抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

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

Part I. Ethnographic Research: Ethnography and Culture. Language and Field Work. Informants. Part II. The Developmental Research Sequences: Locating an Informant. Interviewing an Informant. Making an Ethnographic Record. Asking Descriptive Questions. Analyzing Ethnographic Interviews. Making a Domain Analysis. Asking Structural Questions. Making a Taxonomic Analysis. Asking Contrast Questions. Making a Componential Analysis. Discovering Cultural Themes. Writing an Ethnography. Notes. Appendices: A Taxonomy of Ethnographic Questions. Developmental Research Sequence Writing Tasks. The Development Research Sequence Method. Bibliography. Index.

The ethnographic interview

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)

Land use has generally been considered a local environmental issue, but it is becoming a force of global importance. Worldwide changes to forests, farmlands, waterways, and air are being driven by the need to provide food, fiber, water, and shelter to more than six billion people. Global croplands, pastures, plantations, and urban areas have expanded in recent decades, accompanied by large increases in energy, water, and fertilizer consumption, along with considerable losses of biodiversity. Such changes in land use have enabled humans to appropriate an increasing share of the planet’s resources, but they also potentially undermine the capacity of ecosystems to sustain food production, maintain freshwater and forest resources, regulate climate and air quality, and ameliorate infectious diseases. We face the challenge of managing trade-offs between immediate human needs and maintaining the capacity of the biosphere to provide goods and services in the long term.

/pdf/global-consequences-of-land-use-map7a6ziel.pdf

Global Consequences of Land Use

One of the least understood aspects of population biology is community evolution-the evolutionary interactions found among different kinds or organisms where exchange of genetic information among the kinds is assumed to be minimal or absent. Studies of community evolution have, in general, tended to be narrow in scope and to ignore the reciprocal aspects of these interactions. Indeed, one group of organisms is all too often viewed'as a kind of physical constant. In an extreme example a parasitologist might not consider the evolutionary history and responses of hosts, while a specialist in vertebrates might assume species of vertebrate parasites to be invariate entities. This viewpoint is one factor in the general lack of progress toward the understanding of organic diversification. One approach to what we would like to call coevolution is the examination of patterns of interaction between two major groups of organisms with a close and evident ecological relationship, such as plants and herbivores. The considerable amount of information available about butterflies and their food plants make them particularly suitable for these investigations. Further, recent detailed investigations have provided a relatively firm basis for statements about the phenetic relationships of the various higher groups of Papilionoidea (Ehrlich, 1958, and unpubl.). It should, however, be remembered that we are considering the butterflies as a model. They are only one of the many groups of herbivorous organisms coevolving with plants. In this paper, we shall investigate the relationship between butterflies and their food

/pdf/butterflies-and-plants-a-study-in-coevolution-59gysvp1oi.pdf

Butterflies and plants: a study in coevolution

Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them. Different visualizations of species biodiversity. ( A ) The distributions of 9927 bird species. ( B ) The 4964 species with smaller than the median geographical range size. ( C ) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. ( D ) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org. Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity. Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.

The biodiversity of species and their rates of extinction, distribution, and protection

Habitat destruction, especially of the humid forests in the tropics, is the main cause of the species extinctions happening now New work documents the uneven, highly clumped distribution of vulnerable species on the Earth, and pinpoints 25 so-called ‘biodiversity hotspots’ Seventeen of them are tropical forest areas, and here reduction of natural habitat is disproportionately high Nonetheless, identification of this pattern should enable resources for conservation to be better focused

Biodiversity. Extinction by numbers

Angiosperm Biogeography and Past Continental Movements

▪ Abstract Biodiversity, a central component of Earth's life support systems, is directly relevant to human societies. We examine the dimensions and nature of the Earth's terrestrial biodiversity and review the scientific facts concerning the rate of loss of biodiversity and the drivers of this loss. The estimate for the total number of species of eukaryotic organisms possible lies in the 5–15 million range, with a best guess of ∼7 million. Species diversity is unevenly distributed; the highest concentrations are in tropical ecosystems. Endemisms are concentrated in a few hotspots, which are in turn seriously threatened by habitat destruction—the most prominent driver of biodiversity loss. For the past 300 years, recorded extinctions for a few groups of organisms reveal rates of extinction at least several hundred times the rate expected on the basis of the geological record. The loss of biodiversity is the only truly irreversible global environmental change the Earth faces today.

/pdf/global-state-of-biodiversity-and-loss-1t62mkt7ml.pdf

Peter H. Raven

Papers

Butterflies and plants: a study in coevolution

The biodiversity of species and their rates of extinction, distribution, and protection

Biodiversity. Extinction by numbers

Angiosperm Biogeography and Past Continental Movements

Global State of Biodiversity and Loss