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

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the “Plastisphere”. Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vib...

/pdf/life-in-the-plastisphere-microbial-communities-on-plastic-32nw4vsuum.pdf

Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris

What determines the number and size of the seeds produced by a plant? How often should it reproduce them? How often should a plant produce them? Why and how are seeds dispersed, and what are the implications for the diversity and composition of vegetation? These are just some of the questions tackled in this wide-ranging review of the role of seeds in the ecology of plants. The authors bring together information on the ecological aspects of seed biology, starting with a consideration of reproductive strategies in seed plants and progressing through the life cycle, covering seed maturation, dispersal, storage in the soil, dormancy, germination, seedling establishment, and regeneration in the field. The text encompasses a wide range of concepts of general relevance to plant ecology, reflecting the central role that the study of seed ecology has played in elucidating many fundamental aspects of plant community function.

The ecology of seeds

Cholera, a life-threatening diarrhoeal disease, has afflicted human beings and shaped human history for over two millennia. The disease still kills thousands of people annually. Vibrio cholerae, the etiologic agent of cholera, is endemic to aquatic environments [1], but despite intensive research efforts its ecology remains an enigma. The fatal effects of cholera are mainly due to the toxin produced by specific serogroups (O1 and O139) of V. cholerae [1]. Strains of V. cholerae that belong to serogroups other than O1 and O139, collectively referred to as the non-O1, non-O139 V. cholerae, have also been implicated as etiologic agents of moderate to severe human gastroenteritis [2]. The disease is endemic in Southern Asia and in parts of Africa and Latin America, where outbreaks occur widely and are closely associated with poverty and poor sanitation. The epidemic strains spread across countries and continents over time, giving rise to cholera pandemics [1]. It has been suggested that zooplankton function as a carrier of V. cholerae via ocean currents. However, the mechanism that enables V. cholerae to cross freshwater bodies within a continent, as well as oceans between continents, remains unknown. Here, we put forward a strongly neglected hypothesis that deserves more attention, and discuss evidence from the scientific literature that supports this notion: migratory water birds are possible disseminators of V. cholerae within and between continents.

/pdf/waterfowl-the-missing-link-in-epidemic-and-pandemic-cholera-1iluhofb94.pdf

Waterfowl: the missing link in epidemic and pandemic cholera dissemination?

There are two contradictory approaches to explaining the presence of secondary metabolites in ripe fruits. One holds that they evolved toward enhancing dispersal success (adaptive approach); the other claims that they evolved primarily to deter herbivores from eating leaves and seeds and that their presence in ripe fruits is a byproduct of that function (non-adaptive approach). We tested the validity of three hypotheses of the adaptive approach that explain the presence of secondary metabolites in ripe fruits. We explored the current function of a secondary metabolite, emodin, in Mediterranean buckthorn (Rhamnus alaternus, Rhamnaceae) fruits by relating intraspecific variation and seasonal patterns of concentration to fruit removal and seed damage and by conducting feeding trials with captive birds presented artificial fruits that varied in emodin concentration. The concentration of emodin in the pulp of 10–13 Rhamnus plants from the same population was determined by HPLC every month during two fruiting seasons. Fruit removal by birds and seed predation by invertebrates and microbes were determined for the same plants. Emodin concentration rose during the first stages of ripening, reaching a peak before the fruits were ripe, and then decreased to a minimum when the fruits were ripe. No significant correlation between emodin concentration and ripe fruit removal rate among trees was observed in the first year, whereas in the second year the correlation was positive and significant. Thus, the impact of emodin on fruit selection varied between years, suggesting that emodin concentration does not solely govern fruit selection. A significant negative correlation was found in the first year between emodin concentration and seed predation during the first fruiting month. The yellow-vented bulbul (Pycnonotus xanthopygos), a seed dispersing bird, distinguished between artificial foods that differed in emodin concentration (control, 0.001% and 0.002%), always preferring the lower concentration. In contrast, house sparrows, (Passer domesticus), a seed predator, did not detect such differences in emodin concentration but did distinguish between control foods and food with 0.005% and 0.001% emodin. We suggest that emodin has an ecological role, preventing seed predation by invertebrates and microbes without decreasing fruit removal by avian dispersers.

