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

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

Citation classic - optimal foraging - a selective review of theory and tests

List of contributors Habitats and regional perspectives: S.J. Hawkins, R.G. Hartnoll, J.M. Kain, & T.A. Norton: Plant-animal interactions on hard substrata in the Northeast Atlantic R.L. Vadas & R.W. Elner: Plants-animal interactions in the Northwest Atlantic M.S. Foster: Plant animal interactions in the Northeast Pacific: the importance of grazing to seaweed evolution and assemblage structure D.M. John, J.H. Price, & G.W. Lawson: Tropical East Atlantic and islands: plant-animal interactions on tropical shores free of biotic reefs Deborah M. Brosnan: Ecology of tropical rocky shores: plant-animal interactions in tropical and temperate latitudes K. Reise: Grazing on sediment shores R.J. Orth: A perspective on plant-animal interactions in seagrasses: physical and biological determinants influencing plant and animal abundance L. Mazzella, M.C. Buia, M.C. Gambi, M. Lorenti, G.F. Russo, M.B. Scipione, & V. Zupo: Plant-animal trophic relationships in the posidonia oceanica ecosystem of the Mediterranean Sea: a review G.A. Williams & R. Seed: Interactions between macrofaunal epiphytes and their host algae N.V.C. Polunin & D.W. Klumpp: A trophodynamic model of fish production on a windward reef tract Processes and types of plant-animal interaction: Susan H. Brawley: Mesograzers B.L. Bayne & A.J.S. Hawkins: Herbivory in benthic suspension-feeding molluscs M.G. Chapman & A.J. Underwood: Foraging behaviour of marine benthic grazers M.E. Hay & W. Fenical: Chemical mediation of seaweed-herbivore interactions M.H. Horn: Herbivorous fish: feeding and digestion mechanisms B. Santelices: Digestion survival of algae: an overview A.N.C. Morse: Role of algae in the recruitment of marine invertebrate G.M. Branch, J.M. Harris, C. Parkins, R.H. Bustamente, & S. Eckhout: Algal gardening by marine grazers: a comparison of the ecological effects of territorial fish and limpets W.P. Sousa & J.H. Connell: Grazing and succession A.J. Underwood: Competition and marine plant-animal interactions R.S. Steneck: Plant-herbivore coevolution: a reappraisal from the marine realm and its fossil record T. Spencer: Bioerosion and biogeomorphology Endosymbiosis: P.S. Spencer-Davies: Endosymbiosis in marine cnidarians Summary and future view: A.J. Underwood: Summary and future prospects for plant-animal interactions Index List of Systematics Association Publications.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0025315400053492

Plant-animal interactions in the marine benthos

Preface 1 The shore environment 2 The diversity of shore organisms 3 Coping with life on the shore: adaptations of littoral organisms 4 Primary producers on the shore: the autotrophs 5 Utilizing autotrophic resources: the grazers 6 Suspension feeders: how to live on floating food 7 Eating flesh: the predators 8 Vertical distributions: 'zonation' and its causes 9 How organisms are gathered together: communities on the shore and the effects of wave exposure 10 The functioning of rocky shore communities 11 Human influences on rocky shores 12 Methods and experimental approaches Appendix: Name changes of ecologically important taxa Further reading References Index

The biology of rocky shores

/pdf/habitat-partitioning-and-thermal-tolerance-in-a-tropical-exuu0j21en.pdf

Habitat partitioning and thermal tolerance in a tropical limpet, Cellana grata

The relative importance of habitat complexity and surface area in assessing biodiversity: Fractal application on rocky shores

SUMMARY Contemporary theory for thermal adaptation of ectothermic metazoans focuses on the maximization of energy gain and performance (locomotion and foraging). Little consideration is given to the selection for mechanisms that minimize resting energy loss in organisms whose energy gain is severely constrained. We tested a hypothetical framework for thermal performance of locomotor activity (a proxy for energy gain) and resting metabolism (a proxy for energy loss) in energetically compromised snails in the littoral fringe zone, comparing this with existing theory. In contrast to theory, the thermal ranges and optima for locomotor performance and metabolic performance of Echinolittorina malaccana are mismatched, and energy gain is only possible at relatively cool temperatures. To overcome thermal and temporal constraints on energy gain while experiencing high body temperatures (23–50°C), these snails depress resting metabolism between 35 and 46°C (thermally insensitive zone). The resulting bimodal relationship for metabolism against temperature contrasts with the unimodal or exponential relationships of most ectotherms. Elevation of metabolism above the breakpoint temperature for thermal insensitivity (46°C) coincides with the induction of a heat shock response, and has implications for energy expenditure and natural selection. Time-dependent mortality is initiated at this breakpoint temperature, suggesting a threshold above which the rate of energy demand exceeds the capacity for cellular energy generation (rate of ATP turnover). Mortality in a thermal range that elevates rather than limits aerobic metabolism contrasts with the hypothesis that cellular oxygen deficiency underlies temperature-related mortality. The findings of this study point to the need to incorporate aspects of resting metabolism and energy conservation into theories of thermal adaptation.

Gray A. Williams

Papers

Plant-animal interactions in the marine benthos

The biology of rocky shores

Habitat partitioning and thermal tolerance in a tropical limpet, Cellana grata

The relative importance of habitat complexity and surface area in assessing biodiversity: Fractal application on rocky shores

Thermal adaptation in the intertidal snail Echinolittorina malaccana contradicts current theory by revealing the crucial roles of resting metabolism