites in eight catchments in the Taieri River drainage of the South Island, New Zealand, and found a strong negative association between the distributions of introduced brown trout and native Galaxias vulgaris. Although habitat degradation due to agricultural and forestry practices was associated with lower densities of fish, these reductions were found in all fish species and did not help to explain the trout/galaxiid pattern. Statistical analyses incorporating a variety of physical, chemical and biological variables showed that presence and abundance of G. vulgaris were best predicted by the absence of trout

http://www.jstor.org/stable/pdfplus/3545242.pdf

Fragmented population structure in a native New Zealand fish: an effect of introduced brown trout?

This overview of non-visual communication in freshwater benthic animals emphasizes recent studies of the effect of chemical and mechanical signals on predator-prey interactions of benthic macroinvertebrates and amphibians. Prey species use chemical signals to modify their morphological development, life history strategy, feeding, and predator avoidance behavior. The advantages of chemical signals are that they can be used in dark or turbid environments by animals that do not have image-forming eyes. Chemical signals are more persistent than mechanical signals, and they allow species-level identification of predator species. In streams, prey species may use mechanical signals (hydrodynamic pressure waves or sound) to avoid predators approaching from downstream (a situation characteristic of streams and in which chemical signals are unreliable) and to initiate escape responses. Predators often depend on chemical signals to stimulate or inhibit feeding, and they use species-specific mechanical signals to locate or track prey or potential mates. The exact nature of non-visual signals depends on ecological constraints of both the sender and receiver. Responses to non-visual signals may be adapted to local predator conditions. Non-visual signals are effectively used over a wide range of temporal and spatial scales in all aquatic habitats. Organisms often adjust their responses as ontogenic development results in changing size, diet, and habitat.

Todd A. Crowl

Papers

The Role of Benthic Invertebrate Species in Freshwater Ecosystems: Zoobenthic species influence energy flows and nutrient cycling

Predator-Induced Life-History Shifts in a Freshwater Snail

The spread of invasive species and infectious disease as drivers of ecosystem change

Fragmented population structure in a native New Zealand fish: an effect of introduced brown trout?

Non-visual communication in freshwater benthos: an overview