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- Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islandsPublication . Emerson, Brent C.; Borges, Paulo A. V.; Cardoso, Pedro; Convey, Peter; deWaard, Jeremy R.; Economo, Evan P.; Gillespie, Rosemary G.; Kennedy, Susan; Krehenwinkel, Henrik; Meier, Rudolf; Roderick, George K.; Strasberg, Dominique; Thébaud, Christophe; Traveset, Anna; Creedy, Thomas J.; Meramveliotakis, Emmanouil; Noguerales, Víctor; Overcast, Isaac; Morlon, Hélène; Papadopoulou, Anna; Vogler, Alfried P.; Arribas, Paula; Andújar, CarmeloABSTRACT: Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
- How genomics can help biodiversity conservationPublication . Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul R.; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R.; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A.; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; De Vries, Jan; Waldvogel, Ann-Marie; Zhang, Guojie; Jarvis, Erich D.; Bálint, Miklós; CIOFI, CLAUDIO; Waterhouse, Robert M.; Mazzoni, Camila J.; Höglund, Jacob; Aghayan, Sargis A.; Alioto, Tyler; Alvarez, Nadir; Alves, Paulo C.; Rosário, Isabel Amorim do; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, Luis Filipe; Chueca, Luis J.; Čiampor, Fedor; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V.; Delsuc, Frédéric; Dennis, Alice B.; Dimitrov, Dimitar; Faria, Rui; Favre, Adrien; Fedrigo, Olivier D.; Fernández, Rosa; Ficetola, Gentile; Flot, Jean-François; Gabaldón, Toni; Agius, Dolores R.; Giani, Alice M.; Gilbert, M Thomas P; Grebenc, Tine; Guschanski, Katerina; Guyot, Romain; Hausdorf, Bernhard; Hawlitschek, Oliver; Heintzman, Peter D.; Heinze, Berthold; Hiller, Michael; Husemann, Martin; Iannucci, Alessio; Irisarri, Iker; Jakobsen, Kjetill S.; Klinga, Peter; Kloch, Agnieszka; Kratochwil, Claudius F; Kusche, Henrik; Layton, Kara K.S.; Leonard, Jennifer A.; LERAT, Emmanuelle; Liti, Gianni; Manousaki, Tereza; Marques-Bonet, Tomas; Matos-Maraví, Pável; Matschiner, Michael; Maumus, Florian; Mc Cartney, Ann M.; Meiri, Shai; Melo-Ferreira, José; Mengual, Ximo; Monaghan, Michael T.; Montagna, Matteo; Mysłajek, Robert; Neiber, Marco T.; Nicolas, Violaine; Novo, Marta; Ozretić, Petar; Palero, Ferran; Pârvulescu, Lucian; Pascual, Marta; Paulo, Octávio S.; Pavlek, Martina; Pegueroles, Cinta; Pellissier, Loïc; Pesole, Graziano; Primmer, Craig R.; Riesgo, Ana; Rüber, Lukas; RUBOLINI, DIEGO; Salvi, Daniele; Seehausen, Ole; Seidel, Matthias; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara; Vasemägi, Anti; Vella, Adriana; Vella, Noel; Vernes, Sonja C.; Vernesi, Cristiano; Vieites, David R.; Wheat, Christopher W.; Wörheide, Gert; Wurm, Yannick; Zammit, GabrielleABSTRACT: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.