All Outputs (40)

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure (2024)
Journal Article
Winter, M. R., Taranto, A. P., Yimer, H. Z., Coomer Blundell, A., Siddique, S., Williamson, V. M., & Lunt, D. H. (2024). Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure. PLoS ONE, 19(6), Article e0302506. https://doi.org/10.1371/journal.pone.0302506

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

A catalogue of chromosome counts for Phylum Nematoda (2024)
Preprint / Working Paper
Blaxter, M., Leech, C., & Lunt, D. H. 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 e... Read More about A catalogue of chromosome counts for Phylum Nematoda.

Identification of individual root-knot nematodes using low coverage long-read sequencing (2021)
Journal Article
Sellers, G. S., Jeffares, D. C., Lawson, B., Prior, T., & Lunt, D. H. (2021). Identification of individual root-knot nematodes using low coverage long-read sequencing. PLoS ONE, 16(12), Article e0253248. https://doi.org/10.1371/journal.pone.0253248

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 i... Read More about Identification of individual root-knot nematodes using low coverage long-read sequencing.

Using network ecology to understand and mitigate long-term insect declines (2021)
Journal Article
Petsopoulos, D., Lunt, D. H., Bell, J. R., Kitson, J. J., Collins, L., Boonham, N., Morales-Hojas, R., & Evans, D. M. (2021). Using network ecology to understand and mitigate long-term insect declines. Ecological entomology, 46(4), 693-698. https://doi.org/10.1111/een.13035

Genome sequence of the root-knot nematode Meloidogyne luci (2020)
Journal Article
Susič, N., Koutsovoulos, G. D., Riccio, C., Danchin, E. G., Blaxter, M. L., Lunt, D. H., Strajnar, P., Širca, S., Urek, G., & Stare, B. G. (2020). Genome sequence of the root-knot nematode Meloidogyne luci. Journal of Nematology, 52(1), 1-5. https://doi.org/10.21307/jofnem-2020-025

Root-knot nematodes from the genus Meloidogyne are polyphagous plant endoparasites and agricultural pests of global importance. Here, we report the high-quality genome sequence of Meloidogyne luci population SI-Smartno V13. The resulting genome assem... Read More about Genome sequence of the root-knot nematode Meloidogyne luci.

The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species (2019)
Journal Article
Faber-Hammond, J. J., Renn, S. C., Venkatesh, B., Faber-Hammond, J. J., Bezault, E., Lunt, D. H., Joyce, D. A., & Renn, S. C. P. (2019). The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biology and Evolution, 11(10), 2856-2874. https://doi.org/10.1093/gbe/evz185

© 2019 Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2019. This work is written by US Government employees and is in the public domain in the US. The initial sequencing of five cichlid genomes revea... Read More about The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.

Climate-warming alters the structure of farmland tri-trophic ecological networks and reduces crop yield (2018)
Journal Article
Derocles, S. A., Lunt, D. H., Berthe, S. C., Nichols, P. C., Moss, E. D., & Evans, D. M. (2018). Climate-warming alters the structure of farmland tri-trophic ecological networks and reduces crop yield. Molecular ecology, 27(23), 4931-4946. https://doi.org/10.1111/mec.14903

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 cha... Read More about Climate-warming alters the structure of farmland tri-trophic ecological networks and reduces crop yield.

Construction, validation, and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using light microscopy and DNA metabarcoding (2018)
Journal Article
Macgregor, C. J., Kitson, J. J., Fox, R., Hahn, C., Lunt, D. H., Pocock, M. J., & Evans, D. M. (2019). Construction, validation, and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using light microscopy and DNA metabarcoding. Ecological entomology, 44(1), 17-29. https://doi.org/10.1111/een.12674

1. Moths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant–pollinator interaction networks are traditionally constructed using either flower‐visitor observations or pollen‐transport detection using micros... Read More about Construction, validation, and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using light microscopy and DNA metabarcoding.

Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding (2018)
Journal Article
Kitson, J. J. N., Hahn, C., Sands, R. J., Straw, N. A., Evans, D. M., & Lunt, D. H. (2019). Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding. Molecular ecology, 28(2), 471-483. https://doi.org/10.1111/mec.14518

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 tec... Read More about Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding.

Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA-metabarcoding (2018)
Journal Article
Kitson, J. J. N., Hahn, C., Sands, R. J., Straw, N. A., Evans, D. M., & Lunt, D. H. (2019). Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA-metabarcoding. Molecular ecology, 28(2), 471-483. https://doi.org/10.1101/035071

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 tec... Read More about Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA-metabarcoding.

Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change (2017)
Journal Article
Szitenberg, A., Salazar-Jaramillo, L., Blok, V. C., Laetsch, D. R., Joseph, S., Williamson, V. M., Blaxter, M. L., & Lunt, D. H. (2017). Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change. Genome Biology and Evolution, 9(10), 2844-2861. https://doi.org/10.1093/gbe/evx201

The Root-Knot Nematodes (RKN; 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 poly... Read More about Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change.

