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.

Rejoinder to Wiens (2008): Phylogenetic niche conservatism, its occurrence and importance

-We report a phylogenetic analysis of approximately 1330 bases of mitochondrial DNA sequence for eight species of the Anolis roquet series (Anolis aeneus, Anolis bonairensis, Anolis extremus, Anolis griseus, Anolis luciae, Anolis richardi, Anolis roquet, Anolis trinitatus). These data contain 410 characters that are parsimony informative for the A. roquet series plus three outgroup species. A parsimony analysis of these data, combined with previously published allozymic data, reveals a single most parsimonious tree with strong support for seven internal branches. Anolis bonairensis and A. luciae are sister taxa and together form a sister taxon to a group containing the other species. Relationships among A. griseus, A. trinitatus, and a clade containing the remaining species are unresolved. Within the latter clade, A. richardi is the sister taxon to a group containing A. aeneus, A. extremus, and A. roquet, with the latter two species being sister taxa. Reanalysis of previously published allozymic data produces no conflicts with the mtDNA tree for wellsupported branches. Parsimony analysis of the combined allozymic and DNA data gives a tree identical in topology to the tree resulting from the DNA analysis alone. In contrast to earlier studies, our phylogenetic analyses indicate that neither the small-bodied (A. aeneus, A. trinitatus) nor the large-bodied (A. griseus, A. richardi) species form monophyletic groups. The Anolis roquet series occupies the southern Lesser Antilles from Martinique to Grenada, including Barbados to the east, as well as two islands in the Venezuelan and Netherlands Antilles to the west (see Fig. 1; Underwood, 1959; Gorman and Dessauer, 1966; Gorman and Atkins, 1967, 1969; Gorman, 1968). Monophyly of this group is supported by allozymic and behavioral data (Gorman and Atkins, 1969). The A. roquet series is phylogenetically distinct from the Anolis bimaculatus species group occupying the northern Lesser Antilles (from Dominica northward), to which it appears not to be closely related (Etheridge, 1960; Gorman and Dessauer, 1966; Gorman and Atkins, 1969; Gorman et al., 1980; Guyer and Savage, 1986, 1992; Jackman et al., 1999). The Grenada and St. Vincent island banks each contain a pair of sympatric species, one large-bodied and the other considerably smaller. The other banks as well as the two western islands each contain single species intermediate in body size (Lazell, 1972; Schoener and Gorman, 1968; Roughgarden, 1995). The natural history of this group has been described by Gorman (1968), Schoener and Gorman (1968), Lazell (1972), and Gorman and Stamm (1975). 2 Corresponding Author. E-mail: creer@biology. wustl.edu Phylogenetic hypotheses for the A. roquet series have been proposed previously by Gorman and Atkins (1969) and Yang et al. (1974), based on karyotypic and allozymic data, and by Lazell (1972), based on morphology. Some immunological data have also been reported (Wyles and Gorman, 1980; Schochat and Dessauer, 1981). Roughgarden (1995) included the A. roquet series in a phylogenetic tree of the entire genus, in which he showed those relationships that appear well supported by the above works. Since the 1970s, many new techniques have been developed for systematic analysis, including statistical methods for assessing confidence in the results, both in terms of whole trees and individual branches. It is now possible to compare trees derived from different datasets in terms of branch support and test a variety of specific phylogenetic hypotheses in a statistically rigorous fashion. Most recently, Giannasi et al. (2000) have published trees derived from analysis of cytochrome b mitochondrial DNA sequence. Jackman et al. (1999) used sequences from the ND2 gene of the mitochondrial genome and adjacent regions to identify large-scale relationships among Anolis lizards. Based on their study, this particular region also appears suitable for analyzing relationships within various Anolis subclades. Here, we present mtDNA sequences from this region for species in the A. This content downloaded from 207.46.13.128 on Wed, 07 Sep 2016 06:32:03 UTC All use subject to http://about.jstor.org/terms SYSTEMATICS OF THE ANOLIS ROQUET SERIES

