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2. Outstanding Challenges in the Transferability of Ecological Models

Author

Yates, Katherine L, Bouchet, Phil J, Caley, M Julian, Mengersen, Kerrie, Randin, Christophe F, Parnell, Stephen, Fielding, Alan H, Bamford, Andrew J, Ban, Stephen, Barbosa, A Márcia, Dormann, Carsten F, Elith, Jane, Embling, Clare B, Ervin, Gary N, Fisher, Rebecca, Gould, Susan, Graf, Roland F, Gregr, Edward J, Halpin, Patrick N, Heikkinen, Risto K, Heinänen, Stefan, Jones, Alice R, Krishnakumar, Periyadan K, Lauria, Valentina, Lozano-Montes, Hector, Mannocci, Laura, Mellin, Camille, Mesgaran, Mohsen B, Moreno-Amat, Elena, Mormede, Sophie, Novaczek, Emilie, Oppel, Steffen, Crespo, Guillermo Ortuño, Peterson, A Townsend, Rapacciuolo, Giovanni, Roberts, Jason J, Ross, Rebecca E, Scales, Kylie L, Schoeman, David, Snelgrove, Paul, Sundblad, Göran, Thuiller, Wilfried, Torres, Leigh G, Verbruggen, Heroen, Wang, Lifei, Wenger, Seth, Whittingham, Mark J, Zharikov, Yuri, Zurell, Damaris, and Sequeira, Ana MM

Subjects
Ecology, Models, Biological, Predictive modeling, extrapolation, generality, habitat models, model transfers, species distribution models, uncertainty, Environmental Sciences, Biological Sciences, Evolutionary Biology
Abstract

Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.

Published
2018

5. Open access solutions for biodiversity journals : Do not replace one problem with another

Author

Peterson, A. Townsend, Anderson, Robert P., Beger, Maria, Bolliger, Janine, Brotons, Lluís, Burridge, Christopher P., Cobos, Marlon E., Cuervo-Robayo, Angela P., Di Minin, Enrico, Diez, Jeffrey, Elith, Jane, Embling, Clare B., Escobar, Luis E., Essl, Franz, Feeley, Kenneth J., Hawkes, Lucy, Jiménez-García, Daniel, Jimenez, Laura, Green, David M., Knop, Eva, Kühn, Ingolf, Lahoz-Monfort, José J., Lira-Noriega, Andres, Lobo, Jorge M., Loyola, Rafael, Nally, Ralph Mac, Machado-Stredel, Fernando, Martínez-Meyer, Enrique, McCarthy, Michael, Merow, Cory, Nori, Javier, Nuñez-Penichet, Claudia, Osorio-Olvera, Luis, Pyšek, Petr, Rejmánek, Marcel, Ricciardi, Anthony, Robertson, Mark, Soto, Octavio Rojas, Romero-Alvarez, Daniel, Roura-Pascual, Núria, Santini, Luca, Schoeman, David S., Schröder, Boris, Soberon, Jorge, Strubbe, Diederik, Thuiller, Wilfried, Traveset, Anna, Treml, Eric A., Václavík, Tomáš, Varela, Sara, Watson, James E. M., Wiersma, Yolanda, Wintle, Brendan, Yañez-Arenas, Carlos, and Zurell, Damaris

Published
2019

6. Predictive models of cetacean distributions off the west coast of Scotland

Author

Embling, Clare B., Hammond, Philip S., and Gordon, Jonathan

Subjects
591.7, Cetacean, GAM, Harbour porpoise, Phocoena phocoena, Delphinid, Sperm whale, Physeter macrocephalus, Habitat model, Predictive model, Scotland
Abstract

