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

A catalogue of the marine macroalgae found in the western islands of the Recherche Archipelago, Western Australia, with notes on their distribution in relation to island location, depth, and exposure to wave energy

Seeds of Australian species of the seagrass genus Posidonia are covered by a membranous wing that we hypothesize plays a fundamental role in seed establishment in sandy, wave swept marine environments. Dimensions of the seed and membrane were quantified under electron microscopy and micro-CT scans, and used to model rotational, drag and lift forces. Seeds maintain contact with the seabed in the presence of strong turbulence: the larger the wing, the more stable the seed. Wing surface area increases from P. sinuosa < P. australis < P.coriacea correlating with their ability to establish in increasingly energetic environments. This unique seed trait in a marine angiosperm corresponds to adaptive pressures imposed on seagrass species along 7,500 km of Australia’s coastline, from open, high energy coasts to calmer environments in bays and estuaries.

/pdf/a-novel-adaptation-facilitates-seed-establishment-under-1sbo73vnp2.pdf

A novel adaptation facilitates seed establishment under marine turbulent flows

Dynamic Bayesian Networks (DBNs) provide a versatile platform for predicting and analysing the behaviour of complex systems As such, they are well suited to the prediction of complex ecosystem population trajectories under anthropogenic disturbances such as the dredging of marine seagrass ecosystems However, DBNs assume a homogeneous Markov chain whereas a key characteristics of complex ecosystems is the presence of feedback loops, path dependencies and regime changes whereby the behaviour of the system can vary based on past states This paper develops a method based on the small world structure of complex systems networks to modularise a non-homogeneous DBN and enable the computation of posterior marginal probabilities given evidence in forwards inference It also provides an approach for an approximate solution for backwards inference as convergence is not guaranteed for a path dependent system When applied to the seagrass dredging problem, the incorporation of path dependency can implement conditional absorption and allows release from the zero state in line with environmental and ecological observations As dredging has a marked global impact on seagrass and other marine ecosystems of high environmental and economic value, using such a complex systems model to develop practical ways to meet the needs of conservation and industry through enhancing resistance and/or recovery is of paramount importance

/pdf/dynamic-bayesian-network-inferencing-for-non-homogeneous-23gatzr4k7.pdf

Dynamic Bayesian network inferencing for non‐homogeneous complex systems

As concentrations of atmospheric CO2 increase, mean temperatures across the globe rise, the carbon system equilibrium in the ocean shifts, and pH is reduced in a process termed Ocean Acidification (OA). These changes can dramatically alter seagrass meadows as both temperature and pH fundamentally influence biochemistry and physiology of plants. Seagrass responses to climate change are species-specific and dependent on interactions with other factors such as light intensity, nutrient availability and competition. The majority of seagrasses appear limited by the availability of dissolved inorganic carbon at current ocean pH, suggesting that rates of photosynthesis and growth are likely to increase with OA. Short- and intermediate term laboratory experiments have shown an increase in photosynthetic rates to increased pCO2. Longer-term studies (>1 year) indicate enhanced shoot proliferation resulting in meadows with high shoot density. Studies utilizing natural gradients in pCO2 that exist near shallow volcanic CO2 vents have shown that, overall, seagrasses appear to benefit from OA. Seagrasses photosynthesize across a range in temperatures, but rapidly decline above thermal optima. Respiration rates increase with warming at a faster rate than photosynthesis and reduces the overall photosynthesis-to-respiration ratio, and thus growth. While seagrasses can recover from moderate temperature stress, extreme temperatures result in mortality. Future changes in seagrass species distributions are predicted as sensitive species shift poleward. Foundation species, like seagrasses, have a large influence on their environment and their loss can significantly impact the functioning of the whole ecosystem. Despite a recent increase in climate-change research, we lack an understanding of how seagrass meadows are going to respond to the combined pressures of warming and OA. It is particularly difficult to predict longer-term responses and possible adaptation, and efforts should be focused in this area to determine how we can manage seagrasses to maximize resilience to climate change.

Global Warming and Ocean Acidification: Effects on Australian Seagrass Ecosystems

A recent analysis of herbarium records back to the 1940s suggests temperate
seaweeds on both east and west coasts of Australia have retreated south 10-50 km per
decade as waters have warmed. A recent extreme warming event (marine heatwave)
in Western Australia caused substantial changes to seaweed habitats, including a
reduction in large habitat forming species. In eastern Tasmania, a substantial decline
in algal habitat is associated with southward expansion of a grazing sea urchin aided
by the strengthening of the East Australian Current and warmer temperatures. Warming will reduce the resilience of macroalgal habitats to other stressors such as
pollution. Temperate species will contract their ranges southwards and tropical
species expand their ranges further south. Many temperate species, found only in
Australia, are at risk of extinction in the next 50-100 years. Extreme events (storms,
heat waves, etc) will increase in frequency and magnitude and drive shifts in species’
distributions and interactions. 

IMOS Autonomous Underwater Vehicle Facility will provide long-term monitoring
of water properties and temperate reefs at key locations in Qld, NSW, Tas and WA.
Several research projects focusing on climate change and temperate macroalgae are
under way. These focus both on establishing the range of impacts as well as the
mechanistic relationships which drive impacts of climate change.

Gary A. Kendrick

Papers

A catalogue of the marine macroalgae found in the western islands of the Recherche Archipelago, Western Australia, with notes on their distribution in relation to island location, depth, and exposure to wave energy

A novel adaptation facilitates seed establishment under marine turbulent flows

Dynamic Bayesian network inferencing for non‐homogeneous complex systems

Global Warming and Ocean Acidification: Effects on Australian Seagrass Ecosystems

Macroalgae and Temperate Rocky Reefs