NatureMetrics Publications

Aylagas, E., Borja, A., Pochon, X., Zaiko, A., Keeley, N., Bruce, K., Hong, P., Ruiz, G.M., Stein, E.D., Theroux, S., Geraldi, N., Ortega, A., Gajdzik, L., Coker, D.J., Katan, Y., Hikmawan, T., Saleem, A., Alamer, S., Jones, B.H., Duarte, C.M., Pearman, J., Carvalho, S. 2020. Translational molecular ecology in practice: linking DNA-based methods to actionable marine environmental management. Science of the Total Environment.
DOI: https://doi.org/10.1016/j.scitotenv.2020.140780
Keywords: Molecular methods, Marine policy, Translational molecular ecology, Metabarcoding, Marine bioassessments

Breeze, T.D., Bailey, A.P., Balcombe, K.G., Brereton, T., Comont, R., Edwards, M., Garratt, M.P., Harvey, M., Hawes, C., Isaac, N., Jitlal, M., Jones, C.M., Kunin, W.E., Lee, P., Morris, R.K.A., Musgrove, A., O’Connor, R.S., Peyton, J., Potts, S.G., Roberts, S.P.M., Roy, D.B., Roy, H.E., Tang, C.Q., Vanbergen, A.J., Carvell, C. 2020. Pollinator monitoring more than pays for itself. Journal of Applied Ecology.
DOI: https://doi.org/10.1111/1365-2664.13755

Craig, H., Kennedy, J.P., Devlin, D.J., Bardgett, R.D., Rowntree, J.K. 2020. Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field‐based experiment. Ecology and Evolution.
DOI: https://doi.org/10.1002/ece3.6989

Díaz, C., Wege, F.F., Tang, C.Q., Crampton-Platt, A., Rüdel, H., Eilebrecht, E., Koschorreck, J . 2020. Aquatic suspended particulate matter as a source of eDNA for fish metabarcoding. Scientific Reports.
DOI: https://doi.org/10.1101/2020.04.27.063990

Egeter, Bastian; Veríssimo, Joana; Lopes_Lima, Manuel; Chaves, Cátia; Pinto, Joana; Riccardi, Nicoletta; Beja, Pedro; Fonseca, Nuno A. 2020. Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing. bioRxiv.
DOI: https://doi.org/10.1101/2020.06.09.142521

Hupało, K., Majaneva, M., Czachur, M.V., et al. An urban Blitz with a twist: rapid biodiversity assessment using aquatic environmental DNA. 2020. Environmental DNA.
DOI: https://doi.org/10.1002/edn3.152

Ikoyi, Israel; Egeter, Bastian; Chaves, Cátia; Ahmed, Mohammed; Fowler, Andrew; Schmalenberger, Achim. 2020. Responses of soil microbiota and nematodes to application of organic and inorganic fertilizers in grassland columns. Biology and Fertility of Soils.
DOI: https://doi.org/10.1007/s00374-020-01440-5

Ji, Y., Baker, C.C.M., Li, Y., Popescu, V.D., Wang, Z., Wang, J., Wang, L., Wu, C., Hua, C., Yang, Z., Yang, C., Xu, C.C.Y., Wen, Q., Pierce, N.E. & Yu, D.W. 2020. Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA. bioRxiv.
DOI: https://doi.org/10.1101/2020.02.10.941336
Keywords: environmental DNA, metabarcoding, occupancy, leeches, China, monitoring, conservation, biodiversity

Kennedy, J.P., Craig, H., Jara-Cavieres, A., Lundy, A., Preziosi, R.F., Rowntree, J.K. 2020. Multiplex microsatellite PCR panels for the neotropical red mangrove, Rhizophora mangle: combining efforts towards a cost-effective and modifiable tool to better inform conservation and management. Conservation Genetics Resources.
DOI: https://doi.org/10.1007/s12686-020-01138-8

Martins, Filipa MS; Porto, Miguel; Feio, Maria J; Egeter, Bastian; Bonin, Aurélie; Serra, Sónia RQ; Taberlet, Pierre; Beja, Pedro. 2020. Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers. Molecular Ecology.
DOI:  https://doi.org/10.1111/mec.15620

Thalinger, B., Deiner, K., Harper, L.R., Rees. H.C., Blackman, R.C., Sint, D., Traugott, M., Goldberg, C.S., Bruce, K. 2020. A validation scale to determine the readiness of environmental DNA assays for routine species monitoring. bioRxiv.
DOI: https://doi.org/10.1101/2020.04.27.063990

