February 22, 2018

Changing Landscape of Science Publishing

I was asked to provide some background for a class on Ethics in the Darwinian Sciences on the topic of the Changing Landscape of Science Publishing. Here's the list of resources I thought made a starting point into the ethical questions and changes going on.--Trish


To sort out thorny issues (e.g., authorship disputes, accusations of plagiarism, retractions): Committee on Publication Ethics [COPE]: https://publicationethics.org/

To cover the basic responsibilities and ethics of each role in publishing: Council of Science Editors [CSE]: https://www.councilscienceeditors.org/

To get an overview on copyright, publication agreements, and creative commons licenses: https://dynamicecology.wordpress.com/2018/02/07/intellectual-property-law-101-for-academics/

Guides on how to


Solve the questions of authorship BEFORE you write the paper

Peer Review

Open Science

Learn what your funders require--Gold OA, Green OA, self-archiving, opening the paywall, APCs, licenses. Read anything you sign.

Arguments for Open Science at all project stages


Early sharing, green open access, disrupting traditional publishing

Evaluation Metrics

Science Social Media


Blog by Publishers on the Changing Landscape

February 15, 2018

Syntheses and Perspectives

The Synthesis and Perspectives section publishes visionary re-evaluations designed to move fields of ecology, evolution, and behavior forward.

Open Access
Coupling, Reinforcement, and Speciation
Roger K. Butlin and Carole M. Smadja

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective
Sébastien Lion
Lay summary: http://amnat.org/an/newpapers/JanLion.html

Mechanisms of Assortative Mating in Speciation with Gene Flow: Connecting Theory and Empirical ResearchMichael Kopp, Maria R. Servedio, Tamra C. Mendelson, Rebecca J. Safran, Rafael L. Rodríguez, Mark E. Hauber, Elizabeth C. Scordato, Laurel B. Symes, Christopher N. Balakrishnan, David M. Zonana, and G. Sander van Doorn

Comparative Analyses of Phenotypic Trait Covariation within and among Populations
Kathryn S. Peiman and Beren W. Robinson
Lay summary: http://amnat.org/an/newpapers/OctPeiman.html

An Ecological Perspective on Sleep Disruption
Kévin Tougeron and Paul K. Abram
Lay summary: http://amnat.org/an/newpapers/SepTougeron.html

Cannibalism and Infectious Disease: Friends or Foes?
Benjamin G. Van Allen, Forrest P. Dillemuth, Andrew J. Flick, Matthew J. Faldyn, David R. Clark, Volker H. W. Rudolf, and Bret D. Elderd
Lay summary: http://amnat.org/an/newpapers/SepVanAllen.html

Open Access
Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures
Rachael A. Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K. Ghalambor, Jesse R. Lasky, Rachel B. Brem, Stephen R. Palumbi, and Peter Ralph 

Open Access
Fundamental Theorems of Evolution, David C. Queller 

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography, David Jablonski, Shan Huang, Kaustuv Roy, and James W. Valentine 

Open Access
The Case of the Missing Ancient Fungal Polyploids, Matthew A. Campbell, Austen R. D. Ganley, Toni Gabaldón, and Murray P. Cox 

Open Access
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (Sean Hoban, Joanna L. Kelley, Katie E. Lotterhos, Michael F. Antolin, Gideon Bradburd, David B. Lowry, Mary L. Poss, Laura K. Reed, Andrew Storfer, and Michael C. Whitlock

See  http://www.journals.uchicago.edu/journals/an/instruct for details and submission instructions. A short proposal is required for Syntheses and Perspectives; it will be given full and constructive attention.

