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Outputs (36)

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.

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., …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., …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., 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.

Gene duplication in an African cichlid adaptive radiation (2014)
Journal Article
Machado, H. E., Jui, G., Joyce, D. A., Reilly, C. R. L., Lunt, D. H., & Renn, S. C. (2014). Gene duplication in an African cichlid adaptive radiation. BMC Genomics, 15(1), 161. https://doi.org/10.1186/1471-2164-15-161

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 r... Read More about Gene duplication in an African cichlid adaptive radiation.

Divergence of scent pheromones in allopatric populations of Acanthodactylus boskianus (Squamata: Lacertidae) (2013)
Journal Article
Khannoon, E. R., Lunt, D. H., Schulz, S., & Hardege, J. (2013). Divergence of scent pheromones in allopatric populations of Acanthodactylus boskianus (Squamata: Lacertidae). Zoological Science, 30(5), 380-385. https://doi.org/10.2108/zsj.30.380

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. Compariso... Read More about Divergence of scent pheromones in allopatric populations of Acanthodactylus boskianus (Squamata: Lacertidae).

Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage (2011)
Journal Article
Moss, S. P., Joyce, D. A., Humphries, S., Tindall, K. J., & Lunt, D. H. (2011). Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biology and Evolution, 3(1), 1187-1196. https://doi.org/10.1093/gbe/evr090

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

Latitudinal variations in the physiology of marine gammarid amphipods (2011)
Journal Article
Whiteley, N. M., Rastrick, S. P. S., Lunt, D. H., & Rock, J. (2011). Latitudinal variations in the physiology of marine gammarid amphipods. Journal of experimental marine biology and ecology, 400(1-2), 70-77. https://doi.org/10.1016/j.jembe.2011.02.027

In order to examine the physiological capabilities of marine invertebrates in their natural environment, a series of physiological measurements were conducted on congeneric amphipod species (Genus Gammarus) distributed along a natural thermal gradien... Read More about Latitudinal variations in the physiology of marine gammarid amphipods.

Repeated colonization and hybridization in Lake Malawi cichlids (2011)
Journal Article
Joyce, D., Lunt, D. H., Genner, M. J., Turner, G. F., Bills, R., & Seehausen, O. (2011). Repeated colonization and hybridization in Lake Malawi cichlids. Current biology : CB, 21(3), R108-R109. https://doi.org/10.1016/j.cub.2010.11.029

Through adaptive radiation, ancestral species rapidly diversify into multiple species with different ecological adaptations. The haplochromine cichlid fishes of the East African Great Lakes are considered classic examples of adaptive radiation, but o... Read More about Repeated colonization and hybridization in Lake Malawi cichlids.

Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida) (2010)
Journal Article
Bik, H. M., Thomas, W. K., Lunt, D. H., & Lambshead, P. J. D. (2010). Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC evolutionary biology, 10(1), 389. https://doi.org/10.1186/1471-2148-10-389

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

Moving towards a complete molecular framework of the Nematoda: A focus on the Enoplida and early-branching clades (2010)
Journal Article
Lunt, D. H., Bik, H. M., Lambshead, P. J. D., & Thomas, W. K. (2010). Moving towards a complete molecular framework of the Nematoda: A focus on the Enoplida and early-branching clades. BMC evolutionary biology, 10(1), Article ARTN 353. https://doi.org/10.1186/1471-2148-10-353

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

Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes (2009)
Journal Article
Costa, F. O., Henzler, C. M., Lunt, D. H., Whiteley, N. M., & Rock, J. (2009). Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Systematics and Biodiversity, 7(4), 365-379. https://doi.org/10.1017/S1477200009990120

The genus Gammarus (Amphipoda) is one of the most speciose genera of Crustacea, yet much uncertainty remains concerning taxonomy and systematic relationships, particularly for brackish and marine forms. We used DNA barcode sequences from the mitochon... Read More about Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes.

Linking functional molecular variation with environmental gradients: myosin gene diversity in a crustacean broadly distributed across variable thermal environments (2009)
Journal Article
Rock, J., Magnay, J. L., Beech, S., El Haj, A. J., Goldspink, G., Lunt, D. H., & Whiteley, N. M. (2009). Linking functional molecular variation with environmental gradients: myosin gene diversity in a crustacean broadly distributed across variable thermal environments. Gene, 437(1-2), 60-70. https://doi.org/10.1016/j.gene.2009.02.008

To investigate the molecular basis of temperature adaptation in natural populations we used the candidate gene approach, targeting the myosin heavy chain (MyHC) gene. The functional effects of genetic variation in MyHC have been well characterised, a... Read More about Linking functional molecular variation with environmental gradients: myosin gene diversity in a crustacean broadly distributed across variable thermal environments.