Abrams, J.F., Hörig, L.A.,  Brozovic, R., Axtner, J., Crampton‐Platt, A., Mohamed, A., Wong, S.T., Sollmann, R., Yu, D.W. & Wilting, A. 2019. Shifting up a gear with iDNA: From mammal detection events to standardised surveys. Journal of Applied Ecology. 56(7).
DOI: https://doi.org/10.1111/1365-2664.13411
Keywords: biodiversity, Borneo, conservation, environmental DNA, invertebrate DNA, leeches, mammals, Southeast Asia

Axtner, J., Crampton-Platt, A., Hörig, L.A., Mohamed, A., Xu, C.C.Y., Yu, D.W. & Wilting, A. 2019 An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. GigaScience. 8(4).
DOI: https://doi.org/10.1093/gigascience/giz029
Keywords: metabarcoding; invertebrate-derived -DNA; environmental DNA; leeches

Blackman, Rosetta C; Mächler, Elvira; Altermatt, Florian; Arnold, Amanda; Beja, Pedro; Boets, Pieter; Egeter, Bastian; Elbrecht, Vasco; Filipe, Ana Filipa; Jones, J Iwan. 2019. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring–the need for calibration experiments. Metabarcoding and Metagenomics.
DOI: https://doi.org/10.3897/mbmg.3.34735

Creedy, T.J., Norman, H., Tang, C.Q., Chin, K.Q., Andujar, C., Arribas, P., O’Connor, R.S., Carvell, C., Notton, D.G., Notton, D.G. & Vogler, A.P. 2019. A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding. Molecular Ecology Resources. 20(1).
DOI: https://doi.org/10.1111/1755-0998.13056
Keywords: community barcoding, contamination, double dual tagging, illumina sequencing, pollinators

Egeter, Bastian; Roe, Cailín; Peixoto, Sara; Puppo, Pamela; Easton, Luke J; Pinto, Joana; Bishop, Phillip J; Robertson, Bruce C. 2019. Using molecular diet analysis to inform invasive species management: a case study of introduced rats consuming endemic New Zealand frogs.Ecology and Evolution.
DOI: https://doi.org/10.1002/ece3.4903

Ji, Y., Huotari, T., Roslin, T., Schmidt, N.M., Wang, J., Yu, D.W. & Ovaskainen, O. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. 2019. Molecular Ecology Resources, 20(1).
DOI: https://doi.org/10.1111/1755-0998.13057
Keywords: Araneae, Arthropoda, biomonitoring, COI internal standard, community composition, DNA barcoding, insecta, metagenomics, mitogenomes, mitogenomics

Lopes, Ricardo J; Pinho, Catarina J; Santos, Bárbara; Seguro, Mariana; Mata, Vanessa A; Egeter, Bastian; Vasconcelos, Raquel. 2019. Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean. Ecology and Evolution.
DOI: https://doi.org/10.1002/ece3.5105

Peel, N., Dicks, L.V., Clark, M.D., Heavens, D., Percival-Alwyn, L., Cooper, C., Davies, R.G., Leggett, R.M. & Yu, D.W. 2019. Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet). Methods in Ecology and Evolution. 10(10).
DOI: https://doi.org/10.1111/2041-210X.13265
Keywords: bees, diet analysis, genome skim, metabarcoding, metagenomics, MinION, pollen, quantitative

Pochardt, M., Allen, J.M., Hart, T., Miller, S.D.L., Yu, D.W. & Levi, T. 2019. Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish. Molecular Ecology Resources. 20(2).
DOI: https://doi.org/10.1111/1755-0998.13123
Keywords: Alaska, anadromous, eDNA, eulachon, fisheries, Thaleichthys pacificus, Tlingit

Barsoum, N., Bruce, K., Forster, J., Yin-QiuJi., Yu, D.W. 2018. Metabarcoding of arthropods provides a sensitive measure of biodiversity response to forest stand composition compared with surrogate measures of biodiversity. Ecological Indicators, Volume 101, June 2019, Pages 313-323.
DOI: https://doi.org/10.1016/j.ecolind.2019.01.023
Keywords: DNA metabarcoding, Malaise traps, Surrogate measures of biodiversity, Biodiversity indicators, Forest management, Tree identity