The main purpose of this study was to produce and test the reliability of predictive models of cetacean distributions off the west coast of Scotland. Passive acoustic and visual surveys were carried out from platforms of opportunity between 2003 and 2005. Acoustic identifications were made primarily of harbour porpoises (Phocoena phocoena), delphinids, and sperm whales (Physeter macrocephalus). Generalised Additive Models (GAMs) were used to relate species’ distributions to a range of environmental variables over a range of temporal and spatial scales. Predictive models of delphinid distributions showed both inter-annual and inter-month variations. Combining all data for all months and years resulted in a model that combined the environmental influences from each monthly and yearly model. Overall, delphinids were found to associate with the deep (> 400m) warm water (10.5°C-12.5°C), and in areas of deep thermocline. Relationships between sperm whales and environmental variables were consistent over changes in grain size (9 km or 18 km), but not between areas. Although sperm whales were distributed in deep water characterised by weak thermoclines and strong haloclines in the most northerly area (Faroe-Shetland Channel), they were found in deep productive areas with cold surface temperature in the more southerly waters (Rockall Trough). Within the southern Inner Hebrides, high use areas for harbour porpoises were consistently predicted over time (in years) and with differing survey techniques (acoustic versus visual), but not over space (southern Inner Hebrides versus whole of the Inner Hebrides). Harbour porpoises were mainly distributed in areas with low tidal currents and with higher detection rates during spring tides. The use of prey as a predictor variable within models of delphinid distribution shows some promise: there were correlations between delphinid and herring (Clupea harengus) in shelf-waters in 2005 but not in 2004. These models can be used in mitigating acoustic threats to cetaceans in predicted high use areas off the west coast of Scotland.

Published
2008

7. A review of a decade of lessons from one of the world’s largest MPAs: conservation gains and key challenges

Author

Hays, Graeme C., Koldewey, Heather J., Andrzejaczek, Samantha, Attrill, Martin J., Barley, Shanta, Bayley, Daniel T. I., Benkwitt, Cassandra E., Block, Barbara, Schallert, Robert J., Carlisle, Aaron B., Carr, Pete, Chapple, Taylor K., Collins, Claire, Diaz, Clara, Dunn, Nicholas, Dunbar, Robert B., Eager, Dannielle S., Engel, Julian, Embling, Clare B., Esteban, Nicole, Ferretti, Francesco, Foster, Nicola L., Freeman, Robin, Gollock, Matthew, Graham, Nicholas A. J., Harris, Joanna L., Head, Catherine E. I., Hosegood, Phil, Howell, Kerry L., Hussey, Nigel E., Jacoby, David M. P., Jones, Rachel, Sannassy Pilly, Sivajyodee, Lange, Ines D., Letessier, Tom B., Levy, Emma, Lindhart, Mathilde, McDevitt-Irwin, Jamie M., Meekan, Mark, Meeuwig, Jessica J., Micheli, Fiorenza, Mogg, Andrew O. M., Mortimer, Jeanne A., Mucciarone, David A., Nicoll, Malcolm A., Nuno, Ana, Perry, Chris T., Preston, Stephen G., Rattray, Alex J., Robinson, Edward, Roche, Ronan C., Schiele, Melissa, Sheehan, Emma V., Sheppard, Anne, Sheppard, Charles, Smith, Adrian L., Soule, Bradley, Spalding, Mark, Stevens, Guy M. W., Steyaert, Margaux, Stiffel, Sarah, Taylor, Brett M., Tickler, David, Trevail, Alice M., Trueba, Pablo, Turner, John, Votier, Stephen, Wilson, Bry, Williams, Gareth J., Williamson, Benjamin J., Williamson, Michael J., Wood, Hannah, and Curnick, David J.

Published
2020
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14. Outstanding challenges in the transferability of ecological models

