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

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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

Cause, conseguenze e strategie di mitigazione Proponiamo il primo di una serie di articoli in cui affronteremo l’attuale problema dei mutamenti climatici. Presentiamo il documento redatto, votato e pubblicato dall’Ipcc - Comitato intergovernativo sui cambiamenti climatici - che illustra la sintesi delle ricerche svolte su questo tema rilevante.

/pdf/climate-change-2007-the-physical-science-basis-1x93ttz9jt.pdf

Climate Change 2007: The Physical Science Basis.

Most heat shock proteins (Hsp) function as molecular chaperones that help organisms to cope with stress of both an internal and external nature. Here, we review the recent evidence of the relationship between stress resistance and inducible Hsp expression, including a characterization of factors that induce the heat shock response and a discussion of the associated costs. We report on studies of stress resistance including mild stress, effects of high larval densities, inbreeding and age on Hsp expression, as well as on natural variation in the expression of Hsps. The relationship between Hsps and life history traits is discussed with special emphasis on the ecological and evolutionary relevance of Hsps. It is known that up-regulation of the Hsps is a common cellular response to increased levels of non-native proteins that facilitates correct protein folding/refolding or degradation of non-functional proteins. However, we also suggest that the expression level of Hsp in each species and population is a balance between benefits and costs, i.e. a negative impact on growth, development rate and fertility as a result of overexpression of Hsps. To date, investigations have focused primarily on the Hsp70 family. There is evidence that representatives of this Hsp family and other molecular chaperones play significant roles in relation to stress resistance. Future studies including genomic and proteonomic analyses will increase our understanding of molecular chaperones in stress research.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1461-0248.2003.00528.x

The evolutionary and ecological role of heat shock proteins

Adaptation of Drosophila to temperature extremes: bringing together quantitative and molecular approaches

Upper thermal limits vary less than lower limits among related species of terrestrial ectotherms. This pattern may reflect weak or uniform selection on upper limits, or alternatively tight evolutionary constraints. We investigated this issue in 94 Drosophila species from diverse climates and reared in a common environment to control for plastic effects that may confound species comparisons. We found substantial variation in upper thermal limits among species, negatively correlated with annual precipitation at the central point of their distribution and also with the interaction between precipitation and maximum temperature, showing that heat resistance is an important determinant of Drosophila species distributions. Species from hot and relatively dry regions had higher resistance, whereas resistance was uncorrelated with temperature in wetter regions. Using a suite of analyses we showed that phylogenetic signal in heat resistance reflects phylogenetic inertia rather than common selection pressures. Current species distributions are therefore more likely to reflect environmental sorting of lineages rather than local adaptation. Similar to previous studies, thermal safety margins were small at low latitudes, with safety margins smallest for species occupying both humid and dry tropical environments. Thus, species from a range of environments are likely to be at risk owing to climate change. Together these findings suggest that this group of insects is unlikely to buffer global change effects through marked evolutionary changes, highlighting the importance of facilitating range shifts for maintaining biodiversity.

Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically

Extreme environments and adaptation.- The evolution of plants in metal-contaminated environments.- Responses of aquatic organisms to pollutant stress: Theoretical and practical implications.- Conifers from the cold.- Genetic variation and environmental stress.- Phenotypic plasticity and fluctuating asymmetry as responses to environmental stress in the butterflyBicyclus anynana.- Environmental stress and the expression of genetic variation.- Worldwide latitudinal clines for the alcohol dehydrogenase polymorphism in Drosophila melanogaster: What is the unit of selection?.- Stress and metabolic regulation inDrosophila.- Acclimation and response to thermal stress.- Phenotypic and evolutionary adaptation of a model bacterial system to stressful thermal environments.- Ecological and evolutionary physiology of heat shock proteins and the stress response inDrosophila: Complementary insights from genetic engineering and natural variation.- High-temperature stress and the evolution of thermal resistance inDrosophila.- Stress, selection and extinction.- Genetic and environmental stress, and the persistence of populations.- Adaptation and extinction in changing environments.- Environmental stress and evolution: A theoretical study.- Stress, developmental stability and sexual selection.- Evolution and stress.- Genetic variability and adaptation to stress.- Stress-resistance genotypes, metabolic efficiency and interpreting evolutionary change.- The Plus ca change model: Explaining stasis and evolution in response to abiotic stress over geological timescales.

/pdf/environmental-stress-adaptation-and-evolution-an-overview-53i2gihmn7.pdf

Environmental stress, adaptation and evolution: an overview

http://www.mus-nh.city.osaka.jp/yokogawa/document/20101214TRG.pdf

Volker Loeschcke

Papers

The evolutionary and ecological role of heat shock proteins

Adaptation of Drosophila to temperature extremes: bringing together quantitative and molecular approaches

Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically

Environmental stress, adaptation and evolution: an overview

Conservation genetics in transition to conservation genomics