Genetic drift, not life history or RNAi, determine long term evolution of transposable elements (2016)
Journal Article
Szitenberg, A., Cha, S., Opperman, C. H., Bird, D. M., Blaxter, M. L., & Lunt, D. H. (2016). Genetic drift, not life history or RNAi, determine long term evolution of transposable elements. Genome Biology and Evolution, 8(9), 2964-2978. https://doi.org/10.1093/gbe/evw208

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... Read More about Genetic drift, not life history or RNAi, determine long term evolution of transposable elements.

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems (2016)
Journal Article
Evans, D. M., Kitson, J. J. N., Lunt, D. H., Straw, N. A., & Pocock, M. J. O. (2016). Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems. Functional ecology, 30(12), 1904-1916. https://doi.org/10.1111/1365-2435.12659

Summary 1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying str... Read More about Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems.

Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes? (2015)
Journal Article
Derocles, S. A. P., Plantegenest, M., Rasplus, J.-Y., Marie, A., Evans, D. M., Lunt, D. H., & Le Ralec, A. (2016). Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?. Systematic Entomology, 41(2), 379--391. https://doi.org/10.1111/syen.12160

Aphidiinae are mostly composed of specialist parasitoids and the few species described as generalist are suspected to be composed of cryptic specialists, almost indistinguishable based on morphological characteristics. The use of molecular markers ha... Read More about Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?.

ReproPhylo: An Environment for Reproducible Phylogenomics (2015)
Journal Article
Szitenberg, A., John, M., Blaxter, M. L., & Lunt, D. H. (2015). ReproPhylo: An Environment for Reproducible Phylogenomics. PLoS Computational Biology, 11(9), Article ARTN e1004447. https://doi.org/10.1371/journal.pcbi.1004447

© 2015 Szitenberg et al. 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 envi... Read More about ReproPhylo: An Environment for Reproducible Phylogenomics.

Simulated climate-warming increases Coleoptera activity-densities and reduces community diversity in a cereal crop (2015)
Journal Article
Berthe, S. C., Derocles, S. A., Lunt, D. H., Kimball, B. A., & Evans, D. M. (2015). Simulated climate-warming increases Coleoptera activity-densities and reduces community diversity in a cereal crop. Agriculture, ecosystems & environment, 210, 11-14. https://doi.org/10.1016/j.agee.2015.05.001

Abstract Simulated climate-warming experiments have provided important insights into the response of terrestrial ecosystems, but few have examined the impacts on agricultural insects, particularly those associated with the ecosystem service of biolog... Read More about Simulated climate-warming increases Coleoptera activity-densities and reduces community diversity in a cereal crop.

Determining Plant – Leaf Miner – Parasitoid Interactions: A DNA Barcoding Approach (2015)
Journal Article
Derocles, S. A., Evans, D. M., Nichols, P. C., Evans, S. A., & Lunt, D. H. (2015). Determining Plant – Leaf Miner – Parasitoid Interactions: A DNA Barcoding Approach. PLoS ONE, 10(2), Article e0117872. https://doi.org/10.1371/journal.pone.0117872

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 o... Read More about Determining Plant – Leaf Miner – Parasitoid Interactions: A DNA Barcoding Approach.

The Evolution of Tyrosine-Recombinase Elements in Nematoda (2014)
Journal Article
Szitenberg, A., Koutsovoulos, G., Blaxter, M. L., & Lunt, D. H. (2014). The Evolution of Tyrosine-Recombinase Elements in Nematoda. PLoS ONE, 9(9), Article e106630. https://doi.org/10.1371/journal.pone.0106630

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 elemen... Read More about The Evolution of Tyrosine-Recombinase Elements in Nematoda.

The contribution of Anatolia to European phylogeography: The centre of origin of the meadow grasshopper, Chorthippus parallelus (2014)
Journal Article
Korkmaz, E. M., Lunt, D. H., Çiplak, B., Deǧerli, N., & Başibüyük, H. H. (2014). The contribution of Anatolia to European phylogeography: The centre of origin of the meadow grasshopper, Chorthippus parallelus. Journal of Biogeography, 41(9), 1793-1805. https://doi.org/10.1111/jbi.12332

Aim: Chorthippus parallelus is one of the classic model systems for studying genetic structure and phylogeography in the Western Palaearctic. Here, we investigate the regional genetic differentiation of C. parallelus and evaluate the historical and e... Read More about The contribution of Anatolia to European phylogeography: The centre of origin of the meadow grasshopper, Chorthippus parallelus.

The complex hybrid origins of the root knot nematodes revealed through comparative genomics (2014)
Journal Article
Lunt, D. H., Kumar, S., Koutsovoulos, G., & Blaxter, M. L. (2014). The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ, 2014(1), Article e356. https://doi.org/10.7717/peerj.356

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