Impact on fruit removal and seed predation of a secondary metabolite, emodin, in Rhamnus alaternus fruit pulp

The protein content of pulps of 26 fleshy fruit species from east Mediterranean habitats in Israel were estimated using two different methods: (1) the Kjeldahl procedure in which the total recovered nitrogen is multiplied by 6.25 to estimate total proteins, and (2) amino acid analysis by amino acid analyzer. The average protein content obtained by the Kjeldahl procedure was 5.75% (dry weight) while it was only 3.90% when amino acids were analyzed. The higher value of protein content by the Kjeldahl procedure is most likely the result of a relatively high proportion of nonprotein nitrogen compounds (31%) in these pulps. Therefore the 6.25 factor is not valid and a 4.05 factor may be more accurate for assessing the true protein content of these fleshy fruits. The data also suggest that the more accurate estimate of true protein (Y) from Kjeldahl total nitrogen (X) should be based on the highly significant linear regression between these two variables:Y=4.885X−0.6.

Influence of nonprotein nitrogen on estimation of protein from total nitrogen in fleshy fruits

Nectar of many bee flowers contains secondary compounds, which are considered toxic for honeybees on repeated exposure. Although many anecdotal reports indicate the toxicity of secondary compounds to bees, only a few studies have tested the extent of toxicity at different honeybee ages, especially at the larval stages. Honeybees encounter nicotine at trace con- centrations (between 0.1 and 5 ppm) in floral nectar of a few Nicotiana spp. and in Tilia cordata. Adult honeybee workers tolerate these nicotine con- centrations. In controlled nonchoice feeding experiments with caged bees, we investigated the effect of nicotine on hatching success and larval and forager survival. Naturally occurring concentrations of nectar-nicotine did not affect hatching success of larvae or their survival, but the latter was negatively affected by higher concentrations of nicotine (50 ppm). Concentrations of nicotine in fresh honey samples from the hives were 90% lower than the concentrations in the offered experimental sucrose solutions. Our results indi- cate that honeybees can cope with naturally occurring concentrations of nic- otine, without notable mortality, even when consumed in large quantities for more than 3 weeks.

/pdf/the-effects-of-nectar-nicotine-on-colony-fitness-of-caged-4i6forfa5g.pdf

The effects of nectar-nicotine on colony fitness of caged honeybees.

Fire is a common disturbance in the Mediterranean ecosystem. A fire that broke out in the eastern Mediterranean pine forest on Mount Carmel in September 1989 destroyed thousands of hectares of natural forest. We carried out a comparative study of rodent recovery after fire under three different management regimes in order to establish the best treatment for recovery. Rodents were used as ‘bio-indicators’, because of their limited home range, to assess the best management practice to be used in the recovery of the post-fire habitat. Our results show that the three arboreal Palaeoarctic species which lived in this habitat before the fire either died during the fire or left the habitat as a result of its destruction. A succession of rodent species was observed. The untreated burned forest had the highest species diversity in the initial stage, while during a later stage the highest diversity was observed in plots where the burned trees were cut down, the trunks removed and the twigs collected into small piles. The results also suggest that removing the trunks and twigs at the initial stage of recolonization results in a more xeric and warm habitat which will postpone the reinvasion of the forest species.

Ido Izhaki

Papers

Waterfowl: the missing link in epidemic and pandemic cholera dissemination?

Impact on fruit removal and seed predation of a secondary metabolite, emodin, in Rhamnus alaternus fruit pulp

Influence of nonprotein nitrogen on estimation of protein from total nitrogen in fleshy fruits

The effects of nectar-nicotine on colony fitness of caged honeybees.

Changes in rodent community during recovery from fire: relevance to conservation