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

https://www.cs.princeton.edu/~schapire/papers/ecolmod.pdf

Maximum entropy modeling of species geographic distributions

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

This book brings together a wealth of scientific findings and ecological knowledge to survey what we have learned about the "Wet Tropics" rainforests of North Queensland, Australia This interdisciplinary text is the first book to provide such a holistic view of any tropical forest environment, including the social and economic dimensions

Towards an understanding of vertebrate biodiversity in the Australian wet tropics

https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05776

Predicting species abundance by implementing the ecological niche theory

The patterns of composition and distribution of vertebrate fauna in Queensland's tropical savannas are poorly known. The sandstone landscapes of White Mountains National Park are considered to be significant for fauna given its geographical position on the Great Dividing Range. A survey at White Mountains National Park was undertaken in order to determine the species present, and place them in the context of the assemblages recorded within the Desert Uplands Bioregion. Standardised trapping and incidental data collection techniques were used and a total of 122 vertebrate fauna species (53 being new to the park) were identified. The fauna assemblage contains a mix of vertebrates with some affiliation to north-eastern Queensland tropical savannas (e.g. Anomalopus gowi, Uperoleia lithomoda, Chaerephon jobensis), more mesic east coastal environments (e.g. Glaphyromorphus punctulatus, Planigale maculata, Rattus sordidus) and species distributed generally within and west of the Desert Uplands (e.g. Pseudomys desertor, Ctenotus rosarium, Gehyra variegata, Lerista wilkinsi).

/pdf/vertebrate-fauna-survey-of-white-mountains-national-park-in-4sepvwoi1d.pdf

Vertebrate fauna survey of White Mountains National Park in the Desert Uplands Bioregion, central-north Queensland

This study examined the spatial patterns of vertebrate biodiversity, with an emphasis on mammals, in the Australian Wet Tropics biogeographic region over a range of spatial scales. Regional patterns of diversity were described on the basis of a review and collation of all available data on vertebrate distributions. The highest species diversity of vertebrates was found in sclerophyll habitats (approximately 388 species). Rainforest was considerably less species-rich with about 259 vertebrate species; however, regional endemism was much higher in rainforest (25%) than in the combined sclerophyll habitats (4%). Although there was no consistent latitudinal or altitudinal dine in diversity, there was a consistent turnover in the assemblage composition of vertebrates, both altitudinally and latitudinally. Habitat diversity at the landscape scale was consistently important in explaining the variance in patterns of species richness.

The number of regionally endemic species of vertebrates and the proportion of regional endemics present in each sub-region were both related to the geographic shape and area of sub-regional patches of rainforest. Shape had a more significant influence on regional endemism than area, while area had a stronger influence on species richness. These patterns were similar for all terrestrial vertebrate classes.

Mammal assemblages were examined in more detail: multivariate analyses suggested five different geographically separated rainforest mammal assemblages. The most diverse was found in the central uplands (Atherton Tableland) with a decrease in diversity to the north and south, and with decreasing altitude. The most diverse areas were characterised by large areas of rainforest with a rounder shape (low shape index), high annual rainfall, consistent rainfall in the dry season and a diversity of rainfall regimes.

The combination of rainforest area and shape explained most of the variance (r2 = 0.74) in the patterns of species richness of rainforest mammals. Various measures of habitat diversity were also dependent on area, and a similar degree of the variance in species richness (r2 = 0.78) was explained by using rainforest shape and habitat diversity variables (rainfall and vegetation diversity) and excluding area. This suggests that the effect of area on the patterns of species richness was primarily due to its positive influence on habitat heterogeneity. Analysis of the mammalian guild structure indicated that it was the number of species within guilds that most strongly affected patterns of species richness, although the number of guilds also had an effect. Most of the variance in species richness could be attributed to three guilds: arboreal folivores, small scansorial and small scansorial folivore-omnivores.

The results suggest that habitat heterogeneity and patterns of localised extinctions (species sifting) during historical contractions of the rainforest have been extremely important processes in determining regional patterns of vertebrate biodiversity in Australia's wet tropical rainforests.

An investigation of the local-scale patterns of mammal diversity was undertaken on the southern Atherton Tableland Spotlighting and live trapping were used to examine the relationships between the composition of the mammal assemblage and habitat structure over several spatial scales. The results showed that the structure of the mammal assemblages was closely correlated with vegetation structure. The presence or absence of specific guilds was related to vegetation complexity, although total species richness was not. Local species richness of ground-dwelling mammals was mostly a product of the spatial variability in assemblage structure (b diversity), which was related to the spatial variability in vegetation structure.

The effect of spatial scale is crucial to the understanding of the generality of processes which limit or promote biodiversity. Each spatial scale represents a nested hierarchy within the larger scales. The available species pool at a given spatial scale constrains the upper limit of species richness possible at the smaller scales while spatial patterns within a scale are determined by processes acting at that scale. This study examined patterns of diversity over a range of spatial scales and conceptual models are presented which describe the different spatial scales and the variety of processes which act at each spatial scale.

Spatial patterns of vertebrate biodiversity and assemblage structure in the rainforests of the Australian wet tropics

CLIMATE CHANGE is predicted to result in a worldwide loss of biodiversity, with extinctions becoming increasingly common in the future. The climate is changing at an ever more rapid rate, impacting on individuals and populations, through to community interactions and ecosystem function. Climate change will likely reduce worldwide biodiversity through negative effects on already extinction-prone species, such as endemics and those at the top of the food chain. This will likely result in a more homogeneous fauna and flora worldwide which is dominated by generalist taxa, which are able to adapt to the changing climatic conditions.

Stephen E. Williams

Papers

Towards an understanding of vertebrate biodiversity in the Australian wet tropics

Predicting species abundance by implementing the ecological niche theory

Vertebrate fauna survey of White Mountains National Park in the Desert Uplands Bioregion, central-north Queensland

Spatial patterns of vertebrate biodiversity and assemblage structure in the rainforests of the Australian wet tropics

Climate Change and Extinctions