Harper, L.R., Buxton, A.S., Rees, H.C., Bruce, K. et al. 2018. Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia 826: 25.
DOI: : https://doi.org/10.1007/s10750-018-3750-5
Keywords: Aquatic, Biodiversity, Lentic, Metabarcoding, Quantitative PCR, Survey

Hering, Daniel., Borja, Angel., Jones, John., Pont, Didier., Boets, Pieter., Bouchez, Agnès., Bruce, Kat. et al. 2018. Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research.
DOI: https://doi.org/10.1016/j.watres.2018.03.003
Keywords: Metabarcoding, eDNA, Biological quality elements, Rivers, Lakes

Levi, T., Allen, J.M., Bell, D., Joyce, J., Russel, J.R., Tallmon, D.A., Vulstek, S.C., Yang, C. & Yu, D.W. 2018. Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources. 19(3).
DOI: https://doi.org/10.1111/1755-0998.12987
Keywords: environmental DNA, qPCR, Southeast Alaska, fisheries management, Oncorhynchus, ecosystem services, ecosystem functions

Tang, C.Q., Crampton-Platt, A., Townend, S., Bruce, K., Bista, I. & Creer, S. 2018. Development of DNA applications in Natural England. Natural England Commissioned Reports, Number 252.
Keywords: DNA, eDNA, sequencing, metabarcoding, monitoring, invertebrates, fish, vascular plants

Andújar, Carmelo., Arribas, Paula., Gray, Clare., Bruce, Kat., Woodward, Guy., Yu, Douglas., & Vogler, Alfried. (2017). Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill. Molecular Ecology.
DOI: https://doi.org/10.1111/mec.14410
Keywords: Biomonitoring, Community ecology, DNA barcoding, Freshwater ecosystems, Invertebrates

Bush, A., Sollmann, R., Wilting, A., Bohmann, K., Cole, B., Balzter, H., … & Dawson, T. P. (2017). Connecting Earth Observation to High-Throughput Biodiversity Data. Nature Ecology & Evolution.

Somervuo, P., Yu, D. W., Xu, C. C., Ji, Y., Hultman, J., Wirta, H., & Ovaskainen, O. (2017). Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding. Methods in Ecology and Evolution, 8(4), 398-407.
DOI: https://doi.org/10.1111/2041-210X.12721
Keywords: Biodiversity, DNA barcoding, eDNA, Metabarcoding

Rodgers, T. W., Xu, C., Giacalone, J., Kapheim, K., Saltonstall, K., Vargas, M., … & Jansen, P. (2017). Carrion Fly-Derived DNA Metabarcoding Is An Effective Tool For Mammal Surveys: Evidence From A Known Tropical Mammal Community. bioRxiv, 133405.
DOI: https://doi.org/10.1101/133405
Keywords: DNA barcoding, DNA metabarcoding, molecular species identification, multinomial regression, statistical model, taxonomic assignment, taxonomic placement

Cai W, Ma Z, Yang C, Wang L, Wang W, Zhao G, … & Douglas, W. Y. (2017) Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site. PLoS ONE 12(5): e0177724.
DOI: https://doi.org/10.1371/journal.pone.0177724
Keywords: eDNA, Invasive crayfish, pPCR,

Hudson, L. N., Newbold, T., Contu, S., Hill, S. L., Lysenko, I., De Palma, A., … & Booth, H. (2017). The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project. Ecology and Evolution, 7(1), 145-188.
DOI: https://doi.org/10.1002/ece3.2579
Keywords: Data sharing, Global biodiversity modeling, Global change, Habitat destruction, Land use

Tang, P. and Vogler, A.P., 2017. Evolution: Taking the Sting out of Wasp Phylogenetics. Current Biology, vol:27 pp.R358-R360.

Bush, A., Sollmann, R., Wilting, A., Bohmann, K., Cole, B., Balzter, H., Martius, C., Zlinszky, A., Calvignac-Spencer, S., Cobbold, C.A. and Dawson, T.P., 2017 Connecting Earth Observation to High-Throughput Biodiversity Data. Nature Ecology & Evolution.
Keywords: Biodiversity, Conservation biology, Decision making, Ecosystem services, Environmental impact

Andujar, C., Arribas, P., Linard, B., Kundrata, R., Bocak, L. and Vogler, A.P., 2017. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles. Mitochondrial DNA Part A, vol:28, pp.156-158.
Keywords: Coleoptera, Elateroidea, Gene rearrangement, Mitochondrial metagenomics, Mitochondrion

