A novel exploratory method for visual recombination detection

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the highway plot and the occupancy plot - that graphically portray phylogenetic inhomogeneity along an alignment, and can be viewed as a synthesis of two widely used but unrelated methods: bootscanning and quartet-mapping. To illustrate the method, simulated data and HIV-1 and influenza A datasets are investigated

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants

Noroviruses are the most common cause of viral gastroenteritis. An increase in the number of globally reported norovirus outbreaks was seen the past decade, especially for outbreaks caused by successive genogroup II genotype 4 (GII.4) variants. Whether this observed increase was due to an upswing in the number of infections, or to a surveillance artifact caused by heightened awareness and concomitant improved reporting, remained unclear. Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s. We collected 1383 partial polymerase and 194 full capsid GII.4 sequences. A Bayesian MCMC coalescent analysis revealed an increase in the number of GII.4 infections during the last decade. The GII.4 strains included in our analyses evolved at a rate of 4.3–9.0×10−3 mutations per site per year, and share a most recent common ancestor in the early 1980s. Determinants of adaptation in the capsid protein were studied using different maximum likelihood approaches to identify sites subject to diversifying or directional selection and sites that co-evolved. While a number of the computationally determined adaptively evolving sites were on the surface of the capsid and possible subject to immune selection, we also detected sites that were subject to constrained or compensatory evolution due to secondary RNA structures, relevant in virus-replication. We highlight codons that may prove useful in identifying emerging novel variants, and, using these, indicate that the novel 2008 variant is more likely to cause a future epidemic than the 2007 variant. While norovirus infections are generally mild and self-limiting, more severe outcomes of infection frequently occur in elderly and immunocompromized people, and no treatment is available. The observed pattern of continually emerging novel variants of GII.4, causing elevated numbers of infections, is therefore a cause for concern

Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean)

Phaseolus vulgaris is a major food crop grown and consumed around the world. A new world vegetable, the common bean underwent two separate domestication events, both pre-Columbus. These events generated two different land races, the Mesoamerican and Andean, named for the area where the domestication took place. Since the initial domestications the land races have been generally evenly cultivated, but despite its popularity the common bean has only very recently been fully sequenced. One of the issues faced by bean growers worldwide is Common Bacterial Blight (CBB). A disease caused by Xanthomonas axonopodis, CBB causes crop loses ranging from 20–40% every year but does not affect all species within Phaseolus evenly; P. acutifolius, for example, shows an innate resistance to CBB. To leverage this advantage, researchers at the University of Guelph, in partnership with the Ontario Agricultural College, developed a cultivar of Mesoamerican P. vulgaris that was introgressed with PI440795, a P. acutifolius accession, and backcrossed repeatedly with several other Mesoamerican P. vulgaris accessions to generate ‘OAC-Rex’, a plant that displays the crop-desired traits of P. vulgaris and the disease resistance traits of P. acutifolius. Genetic introgression is the process of crossing distantly related organisms followed by repeated backcrossing, resulting in a viable offspring that displays characteristics of each parent. Though rarely occurring, it can be observed in both plants and animals and is often exploited in a crop development context to generate new cultivars. Unfortunately, though regularly observed, introgression has been followed on a predominantly phenotypic level, usually many generations after the event, and as such molecular aspects of this phenomenon are largely unknown.By studying OAC-Rex, PI440795, and G-19833 (an Andean cultivar whose whole-genome has been published) introgression was examined directly and a method for the detection of regions within the introgressed genome uniquely donated from either paren

A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations

Analysing pig class II mayor histocompatibility complex (MHC) molecules is mainly related to antigen presentation. Identifying frequently-occurring alleles in pig populations is an important aspect to be considered when developing peptide-based vaccines. Colombian creole pig populations have had to adapt to local conditions since entering Colombia; a recent census has shown low amounts of pigs which is why they are considered protected by the Colombian government. Commercial hybrids are more attractive regarding production. This research has been aimed at describing the allele distribution of Colombian pigs from diverse genetic backgrounds and comparing Colombian SLA-DRB1 locus diversity to that of internationally reported populations. Twenty SLA-DRB1 alleles were identified in the six populations analysed here using sequence-based typing. The amount of alleles ranged from six (Manta and Casco Mula) to nine (San Pedreño). Only one allele (01:02) having > 5% frequency was shared by all three commercial line populations. Allele 02:01:01 was shared by five populations (around > 5% frequency). Global FST indicated that pig populations were clearly structured, as 20.6% of total allele frequency variation was explained by differences between populations (FST = 0.206). This study’s results confirmed that the greatest diversity occurred in wild boars, thereby contrasting with low diversity in domestic pig populations.This work was supported by the Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A)

