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3. ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Author

Kandlikar, Gaurav S, Gold, Zachary J, Cowen, Madeline C, Meyer, Rachel S, Freise, Amanda C, Kraft, Nathan JB, Moberg-Parker, Jordan, Sprague, Joshua, Kushner, David J, and Curd, Emily E

Subjects
DNA, Microbiology, Environment, Biodiversity, Principal Component Analysis, Curriculum, Internet, Software, Statistics as Topic, DNA Barcoding, Taxonomic, citizen science, community ecology, community science, data visualization, education, environmental DNA, metabarcoding, shiny, Biochemistry and Cell Biology, Clinical Sciences, Oncology and Carcinogenesis
Abstract

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.

Published
2018

4. Soundscapes indicate kelp forest condition

Author

Gottesman, Benjamin L., Sprague, Joshua, Kushner, David J., Bellisario, Kristen, Savage, David, McKenna, Megan F., Conlin, David L., DiDonato, Eva, Barkaszi, Mary J., Halvorsen, Michele B., and Pijanowski, Bryan C.

Published
2020

5. Global patterns of kelp forest change over the past half-century

Author

Krumhansl, Kira A, Okamoto, Daniel K, Rassweiler, Andrew, Novak, Mark, Bolton, John J, Cavanaugh, Kyle C, Connell, Sean D, Johnson, Craig R, Konar, Brenda, Ling, Scott D, Micheli, Fiorenza, Norderhaug, Kjell M, Pérez-Matus, Alejandro, Sousa-Pinto, Isabel, Reed, Daniel C, Salomon, Anne K, Shears, Nick T, Wernberg, Thomas, Anderson, Robert J, Barrett, Nevell S, Buschmann, Alejandro H, Carr, Mark H, Caselle, Jennifer E, Derrien-Courtel, Sandrine, Edgar, Graham J, Edwards, Matt, Estes, James A, Goodwin, Claire, Kenner, Michael C, Kushner, David J, Moy, Frithjof E, Nunn, Julia, Steneck, Robert S, Vásquez, Julio, Watson, Jane, Witman, Jon D, and Byrnes, Jarrett EK

Subjects
Life on Land, Arctic Regions, Climate Change, Ecosystem, Forests, Kelp, Oceans and Seas, kelp forest, Laminariales, global change, climate change, coastal ecosystems
Abstract

Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = -0.018 y-1). Our analysis identified declines in 38% of ecoregions for which there are data (-0.015 to -0.18 y-1), increases in 27% of ecoregions (0.015 to 0.11 y-1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.