Timmermans, M.J., Thompson, M.J., Collins, S. and Vogler, A.P., 2017. Independent evolution of sexual dimorphism and female‐limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas). Molecular ecology, vol:26, pp.1273-1284.
Keywords: Batesian mimicry, Papilio phorcas, Phylogenomics, Polymorphism, Sexual selection, Transcriptome

Gómez‐Rodríguez, C., Timmermans, M.J., Crampton‐Platt, A. and Vogler, A.P., 2017. Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes. Methods in Ecology and Evolution, vol:8, pp.248-256.
Keywords: Chrysomelidae, DNA barcodes, genome skimming, intraspecific variability, mitochondrial metagenomics, mito‐metagenomics, population genetics

Linard, B., Arribas, P., Andújar, C., Crampton-Platt, A. and Vogler, A.P., 2017. The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera. Mitochondrial DNA Part A, vol:28, pp.71-72.
Keywords: Biomonitoring, Hydropsychoidae, Mitochondrial rearrangement, Mitochondrial metagenomics

Nie, R.E., Breeschoten, T., Timmermans, M.J., Nadein, K., Xue, H.J., Bai, M., Huang, Y., Yang, X.K. and Vogler, A.P., 2017. The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics.

Crampton-Platt, A., Douglas, W. Y., Zhou, X., & Vogler, A. P. (2016). Mitochondrial metagenomics: letting the genes out of the bottle. GigaScience, 5(1), 15.
DOI: https://doi.org/10.1186/s13742-016-0120-y
Keywords: Shotgun sequencing, Illumina, Biodiversity, Phylogenetics, Community ecology, Genome assembly

Zhang, K., Lin, S., Ji, Y., Yang, C., Wang, X., Yang, C., … & Yu, D. W. (2016). Plant diversity accurately predicts insect diversity in two tropical landscapes. Molecular Ecology, 25(17), 4407-4419.
DOI: https://doi.org/10.1111/mec.13770
Keywords: Hropoda, Biodiversity, Biomonitoring, Host specificity, Insect–plant interactions, Surrogate species

Orkin, J. D., Yang, Y., Yang, C., Yu, D. W., & Jiang, X. (2016). Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology. Scientific Reports, 6.
DOI: https://doi.org/10.1038/srep34758

Hua, F., Wang, X., Zheng, X., Fisher, B., Wang, L., Zhu, J., … & Wilcove, D. S. (2016). Opportunities for biodiversity gains under the world/’s largest reforestation programme. Nature Communications, 7.
DOI: https://doi.org/10.1038/ncomms12717

Notton, D.G., Tang, C.Q., and Day, A.R., 2016. Viper’s Bugloss Mason Bee, Hoplitis (Hoplitis) adunca, new to Britain (Hymenoptera, Megachilidae, Megachilinae, Osmiini). British Journal of Entomology & Natural History, 29, pp. 134-143.

Tang, C.Q., Orme, C.D.L., Bunnefeld, L., Jones, F.A., Powell, S., Chase, M.W., Barraclough, T.G. and Savolainen, V., 2016. Global monocot diversification: geography explains variation in species richness better than environment or biology. Botanical Journal of the Linnean Society.
DOI: https://doi.org/10.1111/boj.12497

Gill, R.J., Baldock, K.C., Brown, M.J., Cresswell, J.E., Dicks, L.V., Fountain, M.T., Garratt, M.P., Gough, L.A., Heard, M.S., Holland, J.M., Ollerton, J., Stone, G.N., Tang, C.Q., et al., 2016. Chapter Four-Protecting an Ecosystem Service: Approaches to Understanding and Mitigating Threats to Wild Insect Pollinators. Advances in Ecological Research, 54, pp.135-206.
DOI: https://doi.org/10.1016/bs.aecr.2015.10.007

Breeschoten, T., Doorenweerd, C., Tarasov, S. and Vogler, A.P., 2016. Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes. Molecular Phylogenetics and Evolution, vol:105, pp.86-95.

Linard, B., Arribas, P., Andújar, C., Crampton‐Platt, A. and Vogler, A.P., 2016. Lessons from genome skimming of arthropod‐preserving ethanol. Molecular ecology resources, vol:16, pp.1365-1377.

Paula, D.P., Linard, B., Crampton-Platt, A., Srivathsan, A., Timmermans, M.J., Sujii, E.R., Pires, C.S., Souza, L.M., Andow, D.A. and Vogler, A.P., 2016. Uncovering trophic interactions in arthropod predators through DNA shotgun-sequencing of gut contents. PloS one, vol: 11, p.e0161841.

Arribas, P., Andújar, C., Hopkins, K., Shepherd, M. and Vogler, A.P., 2016. Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil. Methods in Ecology and Evolution, vol:7, pp.1071-1081.

Andújar, C., Faille, A., Pérez-González, S., Zaballos, J.P., Vogler, A.P. and Ribera, I., 2016. Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles. Molecular phylogenetics and evolution, vol:99, pp.235-246.

Bocak, L., Kundrata, R., Fernández, C.A. and Vogler, A.P., 2016, May. The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing. Proceedings of the Royal Society Biological sciences Vol: 283,  pp. 20152350.

Song, F., Li, H., Jiang, P., Zhou, X., Liu, J., Sun, C., Vogler, A.P. and Cai, W., 2016. Capturing the phylogeny of Holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models. Genome biology and evolution, vol:8,  pp.1411-1426.

Ahrens, D., Fujisawa, T., Krammer, H.J., Eberle, J., Fabrizi, S. and Vogler, A.P., 2016. Rarity and incomplete sampling in DNA-based species delimitation. Systematic biology, vol:65, pp.478-494.

Srivathsan, A., Ang, A., Vogler, A.P. and Meier, R., 2016. Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Frontiers in zoology, vol:13, pp.17.

Bidegaray-Batista, L., Sánchez-Garcia, A., Santulli, G., Maiorano, L., Guisan, A., Vogler, A. and Arnedo, M., 2016. Data from: Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider.

Bidegaray‐Batista, L., Sánchez‐Garcia, A., Santulli, G., Maiorano, L., Guisan, A., Vogler, A.P. and Arnedo, M.A., 2016. Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and paleodistribution modelling of an endemic spider. Molecular ecology, Vol: 25, Pages: 2046-2064.

Leese, F., Altermatt, F., Bouchez, A., Ekrem, T., Hering, D., Csabai, Z.S., Padisák, J., …. Vogler, A.P. and Várbíró, G., 2016. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes (RIO), vol:2, p.e11321.

Miller, K.E., Hopkins, K., Inward, D.J. and Vogler, A.P., 2016. Metabarcoding of fungal communities associated with bark beetles. Ecology and evolution. Vol: 6, Pages: 1590-1600.

Timmermans, M.J., Barton, C., Haran, J., Ahrens, D., Culverwell, C.L., Ollikainen, A., Dodsworth, S., Foster, P.G., Bocak, L. and Vogler, A.P., 2016. Family-level sampling of mitochondrial genomes in Coleoptera: compositional heterogeneity and phylogenetics. Genome biology and evolution, Vol: 8 pp.161-175.

Bocakova, M., Bocak, L., Gimmel, M.L., Motyka, M. and Vogler, A.P., 2016. Aposematism and mimicry in soft‐bodied beetles of the superfamily Cleroidea (Insecta). Zoologica Scripta, vol:45 pp.9-21.

Timmermans, M.J., Viberg, C., Martin, G., Hopkins, K. and Vogler, A.P., 2016. Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections. Biological Journal of the Linnean Society, vol:117, pp.83-95.

Schnell, I. B., Sollmann, R., Calvignac-Spencer, S., Siddall, M. E., Douglas, W. Y., Wilting, A., & Gilbert, M. T. P. (2015). iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool–prospects, pitfalls and avenues to be developed.  Frontiers in zoology, 12(1), 24.
DOI: https://doi.org/10.1186/s12983-015-0115-z

Tang, M., Hardman, C.J., Ji, Y., Meng, G., Liu, S., Tan, M., Yang, S., Moss, E.D., Wang, J., Yang, C. and Bruce, C., 2015. High‐throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution, 6(9), pp.1034-1043.
DOI: https://doi.org/10.1111/2041-210X.12416

Fontaneto, D., Flot, J.F. and Tang, C.Q., 2015. Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity, 45(3), pp.433-451.
DOI: https://doi.org/10.1007/s12526-015-0319-7

Elfekih, S., Shannon, M., Haran, J. and Vogler, A.P., 2014. Detection of the Acetylcholinesterase Insecticide Resistance Mutation (G328A) in Natural Populations of Ceratitis capitata. Journal of economic entomology, vol :107, pp.1965-1968.