Author

Yates, Katherine L., Bouchet, Phil J., Caley, M Julian, Mengersen, Kerrie, Randin, Christophe F., Parnell, Stephen, Fielding, Alan H., Bamford, Andrew J., Ban, Stephen, Barbosa, A Márcia, Dormann, Carsten F., Elith, Jane, Embling, Clare B., Ervin, Gary N., Fisher, Rebecca, Gould, Susan, Graf, Roland Felix, Gregr, Edward J., Halpin, Patrick N., Heikkinen, Risto K., Heinänen, Stefan, Jones, Alice R., Krishnakumar, Periyadan K., Lauria, Valentina, Lozano-Montes, Hector, Mannocci, Laura, Mellin, Camille, Mesgaran, Mohsen B., Moreno-Amat, Elena, Mormede, Sophie, Novaczek, Emilie, Oppel, Steffen, Ortuño Crespo, Guillermo, Peterson, A. Townsend, Rapacciuolo, Giovanni, Roberts, Jason J., Ross, Rebecca E., Scales, Kylie L., Schoeman, David, Snelgrove, Paul, Sundblad, Göran, Thuiller, Wilfried, Torres, Leigh G., Verbruggen, Heroen, Wang, Lifei, Wenger, Seth, Whittingham, Mark J., Zharikov, Yuri, Zurell, Damaris, Sequeira, Ana M. M., Yates, Katherine L., Bouchet, Phil J., Caley, M Julian, Mengersen, Kerrie, Randin, Christophe F., Parnell, Stephen, Fielding, Alan H., Bamford, Andrew J., Ban, Stephen, Barbosa, A Márcia, Dormann, Carsten F., Elith, Jane, Embling, Clare B., Ervin, Gary N., Fisher, Rebecca, Gould, Susan, Graf, Roland Felix, Gregr, Edward J., Halpin, Patrick N., Heikkinen, Risto K., Heinänen, Stefan, Jones, Alice R., Krishnakumar, Periyadan K., Lauria, Valentina, Lozano-Montes, Hector, Mannocci, Laura, Mellin, Camille, Mesgaran, Mohsen B., Moreno-Amat, Elena, Mormede, Sophie, Novaczek, Emilie, Oppel, Steffen, Ortuño Crespo, Guillermo, Peterson, A. Townsend, Rapacciuolo, Giovanni, Roberts, Jason J., Ross, Rebecca E., Scales, Kylie L., Schoeman, David, Snelgrove, Paul, Sundblad, Göran, Thuiller, Wilfried, Torres, Leigh G., Verbruggen, Heroen, Wang, Lifei, Wenger, Seth, Whittingham, Mark J., Zharikov, Yuri, Zurell, Damaris, and Sequeira, Ana M. M.

Abstract

Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.

Published
2019

15. Open access solutions for biodiversity journals: do not replace one problem with another

Author

Peterson, Andrew Townsend, Anderson, Robert P., Beger, Maria, Bolliger, Janine, Brotons, Lluís, Burridge, Christopher P., Cobos, Marlon E., Cuervo-Robayo, Angela P., Di Minin, Enrico, Díez, Jeffrey M., Elith, Jane, Embling, Clare B., Escobar, Luis E., Essl, Franz, Feeley, Kenneth J., Hawkes, Lucy, Jiménez-García, Daniel, Jiménez, Laura, Green, David M., Knop, Evan, Kühn, Ingolf, Lahoz-Monfort, José J., Lira-Noriega, Andres, Lobo, Jorge M., Loyola, Rafael, Mac Nally, Ralph, Machado-Stredel, Fernando, Martínez-Meyer, Enrique, McCarthy, Michael, Merow, Cory, Nori, Javier, Nuñez-Penichet, Claudia, Osorio-Olvera, Luis, Pyšek, Petr, Rejmánek, Marcel, Ricciardi, Anthony, Robertson, Mark, Rojas Soto, Octavio, Romero-Alvarez, Daniel, Roura-Pascual, Núria, Santini, Luca, Schoeman, David S., Schröder, Boris, Soberon, Jorge, Strubbe, Diederik, Thuiller, Wilfried, Traveset, Anna, Treml, Erik A., Václavík, Tomas, Varela, Sara, Watson, James E.M., Wiersma, Yolanda, Wintle, Brendan A., Yanez-Arenas, Carlos, Zurell, Damaris, Peterson, Andrew Townsend, Anderson, Robert P., Beger, Maria, Bolliger, Janine, Brotons, Lluís, Burridge, Christopher P., Cobos, Marlon E., Cuervo-Robayo, Angela P., Di Minin, Enrico, Díez, Jeffrey M., Elith, Jane, Embling, Clare B., Escobar, Luis E., Essl, Franz, Feeley, Kenneth J., Hawkes, Lucy, Jiménez-García, Daniel, Jiménez, Laura, Green, David M., Knop, Evan, Kühn, Ingolf, Lahoz-Monfort, José J., Lira-Noriega, Andres, Lobo, Jorge M., Loyola, Rafael, Mac Nally, Ralph, Machado-Stredel, Fernando, Martínez-Meyer, Enrique, McCarthy, Michael, Merow, Cory, Nori, Javier, Nuñez-Penichet, Claudia, Osorio-Olvera, Luis, Pyšek, Petr, Rejmánek, Marcel, Ricciardi, Anthony, Robertson, Mark, Rojas Soto, Octavio, Romero-Alvarez, Daniel, Roura-Pascual, Núria, Santini, Luca, Schoeman, David S., Schröder, Boris, Soberon, Jorge, Strubbe, Diederik, Thuiller, Wilfried, Traveset, Anna, Treml, Erik A., Václavík, Tomas, Varela, Sara, Watson, James E.M., Wiersma, Yolanda, Wintle, Brendan A., Yanez-Arenas, Carlos, and Zurell, Damaris

