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

Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

http://www.therenegadecell.com/wiki/images/0/0d/NEJM-2012-366%2810%29-883.pdf

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-kappaBeta pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.

/pdf/the-landscape-of-somatic-copy-number-alteration-across-human-2stjg261iq.pdf

The landscape of somatic copy-number alteration across human cancers

Cancers evolve by a reiterative process of clonal expansion, genetic diversification and clonal selection within the adaptive landscapes of tissue ecosystems. The dynamics are complex, with highly variable patterns of genetic diversity and resulting clonal architecture. Therapeutic intervention may destroy cancer clones and erode their habitats, but it can also inadvertently provide a potent selective pressure for the expansion of resistant variants. The inherently Darwinian character of cancer is the primary reason for this therapeutic failure, but it may also hold the key to more effective control.

Clonal evolution in cancer

We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence. Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets.

/pdf/gistic2-0-facilitates-sensitive-and-confident-localization-5clseou2er.pdf

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.

Neoplasms are microcosms of evolution. Within a neoplasm, a mosaic of mutant cells compete for space and resources, evade predation by the immune system and can even cooperate to disperse and colonize new organs. The evolution of neoplastic cells explains both why we get cancer and why it has been so difficult to cure. The tools of evolutionary biology and ecology are providing new insights into neoplastic progression and the clinical control of cancer.

Cancer as an evolutionary and ecological process.

Patterns of association among bottlenose dolphins resident in Shark Bay, Western Australia were analyzed using party membership data. Parties contained an average of 4.8 individuals, but party size and composition were unstable. While these temporary parties often contained both males and females, long term consistent associations generally were between members of the same sex. The highest association coefficients, resulting from very frequent co-occurrence within parties were between males and between mothers and offspring. Males formed subgroups of two or three individuals who consistently associated with each other, and these were stable over periods of at least seven years in some cases. Male subgroups preferentially associated with particular other male subgroups. Females associated most consistently with other females, although not to the same extent as some males. Female associations were better described as a network rather than discrete subgroups. Male-female associations were generally inconsistent and depended in part on female reproductive state. Mothers and their offspring associated very consistently for at least 4 years.

https://www.jstor.org/stable/pdfplus/4535060.pdf

Sex Differences in Patterns of Association Among Indian Ocean Bottlenose Dolphins

Wild chimpanzees form temporary parties that vary in size and composition. Previous studies have revealed considerable intraspecific variation in party compositions. We examined patterns of association among age, sex, and reproductive classes of chimpanzees at Ngogo in the Kibale National Park, Uganda. We employed a class-based association index and a randomization procedure to control for confounding factors and to test for differences between classes. Results indicate that males associated with other males significantly more than expected if all classes behaved equivalently, while females generally associated with individuals of the same sex less than expected. To interpret these patterns we used two additional indices that separate associations into two components: general gregariousness and preference for particular classes of associates. Males and estrous females were more gregarious than other classes, while anestrous females were less so. After controlling for general gregariousness, adult males as a class showed no specific preference for associating with each other. Anestrous females preferred each other as party members, and estrous females avoided each other. These results are consistent with previous findings that adult males are more gregarious than females. They diverge from the standard picture of chimpanzee society, however, by suggesting a mutual affinity among anestrous females, but not among adult males as a class.

/pdf/general-gregariousness-and-specific-social-preferences-among-4uhbmbhpic.pdf

John W. Pepper

Papers

Cancer as an evolutionary and ecological process.

Sex Differences in Patterns of Association Among Indian Ocean Bottlenose Dolphins

General Gregariousness and Specific Social Preferences among Wild Chimpanzees

Relatedness in Trait Group Models of Social Evolution

Influence of competitors on caching behaviour in the common raven,Corvus corax