Systematics of the Anolis roquet Series of the Southern Lesser Antilles

We analyzed the impact of interspecific interactions between two ecologically and morphologically distinct Puerto Rican lizards, Anolis gundlachi and A. evermanni, in an experimental design consisting of six 20 × 20 m plots divided into three blocks, each consisting of a pair of experimental and control plots. We removed A. gundlachi from experimental plots and monitored the response of A. evermanni. The reduction in the number of A. gundlachi resulted in a significant increase in the abundance of both adult and juvenile A. evermanni. We found no evidence for a shift in structural habitat use in A. evermanni in experimental plots. Two possible mechanisms, interspecific competition and intraguild predation, could explain the increase in abundance of A. evermanni after the removal of A. gundlachi. These results make clear that interactions still occur between A. gundlachi and A. evermanni even given their morphological and ecological differences.

An experimental study of interspecific interactions between two Puerto Rican Anolis lizards

revealed an interesting pattern: on most islands with only one species, that species is of intermediate size, but two-species islands usually contain both a large and a small species (Schoener, 1970; Table 1). The evolution of large and small size has often been interpreted as an example of character displacement (e.g., Schoener, 1988b; Williams 1972; Losos, 1990). Roughgarden and associates (e.g., Roughgarden et al., 1987; Roughgarden and Pacala, 1989; Rummel and Roughgarden 1985a) have proposed an alternative hypothesis; they argue that a taxon cycle is operating in the northern Lesser Antilles in which a larger species invades an island occupied by an intermediate-sized species, and both evolve smaller size until the former species is intermediate in size and the latter species is extinct (Fig. 1). Roughgarden and Pacala (1989) reviewed the pertinent data and concluded that the available evidence overwhelmingly favors the taxon-cycle model. Here I argue that much of this evidence is either inconclusive, incorrect, or more consistent with the character-displacement model.

A critical comparison of the taxon-cycle and character-displacement models for size evolution of Anolis lizards in the lesser Antilles

Aim To test the role of climate, dispersal limitation and biotic interactions in limiting species’ distributions within an island adaptive radiation by integrating species traits, phylogeny and estimates of dispersal cost into climate-based species distribution models. Location Hispaniola. Methods Focusing on 26 species of Anolis lizards, we used multivariate adaptive regression splines to evaluate the contribution of climate, species interactions, phylogenetic history and dispersal limitation to species distributional limits. For each species, we mapped the morphological similarity of congenerics using traits of known ecological import and predicted that species would be less likely to occur in climatically suitable areas if they were inhabited by ecologically similar species. Dispersal limitation was incorporated by generating spatially explicit estimates of dispersal cost, based on inferred habitat suitability. We compared models including morphological similarity, dispersal cost, phylogeny and climate with climate-only models. Results were evaluated against a null model that conserved the spatial structure of species occurrences. Results Climate had a dominant role in shaping species distributions. However, for over one-third of species we also found evidence consistent with supplemental effects of species interactions, i.e. ecological niche incumbency. These species were less likely to occur in climatically suitable areas inhabited by a morphologically similar species. Dispersal limitation also supplemented climatic limits in most species. These results were robust to co-variation with phylogeny and to comparison with our null model. Conclusions These results suggest that, rather than act as mutually exclusive alternatives, multiple dimensions of the ecological niche, including climatic limits, biotic interactions and dispersal capacity, interact to shape species distributions and that local interactions can influence the broad-scale geography of species in a predictable way.

Jonathan B. Losos

Papers

Rejoinder to Wiens (2008): Phylogenetic niche conservatism, its occurrence and importance

Systematics of the Anolis roquet Series of the Southern Lesser Antilles

An experimental study of interspecific interactions between two Puerto Rican Anolis lizards

A critical comparison of the taxon-cycle and character-displacement models for size evolution of Anolis lizards in the lesser Antilles

Niche incumbency, dispersal limitation and climate shape geographical distributions in a species-rich island adaptive radiation