Abstract

For much of the twentieth century, many or most scholarly journals in biodiversity, ecology, biogeography and conservation were owned and published by scientific societies and made available to the broader scientific community at relatively low cost. However, the past several decades have seen a dominant process of commercialization of the publication process in this field, either by commercial publishing firms taking over publication of journals owned by a society (e.g., Evolution), or by commercial publishers starting new journals to fill “niches” that were until then empty in the scholarly publishing ecosystem. Diversity and Distributions is an example of this latter category of journals, having been created by Wiley Publishers in 1993 (as Biodiversity Letters). Being a journal owned by a commercial publisher, it has always been accessed by readers via subscription, but the publication process has been free to potential authors whose work has passed peer review.

Published
2019

17. Outstanding Challenges in the Transferability of Ecological Models

Author

Yates, Katherine L., Bouchet, Phil J., Caley, M. Julian, Mengersen, Kerrie, Randin, Christophe F., Parnell, Stephen, Fielding, Alan H., Bamford, Andrew J., Ban, Stephen, Marcia Barbosa, A., Dormann, Carsten F., Elith, Jane, Embling, Clare B., Ervin, Gary N., Fisher, Rebecca, Gould, Susan, Graf, Roland F., Gregr, Edward J., Halpin, Patrick N., Heikkinen, Risto K., Heinanen, Stefan, Jones, Alice R, Krishnakumar, Periyadan K., Lauria, Valentina, Lozano-montes, Hector, Mannocci, Laura, Mellin, Camille, Mesgaran, Mohsen B., Moreno-amat, Elena, Mormede, Sophie, Novaczek, Emilie, Oppel, Steffen, Crespo, Guillermo Ortuno, Peterson, A. Townsend, Rapacciuolo, Giovanni, Roberts, Jason J., Ross, Rebecca E., Scales, Kylie L., Schoeman, David, Snelgrove, Paul, Sundblad, Goran, Thuiller, Wilfried, Torres, Leigh G., Verbruggen, Heroen, Wang, Lifei, Wenger, Seth, Whittingham, Mark J., Zharikov, Yuri, Zurell, Damaris, Sequeira, Ana M. M., Yates, Katherine L., Bouchet, Phil J., Caley, M. Julian, Mengersen, Kerrie, Randin, Christophe F., Parnell, Stephen, Fielding, Alan H., Bamford, Andrew J., Ban, Stephen, Marcia Barbosa, A., Dormann, Carsten F., Elith, Jane, Embling, Clare B., Ervin, Gary N., Fisher, Rebecca, Gould, Susan, Graf, Roland F., Gregr, Edward J., Halpin, Patrick N., Heikkinen, Risto K., Heinanen, Stefan, Jones, Alice R, Krishnakumar, Periyadan K., Lauria, Valentina, Lozano-montes, Hector, Mannocci, Laura, Mellin, Camille, Mesgaran, Mohsen B., Moreno-amat, Elena, Mormede, Sophie, Novaczek, Emilie, Oppel, Steffen, Crespo, Guillermo Ortuno, Peterson, A. Townsend, Rapacciuolo, Giovanni, Roberts, Jason J., Ross, Rebecca E., Scales, Kylie L., Schoeman, David, Snelgrove, Paul, Sundblad, Goran, Thuiller, Wilfried, Torres, Leigh G., Verbruggen, Heroen, Wang, Lifei, Wenger, Seth, Whittingham, Mark J., Zharikov, Yuri, Zurell, Damaris, and Sequeira, Ana M. M.

Abstract

Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.

Published
2018
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20. Navigating uncertain waters: a critical review of inferring foraging behaviour from location and dive data in pinnipeds

Author

Carter, Matt Ian Daniel, Bennett, Kimberley A., Embling, Clare B., Hosegood, Philip J., and Russell, Debbie J. F.