February 14, 2018

Ecosystem Ecology

Rising Variability, Not Slowing Down, as a Leading Indicator of a Stochastically Driven Abrupt Transition in a Dryland Ecosystem
Ning Chen, Ciriyam Jayaprakash, Kailiang Yu, and Vishwesha Guttal

 Lay summary: http://amnat.org/an/newpapers/JanChen.html

Open Access
Catastrophic Shifts in Semiarid Vegetation-Soil Systems May Unfold Rapidly or Slowly
Derek Karssenberg, Marc F. P. Bierkens, and Max Rietkerk

Countdown to 150, Open Access
A Modest Proposal for Unifying Macroevolution and Ecosystem Ecology
Matthew W. Pennell and Mary I. O’Connor

Fear Mediates Trophic Cascades: Nonconsumptive Effects of Predators Drive Aquatic Ecosystem Function
Crasso Paulo B. Breviglieri, Paulo S. Oliveira, and Gustavo Q. Romero
Lay summaryhttp://amnat.org/an/newpapers/MayBrevigl.html
"Terrestrial predators influence aquatic ecosystems"

Countdown to 150, Open Access
A Modest Proposal for Unifying Macroevolution and Ecosystem Ecology
Matthew W. Pennell and Mary I. O’Connor

Longer Food Chains in Pelagic Ecosystems: Trophic Energetics of Animal Body Size and Metabolic Efficiency
Richard McGarvey, Natalie Dowling, and Joel E. Cohen

Complexity Increases Predictability in Allometrically Constrained Food Webs
Alison C. Iles and Mark Novak

A General, Synthetic Model for Predicting Biodiversity Gradients from Environmental Geometry
Kevin Gross and Andrew Snyder-Beattie
Lay summary: http://amnat.org/an/newpapers/OctGross.html

The Evolutionary Legacy of Diversification Predicts Ecosystem Function
Benjamin Yguel, Hervé Jactel, Ian S. Pearse, Daniel Moen, Marten Winter, Joaquin Hortal, Matthew R. Helmus, Ingolf Kühn, Sandrine Pavoine, Oliver Purschke, Evan Weiher, Cyrille Violle, Wim Ozinga, Martin Brändle, Igor Bartish, and Andreas Prinzing
Lay summary: http://amnat.org/an/newpapers/OctYguel.html


Shared Genes but Not Shared Genetic Variation: Legume Colonization by Two Belowground Symbionts 
Julia N. Ossler and Katy D. Heath
Lay summary: http://amnat.org/an/newpapers/MarOssler.html

Open AccessCoevolution between Mutualists and Parasites in Symbiotic Communities May Lead to the Evolution of Lower Virulence
Paul G. Nelson and Georgiana May

Natural History Note
Hollow Internodes Permit a Neotropical Understory Plant to Shelter Multiple Mutualistic Ant Species, Obtaining Protection and Nutrient Provisioning (Myrmecotrophy)
Alain Dejean, Frédéric Petitclerc, Arthur Compin, Frédéric Azémar, Bruno Corbara, Jacques H. C. Delabie, and Céline Leroy

Sanctions, Partner Recognition, and Variation in Mutualism
Jeremy B. Yoder and Peter Tiffin
Lay summary: http://amnat.org/an/newpapers/OctYoder.html

Natural History Note
Ants at Plant Wounds: A Little-Known Trophic Interaction with Evolutionary Implications for Ant-Plant Interactions
Michael Staab, Felix Fornoff, Alexandra-Maria Klein, and Nico Blüthgen
Lay summary: http://amnat.org/an/newpapers/SepStaab-A.html

Natural History Note, Open Access
Bees without Flowers: Before Peak Bloom, Diverse Native Bees Find Insect-Produced Honeydew Sugars

Joan M. Meiners, Terry L. Griswold, David J. Harris, and S. K. Morgan Ernest
Lay summary: http://amnat.org/an/newpapers/AugMeiners.html

Countdown to 150, Open Access

Open Access
Three’s a Crowd: Trade-Offs between Attracting Pollinators and Ant Bodyguards with Nectar Rewards in Turnera
Emily M. Dutton, Elaine Y. Luo, Adam R. Cembrowski, Joel S. Shore, and Megan E. Frederickson

Natural History Note
Lay summary: http://amnat.org/an/newpapers/DecSchwab.html

Natural History Note
Selene Báez, David A. Donoso, Simon A. Queenborough, Liliana Jaramillo, Renato Valencia, and Olivier Dangles

