Relevant publications
The following list of selected publications provides an idea of the workshop's general framework, as well as the instructors' background. Publications marked with stars (***) are strongly recommended as basic background before attending the workshop.
Metabarcoding
Mitochondrial Metagenetics
Analysing metagenetic communities
- Alberdi, A., Aizpurua, O., Gilbert, M. T. P., & Bohmann, K. (2018). Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods in Ecology and Evolution, 9(1), 134–147. https://doi.org/10.1111/2041-210X.12849
- Creedy, T. J., Norman, H., Tang, C. Q., Chin, K. Q., Andujar, C., Arribas, P., … Vogler, A. P. (2019). A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput barcoding. BioRxiv, 575308. https://doi.org/10.1101/575308
- Creedy, T. J., Ng, W. S., & Vogler, A. P. (2019). Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy. Ecology and Evolution, 9(6), 3105–3116. https://doi.org/10.1002/ece3.4839
- Ji, Y., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., … Yu, D. W. (2013). Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters, 16(10), 1245–1257. https://doi.org/10.1111/ele.12162
- Joly, S., Davies, T. J., Archambault, A., Bruneau, A., Derry, A., Kembel, S. W., … Wheeler, T. A. (2014). Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Molecular Ecology Resources, 14(2), 221–232. https://doi.org/10.1111/1755-0998.12173
- Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: diet assessment using next generation sequencing. Molecular Ecology, 21(8), 1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
- Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428
- *** Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012). Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3(4), 613–623. https://doi.org/10.1111/j.2041-210X.2012.00198.x ***
Mitochondrial Metagenetics
- *** Andújar, C., Arribas, P., Ruzicka, F., Platt, A. C., Timmermans, M. J. T. N., & Vogler, A. P. (2015). Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Molecular Ecology, 24, 3603–3617. https://doi.org/10.1111/mec.13195 ***
- Choo, L. Q., Crampton-Platt, A., & Vogler, A. P. (2017). Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum. Molecular Ecology, 26(19), 5086–5098. https://doi.org/10.1111/mec.14258
- Crampton-Platt, A., Yu, D. W., Zhou, X., & Vogler, A. P. (2016). Mitochondrial metagenomics: letting the genes out of the bottle. GigaScience, 5(1), 15. https://doi.org/10.1186/s13742-016-0120-y
- Gómez-Rodríguez, C., Crampton-Platt, A., Timmermans, M. J. T. N., Baselga, A., & Vogler, A. P. (2015). Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages. Methods in Ecology and Evolution, 6(8), 883–894. https://doi.org/10.1111/2041-210X.12376
- Tang, M., Hardman, C. J., Ji, Y., Meng, G., Liu, S., Tan, M., … Yu, D. W. (2015). High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution, 6(9), 1034–1043. https://doi.org/10.1111/2041-210X.12416
Analysing metagenetic communities
- Baselga, A. (2008). Determinants of species richness, endemism and turnover in European longhorn beetles. Ecography, 31(2), 263–271. https://doi.org/10.1111/j.0906-7590.2008.5335.x
- Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19(1), 134–143. https://doi.org/10.1111/j.1466-8238.2009.00490.x
- *** Baselga, A., Gómez-Rodríguez, C., & Vogler, A. P. (2015). Multi-hierarchical macroecology at species and genetic levels to discern neutral and non-neutral processes. Global Ecology and Biogeography, 24(8), 873–882. https://doi.org/10.1111/geb.12322 ***
- García-López, A., Micó, E., Múrria, C., Galante, E., & Vogler, A. P. (2013). Beta diversity at multiple hierarchical levels: explaining the high diversity of scarab beetles in tropical montane forests. Journal of Biogeography, 40(11), 2134–2145. https://doi.org/10.1111/jbi.12148
- Nekola, J. C., & White, P. S. (1999). The distance decay of similarity in biogeography and ecology. Journal of Biogeography, 26(4), 867–878. https://doi.org/10.1046/j.1365-2699.1999.00305.x
You might also find this BES blog post by two of the course instructors interesting:
