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

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)

How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.

/pdf/generalized-linear-mixed-models-a-practical-guide-for-3gh61pkir0.pdf

Generalized linear mixed models: a practical guide for ecology and evolution

The harmful effects of close inbreeding have been noticed for many centuries (34, 35, 165). With the rise of Mendelian genetics, it was realized that the main genetic consequence of inbreeding is homozygosis (165, Ch. 2). Two main theories were early proposed to account for inbreeding depression and its converse, heterosis (the increase in vigor observed in an F1 between two inbred lines). These are the overdominance and partial dominance hypotheses, discussed in more detail below. Research into this question has continued up to the present, and this is one of the topics that we discuss. Darwin (35, 36) was the first to point out that the evident adaptations of many plants for ensuring outcrossing could be understood in terms of the selective advantage of avoiding inbreeding depression. We review the evidence that the evolution of breeding systems of animals and plants has been significantly influenced by the occurrence of inbreeding depression. In order to do this, we consider the contemporary genetic theory of inbreeding depression and heterosis, and the experimental data concerning the strength of inbreeding depression. We emphasize data and theory relevant to natural, rather than domesticated, populations as we are chiefly concerned to evaluate the evolutionary significance of inbreeding depression. We do not attempt to give a complete bibliography of this very extensive field but try to concentrate on what seem to be the most significant findings in relation to this aim.

https://www.jstor.org/stable/pdf/2097132.pdf

Inbreeding depression and its evolutionary consequences

Chloroplast DNA (cpDNA) markers and 12 nuclear (random amplified polymorphic DNA, or RAPD) markers were used to examine the distribution of genetic variation among individuals and the genetic and ecological associations in a hybrid iris population. Plants in the population occurred at various distances from the edge of a bayou in a relatively undisturbed mixed hardwood forest and in an adjacent pasture dominated by herbaceous perennials with interspersed oak and cypress trees. The majority of plants sampled possessed combinations of markers from the different Iris species. Genetic markers diagnostic for Iris fulva and I. brevicaulis occurred at high frequencies, whereas markers diagnostic for I. hexagona were infrequent. For the majority of the nuclear markers, significant levels of cytonuclear disequilibria existed because of intraspecific associations among the markers in both the pasture and the forest. The distribution of nuclear markers among individuals was bimodal; intermediate genotypes were absent and the majority of RAPD markers were associated with their intraspecific cpDNA haplotypes. Strong intraspecific associations existed among RAPD markers in the forest, but associations tended to be weaker in the pasture area. Ecological correlations were detected for all but one of the I. fulva and I. brevicaulis RAPD markers. The ecological associations of hybrids similar to I. brevicaulis resembled associations of I. brevicaulis parental genotypes, suggesting that these hybrid genotypes may be relatively fit in the same habitats. The hybrids similar to I. fulva, however, were distributed in habitats that were unique relative to the parental species. The patterns of genetic and environmental associations along with other available data suggest that (1) only advanced generation hybrids were present in the population; (2) formation of F1 hybrids among Louisiana irises is rare, leading to sporadic formation of hybrid populations; and (3) selection and assortative mating have contributed to the formation of hybrid genotypes that tend to be similar to parental genotypes. The patterns of ecological and genetic associations detected in this population suggest that assortative mating and environmental and viability selection are important in the structuring and maintenance of this hybrid zone.

Ecological and genetic associations in an iris hybrid zone.

The application of principles from coalescence theory to genealogical relationships within species can provide insights into the process of diversification and the influence of biogeography on distributional patterns. There are several features that make some organisms more suitable for detailed studies of historical processes; in particular, limited dispersal, which serves to conserve the patterns of genetic variation that developed during colonization. We describe the potential benefits of studies that integrate analyses of genetic variation with information from the fossil pollen record and present recent examples of the application of quantitative methods of phylogeographic analysis.

Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record.

The measurement of fitness is critical to biological research. Although the determination of fitness for some organisms may be relatively straightforward under controlled conditions, it is often a difficult or nearly impossible task in nature. Plants are no exception. The potential for long-distance pollen dispersal, likelihood of multiple reproductive events per inflorescence, varying degrees of reproductive growth in perennials, and asexual reproduction all confound accurate fitness measurements. For these reasons, biomass is frequently used as a proxy for plant fitness. However, the suitability of indirect fitness measurements such as plant size is rarely evaluated. This review outlines the important associations between plant performance, fecundity, and fitness. We make a case for the reliability of biomass as an estimate of fitness when comparing conspecifics of the same age class. We reviewed 170 studies on plant fitness and discuss the metrics commonly employed for fitness estimations. We find that biomass or growth rate are frequently used and often positively associated with fecundity, which in turn suggests greater overall fitness. Our results support the utility of biomass as an appropriate surrogate for fitness under many circumstances, and suggest that additional fitness measures should be reported along with biomass or growth rate whenever possible.

/pdf/is-biomass-a-reliable-estimate-of-plant-fitness-2m1y2dfryd.pdf

Is biomass a reliable estimate of plant fitness

A database of the county distribution of rare vascular plant species endemic to the southeastern United States was compiled in order to review geographic trends. A total of 482 species representing 246 genera in 95 families were identified as rare southeastern endemics. The histogram of total county occurrences for these endemic species is significantly skewed to the right, indicating that those taxa that are endemic to the southeastern United States are typically rare within the region. Six centers of endemism were identified: Central Peninsular Florida, Florida Panhandle, Southern Appalachian Mountains, Tennessee Central Basin, Mid-Atlantic Coastal Plain, and West Gulf Coastal Plain. This identification of geographic trends will assist in the proactive conservation of areas harboring large numbers of endemic taxa, and these data provide the first step towards an integrative understanding of the evolutionary ecology of endemic floras.

Phytogeography of rare plant species endemic to the Southeastern United States.

We compared the levels and distribution of genetic diversity in Eurasian and North American populations of Brachypodium sylvaticum (Huds.) Beauv. (false brome), a newly invasive perennial bunchgrass in western North America. Our goals were to identify source regions for invasive populations, determine the number of independent invasion events, and assess the possibility that postinvasion bottlenecks and hybridization have affected patterns of genetic diversity in the invaded range. We tested the hypothesis that this Eurasian grass was accidentally introduced into two areas in Oregon and one site in California by examining nuclear microsatellites and chloroplast haplotype variation in 23 introduced and 25 native populations. In the invaded range, there was significantly lower allelic richness (RS), observed heterozygosity (HO) and within-population gene diversity (HS), although a formal test failed to detect a significant genetic bottleneck. Most of the genetic variation existed among populations in the native range but within populations in the invaded range. All of the allelic variation in the invaded range could be explained based on alleles found in western European populations. The distribution of identified genetic clusters in the North American populations and the unique alleles associated with them is consistent with two historical introductions in Oregon and a separate introduction to California. Further analyses of population structure indicate that intraspecific hybridization among genotypes from geographically distinct regions of western Europe occurred following colonization in Oregon. The California populations, however, are more likely to be derived from one or perhaps several genetically similar regions in the native range. The emergence and spread of novel recombinant genotypes may be facilitating the rapid spread of this invasive species in Oregon.

Mitchell B. Cruzan

Papers

Ecological and genetic associations in an iris hybrid zone.

Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record.

Is biomass a reliable estimate of plant fitness

Phytogeography of rare plant species endemic to the Southeastern United States.

Evidence for multiple sources of invasion and intraspecific hybridization in Brachypodium sylvaticum (Hudson) Beauv. in North America.