Published
2016

6. BioTIME: A database of biodiversity time series for the Anthropocene

Author

Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błazewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Collier, Laura Siegwart, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J. Hans C., Cotano, Unai, Crow, Shannan Kyle, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Farah, Fabiano Turini, Fernandes, Luiz Loureiro, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Franco, Geraldo Antonio Daher Correa, Frank, Grace E., Fraser, William R., García, Hernando, Gatti, Roberto Cazzolla, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Ivanauskas, Natália Macedo, Janík, David, Jandt, Ute, Jazdzewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. M., Kang, Jungwon, Kartawijaya, Tasrif, Keeley, Erin C., Kelt, Douglas A., Kinnear, Rebecca, Klanderud, Kari, Knutsen, Halvor, Koenig, Christopher C., Kortz, Alessandra R., Král, Kamil, Kuhnz, Linda A., Kuo, Chao-Yang, Kushner, David J., Laguionie-Marchais, Claire, Lancaster, Lesley T., Lee, Cheol Min, Lefcheck, Jonathan S., Lévesque, Esther, Lightfoot, David, Lloret, Francisco, Lloyd, John D., López-Baucells, Adrià, Louzao, Maite, Madin, Joshua S., Magnússon, Borgþór, Malamud, Shahar, Matthews, Iain, McFarland, Kent P., McGill, Brian, McKnight, Diane, McLarney, William O., Meador, Jason, Meserve, Peter L., Metcalfe, Daniel J., Meyer, Christoph F. J., Michelsen, Anders, Milchakova, Nataliya, Moens, Tom, Moland, Even, Moore, Jon, Moreira, Carolina Mathias, Müller, Jörg, Murphy, Grace, Myers-Smith, Isla H., Myster, Randall W., Naumov, Andrew, Neat, Francis, Nelson, James A., Nelson, Michael Paul, Newton, Stephen F., Norden, Natalia, Oliver, Jeffrey C., Olsen, Esben M., Onipchenko, Vladimir G., Pabis, Krzysztof, Pabst, Robert J., Paquette, Alain, Pardede, Sinta, Paterson, David M., Pélissier, Raphaël, Peñuelas, Josep, Pérez-Matus, Alejandro, Pizarro, Oscar, Pomati, Francesco, Post, Eric, Prins, Herbert H. T., Priscu, John C., Provoost, Pieter, Prudic, Kathleen L., Pulliainen, Erkki, Ramesh, B. R., Ramos, Olivia Mendivil, Rassweiler, Andrew, Remillard, Suzanne M., Richardson, Anthony J., Richardson, J. Paul, van Rijn, Itai, Rocha, Ricardo, Rivera-Monroy, Victor H., Rixen, Christian, Robinson, Kevin P., Rodrigues, Ricardo Ribeiro, de Cerqueira Rossa-Feres, Denise, Rudstam, Lars, Ruhl, Henry, Ruz, Catalina S., Sampaio, Erica M., Rybicki, Nancy, Rypel, Andrew, Sal, Sofia, Salgado, Beatriz, Santos, Flavio A. M., Savassi-Coutinho, Ana Paula, Scanga, Sara, Schmidt, Jochen, Schooley, Robert, Setiawan, Fakhrizal, Shao, Kwang-Tsao, Shaver, Gaius R., Sherman, Sally, Sherry, Thomas W., Siciński, Jacek, Sievers, Caya, da Silva, Ana Carolina, da Silva, Fernando Rodrigues, Silveira, Fabio L., Slingsby, Jasper, Smart, Tracey, Snell, Sara J., Soudzilovskaia, Nadejda A., Souza, Gabriel B. G., Souza, Flaviana Maluf, Souza, Vinícius Castro, Stallings, Christopher D., Stanforth, Rowan, Stanley, Emily H., Sterza, José Mauro, Stevens, Maarten, Stuart-Smith, Rick, Suarez, Yzel Rondon, Supp, Sarah, Tamashiro, Jorge Yoshio, Tarigan, Sukmaraharja, Thiede, Gary P., Thorn, Simon, Tolvanen, Anne, Toniato, Maria Teresa Zugliani, Totland, Ørjan, Twilley, Robert R., Vaitkus, Gediminas, Valdivia, Nelson, Vallejo, Martha Isabel, Valone, Thomas J., Van Colen, Carl, Vanaverbeke, Jan, Venturoli, Fabio, Verheye, Hans M., Vianna, Marcelo, Vieira, Rui P., Vrška, Tomáš, Vu, Con Quang, Van Vu, Lien, Waide, Robert B., Waldock, Conor, Watts, Dave, Webb, Sara, Wesołowski, Tomasz, White, Ethan P., Widdicombe, Claire E., Wilgers, Dustin, Williams, Richard, Williams, Stefan B., Williamson, Mark, Willig, Michael R., Willis, Trevor J., Wipf, Sonja, Woods, Kerry D., Woehler, Eric J., Zawada, Kyle, and Zettler, Michael L.

