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 lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

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 global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat-fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat-fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land-sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options.

https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/10-1510.1

The value of estuarine and coastal ecosystem services

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 km(2) yr(-1) since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% yr(-1) before 1940 to 7% yr(-1) since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

/pdf/accelerating-loss-of-seagrasses-across-the-globe-threatens-a5a3ugal7q.pdf

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

Changes in seagrass coverage on Success and Parmelia Banks, Western Australia (1965 to 1995)

Communities: Herbivory Mat Vanderklift1,7, Richard Pillans1,7 , Lisa De Wever1,7, Gary Kendrick2,7, Andrea Zavala-Perez2,7, Adriana Verges3,7, Ruby Garthwin3,7, Grzegorz Skrzypek4,7, Katherine Cure5,7, Camilla Piggott2,7, Daniel Oades6,7, Phillip McCarthy6,7, Kevin George6,7, Trevor Sampi6,7, Dwayne George6,7, Chris Sampi6,7, Zac Edgar6,7, Kevin Dougal6,7, Azton Howard6,7 1CSIRO Marine and Atmosphere, Indian Ocean Marine Research Centre, Crawley, Western Australia 2School of Biological Sciences and Oceans Institute, The University of Western Australia, Crawley, Western Australia 3School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 4West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Western Australia 5Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Western Australia 6Bardi Jawi Rangers, One Arm Point, Western Australia 7Western Australian Marine Science Institution, Perth, Western Australia

Key Ecological Processes in Kimberley Benthic Communities: Herbivory

This project was funded by the Western Australian Marine Science Institution as part of the WAMSI Dredging Science Node, Theme 9 (Effects of dredging-related pressures on critical ecological processes), and made possible through investment from Chevron Australia, Woodside Energy Limited, BHP Billiton and coinvestment from the WAMSI Joint Venture partners.

/pdf/predicting-the-temporal-response-of-seagrass-meadows-to-ge48ryrfwb.pdf

Predicting the temporal response of seagrass meadows to dredging using Dynamic Bayesian Networks

ABSTRACT Plants endure environmental stressors via adaptation and phenotypic plasticity. Studying these mechanisms in seagrasses is extremely relevant as they are important primary producers and functionally significant carbon sinks. These mechanisms are not well understood at the tissue level in seagrasses. Using RNA-seq, we generated transcriptome sequences from tissue of leaf, basal leaf meristem and root organs of Posidonia australis, establishing baseline in situ transcriptomic profiles for tissues across a salinity gradient. Samples were collected from four P. australis meadows growing in Shark Bay, Western Australia. Analysis of gene expression showed significant differences between tissue types, with more variation among leaves than meristem or roots. Gene ontology enrichment analysis showed the differences were largely due to the role of photosynthesis, plant growth and nutrient absorption in leaf, meristem and root organs, respectively. Differential gene expression of leaf and meristem showed upregulation of salinity regulation processes in higher salinity meadows. Our study highlights the importance of considering leaf meristem tissue when evaluating whole-plant responses to environmental change. This article has an associated First Person interview with the first author of the paper.

/pdf/tissue-specific-transcriptome-profiles-identify-functional-2imy6zt4.pdf

Tissue-specific transcriptome profiles identify functional differences key to understanding whole plant response to life in variable salinity

Shellsand Dredging Environmental Management Programme. Project S1: ecological significance of seagrasses calcium carbonate and nitrogen turnover on Success Bank, Western Australia.

Gary A. Kendrick

Papers

Changes in seagrass coverage on Success and Parmelia Banks, Western Australia (1965 to 1995)

Key Ecological Processes in Kimberley Benthic Communities: Herbivory

Predicting the temporal response of seagrass meadows to dredging using Dynamic Bayesian Networks

Tissue-specific transcriptome profiles identify functional differences key to understanding whole plant response to life in variable salinity

Shellsand Dredging Environmental Management Programme. Project S1: ecological significance of seagrasses calcium carbonate and nitrogen turnover on Success Bank, Western Australia.