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

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

/pdf/paml-4-phylogenetic-analysis-by-maximum-likelihood-2gg19rsgos.pdf

PAML 4: Phylogenetic Analysis by Maximum Likelihood

http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

Thank you very much for downloading modern applied statistics with s. As you may know, people have search hundreds times for their favorite readings like this modern applied statistics with s, but end up in harmful downloads. Rather than reading a good book with a cup of coffee in the afternoon, instead they cope with some harmful virus inside their laptop. modern applied statistics with s is available in our digital library an online access to it is set as public so you can download it instantly. Our digital library saves in multiple countries, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the modern applied statistics with s is universally compatible with any devices to read.

Modern Applied Statistics With S

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

/pdf/phylogenies-and-community-ecology-52euwskuu7.pdf

Phylogenies and Community Ecology

The {ITS} region of nuclear ribosomal {DNA}: {A} valuable source of evidence on angiosperm phylogeny

Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here, we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness.

/pdf/historical-biogeography-ecology-and-species-richness-1m3f4luxtw.pdf

Historical biogeography, ecology and species richness

THE SCIENCE OF PLANT SYSTEMATICS - What Do We Mean by Plant? - What Do We Mean by Systematics? - A Phylogenetic Approach - The Practice of Plant Systematics - Why is Systematics Important? - Aims and Organization of This Book - PRINCIPLES OF BIOLOGICAL SYSTEMATICS - What is a Phylogeny? - Determining Evolutionary History - Constructing a Classification - Summary - CLASSIFICATION AND SYSTEM IN FLOWERING PLANTS: THE HISTORICAL BACKGROUND - Classification, Nature, and Stability - Understanding Relationships - Classifications and Memory - Higher Taxa and Their Formation - Plant Groupings - Summary - TAXONOMIC EVIDENCE: STRUCTURAL AND BIOCHEMICAL CHARACTERS - Morphology - Pollination Biology - Inflorescences, Fruits, and Seeds - Anatomy - Embryology - Chromosomes - Palynology - Secondary Plant Compounds - Proteins - Summary - MOLECULAR SYSTEMATICS - Plant Genomes - Generating Molecular Data - Types of Molecular Data - Analysis of Molecular Data - Molecular Characters - Summary - THE EVOLUTION OF PLANT DIVERSITY - Plant Diversity Is the Result of Evolution - Variation in Plant Populations and Species - Speciation - Species Concepts - Summary - AN OVERVIEW OF PLANT EVOLUTION - Endosymbiotic Events - Miscellaneous 'Algae' - Green Plants - Land Plants - Vascular Plants - Seed Plants - Flowering Plants - PHYLOGENETIC RELATIONSHIPS OF LYCOPHYTES, FERNS AND THEIR ALLIES, AND GYMNOSPERMS - Lycophytes - Ferns and Their Allies - Gymnosperms - Cycads - Ginkgos - Conifers - Gnetophytes - PHYLOGENETIC RELATIONSHIPS OF ANGIOSPERMS - 'Basal Families' - Amborellales - Nymphaeales - Austrobaileyales - Magnoliid Complex - Magnoliales - Laurales - Canellales - Piperales - Monocots - Alismatales - Petaloid Monocots (Liliales, Asparagales, Dioscoreales) - Commelinoid Monocots (Arecales, Commelinales, Poales, Zingiberales) - Eudicots (Tricolpates) - 'Basal Tricolpates' - Ranunculales, Proteales, and several small groups - Core Eudicots - Caryophyllid Clade (Caryophyllales, Polygonales) - Santalales - Rosid Clade - Saxifragales - Vitales - Myrtales - Eurosids I (Zygophyllales, Oxalidales, Celastrales, Malpighiales, - Fabales, Rosales, Cucurbitales, Fagales) - Eurosids II (Brassicales, Malvales, Sapindales) - Asterid clade (Sympetalae) - Cornales - Ericales - Euasterids I (Solanales, Gentianales, Lamiales) - Euasterids II (Aquifoliales, Apiales, Dipsacales, Asterales) - - Appendix 1. Botanical Nomenclature - Appendix 2. Specimen Preparation and Identification - Glossary - Taxonomic Index - Subject Index

Plant Systematics: A Phylogenetic Approach

-Methods that use outgroups in the reconstruction of phylogeny are described and evaluated by the criterion of parsimony. By considering the character states and relationships of outgroups, one can estimate the states ancestral for a study group or ingroup, even when several character states are found among the outgroups. Algorithms and rules are presented that find the most parsimonious estimates of ancestral states for binary and multistate characters when outgroup relationships are well resolved. Other rules indicate the extent to which uincertainty about outgroup relationships leads to uncertainty about the ancestral states. The algorithms and rules are based on "simple parsimony" in that convergences and reversals are counted equally. After parsimony is measured locally among the outgroups to estimate ancestral states, parsimony is measured locally within the ingroup, given the ancestral states, to find the ingroup cladogram. This two-step procedure is shown to find the ingroup cladograms that are most parsimonious globally; that is, most parsimonious when parsimony is measured simultaneously over the ingroup and outgroups. However, the two-step procedure is guaranteed to achieve global parsimony only when: (a) outgroup relationships are sufficiently resolved beforehand; (b) outgroup analysis is taken to indicate the state not in the most recent common ancestor of the ingroup, but in a more distant ancestor; and (c) ancestral states are considered while the ingroup is being resolved, not merely added afterward to root an unrooted network. The criterion of global parsimony is then applied to evaluate procedures used when outgroup relationships are poorly resolved. The procedure that chooses as ancestral the state occurring most commonly among the outgroups can sometimes yield cladograms that are not globally parsimonious. By the criterion of global parsimony, the best procedure is one that simultaneously resolves the outgroups and ingroup with the data at hand. Finally, simple parsimony can choose among competing hypotheses, but it often fails to indicate how much confidence can be placed in that choice. [Phylogeny reconstruction; cladistic methods; outgroup analysis; character polarity; parsimony.] This paper explores the use of outgroup analysis in phylogeny reconstruction. When reconstructing a phylogeny, a systematist asks: Given a group of organisms (the ingroup), what are the monophyletic subgroups? If the members of a subgroup share a character state that is derived within the group, the monophyly of this subgroup is corroborated (Hennig, 1966; Wiley, 1975). Hence, systematists attempting to infer phylogenies have sought methods for determining whether a given character state is derived (apomorphic) or ancestral (plesiomorphic). Many methods for assessing the evolutionary polarity of characters have been proposed, including outgroup analysis, ingroup analysis, the ontogenetic method, and the paleontological method. These approaches have been reviewed recently by Crisci and Stuessy (1980), de Jong (1980), Stevens (1980), Arnold (1981), Nelson and Platnick (1981), and others. The methods perhaps most widely accepted today are outgroup analysis and the ontogenetic method, the relative merits of which are still being debated (contrast Nelson [1978] and Patterson [1982] with Lundberg [1973], Wheeler [1981] and Voorzanger and van der Steen [1982]). In its simplest form, outgroup analysis can be summarized by the following rule (Watrous and Wheeler, 1981): For a given character with two or more states within a group, the state occurring in related groups is assumed to be the plesiomorphic state. This rule is inadequate, however, when characters vary among the related groups (the outgroups). Arnold (1981) and Farris (1982) have dealt with some cases of

Michael J. Donoghue

Papers

Phylogenies and Community Ecology

The {ITS} region of nuclear ribosomal {DNA}: {A} valuable source of evidence on angiosperm phylogeny

Historical biogeography, ecology and species richness

Plant Systematics: A Phylogenetic Approach

Outgroup analysis and parsimony