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins (2008)
Journal Article
Lunt, D. H. (2008). Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins. BMC evolutionary biology, 8(1), 194. https://doi.org/10.1186/1471-2148-8-194

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 repr... Read More about Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins.

Global isolation by distance despite strong regional phylogeography in a small metazoan (2007)
Journal Article
Mills, S., Lunt, D. H., & Gómez, A. (2007). Global isolation by distance despite strong regional phylogeography in a small metazoan. BMC evolutionary biology, 7, Article 225. https://doi.org/10.1186/1471-2148-7-225

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 inve... Read More about Global isolation by distance despite strong regional phylogeography in a small metazoan.

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula (2007)
Journal Article
Gomez, A., Montero-Pau, J., Lunt, D. H., Serra, M., & Campillo, S. (2007). Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula. Molecular ecology, 16(15), 3228-3240. https://doi.org/10.1111/j.1365-294X.2007.03372.x

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between... Read More about Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula.

Mitochondrial DNA phylogeography and mating compatibility reveal marked genetic structuring and speciation in the NE Atlantic bryozoan Celleporella hyalina (2007)
Journal Article
Gomez, A., Hughes, R. N., Wright, P. J., Carvalho, G. R., & Lunt, D. H. (2007). Mitochondrial DNA phylogeography and mating compatibility reveal marked genetic structuring and speciation in the NE Atlantic bryozoan Celleporella hyalina. Molecular ecology, 16(10), 2173-2188. https://doi.org/10.1111/j.1365-294X.2007.03308.x

The marine bryozoan Celleporella hyalina is a species complex composed of many highly divergent and mostly allopatric genetic lineages that are reproductively isolated but share a remarkably similar morphology. One such lineage commonly encrusts macr... Read More about Mitochondrial DNA phylogeography and mating compatibility reveal marked genetic structuring and speciation in the NE Atlantic bryozoan Celleporella hyalina.

Age of cichlids: New dates for ancient lake fish radiations (2007)
Journal Article
Genner, M. J., Seehausen, O., Lunt, D. H., Joyce, D. A., Shaw, P. W., Carvalho, G. R., & Turner, G. F. (2007). Age of cichlids: New dates for ancient lake fish radiations. Molecular biology and evolution, 24(5), 1269-1282. https://doi.org/10.1093/molbev/msm050

Timing divergence events allow us to infer the conditions under which biodiversity has evolved and gain important insights into the mechanisms driving evolution. Cichlid fishes are a model system for studying speciation and adaptive radiation, yet, w... Read More about Age of cichlids: New dates for ancient lake fish radiations.

Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon (2007)
Journal Article
Gómez, A., Wright, P. J., Lunt, D. H., Cancino, J. M., Carvalho, G. R., & Hughes, R. N. (2007). Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society B: Biological Sciences, 274(1607), 199-207. https://doi.org/10.1098/rspb.2006.3718

Despite increasing threats to the marine environment, only a fraction of the biodiversity of the oceans has been described, owing in part to the widespread occurrence of cryptic species. DNA-based barcoding through screening of an orthologous referen... Read More about Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon.

Mitochondrial DNA phylogeography of the Mesoamerican spiny-tailed lizards (Ctenosaura quinquecarinata complex): Historical biogeography, species status and conservation (2005)
Journal Article
Hasbún, C. R., Gomez, A., Köhler, G., & Lunt, D. H. (2005). Mitochondrial DNA phylogeography of the Mesoamerican spiny-tailed lizards (Ctenosaura quinquecarinata complex): Historical biogeography, species status and conservation. Molecular ecology, 14(10), 3095-3107. https://doi.org/10.1111/j.1365-294x.2005.02665.x

Through the examination of past and present distributions of plants and animals, historical biogeographers have provided many insights on the dynamics of the massive organismal exchange between North and South America. However, relatively few phyloge... Read More about Mitochondrial DNA phylogeography of the Mesoamerican spiny-tailed lizards (Ctenosaura quinquecarinata complex): Historical biogeography, species status and conservation.

An extant cichlid fish radiation emerged in an extinct Pleistocene lake (2005)
Journal Article
Joyce, D. A., Lunt, D. H., Bills, R., Turner, G. F., Katongo, C., Duftner, N., …Seehausen, O. (2005). An extant cichlid fish radiation emerged in an extinct Pleistocene lake. Nature, 435(7038), 90-95. https://doi.org/10.1038/nature03489

The haplochromine cichlid fish of the East African Great Lakes represent some of the fastest and most species-rich adaptive radiations known(1), but rivers in most of Africa accommodate only a few morphologically similar species of haplochromine cich... Read More about An extant cichlid fish radiation emerged in an extinct Pleistocene lake.