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

Habitat availability underpins the diversity and distribution of benthic marine communities. Sponges are significant structural components of seabeds; therefore, understanding sponge-community associations are important for the effective management of marine biodiversity. Invertebrate communities were quantified from 11 sponge species having distinct morphologies from Ningaloo Reef (tropical) and Rottnest Island (temperate), Western Australia. Communities from substrate adjacent to sponges were additionally sampled for comparisons to sponge-associated fauna. Gross and fine-scale morphological features of sponge host species were quantified to assess their effects on faunal abundance and diversity. A total of 3966 individuals from 125 taxa were extracted, showing low co-occurrences of taxa from both sponges and the surrounding substrate (Ningaloo 8.9%; Rottnest 11.2%). Four out of the 11 sponges supported higher fauna abundance compared to their surrounding substrate, including Haliclona sp. NTM148 (Ningaloo; 1.21 ± 0.54 N.cm−3, 60 × higher than substrate) and Monanchora clathrata (Rottnest; 2.87 ± 1.7 N.cm−3, 32 × higher than substrate). These communities were dominated by the barnacle Acastinae sp.4 (100%) and sedentary polychaete Spionidae sp. 1 (99%), respectively, highlighting strong host-specific associations. Sponge size (volume), % of internal space, minimum diameter of internal space, and gross morphological complexity were important at explaining variation in faunal assemblage, with larger sponges having more internal space of larger minimum canal diameter supporting higher community abundance. This study highlights the significance of large and long-lived sponges as sources of unique marine biodiversity that are yet to be discovered and the importance of sponge gardens for the conservation of cryptic marine biodiversity.

Sponges in shallow tropical and temperate reefs are important habitats for marine invertebrate biodiversity

On high-relief reefs, research has shown that the abundance and diversity of non-cryptic fishes is greater in kelp beds cleared of their canopy compared to those left intact. Greater abundance may be caused by an increase in the availability of food resources associated with damaged kelp, exposed understory algae and newly colonised turfing algae. We investigate the effect of a disturbance to the kelp canopy on two response variables, the abundance and feeding behaviour of six common non-cryptic fish species. We found that Kyphosus sydneyanus (herbivore) and Notolabrus parilus (generalist carnivore) move preferentially into 1-month old clearance plots to feed, whereas Kyphosus cornelii and Odax cyanomelas only graze in these plots incidentally. Kyphosus sydneyanus responded with greater abundance and feeding rate in 1-month old clearance plots that were dominated by the microscopic filamentous brown alga, Hincksia mitchelliae. Small-scale disturbances that remove kelps from kelp canopies result in a shift...

The effect of kelp bed disturbance on the abundance and feeding behaviour of fishes on high-relief reefs

Ecklonia radiata is the main foundation species in Australian temperate reefs, yet little has been published on its reproduction and how this may change across its depth range (1-50+ m). In this study, we examined differences in sporophyte morphology and zoospore production during a reproductive season and across four depths (7, 15, 25, and 40 m). Additionally, we examined differences in germination rate, survival, and morphological traits of gametophytes obtained from these four depths, cultured under the same light and temperature conditions. Multivariate morphology of sporophytes differed significantly between deep (~40 m) and shallow sites (7 and 15 m), but individual morphological traits were not significantly different across depths. Total spore production was similar across depths but the peak of zoospore release was observed in February at 15 m of depth (6,154 zoospores · mm-2 of tissue) and the minimum observed in January at 7, 25, and 40 m (1,141, 987, and 214 zoospores · mm-2 of tissue, respectively). The source depth of zoospores did not have an influence in the germination rate or the survival of gametophytes, and only gametophytes sourced from 40 m sites presented significantly less surface area and number of branches. Overall, these results indicate that E. radiata's reproductive performance does not change across its depth range and that kelp beds reproducing in deeper areas may contribute to the replenishment of their shallow counterparts. We propose that deep kelps may constitute a mechanism of resilience against climate change and anthropogenic disturbances.

Gary A. Kendrick

Papers

Sponges in shallow tropical and temperate reefs are important habitats for marine invertebrate biodiversity

The effect of kelp bed disturbance on the abundance and feeding behaviour of fishes on high-relief reefs

Reproductive Output, Synchrony across Depth and Influence of Source Depth in the Development of Early Life stages of Kelp.

Designs for remote sampling: review, discussion, examples of sampling methods and layout and scaling issues

Mapping Historical Changes in Seagrass Beds Bordering Owen Anchorage, Western Australia