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

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

Summary
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.

2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.

4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

/pdf/phytools-an-r-package-for-phylogenetic-comparative-biology-yli0omoidd.pdf

phytools: an R package for phylogenetic comparative biology (and other things)

The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal α = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformat...

/pdf/testing-for-phylogenetic-signal-in-comparative-data-3lvcin7t3t.pdf

Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.

/pdf/phylogenetic-niche-conservatism-phylogenetic-signal-and-the-2d4tp4t7ju.pdf

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

A genetic paradox1,2 exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction1,3,4. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs5,6. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed7.

/pdf/genetic-variation-increases-during-biological-invasion-by-a-37rl4o29f0.pdf

Genetic variation increases during biological invasion by a Cuban lizard

The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.

/pdf/contingency-and-determinism-in-replicated-adaptive-1qeufzqe42.pdf

Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards

Adaptive radiation, which results when a single ancestral species gives rise to many descendants, each adapted to a different part of the environment, is possibly the single most important source of biological diversity in the living world. One of the best-studied examples involves Caribbean Anolis lizards. With about 400 species, Anolis has played an important role in the development of ecological theory and has become a model system exemplifying the integration of ecological, evolutionary, and behavioral studies to understand evolutionary diversification. This major work, written by one of the best-known investigators of Anolis, reviews and synthesizes an immense literature. Jonathan B. Losos illustrates how different scientific approaches to the questions of adaptation and diversification can be integrated and examines evolutionary and ecological questions of interest to a broad range of biologists.

Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles

Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods—such as direct measurements of selection or investigations of the functional correlates of trait evolution—to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution.

https://dash.harvard.edu/bitstream/handle/1/9938750/Losos_ConvergenceAdaptation.pdf?sequence=2

Jonathan B. Losos

Papers

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Genetic variation increases during biological invasion by a Cuban lizard

Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards

Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles

Convergence, adaptation, and constraint