Department of Biological Sciences

Abstract DNA degradation, low DNA concentrations and primer‐site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. micro ‐ checker is windows ®‐based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. micro ‐ checker estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. micro ‐ checker can be freely downloaded from http://www.microchecker.hull.ac.uk/ .

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the ∼75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization ∼70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum’s drought tolerance. The Sorghum bicolor genome sequence is published this week. Sorghum is a cereal grown widely as food, animal feed, fibre and fuel. Tolerant to hot, dry conditions, it is a staple for large populations in the West African Sahel region. Comparisons of the genome with those of maize and rice shed light on the evolution of grasses and of C4 photosynthesis, which is particularly efficient at assimilating carbon at high temperatures. In addition, protein coding genes and miRNAs that could contribute to sorghum's drought tolerance may also be found. Sorghum yield improvement has lagged behind that of other crops and the availability of the genome sequence could provide a vital boost to work on its improvement. Sorghum is an African grass that is grown for food, animal feed and fuel. The current paper presents an initial analysis of the ∼730 megabase genome of Sorghum bicolor. Genome analysis and its comparison with maize and rice shed light on grass genome evolution and also provide insights into the evolution of C4 photosynthesis, as well as protein coding genes and miRNAs that might contribute to sorghum's drought tolerance.

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.

We discuss what concepts or models should be used to organize research and management on rangelands. The traditional range succession model is associated with the management objective of achieving an equilibrium condition under an equilibrium grazing policy. In contrast, the state-and-transition model would describe rangelands by means of catalogues of alternative states and catalogues of possible transitions between states. Transitions often require a combination of climatic circumstances and management action (e.g., fire, grazing, or removal of grazing) to bring them about. The catalogue of transitions would describe these combinations as fully as possible. Circumstances which allow favorable transitions represent opportunities. Circumstances which threaten unfavorable transitions represent hazards. Under the state-and-transition model, range management would not see itself as establishing a permanent equilibrium. Rather, it would see itself as engaged in a continuing game, the object of which is to seize opportunities and to evade hazards, so far as possible. The emphasis would be on timing and flexibility rather than on establishing a fixed policy. Research under the state-and-transition model would aim to improve the catalogues. Frequencies of relevant climatic circumstances would be estimated. Hypotheses about transitions would be tested experimentally. Often such experiments would need to be planned so that they could be implemented at short notice, at an unknown future time when the relevant circumstances arise.

PREMISE OF THE STUDY: Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. METHODS: Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. KEY RESULTS: Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. CONCLUSIONS: Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.

Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.

Increasing attention has been focused on understanding bacterial biofilms and this growth modality's relation to human disease. In this review we explore the genetic regulation and molecular components involved in biofilm formation and maturation in the context of the Gram-positive cocci, Staphylococcus aureus. In addition, we discuss diseases and host immune responses, along with current therapies associated with S. aureus biofilm infections and prevention strategies.

Seed mass is a trait that occupies a pivotal position in the ecology of a species. It links the ecology of reproduction and seedling establishment with the ecology of vegetative growth, strategy sectors that are otherwise largely disconnected (Grime et al., 1988; Shipley et al., 1989; Leishman and Westoby, 1992). There is a startling diversity of shapes and sizes of seeds among the plant species of the world. Seeds range from the dust seeds of the Orchidaceae and some saprophytic and parasitic species (around 10 6 g), across ten orders of magnitude to the double coconut Lodoicea seychellarum (104 g) (Harper et al., 1970). Within species, seed size typically spans less than half an order of magnitude (about fourfold: Michaels et al., 1988). Most within-species variation occurs within plant rather than among plants or populations (Michaels et al., 1988; Obeso, 1993; Vaughton and Ramsey, 1998), indicating environmental effects during development rather than genetic differences between mothers. This chapter is concerned with the differences in seed size among species, and the consequences for vegetation dynamics and community composition. During the last 10–15 years, there has been considerable progress in the ecology of seed mass. Unlike many other areas of comparative plant ecology, we have substantial published information from several different scales and research styles. As well as field experiments and demographic studies with a few species at a time, we have simple experiments with larger numbers of species (ten to 50), quantification of seed mass and its correlates in whole-vegetation types (hundreds of species) and tests of consistency across different continents. The wide-scale quantification began as early as Salisbury (1942) and Baker (1972), but has been much added to and consolidated over the past 10 years (e.g. Mazer, 1989, 1990; Leishman and Westoby, 1994a; Leishman et al., 1995; Eriksson and Jakobsson, 1998). The work spanning large numbers of species is complementary to detailed experiments involving only a few species, giving a stronger sense of how widely the results from particular experiments can be generalized. Much of the literature examines how natural selection on seed size might be influenced by various environmental factors. In this context, it is at first glance surprising that seed size varies within communities across a remarkable five to six orders of magnitude (Leishman et al., 1995; Fig. 2.1). Further, there is strong overlap of seed-size distributions between quite different habitats. Within the temperate zone,