Published
2018

7. Size, growth, and density data for shallow-water sea urchins from Mexico to the Aleutian Islands, Alaska, 1956–2016

Author

Ebert, Thomas A., Barr, Louis M., Bodkin, James L., Burcham, DIRK, Bureau, Dominique, Carson, Henry S., Caruso, Nancy L., Caselle, Jennifer E., Claisse, Jeremy T., Clemente, Sabrina, Davis, Kathryn, Detwiler, Paul M., Dixon, John D., Duggins, David O., Engle, John M., Estes, James A., Groth, Scott D., Grupe, Benjamin M., Halmay, Peter, Hebert, Kyle P., Hernández, José C., Jurgens, Laura J., Kalvass, Peter E., Kenner, Michael C., Konar, Brenda, Kushner, David J., Lee, Lynn C., Leighton, David L., Montaño-Moctezuma, Gabriela, Munk, J. Eric, Olguin, Irma, Palleiro, Julio S., Parker, David O., Pearse, John S., Pondella, Daniel J., Rogers-Bennett, Laura, Schroeter, Stephen C., Shelton, Andrew Olaf, Sonnenholzner, Jorge, Taniguchi, Ian K., VanBlaricom, Glenn R., Watson, Jane C., Weitzman, Benjamin P., Williams, Jonathan P., Yakimishyn, Jennifer, and Zhang, Zane

Published
2018

12. Top-down vs. Bottom-up Effects in Kelp Forests [with Response]

Author

Foster, Michael S., Edwards, Matthew S., Reed, Daniel C., Schiel, David R., Zimmerman, Richard C., Steele, Mark A., Schroeter, Stephen C., Carpenter, Robert C., Kushner, David J., Halpern, Benjamin S., Cottenie, Karl, and Broitman, Bernardo R.

Published
2006

13. Global conservation outcomes depend on marine protected areas with five key features

Author

Edgar, Graham J., Stuart-Smith, Rick D., Willis, Trevor J., Kininmonth, Stuart, Baker, Susan C., Banks, Stuart, Barrett, Neville S., Becerro, Mikel A., Bernard, Anthony T.F., Berkhout, Just, Buxton, Colin D., Campbell, Stuart J., Cooper, Antonia T., Davey, Marlene, Edgar, Sophie C., Forsterra, Gunter, Galvan, David E., Irigoyen, Alejo J., Kushner, David J., Moura, Rodrigo, Parnell, P. Ed, Shears, Nick T., Soler, German, Strain, Elisabeth M.A., and Thomson, Russell J.

Subjects
Marine resources conservation -- Research, Environment -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate (1,2). MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve (3-5). Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (> 10 years), large (> 100 [km.sup.2]), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effective MPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (>250 mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity. More emphasis is needed on better MPA design, durable management and compliance to ensure that MPAs achieve their desired conservation value., A multitude of socio-economic and biological factors influence the responses of species to protection within MPA networks, adding considerable uncertainty when making specific predictions regarding the conservation benefits of new [...]

Published
2014

19. ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations

Author

Kandlikar, Gaurav S., primary, Gold, Zachary J., additional, Cowen, Madeline C., additional, Meyer, Rachel S., additional, Freise, Amanda C., additional, Kraft, Nathan J.B., additional, Moberg-Parker, Jordan, additional, Sprague, Joshua, additional, Kushner, David J., additional, and Curd, Emily E., additional

Published
2018
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20. Global conservation outcomes depend on marine protected areas with five key features

Author

Australian Research Council, Australian Government, Edgar, Graham J., Stuart-Smith, Rick D., Willis, Trevor J., Kininmonth, Stuart J., Baker, Susan C., Banks, Stuart, Barrett, Neville S., Becerro, Mikel, Bernard, Anthony T. F., Berkhout, Just, Buxton, Colin D., Campbell, Stuart J., Cooper, Antonia T., Davey, Marlene, Edgar, Sophie C., Försterra, Günter, Galván, David E., Irigoyen, Alejo J., Kushner, David J., Moura, Rodrigo, Parnell, P. Ed, Shears, N., Soler, German, Strain, Elisabeth M. A., Thomson, Russell J., Australian Research Council, Australian Government, Edgar, Graham J., Stuart-Smith, Rick D., Willis, Trevor J., Kininmonth, Stuart J., Baker, Susan C., Banks, Stuart, Barrett, Neville S., Becerro, Mikel, Bernard, Anthony T. F., Berkhout, Just, Buxton, Colin D., Campbell, Stuart J., Cooper, Antonia T., Davey, Marlene, Edgar, Sophie C., Försterra, Günter, Galván, David E., Irigoyen, Alejo J., Kushner, David J., Moura, Rodrigo, Parnell, P. Ed, Shears, N., Soler, German, Strain, Elisabeth M. A., and Thomson, Russell J.

