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.

Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non-ecological factors play the dominant role in the evolution of spatial genetic divergence.

Quantifying the roles of ecology and geography in spatial genetic divergence

We examine phylogenetic relationships among anoles using mitochondrial DNA se- quences from the NADH dehydrogenase subunit 2 gene (ND2) andve transfer-RNA genes repre- senting 1,455 alignable base positions and 866 phylogenetically informative characters (parsimony criterion). We also present 16 morphological characters for phylogenetic analysis. Our analyses yielded poorly-supported nodes deep in the anole tree but many well-supported nodes for more recent phylogenetic divergences. We test the hypothesis that the major clades of anoles form a hard polytomy and present a general statistical framework for testing hypotheses of simultaneous branching of lineages by using molecular sequence data. Our results suggest that rapid diversi- �cation early in the evolutionary history of anoles explains why numerous researchers have had difculty reconstructing well-supported dichotomous phylogenetic trees for anoles. ( Anolis; mito- chondrial DNA; parametric bootstrap; permutation test; phylogeny; polytomy.)

Phylogenetic Relationships and Tempo of Early Diversification in Anolis Lizards

Sexual size dimorphism (SSD) is the evolutionary result of selection operating differently on the body sizes of males and females. Anolis lizard species of the Greater Antilles have been classified into ecomorph classes, largely on the basis of their structural habitat (perch height and diameter). We show that the major ecomorph classes differ in degree of SSD. At least two SSD classes are supported: high SSD (trunk-crown, trunk-ground) and low SSD (trunk, crown-giant, grass-bush, twig). Differences cannot be attributed to an allometric increase of SSD with body size or to a phylogenetic effect. A third explanation, that selective pressures on male and/or female body size vary among habitat types, is examined by evaluating expectations from the major relevant kinds of selective pressures. Although no one kind of selective pressure produces expectations consistent with all of the information, competition with respect to structural habitat and sexual selection pressures are more likely possibilities than competition with respect to prey size or optimal feeding pressures. The existence of habitat-specific sexual dimorphism suggests that adaptation of Anolis species to their environment is more complex than previously appreciated.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/j.0014-3820.2000.tb00026.x

The relationship between sexual size dimorphism and habitat use in greater antillean anolis lizards

Aim We investigate biogeographic relationships within the lizard genus Anolis Daudin, 1802 to test the hypothesis that the mainland (Central and South American) Norops-clade species descended from a West Indian Anolis ancestor. Previous hypotheses have suggested that close island relatives of mainland Norops species (the Cuban Anolis sagrei and Jamaican A. grahami series) represent over-water dispersal from a mainland ancestor. These previous hypotheses predict that the A. sagrei and A. grahami series should be phylogenetically nested within a Norops clade whose ancestral geography traces to the mainland. If Norops is West Indian in origin, then West Indian species should span the deepest phylogenetic divergences within the Norops clade.



Location  Central and South America and West Indian islands.



Methods  The phylogenetic relationships of Anolis lizards are reconstructed from aligned DNA sequences using both parsimony and Bayesian approaches. Hypotheses are tested in two ways: (1) by reconstructing the ancestral geographic location for the Norops clade using Pagel & Lutzoni's (2002) Bayesian approach, and (2) by testing alternative topological arrangements via Wilcoxon Signed-Ranks tests (Templeton, 1983) and Shimodaira–Hasegawa tests (Shimodaira & Hasegawa, 1999).



Results  Our evidence supports an origin of mainland Norops anoles from a West Indian ancestor. A West Indian ancestor to the Norops clade is statistically supported, and alternatives to the biogeographic pattern [Cuban (Jamaican, Mainland)] are statistically rejected by Shimodaira–Hasegawa tests, although not by Wilcoxon Signed-Ranks tests.



Main conclusions  Our data support the hypothesis of a West Indian origin for mainland Norops. This result contradicts previous hypotheses and suggests that island forms may be an important source for mainland biodiversity.

/pdf/mainland-colonization-by-island-lizards-1zxtjqkbjq.pdf

Mainland colonization by island lizards

The role of behaviour in evolutionary change has long been debated. On the one hand, behavioural changes may expose individuals to new selective pressures by altering the way that organisms interact with the environment, thus driving evolutionary divergence. Alternatively, behaviour can act to retard evolutionary change: by altering behavioural patterns in the face of new environmental conditions, organisms can minimize exposure to new selective pressures. This constraining influence of behaviour has been put forward as an explanation for evolutionary stasis within lineages and niche conservatism within clades. Nonetheless, the hypothesis that behavioural change prevents natural selection from operating in new environments has never been experimentally tested. We conducted a controlled and replicated experimental study of selection in entirely natural populations; we demonstrate that lizards alter their habitat use in the presence of an introduced predator, but that these behavioural shifts do not prevent patterns of natural selection from changing in experimental populations.

Jonathan B. Losos

Papers

Quantifying the roles of ecology and geography in spatial genetic divergence

Phylogenetic Relationships and Tempo of Early Diversification in Anolis Lizards

The relationship between sexual size dimorphism and habitat use in greater antillean anolis lizards

Mainland colonization by island lizards

Predator-induced behaviour shifts and natural selection in field-experimental lizard populations