A catalogue of chromosome counts for Phylum Nematoda.

Nematodes are important biological models in genetics and genomics, with research driven by basic biological as well as applied questions. The presence of holocentric chromosomes, clades with frequent polyploidy and the phenomenon of programmed DNA elimination make nematode karyotypic diversity of particular interest. Here we present a catalogue of published karyotypes of nematode species, rationalising and normalising descriptions from the previous 135 years.

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure.

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species.

Identification of individual root-knot nematodes using low coverage long-read sequencing.

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin.

Novel Methods for Recording Stress-Strain Curves in Proton Irradiated Material.

Proton irradiation is often used as a proxy for neutron irradiation but the irradiated layer is typically <50 μm deep; this presents a problem when trying to obtain mechanical test data as a function of irradiation level. Two novel methodologies have been developed to record stress-strain curves for thin proton-irradiated surface layers of SA-508-4N ferritic steel. In the first case, in-situ loading experiments are carried out using a combination of X-ray diffraction and digital image correlation on the near surface region in order to measure stress and strain, thereby eliminating the influence of the non-irradiated volume.

Genome sequence of the root-knot nematode .

Root-knot nematodes from the genus are polyphagous plant endoparasites and agricultural pests of global importance. Here, we report the high-quality genome sequence of population SI-Smartno V13. The resulting genome assembly of SI-Smartno V13 consists of 327 contigs, with an N50 contig length of 1,711,905 bp and a total assembly length of 209.

Producing high-oleic acid beef and the impact of ground beef consumption on risk factors for cardiovascular disease: A review.

This review summarizes the effects of high-oleic acid oil and high-oleic acid ground beef interventions on risk factors for cardiovascular disease (CVD) in human trials, and also summarizes studies designed to increase the amount of oleic acid (18:1n-9) in beef. In three human trials, high-oleic acid oils and high-oleic acid ground beef increased plasma high-density lipoprotein cholesterol over baseline values or over high-carbohydrate diets. Neither low-oleic acid nor high-oleic acid ground beef increased risk factors for CVD, confirming earlier studies that used high-oleic acid oils.

The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.

The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available.

Climate warming alters the structure of farmland tritrophic ecological networks and reduces crop yield.

It is unclear how sustained increases in temperature and changes in precipitation, as a result of climate change, will affect crops and their interactions with agricultural weeds, insect pests and predators, due to the difficulties in quantifying changes in such complex relationships. We simulated the combined effects of increasing temperature (by an average of 1.4°C over a growing season) and applying additional rainwater (10% of the monthly mean added weekly, 40% total) using a replicated, randomized block experiment within a wheat crop.

Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding.

Determining the host-parasitoid interactions and parasitism rates for invasive species entering novel environments is an important first step in assessing potential routes for biocontrol and integrated pest management. Conventional insect rearing techniques followed by taxonomic identification are widely used to obtain such data, but this can be time-consuming and prone to biases. Here, we present a next-generation sequencing approach for use in ecological studies which allows for individual-level metadata tracking of large numbers of invertebrate samples through the use of hierarchically organised molecular identification tags.

Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change.

The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation.

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements.

Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host's genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species.

ReproPhylo: An Environment for Reproducible Phylogenomics.

The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information.

Determining plant-leaf miner-parasitoid interactions: a DNA barcoding approach.

A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant-leaf miner-parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies. We tested the ability of universal primers to amplify the remaining DNA inside leaf miner mines after the emergence of the insect.

Ophthalmic digital image transfer: benefits to triage, patient care and resource.

Purpose: Hospital capacity in the UK is currently significantly challenged due to new treatments, targets and resource limitations. There have been significant improvements in training, equipment and shared care services in community primary care optometry services. Despite this the challenges to ophthalmic service delivery are considerable.

The evolution of tyrosine-recombinase elements in Nematoda.

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda.

The complex hybrid origins of the root knot nematodes revealed through comparative genomics.

Root knot nematodes (RKN) can infect most of the world's agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of their extreme polyphagy. The most damaging pathogens reproduce by obligatory mitotic parthenogenesis and it has been suggested that these species originated from interspecific hybridizations between unknown parental taxa.

Gene duplication in an African cichlid adaptive radiation.

Background: Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis "chilingali") and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei).

Divergence of scent pheromones in allopatric populations of Acanthodactylus boskianus (Squamata: Lacertidae).

The evolutionary phenomena associated with divergence in chemical signals between populations of the same species help to understand the process of speciation. Animals detect and react to semiochemicals and pheromones used in communication. Comparison between populations of the same species that are geographically isolated from one another allows us to determine the genetic or environmental factors responsible for chemical differentiation.

Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage.

We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics. We identify that the zebrafish, Danio rerio, has an unusual distribution of intron sizes, with a greater number of larger introns in general and a notable peak in the frequency of introns of approximately 500 to 2,000 bp compared with the monotonically decreasing frequency distributions of the other fish.

Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida).

Background: Nematodes represent the most abundant benthic metazoa in one of the largest habitats on earth, the deep sea. Characterizing major patterns of biodiversity within this dominant group is a critical step towards understanding evolutionary patterns across this vast ecosystem. The present study has aimed to place deep-sea nematode species into a phylogenetic framework, investigate relationships between shallow water and deep-sea taxa, and elucidate phylogeographic patterns amongst the deep-sea fauna.

Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades.

Background: The subclass Enoplia (Phylum Nematoda) is purported to be the earliest branching clade amongst all nematode taxa, yet the deep phylogeny of this important lineage remains elusive. Free-living marine species within the order Enoplida play prominent roles in marine ecosystems, but previous molecular phylogenies have provided only the briefest evolutionary insights; this study aimed to firmly resolve internal relationships within the hyper-diverse but poorly understood Enoplida. In addition, we revisited the molecular framework of the Nematoda using a rigorous phylogenetic approach in order to investigate patterns of early splits amongst the oldest lineages (Dorylaimia and Enoplia).

Genetic tests of ancient asexuality in root knot nematodes reveal recent hybrid origins.

Background: The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic) reproduction including (i) large "allelic" sequence divergence (ii) lack of phylogenetic clustering of "alleles" within morphological species and (iii) decay and loss of genes specific to meiosis and sexual reproduction.

Global isolation by distance despite strong regional phylogeography in a small metazoan.

Background: Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan Brachionus plicatilis s. s.