Abstract

In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate1,2. MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve3,4,5. Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (>10 years), large (>100 km2), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effective MPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (>250 mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity. More emphasis is needed on better MPA design, durable management and compliance to ensure that MPAs achieve their desired conservation value.

Published
2014

22. Range expansion of a non-native, invasive macroalga Sargassum horneri (Turner) C. Agardh, 1820 in the eastern Pacific.

Author

Marks, Lindsay M., Salinas-Ruiz, Paulina, Reed, Daniel C., Holbrook, Sally J., Culver, Carolynn S., Engle, John M., Kushner, David J., Caselle, Jennifer E., Freiwald, Jan, Williams, Jonathan P., Smith, Jayson R., Aguilar-Rosas, Luis E., and Kaplanis, Nikolas J.

Subjects
SARGASSUM, ALGAL growth, INTRODUCED species, SUSTAINABILITY, MARINE ecology
Abstract

Sargassum horneri (Turner) C. Agardh, 1820 is a fast growing brown alga native to shallow reefs of eastern Asia. It has spread aggressively throughout southern California, USA, and Baja California, México since it was discovered in the eastern Pacific in 2003 and poses a major threat to the sustainability of native marine ecosystems in this region. Here we present a chronology of the rapid geographic expansion of S. horneri in the eastern Pacific and discuss factors that potentially influence its spread. [ABSTRACT FROM AUTHOR]

Published
2015
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24. SEA TEMPERATURE AND WAVE HEIGHT AS PREDICTORS OF POPULATION SIZE STRUCTURE AND DENSITY OF MEGASTRAEA (LITHOPOMA) UNDOSA: IMPLICATIONS FOR FISHERY MANAGEMENT.

Author

Zacharias, Mark A. and Kushner, David J.

Subjects
*FISHERY management, *SEAS, *OCEAN waves, *SNAILS, *OCEAN-atmosphere interaction, *SOUTHERN oscillation
Abstract

The article focuses on a study evaluating sea temperature and wave height as factors of population size structure and density of Megastraea undosa (MU) and its implications on fishery management. A previous hypothesis proved that population characteristics of the wavy turban snail MU in Channel Islands, California could be predicted using temperature and wave height information from a single ocean buoy. MU recruitment and survival is correlated to El-Niño-Southern Oscillation cycles.