Analysis of recombination in molecular sequence data

We present the new and fast method Recco for analyzing a multiple alignment regarding recombination. Recco is based on a dynamic program that explains one sequence in the alignment with the other sequences using mutation and recombination. The dynamic program allows for an intuitive visualization of the optimal solution and also introduces a parameter α controlling the number of recombinations in the solution. Recco performs a parametric analysis regarding α and orders all pareto-optimal solutions by increasing number of recombinations. α is also directly related to the Savings value, a quantitative and intuitive measure for the preference of recombination in the solution. The Savings value and the solutions have a simple interpretation regarding the ancestry of the sequences in the alignment and it is usually easy to understand the output of the method. The distribution of the Savings value for non-recombining alignments is estimated by processing column permutations of the alignment and p-values are provided for recombination in the alignment, in a sequence and at a breakpoint position. Recco also uses the p-values to suggest a single solution, or recombinant structure, for the explained sequence. Recco is validated on a large set of simulated alignments and has a recombination detection performance superior to all current methods. The analysis of real alignments confirmed that Recco is among the best methods for recombination analysis and further supported that Recco is very intuitive compared to other methods.Wir präsentieren Recco, eine neue und schnelle Methode zur Analyse von Rekombinationen in multiplen Alignments. Recco basiert auf einem dynamischen Programm, welches eine Sequenz im Alignment durch die anderen Sequenzen im Alignment rekonstruiert, wobei die Operatoren Mutation und Rekombination erlaubt sind. Das dynamische Programm ermöglicht eine intuitive Visualisierung der optimalen Lösung und besitzt einen Parameter α, welcher die Anzahl der Rekombinationsereignisse in der optimalen Lösung steuert. Recco führt eine parametrische Analyse bezüglich des Parameters α durch, so dass alle pareto-optimalen Lösungen nach der Anzahl ihrer Rekombinationsereignisse sortiert werden können. α steht auch direkt in Beziehung mit dem sogenannten Savings-Wert, der die Neigung zum Einfügen von Rekombinationsereignissen in die optimale Lösung quantitativ und intuitiv bemisst. Der Savings-Wert und die optimalen Lösungen haben eine einfache Interpretation bezüglich der Historie der Sequenzen im Alignment, so dass es in der Regel leicht fällt, die Ausgabe von Recco zu verstehen. Recco schätzt die Verteilung des Savings-Werts für Alignments ohne Rekombinationen durch einen Permutationstest, der auf Spaltenpermutationen basiert. Dieses Verfahren resultiert in p-Werten für Rekombination im Alignment, in einer Sequenz und an jeder Position im Alignment. Basierend auf diesen p-Werten schlägt Recco eine optimale Lösung vor, als Schätzer für die rekombinante Struktur der erklärten Sequenz. Recco wurde auf einem großen Datensatz simulierter Alignments getestet und erzielte auf diesem Datensatz eine bessere Vorhersagegüte in Bezug auf das Erkennen von Alignments mit Rekombination als alle anderen aktuellen Verfahren. Die Analyse von realen Datensätzen bestätigte, dass Recco zu den besten Methoden für die Rekombinationsanalyse gehört und im Vergleich zu anderen Methoden oft leichter verständliche Resultate liefert

Revision of the genus Epiphyas (Lepidoptera, Tortricidae, Tortricinae, Archipini s. Str.)

Epiphyas is the largest genus of moths within the Australian Tortricinae and the only indigenous tortricine genus of economic importance in Australian orchards. Epiphyas postvittana (the light-brown apple moth) is a widely polyphagous horticultural pest that is listed as a serious quarantine threat in many countries. The larvae of four other Epiphyas taxa (E. liadelpha, E. pulla, Epiphyas sp. (1) and E. xylodes) are also pests of horticultural crops in Australia. The larvae of all five pest Epiphyas appear similar and even the adults can be difficult to reliably identify using morphology. To address the concerns of Australia's trading partners and therefore; protect Australia's horticultural exports from unjustified quarantine measures, this revision aims to provide the tools to reliably identify the five economically important Epiphyas, at any life stage. Results on average, the COI sequences sampled from E. postvittana in Australia were 99.7% similar to those sampled from E. dotatana in the Kosciuszko National Park, and 98.8% similar to those sampled from Epiphyas sp. (1) across southern Australia. Epiphyas postvittana, E. dotatana and E. sp. (1) are herein referred to as the "postvittana complex". The average sequence divergence sampled between E. postvittana and E. pulla was 3.4% and between E. postvittana and E. liadelpha (sampled in Western Australia), the average sequence divergence sampled was 5.8%. Between E. postvittana and E. xylodes (sampled in the eastern Australian mainland), the average sequence divergence was 6.8%. In an analysis of nucleotide sequences from the mitochondrial COI gene region, using a Bayesian statistical framework in BEAST v1.4.8 (Drummond and Rambaut, 2002-2007), the postvittana complex, E. pulla and four more species form a monophyletic group that has high statistical support (posterior probability = 1.00). This group, which is highly morphostatic, is herein referred to as the "postvittana species group". In an analysis of concatenated sequence data from four gene regions (COI+IDH+MDH+CPS-CAD) and two genomes (mDNA, nDNA), using a maximum likelihood framework in Tree-puzzle v5.2 (Schmidt et al., 2004), statistical support for the postvittana species group is lower (QP branch reliability = 63%). The horticultural pests E. liadelpha and E. xylodes are not closely related to each other, or to the postvittana species group. Conclusions At any life stage, nucleotide sequences from the nuclear gene region IDH, or MDH, or CPS-CAD, will allow Epiphyas to be distinguished from the Australian crop pest Merophyas divulsana (the lucerne leaf-roller). Adult Epiphyas can be assigned to the appropriate species group using genitalia morphology. However, at all life stages COI nucleotide sequences are required to confirm the identity of a particular Epiphyas pest lineage. For confirmation of typical E. postvittana in non-crop habitats in eastern Australia, it is essential that both the mitochondrial gene region COI and the nuclear gene region CPS-CAD be sequenced. CPS-CAD sequences differentiate typical E. postvittana from E. dotatana, a close relative with an uncertain natural distribution. Reference nucleotide sequences for each taxon are indicated in Appendix I (pages AI:13 and AI:39) and saved in (.txt) format in Appendix III (CD)

VisRD - Visual Recombination Detection

Summary: VisRD, a program for visual recombination detection in a sequence alignment is presented. VisRD is written in Java and is designed to complement the multi-purpose phylogenetic software package SplitsTree4. Availability: The software is freely available from http://www.lcb.uu.se/~vmoulton/software/visrd