Subjects
Movement ecology, Seals, GPS, Marine mammals, Argos, Satellite telemetry, Review, Area-restricted search, TDR, Animal tracking
Abstract

In the last thirty years, the emergence and progression of biologging technology has led to great advances in marine predator ecology. Large databases of location and dive observations from biologging devices have been compiled for an increasing number of diving predator species (such as pinnipeds, sea turtles, seabirds and cetaceans), enabling complex questions about animal activity budgets and habitat use to be addressed. Central to answering these questions is our ability to correctly identify and quantify the frequency of essential behaviours, such as foraging. Despite technological advances that have increased the quality and resolution of location and dive data, accurately interpreting behaviour from such data remains a challenge, and analytical methods are only beginning to unlock the full potential of existing datasets. This review evaluates both traditional and emerging methods and presents a starting platform of options for future studies of marine predator foraging ecology, particularly from location and two-dimensional (time-depth) dive data. We outline the different devices and data types available, discuss the limitations and advantages of commonly-used analytical techniques, and highlight key areas for future research. We focus our review on pinnipeds - one of the most studied taxa of marine predators - but offer insights that will be applicable to other air-breathing marine predator tracking studies. We highlight that traditionally-used methods for inferring foraging from location and dive data, such as first-passage time and dive shape analysis, have important caveats and limitations depending on the nature of the data and the research question. We suggest that more holistic statistical techniques, such as state-space models, which can synthesise multiple track, dive and environmental metrics whilst simultaneously accounting for measurement error, offer more robust alternatives. Finally, we identify a need for more research to elucidate the role of physical oceanography, device effects, study animal selection, and developmental stages in predator behaviour and data interpretation. Electronic supplementary material The online version of this article (doi:10.1186/s40462-016-0090-9) contains supplementary material, which is available to authorized users.

Published
2016

22. Resolving issues with environmental impact assessment of marine renewable energy installations

Author

Maclean, Ilya M. D., primary, Inger, Richard, additional, Benson, David, additional, Booth, Cormac G., additional, Embling, Clare B., additional, Grecian, W. James, additional, Heymans, Johanna J., additional, Plummer, Kate E., additional, Shackshaft, Michael, additional, Sparling, Carol E., additional, Wilson, Ben, additional, Wright, Lucy J., additional, Bradbury, Gareth, additional, Christen, Nadja, additional, Godley, Brendan J., additional, Jackson, Angus C., additional, McCluskie, Aly, additional, Nicholls-Lee, Rachel, additional, and Bearhop, Stuart, additional

Published
2014
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24. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

Author

Foote, Andrew D., Kaschner, Kristin, Schultze, Sebastian E., Garilao, Cristina, Ho, Simon Y.W., Post, Klaas, Higham, Thomas F.G., Stokowska, Catherine, van der Es, Henry, Embling, Clare B., Gregersen, Kristian, Johansson, Friederike, Willerslev, Eske, Gilbert, M. Thomas P., Foote, Andrew D., Kaschner, Kristin, Schultze, Sebastian E., Garilao, Cristina, Ho, Simon Y.W., Post, Klaas, Higham, Thomas F.G., Stokowska, Catherine, van der Es, Henry, Embling, Clare B., Gregersen, Kristian, Johansson, Friederike, Willerslev, Eske, and Gilbert, M. Thomas P.

Abstract

The climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene–Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics.

Published
2013
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25. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

Author

Foote, Andrew David, Kaschner, Kristin, Schultze, Sebastian E., Garilao, Cristina, Ho, Simon Y. W., Post, Klaas, Higham, Thomas F. G., Stokowska, Catherine, van der Es, Henry, Embling, Clare B., Gregersen, Kristian, Johansson, Friederike, Willerslev, Eske, Gilbert, Tom, Foote, Andrew David, Kaschner, Kristin, Schultze, Sebastian E., Garilao, Cristina, Ho, Simon Y. W., Post, Klaas, Higham, Thomas F. G., Stokowska, Catherine, van der Es, Henry, Embling, Clare B., Gregersen, Kristian, Johansson, Friederike, Willerslev, Eske, and Gilbert, Tom

Abstract

The climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene-Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics.

Published
2013

26. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

Author

Foote, Andrew D., primary, Kaschner, Kristin, additional, Schultze, Sebastian E., additional, Garilao, Cristina, additional, Ho, Simon Y.W., additional, Post, Klaas, additional, Higham, Thomas F.G., additional, Stokowska, Catherine, additional, van der Es, Henry, additional, Embling, Clare B., additional, Gregersen, Kristian, additional, Johansson, Friederike, additional, Willerslev, Eske, additional, and Gilbert, M Thomas P., additional

Published
2013
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