SELECTED PUBLICATIONS

Blackman, R., Mächler, E., Altermatt, F., Arnold, A., Beja, P., Boets, P., … Deiner, K. (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

da Silva, L. P., Mata, V. A., Lopes, P. B., Pereira, P., Jarman, S. N., Lopes, R. J., & Beja, P. (2019). Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists. Molecular Ecology Resources. DOI: https://doi.org/10.1111/1755-0998.13060

Corley, M., Ferreira, S., & Mata, V. A. (2019). Ypsolopha rhinolophi sp. nov. (Lepidoptera: Ypsolophidae), a new species from Portugal and France unveiled by bats. Zootaxa, 4609(3), 565. DOI: https://doi.org/10.11646/zootaxa.4609.3.10

Lopes, R. J., Pinho, C. J., Santos, B., Seguro, M., Mata, V. A., Egeter, B., & Vasconcelos, R. (2019). Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean. Ecology and Evolution, 9(8), 4994–5002. DOI: https://doi.org/10.1002/ece3.5105

Egeter, B., Roe, C., Peixoto, S., Puppo, P., Easton, L. J., Pinto, J., … Robertson, B. 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, 9(9), 5032–5048. DOI: https://doi.org/10.1002/ece3.4903

Ferreira, S., Paupério, J., Grosso-Silva, J. M., & Beja, P. (2019). DNA barcoding of Sialis sp. (Megaloptera) in Portugal: the missing tool to species identification. Aquatic Insects. DOI: https://doi.org/10.1080/01650424.2019.1571612

Martins, F. M. S., Galhardo, M., Filipe, A. F., Teixeira, A., Pinheiro, P., Paupério, J., … Beja, P. (2019). Have the cake and eat it: Optimising non‐destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring. Molecular Ecology Resources, 1755–0998.13012. DOI: https://doi.org/10.1111/1755-0998.13012

Proença-Ferreira, A., Ferreira, C., Leitão, I., Paupério, J., Sabino-Marques, H., Barbosa, S., … Pita, R. (2019). Drivers of survival in a small mammal of conservation concern: An assessment using extensive genetic non-invasive sampling in fragmented farmland. Biological Conservation, 230, 131–140. DOI: https://doi.org/10.1016/J.BIOCON.2018.12.021

Agostinho, M., Moniz Alves, C., Aresta, S., Borrego, F., Borlido-Santos, J., Cortez, J., … Vidal, S. (2018). The interface of science: the case for a broader definition of research management. Perspectives: Policy and Practice in Higher Education, 1–9. DOI: https://doi.org/10.1080/13603108.2018.1543215

Egeter, B., Peixoto, S., Brito, J. C., Jarman, S., Puppo, P., & Velo-Antón, G. (2018). Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA. Genome, 61(11), 807–814. DOI: https://doi.org/10.1139/gen-2018-0071

Ferreira, C. M., Sabino-Marques, H., Barbosa, S., Costa, P., Encarnação, C., Alpizar-Jara, R., … Alves, P. C. (2018). Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. European Journal of Wildlife Research, 64(4), 46. DOI: https://doi.org/10.1007/s10344-018-1188-8

Mata, V. A., Rebelo, H., Amorim, F., Mccracken, G. F., Jarman, S., & Beja, P. (2018). How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis. Molecular Ecology. DOI: https://doi.org/10.1111/mec.14779

Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., … Kahlert, M. (2018). The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of The Total Environment, 637–638, 1295–1310. DOI: https://doi.org/10.1016/J.SCITOTENV.2018.05.002

Pinho, C. J., Santos, B., Mata, V. A., Seguro, M., Romeiras, M. M., Lopes, R. J., & Vasconcelos, R. (2018). What is the giant wall gecko having for dinner? Conservation genetics for guiding reserve management in cabo verde. Genes. DOI: https://doi.org/10.3390/genes9120599

Corley, M. F. V., & Ferreira, S. (2017). DNA Barcoding reveals sexual dimorphism in Isotrias penedana Trematerra, 2013 (Lepidoptera: Tortricidae, Chlidanotinae) . Zootaxa. DOI: https://doi.org/10.11646/zootaxa.4221.5.7

Corley, M. F. V., Ferreira, S., Lvovsky, A. L., & Rosete, J. (2017). Borkhausenia crimnodes Meyrick, 1912 (Lepidoptera, Oecophoridae), a southern hemisphere species resident in Portugal. Nota Lepidopterologica, 40(1), 15–24. DOI: https://doi.org/10.3897/nl.40.10938

Curto, M., Puppo, P., Kratschmer, S., & Meimberg, H. (2017). Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons. BMC Evolutionary Biology, 17(1), 198. DOI: https://doi.org/10.1186/s12862-017-1031-y

Mata, V. A., Amorim, F., Guillén-Servent, A., Beja, P., & Rebelo, H. (2017). First complete mitochondrial genomes of molossid bats (Chiroptera: Molossidae). Mitochondrial DNA Part B, 2(1), 152–154. DOI: https://doi.org/10.1080/23802359.2017.1298419