Summary 1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently. 2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation. 3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates. 4. Diversitree is an open source and available on the Comprehensive R Archive Network ( cran ). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree .

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation--lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)--and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.

Mutualistic interactions between ants and plants involve rewards offered by plants and services performed by ants in a mutually advantageous relationship. The rewards are principally food and/or nest sites, and ants in turn perform a number of services for plants: they disperse and plant seeds; they protect foliage, buds, and reproductive structures from enemies such as herbivores and seed predators; they fertilize plants with essential nutrients; and they may sometimes function as pollinators. In this book, initially published in 1985, Professor Beattie reviews the fascinating natural history of ant–plant interactions, discusses the scientific evidence for the mutualistic nature of these relationships, and reaches some conclusions about the ecological and evolutionary processes that mold them. This important work explores the natural history, experimental approach, and integration with contemporary evolutionary and ecological literature of the time will appeal to a wide variety of biologists.

Acinetobacter baumannii is an opportunistic bacterial pathogen primarily associated with hospital-acquired infections. The recent increase in incidence, largely associated with infected combat troops returning from conflict zones, coupled with a dramatic increase in the incidence of multidrug-resistant (MDR) strains, has significantly raised the profile of this emerging opportunistic pathogen. Herein, we provide an overview of the pathogen, discuss some of the major factors that have led to its clinical prominence and outline some of the novel therapeutic strategies currently in development.

The shape of dendritic trees and the density of dendritic spines can undergo significant changes during the life of a neuron. We report here the function of the small GTPases Rac and Rho in the maintenance of dendritic structures. Maturing pyramidal neurons in rat hippocampal slice culture were biolistically transfected with dominant GTPase mutants. We found that expression of dominant-negative Rac1 results in a progressive elimination of dendritic spines, whereas hyperactivation of RhoA causes a drastic simplification of dendritic branch patterns that is dependent on the activity of a downstream kinase ROCK. Our results suggest that Rac and Rho play distinct functions in regulating dendritic spines and branches and are vital for the maintenance and reorganization of dendritic structures in maturing neurons.

We compiled information from the international literature to quantify the relationships between seed mass and survival through each of the hazards plants face between seed production and maturity. We found that small‐seeded species were more abundant in the seed rain than large‐seeded species. However, this numerical advantage was lost by seedling emergence. The disadvantage of small‐seeded species probably results from size‐selective post‐dispersal seed predation, or the longer time small‐seeded species spend in the soil before germination. Seedlings from large‐seeded species have higher survival through a given amount of time as seedlings. However, this advantage seems to be countered by the greater time taken for large‐seeded species to reach reproductive maturity: our data suggested no relationship, or perhaps a weak negative relationship, between seed size and survival from seedling emergence through to adulthood. A previous compilation showed that the inverse relationship between seed mass and the number of seeds produced per unit canopy area per year is countered by positive relationships between seed mass, plant size and plant longevity. Taken together, these data show that our old understanding of a species’ seed mass as the result of a trade–off between producing a few large offspring, each with high survival probability, versus producing many small offspring each with a lower chance of successfully establishing was incomplete. It seems more likely that seed size evolves as part of a spectrum of life history traits, including plant size, plant longevity, juvenile survival rate and time to reproduction.