Published
2006

25. BioTIME: A database of biodiversity time series for the Anthropocene

Author

<p>Funding information available at <a href="https://doi.org/10.1111/geb.12729" target="_blank" title="Link to publication">https://doi.org/10.1111/geb.12729</a></p>, Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błażewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Siegwart Collier, Laura, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J Hans C., Cotano, Unai, Kyle Crow, Shannan, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Turini Farah, Fabiano, Loureiro Fernandes, Luiz, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Daher Correa Franco, Geraldo Antonio, Frank, Grace E., Fraser, William R., García, Hernando, Cazzolla Gatti, Roberto, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-Hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Macedo Ivanauskas, Natália, Janík, David, Jandt, Ute, Jażdżewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. M., Kang, Jungwon, Kartawijaya, Tasrif, Keeley, Erin C., Kelt, Douglas A., Kinnear, Rebecca, Klanderud, Kari, Knutsen, Halvor, Koenig, Christopher C., Kortz, Alessandra R., Král, Kamil, Kuhnz, Linda A., Kuo, Chao-Yang, Kushner, David J., Laguionie-Marchais, Claire, Lancaster, Lesley T., Min Lee, Cheol, Lefcheck, Jonathan S., Lévesque, Esther, Lightfoot, David, Lloret, Francisco, Lloyd, John D., López-Baucells, Adrià, Louzao, Maite, Madin, Joshua S., Magnússon, Borgþór, Malamud, Shahar, Matthews, Iain, McFarland, Kent P., McGill, Brian, McKnight, Diane, McLarney, William O., Meador, Jason, Meserve, Peter L., Metcalfe, Daniel J., Meyer, Christoph F. J., Michelsen, Anders, Milchakova, Nataliya, Moens, Tom, Moland, Even, Moore, Jon, Mathias Moreira, Carolina, Müller, Jörg, Murphy, Grace, Myers-Smith, Isla H., Myster, Randall W., Naumov, Andrew, Neat, Francis, Nelson, James A., Paul Nelson, Michael, Newton, Stephen F., Norden, Natalia, Oliver, Jeffrey C., Olsen, Esben M., Onipchenko, Vladimir G., Pabis, Krzysztof, Pabst, Robert J., Paquette, Alain, Pardede, Sinta, Paterson, David M., Pélissier, Raphaël, Peñuelas, Josep, Pérez-Matus, Alejandro, Pizarro, Oscar, Pomati, Francesco, Post, Eric, Prins, Herbert H. T., Priscu, John C., Provoost, Pieter, Prudic, Kathleen L., Pulliainen, Erkki, Ramesh, B. R., Mendivil Ramos, Olivia, Rassweiler, Andrew, Rebelo, Jose Eduardo, Reed, Daniel C., Reich, Peter B., Remillard, Suzanne M., Richardson, Anthony J., Richardson, J. Paul, van Rijn, Itai, Rocha, Ricardo, Rivera-Monroy, Victor H., Rixen, Christian, Robinson, Kevin P., Ribeiro Rodrigues, Ricardo, de Cerqueira Rossa-Feres, Denise, Rudstam, Lars, Ruhl, Henry, Ruz, Catalina S., Sampaio, Erica M., Rybicki, Nancy, Rypel, Andrew, Sal, Sofia, Salgado, Beatriz, Santos, Flavio A. M., Savassi-Coutinho, Ana Paula, Scanga, Sara, Schmidt, Jochen, Schooley, Robert, Setiawan, Fakhrizal, Shao, Kwang-Tsao, Shaver, Gaius R., Sherman, Sally, Sherry, Thomas W., Siciński, Jacek, Sievers, Caya, da Silva, Ana Carolina, Rodrigues da Silva, Fernando, Silveira, Fabio L., Slingsby, Jasper, Smart, Tracey, Snell, Sara J., Soudzilovskaia, Nadejda A., Souza, Gabriel B. G., Maluf Souza, Flaviana, Castro Souza, Vinícius, Stallings, Christopher D., Stanforth, Rowan, Stanley, Emily H., Mauro Sterza, José, Stevens, Maarten, Stuart-Smith, Rick, Rondon Suarez, Yzel, Supp, Sarah, Yoshio Tamashiro, Jorge, Tarigan, Sukmaraharja, Thiede, Gary P., Thorn, Simon, Tolvanen, Anne, Teresa Zugliani Toniato, Maria, Totland, Ørjan, Twilley, Robert R., Vaitkus, Gediminas, Valdivia, Nelson, Vallejo, Martha Isabel, Valone, Thomas J., Van Colen, Carl, Vanaverbeke, Jan, Venturoli, Fabio, Verheye, Hans M., Vianna, Marcelo, Vieira, Rui P., Vrška, Tomáš, Quang Vu, Con, Van Vu, Lien, Waide, Robert B., Waldock, Conor, Watts, Dave, Webb, Sara, Wesołowski, Tomasz, White, Ethan P., Widdicombe, Claire E., Wilgers, Dustin, Williams, Richard, Williams, Stefan B., Williamson, Mark, Willig, Michael R., Willis, Trevor J., Wipf, Sonja, Woods, Kerry D., Woehler, Eric J., Zawada, Kyle, Zettler, Michael L., <p>Funding information available at <a href="https://doi.org/10.1111/geb.12729" target="_blank" title="Link to publication">https://doi.org/10.1111/geb.12729</a></p>, Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błażewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Siegwart Collier, Laura, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J Hans C., Cotano, Unai, Kyle Crow, Shannan, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Turini Farah, Fabiano, Loureiro Fernandes, Luiz, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Daher Correa Franco, Geraldo Antonio, Frank, Grace E., Fraser, William R., García, Hernando, Cazzolla Gatti, Roberto, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-Hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Macedo Ivanauskas, Natália, Janík, David, Jandt, Ute, Jażdżewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. 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Abstract

Dornelas, M., Antao, L. H., Moyes, F., Bates, A. E., Magurran, A. E., Adam, D., ... Zetter, M. L.. (2018). BioTIME: A database of biodiversity time series for the Anthropocene. Global Ecology and Biogeography, 27(7), 760–786. Available here

28. The use of marine reserves in evaluating the dive fishery for the warty sea cucumber (Parastichopus parvimensis) in California, U.S.A.

