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.

Most studies of adaptive radiations focus on morphological aspects of differentiation, yet behavior is also an important component of evolutionary diversification, often mediating the relationship between animal ecology and morphology. In species within radiations that are convergent in ecology and morphology, we then also expect convergence in behavior. Here, we examined 13 Anolis lizard species to determine whether territorial strategies have evolved convergently with morphology and habitat use. We evaluated two aspects of territoriality: behavioral defense of space via territorial displays, and territory overlap within and between sexes. Controlling for the phylogenetic relationships of the taxa in our study, we found that species similar in perch height and diameter convergently evolved patterns of territory overlap, whereas species similar in habitat visibility (the proportion of space that can be seen from a perch) convergently evolved display behavior. We also found that species with greater display time have more extensive male-male territory overlap. This study provides strong evidence for the role of habitat in the evolution of territoriality and suggests that the social structure of a species ultimately evolves in concert with habitat use and morphology.

/pdf/behavioral-convergence-and-adaptive-radiation-effects-of-2vyu8kj43f.pdf

Behavioral convergence and adaptive radiation: effects of habitat use on territorial behavior in Anolis lizards.

The Princeton Guide to Evolution

We analysed the diversification of squamate reptiles (7488 species) based on a new molecular phylogeny, and compared the results to similar estimates for passerine birds (5712 species). The number of species in each of 36 squamate lineages showed no evidence of phylogenetic conservatism. Compared with a random speciation‐extinction process with parameters estimated from the size distribution of clades, the alethinophidian snakes (2600 species) were larger than expected and 13 clades, each having fewer than 20 species, were smaller than expected, indicating rate heterogeneity. From a lineage-through-time plot, we estimated that a provisional rate of lineage extinction (0.66 per Myr) was 94% of the rate of lineage splitting (0.70 per Myr). Diversification in squamate lineages was independent of their stem age, but strongly related to the area of the region within which they occur. Tropical vs. temperate latitude exerted a marginally significant influence on species richness. In comparison with passerine birds, squamates share several clade features, including: (1) independence of species richness and age; (2) lack of phylogenetic signal with respect to clade size; (3) general absence of exceptionally large clades; (4) over-representation of small clades; (5) influence of region size on clade size; and (6) similar rates of speciation and extinction. The evidence for both groups suggests that clade size has achieved long-term equilibrium, suggesting negative feedback of species richness on the rate of diversification.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1420-9101.2007.01388.x

Evolutionary diversification of clades of squamate reptiles.

We document the decimation and recovery of the commonest lizard species, Anolis sagrei, on 66 islands in the Bahamas that were directly hit by Hurricane Floyd in September 1999. Before the hurricane, an island's area was a better predictor of the occurrence of A. sagrei than was its altitude. Immediately after, altitude was a better predictor: Apparently all lizards on islands lower than about 3 meters maximum elevation perished in the storm surge. After about 1 year, area again became the better predictor. By 19 months after the hurricane, A. sagrei populations occurred on 88% of the islands they formerly occupied. Recovery occurred via overwater colonization and propagation from eggs that survived inundation, mechanisms that were enhanced by larger island area. Thus, natural processes first destroyed and then quickly restored a highly regular species-area distribution.

https://science.sciencemag.org/content/sci/294/5546/1525.full.pdf

Natural restoration of the species-area relation for a lizard after a hurricane.

We artificially invaded a set of small islands with the large lizard Leioce- phalus carinatus to determine effects on food-web elements including an intermediate predator, the lizard Anolis sagrei; the latter was previously found to have major, mostly direct effects on web spiders, as well as detectable indirect effects on aerial arthropods (including parasitoids) and leaf damage. In addition to these food-web elements, we mon- itored ground-surface arthropods; they are expected to be affected directly, as well as indirectly via A. sagrei ,b yL. carinatus. Five islands were randomly selected for invasion while six others served as controls. In addition, four islands without A. sagrei were mon- itored to determine the natural state of the sagrei-free food web. We also monitored a variety of A. sagrei's traits, from behavioral through physiological and demographic to morphological, to elucidate the mechanisms whereby L. carinatus might affect the smaller lizard and to evaluate trait-mediated as well as density-mediated effects. Comparison of unmanipulated islands with and without A. sagrei showed that A. sagrei appeared to be affecting web-spider density and diversity, numbers of small aerial arthro- pods, number of large ground-surface arthropods, and two types of leaf damage, scars and mines. All effects were negative save one: Small aerial arthropods were more abundant with A. sagrei; this variable and parasitoid abundance were negatively related to web-spider density, implicating an indirect effect pathway from A. sagrei via web spiders. Introduction of L. carinatus had major and immediate effects on A. sagrei density and perch height; effects on perch diameter, percentage hatchlings, and the width of the body- size distribution followed over time. Behavioral shifts in habitat use continued to the end of the experiment, after changes in population density had mostly leveled off. Adult-male body condition became poorer after introduction of L. carinatus. Among islands, percentage use of the ground was correlated negatively with percentage vegetated area of the island and positively with premanipulation relative hindlimb length. We hypothesize that longer- legged individuals do better on the ground because they are faster there. Conditional ev- idence for an increase in adult-male relative hindlimb length suggested that, when the ground-inhabiting L. carinatus was introduced, such individuals were differentially able to escape predation. Introduction of L. carinatus significantly reversedA. sagrei's effect on number of species and density of web spiders but had no other major effects on lower level food-web elements. Thus, a relatively short-chained (two links) effect, with a relatively strong second link ( A. sagrei on spiders), showed the greatest indirect effect of the manipulation. Another poten- tially strong indirect effect, that on large ground-surface arthropods, did not occur, possibly because of compensatory (direct) predation by L. carinatus. Thus presence of omnivory may also be relevant to whether reversal of effects occurs. Although most A. sagrei effects were not reversed in the time available for the experiment, this may be typical, as natural L. carinatus colonizations can dwindle away to extinction over about the same time span, producing at best only short-term indirect effects. Population-density estimates from other sites and comparisons to other experimental studies suggest that, in general, predators on Anolis may have erratic effects in space and time.

Jonathan B. Losos

Papers

Behavioral convergence and adaptive radiation: effects of habitat use on territorial behavior in Anolis lizards.

The Princeton Guide to Evolution

Evolutionary diversification of clades of squamate reptiles.

Natural restoration of the species-area relation for a lizard after a hurricane.

Predation on a common anolis lizard: can the food-web effects of a devastating predator be reversed?