Ingo Braasch, John Postlethwait and colleagues report the genome of the spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before genome duplication. Their data provide insights into the evolution of genes involved in immunity, mineralization and development and facilitate the comparison of cis-regulatory elements between teleosts and humans. To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Identifying natal origins of marine fishes is challenging because of difficulties in conducting mark-recapture studies in marine systems. We used natural geochemical signatures in otoliths (ear bones) to determine natal sources in weakfish (Cynoscion regalis), an estuarine-spawning marine fish, in eastern North America. Spawning site fidelity ranged from 60 to 81%, comparable to estimates of natal homing in birds and anadromous fishes. These data were in contrast to genetic analyses of population structure in weakfish. Our findings highlight the need for consideration of spatial processes in fisheries models and have implications for the design of marine reserves in coastal regions.

Dengue virus (DENV) modifies cellular membranes to establish its sites of replication. Although the 3D architecture of these structures has recently been described, little is known about the cellular pathways required for their formation and expansion. In this report, we examine the host requirements for DENV replication using a focused RNAi analysis combined with validation studies using pharmacological inhibitors. This approach identified three cellular pathways required for DENV replication: autophagy, actin polymerization, and fatty acid biosynthesis. Further characterization of the viral modulation of fatty acid biosynthesis revealed that a key enzyme in this pathway, fatty acid synthase (FASN), is relocalized to sites of DENV replication. DENV nonstructural protein 3 (NS3) is responsible for FASN recruitment, inasmuch as (i) NS3 expressed in the absence of other viral proteins colocalizes with FASN and (ii) NS3 interacts with FASN in a two-hybrid assay. There is an associated increase in the rate of fatty acid biosynthesis in DENV-infected cells, and de novo synthesized lipids preferentially cofractionate with DENV RNA. Finally, purified recombinant NS3 stimulates the activity of FASN in vitro. Taken together, these experiments suggest that DENV co-opts the fatty acid biosynthetic pathway to establish its replication complexes. This study provides mechanistic insight into DENV membrane remodeling and highlights the potential for the development of therapeutics that inhibit DENV replication by targeting the fatty acid biosynthetic pathway.

Fluoride was introduced into dentistry over 70 years ago, and it is now recognized as the main factor responsible for the dramatic decline in caries prevalence that has been observed worldwide. However, excessive fluoride intake during the period of tooth development can cause dental fluorosis. In order that the maximum benefits of fluoride for caries control can be achieved with the minimum risk of side effects, it is necessary to have a profound understanding of the mechanisms by which fluoride promotes caries control. In the 1980s, it was established that fluoride controls caries mainly through its topical effect. Fluoride present in low, sustained concentrations (sub-ppm range) in the oral fluids during an acidic challenge is able to absorb to the surface of the apatite crystals, inhibiting demineralization. When the pH is re-established, traces of fluoride in solution will make it highly supersaturated with respect to fluorhydroxyapatite, which will speed up the process of remineralization. The mineral formed under the nucleating action of the partially dissolved minerals will then preferentially include fluoride and exclude carbonate, rendering the enamel more resistant to future acidic challenges. Topical fluoride can also provide antimicrobial action. Fluoride concentrations as found in dental plaque have biological activity on critical virulence factors of S. mutans in vitro, such as acid production and glucan synthesis, but the in vivo implications of this are still not clear. Evidence also supports fluoride's systemic mechanism of caries inhibition in pit and fissure surfaces of permanent first molars when it is incorporated into these teeth pre-eruptively.

This review provides details on the phytochemicals in green coffee beans and the changes that occur during roasting. Key compounds in the coffee beverage, produced from the ground, roasted beans, are volatile constituents responsible for the unique aroma, the alkaloids caffeine and trigonelline, chlorogenic acids, the diterpenes cafestol and kahweol, and melanoidins, which are Maillard reaction products. The fate of these compounds in the body following consumption of coffee is discussed along with evidence of the mechanisms by which they may impact on health. Finally, epidemiological findings linking coffee consumption to potential health benefits including prevention of several chronic and degenerative diseases, such as cancer, cardiovascular disorders, diabetes, and Parkinson's disease, are evaluated.