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)

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Allometric scaling relations, including the 3/4 power law for metabolic rates, are characteristic of all organisms and are here derived from a general model that describes how essential materials are transported through space-filling fractal networks of branching tubes. The model assumes that the energy dissipated is minimized and that the terminal tubes do not vary with body size. It provides a complete analysis of scaling relations for mammalian circulatory systems that are in agreement with data. More generally, the model predicts structural and functional properties of vertebrate cardiovascular and respiratory systems, plant vascular systems, insect tracheal tubes, and other distribution networks.

https://science.sciencemag.org/content/sci/276/5309/122.full.pdf

A general model for the origin of allometric scaling laws in biology

All terrestrial ecosystems consist of aboveground and belowground components that interact to influence community- and ecosystem-level processes and properties. Here we show how these components are closely interlinked at the community level, reinforced by a greater degree of specificity between plants and soil organisms than has been previously supposed. As such, aboveground and belowground communities can be powerful mutual drivers, with both positive and negative feedbacks. A combined aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.

http://science.sciencemag.org/content/sci/304/5677/1629.full.pdf

Ecological linkages between aboveground and belowground biota.

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere.

/pdf/effects-of-above-ground-plant-species-composition-and-3xbj7e1uhc.pdf

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

Plant allometry: The scaling of form and process

Flowers of many angiosperm species are well adapted to avoid self-pollination, for instance by temporal and spatial separation of pollen and stigma within the same flower. However, such adaptations do not prevent the transfer of pollen between flowers on the same plant (geitonogamy). Recent empirical studies, aided by advances in field techniques, statistical methods and modelling, show that geitonogamy often is substantial and increases with plant size. Selfing by geitonogamy incurs a fitness cost of reduced pollen export, and recent reports show that seed set can suffer as well, even in self-incompatible species. Geitonogamy has important implications for sex-allocation theory, the evolution of dioecy and other issues in evolutionary biology.

Geitonogamy: The neglected side of selfing

All individuals of all known populations of Banksia goodii were assessed for seed production. Small populations produced no or only a few seeds per unit canopy area. Effects of population size on seed production per unit area and seed production per plant were present over the whole range of population sizes, indicating that even in large populations seed production may still not be at its maximum. Resource differences could not explain this disproportionate decrease in seed production with decline in population size, because there were no differences in soil properties and understorey or overstorey cover between the small and large populations. Although plants in small and large populations were similar in size, seed production per plant was much lower in small populations. This was not because plants in small populations produced fewer cones but because the fraction of these cones that was fertile was much lower. Five of the nine smallest populations (<200 m2) produced no fertile cones over the last 10 years. The number of seeds per fertile cone did not depend on population size. The results are discussed in relation to pollination biology.

Population fragmentation may reduce fertility to zero in Banksia goodii — a demonstration of the Allee effect

The number of interactions with flower visitor species differs considerably among insect pollinated plants. Knowing the causes for this variation is central to the conservation of single species as well as whole plant � /flower visitor communities. Species specific constraints on flower visitor numbers are seldom investigated at the community level. In this study we tested whether flower size parameters set constraints on the morphology of the potential nectar feeding visitors and thus determine the number of visitor species. We studied three possible constraints: the depth and width of tubular structures hiding the nectar (nectar holder depth and width) and the size of flower parts that visitors can land on (size of the alighting place). In addition we assess the role of flower abundance on this relationship. We hypothesized that the stronger size constraints and the smaller flower abundance, the smaller the number of visitor species will be. Our study of a Mediterranean plant � /flower visitor community revealed that nectar holder depth, nectar holder width and number of flowers explained 71% of the variation in the number of visitor species. The size of the alighting place did not restrict the body length of the visitors and was not related to visitor species number. In a second step of the analyses we calculated for each plant species the potential number of visitors by determining for each insect species of the local visitor pool whether it passed the morphological limits set by the plant. These potential numbers were highly correlated with the observed numbers (r 2 � /0.5, p B /0.001). For each plant species we tested whether the observed visitors were a random selection out of these potential visitors by comparing the mean of the observed and expected proboscis length distributions. For most plant species the observed mean was not significantly different from the random means. Our findings shed light on the way plant � /flower visitor networks are structured. Knowing the constraints on interaction patterns will be an important prerequisite to formulate realistic null models and understand patterns of resource partitioning as well as coevolutionary processes.

/pdf/size-constraints-and-flower-abundance-determine-the-number-1ukrdm0q1u.pdf

Peter G. L. Klinkhamer

Papers

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

Plant allometry: The scaling of form and process

Geitonogamy: The neglected side of selfing

Population fragmentation may reduce fertility to zero in Banksia goodii — a demonstration of the Allee effect

Size constraints and flower abundance determine the number of interactions in a plant /flower visitor web