Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.

Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Contact: peter@biomatters.com

Geneious Basic

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

An overview of the self-organizing map algorithm, on which the papers in this issue are based, is presented in this article.

The Self-Organizing Map

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.

/pdf/founding-events-in-species-invasions-genetic-variation-138f2ii5cu.pdf

Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions

Although genetic methods of species identification, especially DNA barcoding, are strongly debated, tests of these methods have been restricted to a few empirical cases for pragmatic reasons. Here we use simulation to test the performance of methods based on sequence comparison (BLAST and genetic distance) and tree topology over a wide range of evolutionary scenarios. Sequences were simulated on a range of gene trees spanning almost three orders of magnitude in tree depth and in coalescent depth; that is, deep or shallow trees with deep or shallow coalescences. When the query's conspecific sequences were included in the reference alignment, the rate of positive identification was related to the degree to which different species were genetically differentiated. The BLAST, distance, and liberal tree-based methods returned higher rates of correct identification than did the strict tree-based requirement that the query was within, but not sister to, a single-species clade. Under this more conservative approach, ambiguous outcomes occurred in inverse proportion to the number of reference sequences per species. When the query's conspecific sequences were not in the reference alignment, only the strict tree-based approach was relatively immune to making false-positive identifications. Thresholds affected the rates at which false-positive identifications were made when the query's species was unrepresented in the reference alignment but did not otherwise influence outcomes. A conservative approach using the strict tree-based method should be used initially in large-scale identification systems, with effort made to maximize sequence sampling within species. Once the genetic variation within a taxonomic group is well characterized and the taxonomy resolved, then the choice of method used should be dictated by considerations of computational efficiency. The requirement for extensive genetic sampling may render these techniques inappropriate in some circumstances.

Testing the Reliability of Genetic Methods of Species Identification via Simulation

Species Delimitation is a plugin to the Geneious software to support the exploration of species boundaries in a gene tree. The user assigns taxa to putative species and the plugin computes statistics relating to the probability of the observed monophyly or exclusivity having occurred by chance in a coalescent process. It also assesses the within and between species genetic distances to infer the probability with which members of a putative species might be identified successfully with tree-based methods.

Species delimitation – a geneious plugin for the exploration of species boundaries

In recent years, research has shown that geographical variation in mitochondrial DNA of commensal rats provides a strong signal of human dispersal and migration. However, interpretation of genetic variation is complicated by the presence of multiple species of Rattus especially in Island Southeast Asia, by the occurrence of some of these Rattus sp. as subfossils in archaeological and natural sites, and by the difficulty of osteological identification of these remains. Amplification of DNA from ancient sources usually yields only small fragments (∼ 200 bp). We assessed whether we could identify Rattus sp. reliably with DNA barcoding using cytochrome oxidase I (COI) sequences, or tree-based methods using D-loop, cytochrome b and COI sequences. Species forming well-differentiated clades in a molecular phylogeny were accurately identified by both methods, even when we used short DNA fragments. Identification was less accurate for paraphyletic and polyphyletic species. We suggest that taxonomic revisions that recognize cryptic or polytypic species will lead to even greater accuracy of DNA-based identification methods.

Identifying Rattus species using mitochondrial DNA.

Mosaic structure of human coronavirus NL63, one thousand years of evolution.

We know relatively little of the distribution of microbial communities generally. Significant work has examined a range of bacterial communities, but the distribution of microbial eukaryotes is less well characterized. Humans have an ancient association with grape vines (Vitis vinifera) and have been making wine since the dawn of civilization, and fungi drive this natural process. While the molecular biology of certain fungi naturally associated with vines and wines is well characterized, complementary investigations into the ecology of fungi associated with fruiting plants is largely lacking. DNA sequencing technologies allow the direct estimation of microbial diversity from a given sample, avoiding culture-based biases. Here, we use deep community pyrosequencing approaches, targeted at the 26S rRNA gene, to examine the richness and composition of fungal communities associated with grapevines and test for geographical community structure among four major regions in New Zealand (NZ). We find over 200 taxa using this approach, which is 10-fold more than previously recovered using culture-based methods. Our analyses allow us to reject the null hypothesis of homogeneity in fungal species richness and community composition across NZ and reveal significant differences between major areas. Â© 2014 The Authors.

/pdf/pyrosequencing-reveals-regional-differences-in-fruit-2f24v2oczp.pdf

Howard A. Ross

Papers

Testing the Reliability of Genetic Methods of Species Identification via Simulation

Species delimitation – a geneious plugin for the exploration of species boundaries

Identifying Rattus species using mitochondrial DNA.

Mosaic structure of human coronavirus NL63, one thousand years of evolution.

Pyrosequencing reveals regional differences in fruit-associated fungal communities.