McInnes, J. C., Alderman, R., Deagle, B. E., Lea, M.-A., Raymond, B., & Jarman, S. N. (2017). Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates. Methods in Ecology and Evolution, 8(2), 192–202. DOI: https://doi.org/10.1111/2041-210X.12677

 

TECHNICAL REPORTS

Ferreira S, Fonseca N, Egeter B, Paupério J, Galhardo M, Oxelfelt F, Aresta S, Archer J, Corley M, Penado A, Pina S, Jarman S and Beja P (2018). Deliverable 4.2 (D4.2): Protocol for building and organising reference collections of DNA sequences, EnvMetaGen project (Grant Agreement No 668981). European Union Horizon 2020 Research & Innovation Programme - H2020-WIDESPREAD-2014-2 DOI: 10.5281/zenodo.2586893

Egeter B, Fonseca NA, Paupério J, Galhardo M, Ferreira S, Oxelfelt F, Aresta S, Martins FMS, Mata VA, da Silva LP, Peixoto S, Garcia-Raventós A, Vasconcelos S, Gil P, Khalatbari L, Filipe AF, Jarman S and Beja P (2018). Deliverable 4.3 (D4.3): Protocol for field collection and preservation of eDNA samples, EnvMetaGen project (Grant Agreement No 668981). European Union Horizon 2020 Research & Innovation Programme - H2020-WIDESPREAD-2014-2 DOI: 10.5281/zenodo.2579806

Paupério J, Fonseca N, Egeter B, Galhardo M, Ferreira S, Oxelfelt F, Aresta S, Martins F, Mata V, Veríssimo J, Puppo P, Pinto JC, Chaves C, Garcia-Raventós A, Peixoto S, da Silva LP, Vasconcelos S, Gil P, Khalatbari L, Jarman S and Beja P (2018). Deliverable 4.4 (D4.4): Protocol for next-gen analysis of eDNA samples, EnMetaGen project (Grant Agreement No 668981). European Union Horizon 2020 Research & Innovation Programme – H2020-WIDESPREAD-2014-2 DOI: 10.5281/zenodo.2586885

Galhardo M, Fonseca NA, Egeter B, Paupério J, Ferreira S, Oxelfelt F, Aresta S, Muñoz-Merida A, Martins FMS, Mata VA, da silva L, Peixoto S, Garcia-Raventós A, Vasconcelos S, Gil P, Khalatbari L, Jarman S and Beja P (2018). Deliverable 4.5 (D4.5): Protocol for the processing of DNA sequence data generated by next-gen platforms, EnMetaGen project (Grant Agreement No 668981). European Union Horizon 2020 Research & Innovation Programme – H2020-WIDESPREAD-2014-2 DOI: 10.5281/zenodo.2586889

 

OTHER PUBLICATIONS

Correia, E., Granadeiro, J., Mata, V., Regalla, A., & Catry, P. (2019). Trophic interactions between migratory seabirds, predatory fishes and small pelagics in coastal West Africa. Marine Ecology Progress Series, 622, 177–189. DOI: https://doi.org/10.3354/meps13022

Athar, A., Füllgrabe, A., George, N., Iqbal, H., Huerta, L., Ali, A., … Brazma, A. (2019). ArrayExpress update – from bulk to single-cell expression data. Nucleic Acids Research, 47(D1), D711–D715. DOI: https://doi.org/10.1093/nar/gky964

Correia, M., Heleno, R., Silva, L. P., Costa, J. M., & Rodríguez‐Echeverría, S. (2019). First evidence for the joint dispersal of mycorrhizal fungi and plant diaspores by birds. New Phytologist, 222(2), 1054–1060. DOI: https://doi.org/10.1111/nph.15571

da Silva, L. P., Heleno, R. H., Costa, J. M., Valente, M., Mata, V. A., Gonçalves, S. C., … Ramos, J. A. (2019). Natural woodlands hold more diverse, abundant, and unique biota than novel anthropogenic forests: a multi-group assessment. European Journal of Forest Research. DOI: https://doi.org/10.1007/s10342-019-01183-5

Herman, J. S., Wójcik, J. M., Stojak, J., Paupério, J., Jaarola, M., & Searle, J. B. (2019). Genetic variation in field voles (Microtus agrestis) from the British Isles: selective sweeps or population bottlenecks? DOI: https://doi.org/10.1093/biolinnean/bly213

Corley, M. F. V., Rosete, J., Gonçalves, A. R., Mata, V., Nunes, J., & Pires, P. (2018). New and interesting Portuguese Lepidoptera records from 2016 (Insecta: Lepidoptera). SHILAP Revista de Lepidopterología, 46(181), 33–56.

