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

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)

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.

Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx.

Contact: rod.peakall@anu.edu.au

GenAlEx 6.5

Genetics and analysis of quantitative traits

A DNA test to sex most birds.

Population genetic theory predicts that plant populations will exhibit internal spatial autocorrelation when propagule flow is restricted, but as an empirical reality, spatial structure is rarely consistent across loci or sites, and is generally weak. A lack of sensitivity in the statistical procedures may explain the discrepancy. Most work to date, based on allozymes, has involved pattern analysis for individual alleles, but new PCR-based genetic markers are coming into vogue, with vastly increased numbers of alleles. The field is badly in need of an explicitly multivariate approach to autocorrelation analysis, and our purpose here is to introduce a new approach that is applicable to multiallelic codominant, multilocus arrays. The procedure treats the genetic data set as a whole, strengthening the spatial signal and reducing the stochastic (allele-to-allele, and locus-to-locus) noise. We (i) develop a very general multivariate method, based on genetic distance methods, (ii) illustrate it for multiallelic codominant loci, and (iii) provide nonparametric permutational testing procedures for the full correlogram. We illustrate the new method with an example data set from the orchid Caladenia tentaculata, for which we show (iv) how the multivariate treatment compares with the single-allele treatment, (v) that intermediate frequency alleles from highly polymorphic loci perform well and rare alleles poorly, (vi) that a multilocus treatment provides clearer answers than separate single-locus treatments, and (vii) that weighting alleles differentially improves our resolution minimally. The results, though specific to Caladenia, offer encouragement for wider application.

/pdf/spatial-autocorrelation-analysis-of-individual-multiallele-286x81x1b5.pdf

Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure.

The "sexually deceptive" orchid Chiloglottis trapeziformis attracts males of its pollinator species, the thynnine wasp Neozeleboria cryptoides, by emitting a unique volatile compound, 2-ethyl-5-propylcyclohexan-1,3-dione, which is also produced by female wasps as a male-attracting sex pheromone.

The Chemistry of Sexual Deception in an Orchid-Wasp Pollination System

Only orchids affect pollination by the deceptive sexual attraction of male insects, a syndrome particularly well developed in Australia. We examined the ecological and genetic consequences of exclusive pollination by sexually attracted male thynnine wasps in the orchid Caladenia tentaculata. Male wasps respond rapidly to flowers artificially presented in I X I m2 experimental patches. Sixty of 287 wasps approached within centimeters of the flower, but did not land. Of the remaining 79% who made floral, contact, only 7.5% attempted copulation, the step critical for pollination. Wasps only rarely moved among patches (19% of flights) and none attempted copulation a second time, resembling observations in natural populations. We confirmed outcrossing and long distance pollen flow by monitoring how colored pollen moved in natural populations. Pollen movements approximated a linear rather than a leptokurtic distribution (mean distance: 17 m; maximum: 58 m). Pollinator visits varied independently of flower density in three of four populations with most solitary flowers being visited. Allozyme analysis revealed within-population fixation indices (F) close to zero and low levels of differentiation (FST) among populations. Despite behavioral evidence for long distance pollen flow, significant local genetic structure exists, perhaps reflecting restricted seed dispersal. Long distance pollen flow in C. tentaculata may therefore promote outbreeding by minimizing pollen transfers among related neighbors. Although this species is self-compatible, outcrossed progeny develop significantly faster than selfed progeny. Effective pollination at low flower densities could accentuate this advantage. The data are consistent with the predictions that deceptive pollination will result in long distance pollen flow, which may be of selective advantage at low density. Comparative studies of how food reward, food deceptive, and sexual deceptive pollination systems vary within a phylogenetic framework could further illuminate the evolution of sexual deception.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1996.tb03611.x

Ecological and genetic consequences of pollination by sexual deception in the orchid caladenia tentactulata.

Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major driver that shapes patterns of genetic diversity in many natural populations. We outline how disturbance influences genetic diversity through changes in both selective processes and demographically driven, selectively neutral processes. Our review highlights the opportunities and challenges presented by genetic approaches, such as landscape genomics, for better understanding and predicting the demographic and evolutionary responses of natural populations to disturbance. Developing this understanding is now critical because disturbance regimes are changing rapidly in a human-modified world.

/pdf/how-does-ecological-disturbance-influence-genetic-diversity-51ash2qj3e.pdf

Rod Peakall

Papers

GenAlEx 6.5

Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure.

The Chemistry of Sexual Deception in an Orchid-Wasp Pollination System

Ecological and genetic consequences of pollination by sexual deception in the orchid caladenia tentactulata.

How does ecological disturbance influence genetic diversity