Author

Reed, Daniel C., Schroeter, Stephen C., Kushner, David J., Estes, JamesA., and Ono, David S.

Subjects
ICHTHYOLOGY, MARINE resources
Abstract

Management of sustainable fisheries depends upon reliable estimates of stock assessment. Assessment of many stocks is based entirely on fishery-dependent data (e.g., catch per unit effort), which can be problematic. Here we use fishery-independent data on stock size, collected within and outside of no-take reserves before and after the onset of fishing, to evaluate the status of the dive fishery for warty sea cucumbers, Parastichopus parvimensis, in southern California. Long-term monitoring data showed that abundance decreased throughout the Channel Islands within 3-6 years after the onset of fishing. No significant changes in the abundance of P. parvimensis were observed at the two non-fished reserve sites, although densities tended to increase following onset of the fishery. Before-after, control-impact (BACI) analyses of seven fished and two non-fished sites implicated fishing mortality as the cause of 33-83% stock declines. In sharp contrast, stock assessment based on CPUE data showed no declines and a significant increase at one island. To date, most discussion on marine reserves has focused on the protection and enhancement of exploited populations. Our study demonstrates the critically important, but often overlooked, role that marine reserves can play in providing reliable information on stock assessment. [ABSTRACT FROM AUTHOR]

Published
2001

29. Ocean weather, biological rates, and unexplained global ecological patterns.

Author

Li Shing Hiung DLCY, Schuster JM, Duncan MI, Payne NL, Helmuth B, Chu JWF, Baum JK, Brambilla V, Bruno J, Davies SW, Dornelas M, Gagnon P, Guy-Haim T, Jackson JM, Leichter JJ, Madin JS, Monteith ZL, Queirós AM, Schneider EVC, Starko S, Talwar BS, Wyatt ASJ, Aichelman HE, Bensoussan N, Caruso C, Castillo K, Choi F, Dong YW, Garrabou J, Guillemain D, Higgs N, Jiang Y, Kersting DK, Kushner DJ, Longo GO, Neufeld C, Peirache M, Smyth T, Sprague JL, Urvoy G, Zuberer F, and Bates AE

Abstract

As on land, oceans exhibit high temporal and spatial temperature variation. This "ocean weather" contributes to the physiological and ecological processes that ultimately determine the patterns of species distribution and abundance, yet is often unrecognized, especially in tropical oceans. Here, we tested the paradigm of temperature stability in shallow waters (<12.5 m) across different zones of latitude. We collated hundreds of in situ, high temporal-frequency ocean temperature time series globally to produce an intuitive measure of temperature variability, ranging in scale from quarter-diurnal to annual time spans. To estimate organismal sensitivity of ectotherms (i.e. microbes, algae, and animals whose body temperatures depend upon ocean temperature), we computed the corresponding range of biological rates (such as metabolic rate or photosynthesis) for each time span, assuming an exponential relationship. We found that subtropical regions had the broadest temperature ranges at time spans equal to or shorter than a month, while temperate and tropical systems both exhibited narrow (i.e. stable) short-term temperature range estimates. However, temperature-dependent biological rates in tropical regions displayed greater ranges than in temperate systems. Hence, our results suggest that tropical ectotherms may be relatively more sensitive to short-term thermal variability. We also highlight previously unexplained macroecological patterns that may be underpinned by short-term temperature variability., (© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.)

Published
2024
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30. Top-down vs. bottom-up effects in kelp forests.

Author

Steele MA, Schroeter SC, Carpenter RC, and Kushner DJ

Subjects
Animals, California, Fishes, Food Chain, Population Density, Predatory Behavior, Statistics as Topic, Ecosystem, Kelp, Seawater
Published
2006

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