Search Results - "Molecular ecology"

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics by Rochette, Nicolas C., Rivera‐Colón, Angel G., Catchen, Julian M.

“…For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing,…”
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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities by Deiner, Kristy, Bik, Holly M., Mächler, Elvira, Seymour, Mathew, Lacoursière‐Roussel, Anaïs, Altermatt, Florian, Creer, Simon, Bista, Iliana, Lodge, David M., Vere, Natasha, Pfrender, Michael E., Bernatchez, Louis

“…The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid…”
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Population genomics for wildlife conservation and management by Hohenlohe, Paul A., Funk, W. Chris, Rajora, Om P.

“…Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this…”
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Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? by Deagle, Bruce E., Thomas, Austen C., McInnes, Julie C., Clarke, Laurence J., Vesterinen, Eero J., Clare, Elizabeth L., Kartzinel, Tyler R., Eveson, J. Paige

“…Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of…”
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The K = 2 conundrum by Janes, Jasmine K., Miller, Joshua M., Dupuis, Julian R., Malenfant, René M., Gorrell, Jamieson C., Cullingham, Catherine I., Andrew, Rose L.

“…Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow…”
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DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions by Zinger, Lucie, Bonin, Aurélie, Alsos, Inger G., Bálint, Miklós, Bik, Holly, Boyer, Frédéric, Chariton, Anthony A., Creer, Simon, Coissac, Eric, Deagle, Bruce E., De Barba, Marta, Dickie, Ian A., Dumbrell, Alex J., Ficetola, Gentile Francesco, Fierer, Noah, Fumagalli, Luca, Gilbert, M. Thomas P., Jarman, Simon, Jumpponen, Ari, Kauserud, Håvard, Orlando, Ludovic, Pansu, Johan, Pawlowski, Jan, Tedersoo, Leho, Thomsen, Philip Francis, Willerslev, Eske, Taberlet, Pierre

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Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations by Forester, Brenna R., Lasky, Jesse R., Wagner, Helene H., Urban, Dean L.

“…Identifying adaptive loci can provide insight into the mechanisms underlying local adaptation. Genotype–environment association (GEA) methods, which identify…”
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Cryptic species as a window into the paradigm shift of the species concept by Fišer, Cene, Robinson, Christopher T., Malard, Florian

“…The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many…”
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Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding by Valentini, Alice, Taberlet, Pierre, Miaud, Claude, Civade, Raphaël, Herder, Jelger, Thomsen, Philip Francis, Bellemain, Eva, Besnard, Aurélien, Coissac, Eric, Boyer, Frédéric, Gaboriaud, Coline, Jean, Pauline, Poulet, Nicolas, Roset, Nicolas, Copp, Gordon H, Geniez, Philippe, Pont, Didier, Argillier, Christine, Baudoin, Jean‐Marc, Peroux, Tiphaine, Crivelli, Alain J, Olivier, Anthony, Acqueberge, Manon, Le Brun, Matthieu, Møller, Peter R, Willerslev, Eske, Dejean, Tony

“…Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for…”
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Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap by Cordier, Tristan, Alonso‐Sáez, Laura, Apothéloz‐Perret‐Gentil, Laure, Aylagas, Eva, Bohan, David A., Bouchez, Agnès, Chariton, Anthony, Creer, Simon, Frühe, Larissa, Keck, François, Keeley, Nigel, Laroche, Olivier, Leese, Florian, Pochon, Xavier, Stoeck, Thorsten, Pawlowski, Jan, Lanzén, Anders

“…A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic…”
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The long‐standing significance of genetic diversity in conservation by DeWoody, J. Andrew, Harder, Avril M., Mathur, Samarth, Willoughby, Janna R.

“…Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted to characterize gene pools and conserve the…”
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Towards a unified paradigm for sequence-based identification of fungi by Kõljalg, Urmas, Nilsson, R. Henrik, Abarenkov, Kessy, Tedersoo, Leho, Taylor, Andy F. S., Bahram, Mohammad, Bates, Scott T., Bruns, Thomas D., Bengtsson-Palme, Johan, Callaghan, Tony M., Douglas, Brian, Drenkhan, Tiia, Eberhardt, Ursula, Dueñas, Margarita, Grebenc, Tine, Griffith, Gareth W., Hartmann, Martin, Kirk, Paul M., Kohout, Petr, Larsson, Ellen, Lindahl, Björn D., Lücking, Robert, Martín, María P., Matheny, P. Brandon, Nguyen, Nhu H., Niskanen, Tuula, Oja, Jane, Peay, Kabir G., Peintner, Ursula, Peterson, Marko, Põldmaa, Kadri, Saag, Lauri, Saar, Irja, Schüßler, Arthur, Scott, James A., Senés, Carolina, Smith, Matthew E., Suija, Ave, Taylor, D. Lee, Telleria, M. Teresa, Weiss, Michael, Larsson, Karl-Henrik

“…The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of…”
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Biodiversity and species competition regulate the resilience of microbial biofilm community by Feng, Kai, Zhang, Zhaojing, Cai, Weiwei, Liu, Wenzong, Xu, Meiying, Yin, Huaqun, Wang, Aijie, He, Zhili, Deng, Ye

“…The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called…”
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How quantitative is metabarcoding: A meta‐analytical approach by Lamb, Philip D., Hunter, Ewan, Pinnegar, John K., Creer, Simon, Davies, Richard G., Taylor, Martin I.

“…Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA…”
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Best practices in metabarcoding of fungi: From experimental design to results by Tedersoo, Leho, Bahram, Mohammad, Zinger, Lucie, Nilsson, R. Henrik, Kennedy, Peter G., Yang, Teng, Anslan, Sten, Mikryukov, Vladimir

“…The development of high‐throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a…”
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Stacks: an analysis tool set for population genomics by Catchen, Julian, Hohenlohe, Paul A., Bassham, Susan, Amores, Angel, Cresko, William A.

“…Massively parallel short‐read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of…”
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A beginner's guide to low‐coverage whole genome sequencing for population genomics by Lou, Runyang Nicolas, Jacobs, Arne, Wilder, Aryn P., Therkildsen, Nina Overgaard

“…Low‐coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost‐effective approach for population genomic studies in both model and nonmodel…”
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Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods by Hänfling, Bernd, Lawson Handley, Lori, Read, Daniel S., Hahn, Christoph, Li, Jianlong, Nichols, Paul, Blackman, Rosetta C., Oliver, Anna, Winfield, Ian J.

“…Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA)…”
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These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists by O'Leary, Shannon J., Puritz, Jonathan B., Willis, Stuart C., Hollenbeck, Christopher M., Portnoy, David S.

“…Sequencing reduced‐representation libraries of restriction site‐associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming…”
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Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring by Pawlowski, Jan, Apothéloz‐Perret‐Gentil, Laure, Altermatt, Florian

“…The last decade brought a spectacular development of so‐called environmental (e)DNA studies. In general, “environmental DNA” is defined as DNA isolated from…”
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