Aizpurua, O., Budinski, I., Georgiakakis, P., Gopalakrishnan, S., Ibañez, C., Mata, V., … Alberdi, A. (2018). Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding. Molecular Ecology, 27(3), 815–825. DOI: https://doi.org/10.1111/mec.14474

Carvalho, F., Lourenço, A., Carvalho, R., Alves, P. C., Mira, A., & Beja, P. (2018). The effects of a motorway on movement behaviour and gene flow in a forest carnivore: Joint evidence from road mortality, radio tracking and genetics. Landscape and Urban Planning, 178, 217–227. DOI: https://doi.org/https://doi.org/10.1016/j.landurbplan.2018.06.007

Crespo, L., Domènech, M., Enguídanos, A., Malumbres-Olarte, J., Cardoso, P., Moya-Laraño, J., … Arnedo, M. (2018). A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks. Biodiversity Data Journal, 6, e29443. DOI: https://doi.org/10.3897/BDJ.6.e29443

Filipe, A. F., Feio, M. J., Garcia-Raventós, A., Ramião, J. P., Pace, G., Martins, F. M., & Magalhães, M. F. (2018). The European Water Framework Directive facing current challenges: recommendations for a more efficient biological assessment of inland surface waters. Inland Waters, 1–9. DOI: https://doi.org/10.1080/20442041.2018.1494973

Quaglietta, L., Paupério, J., Martins, F. M. S., Alves, P. C., & Beja, P. (2018). Recent range contractions in the globally threatened Pyrenean desman highlight the importance of stream headwater refugia. Animal Conservation, 21(6), 515–525. DOI: https://doi.org/10.1111/acv.12422

Sabino-Marques, H., Ferreira, C. M., Paupério, J., Costa, P., Barbosa, S., Encarnação, C., … Pita, R. (2018). Combining genetic non-invasive sampling with spatially explicit capture-recapture models for density estimation of a patchily distributed small mammal. European Journal of Wildlife Research, 64(4), 44. DOI: https://doi.org/10.1007/s10344-018-1206-x

Barbosa, S., Paupério, J., Herman, J. S., Ferreira, C. M., Pita, R., Vale-Gonçalves, H. M., … Searle, J. B. (2017). Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole. Molecular Ecology, 26(3), 951–967. DOI: https://doi.org/10.1111/mec.13994

Bassett, I. E., Horner, I. J., Hough, E. G., Wolber, F. M., Egeter, B., Stanley, M. C., & Krull, C. R. (2017). Ingestion of infected roots by feral pigs provides a minor vector pathway for kauri dieback disease Phytophthora agathidicida. Forestry: An International Journal of Forest Research, 90(5), 640–648. DOI: https://doi.org/10.1093/forestry/cpx019

McInnes, J. C., Alderman, R., Lea, M.-A., Raymond, B., Deagle, B. E., Phillips, R. A., … Jarman, S. N. (2017). High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding. Molecular Ecology, 26(18), 4831–4845. DOI: https://doi.org/10.1111/mec.14245

Pina, S., Vasconcelos, S., Reino, L., Santana, J., Beja, P., Sánchez-Oliver, J. S., … Ferreira, S. (2017). The Orthoptera of Castro Verde Special Protection Area (Southern Portugal): new data and conservation value. ZooKeys, 691, 19–48. DOI: https://doi.org/10.3897/zookeys.691.14842

Biscontin, A., Frigato, E., Sales, G., Mazzotta, G. M., Teschke, M., De Pittà, C., … Bertolucci, C. (2016). The opsin repertoire of the Antarctic krill Euphausia superba. Marine Genomics, 29, 61–68. DOI: https://doi.org/10.1016/J.MARGEN.2016.04.010

Jarman, S. N., & Deagle, B. E. (2016). Genetics of Antarctic Krill. DOI: https://doi.org/10.1007/978-3-319-29279-3_7

Leese, F., Altermatt, F., Bouchez, A., Ekrem, T., Hering, D., Meissner, K., … Zimmermann, J. (2016). DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes, 2, e11321. DOI: https://doi.org/10.3897/rio.2.e11321

Mata, V. A., Amorim, F., Corley, M. F. V., McCracken, G. F., Rebelo, H., & Beja, P. (2016). Female dietary bias towards large migratory moths in the European free-tailed bat ( Tadarida teniotis ). Biology Letters, 12(3), 20150988. DOI: https://doi.org/10.1098/rsbl.2015.0988

McInnes, J. C., Raymond, B., Phillips, R. A., Jarman, S. N., Lea, M.-A., & Alderman, R. (2016). A review of methods used to analyse albatross diets—assessing priorities across their range. ICES Journal of Marine Science: Journal Du Conseil, 73(9), 2125–2137. DOI: https://doi.org/10.1093/icesjms/fsw105

Toomey, L., Welsford, D., Appleyard, S. A., Polanowski, A., Faux, C., Deagle, B. E., … Jarman, S. (2016). Genetic structure of Patagonian toothfish populations from otolith DNA. Antarctic Science, 28(05), 347–360. DOI: https://doi.org/10.1017/S0954102016000183

Vaz Pinto, P., Beja, P., Ferrand, N., & Godinho, R. (2016). Hybridization following population collapse in a critically endangered antelope. Scientific Reports, 6(1), 18788. DOI: https://doi.org/10.1038/srep18788