Natural History Note
Flávia Delgado Santana, Fabricio Beggiato Baccaro, and Flávia Regina Capellotto Costa1

Andrew J. Bibian, Jennifer A. Rudgers, and Tom E. X. Miller

Samuel Venner, Aurélie Siberchicot, Pierre-François Pélisson, Eliane Schermer, Marie-Claude Bel-Venner, Manuel Nicolas, François Débias, Vincent Miele, Sandrine Sauzet, Vincent Boulanger, and Sylvain Delzon

Hafiz Maherali, Brad Oberle, Peter F. Stevens, William K. Cornwell, and Daniel J. McGlinn

Natural History Note


Testing Range-Limit Hypotheses Using Range-Wide Habitat Suitability and Occupancy for the Scarlet Monkeyflower (Erythranthe cardinalis)Amy L. Angert, Matthew Bayly, Seema N. Sheth, and John R. Paul

Historical Biogeography and Extinction in the Hawaiian HoneycreepersRobert E. Ricklefs
Lay summary: http://amnat.org/an/newpapers/OctRicklefs.html

Open Access
Speciation and the Latitudinal Diversity Gradient: Insights from the Global Distribution of Endemic FishPatrick J. Hanly, Gary G. Mittelbach, and Douglas W. Schemske
Lay summary: http://amnat.org/an/newpapers/JuneHanly.html

The Implications of Eco-Evolutionary Processes for the Emergence of Marine Plankton Community Biogeography
Boris Sauterey, Ben Ward, Jonathan Rault, Chris Bowler and David Claessen
Lay summary: http://amnat.org/an/newpapers/JulySauterey.html

Sixty-Five Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders
Richard Barnes and Adam Thomas Clark
Lay summaryhttp://amnat.org/an/newpapers/JulyBarnes.html

Historical Comment, Open Access“Latitudinal Gradients in Species Diversity”: Reflections on Pianka’s 1966 Article and a Look Forward
Douglas W. Schemske and Gary G. Mittelbach

Antonin Machac and Catherine H. Graham 

Natural History Note
Discovery of a Giant Chameleon-Like Lizard (Anolis) on Hispaniola and Its Significance to Understanding Replicated Adaptive Radiations
D. Luke Mahler, Shea M. Lambert, Anthony J. Geneva, Julienne Ng, S. Blair Hedges, Jonathan B. Losos, and Richard E. Glor
Lay summary: http://amnat.org/an/newpapers/SepMahler.html

Huijie Qiao, Erin E. Saupe, Jorge Soberón, A. Townsend Peterson, and Corinne E. Myers


Southern Ocean Mesopelagic Fish Comply with Bergmann’s Rule
Ryan A. Saunders and Geraint A. Tarling

Lay summary: http://amnat.org/an/newpapers/MarSaunders.html
The Evolution of Energetic Scaling across the Vertebrate Tree of Life

Josef C. Uyeda, Matthew W. Pennell, Eliot T. Miller, Rafael Maia, and Craig R. McClain

Natural History Note
Natural History Constrains the Macroevolution of Foot Morphology in European Plethodontid Salamanders

Dean C. Adams, Dana Korneisel, Morgan Young, and Annamaria Nistri
Lay summary: http://amnat.org/an/newpapers/AugAdams.html

Countdown to 150, Open Access
A Modest Proposal for Unifying Macroevolution and Ecosystem Ecology
Matthew W. Pennell and Mary I. O’Connor

Open Access, Synthesis
The Case of the Missing Ancient Fungal Polyploids
Matthew A. Campbell, Austen R. D. Ganley, Toni Gabaldón, and Murray P. Cox
Lay summary: http://amnat.org/an/newpapers/DecCampbell.html

Micro- and Macroevolutionary Trade-Offs in Plant-Feeding Insects
Daniel A. Peterson,, Nate B. Hardy, and Benjamin B. Normark
Lay summary: http://amnat.org/an/newpapers/DecPeterson.html

Impacts of Niche Breadth and Dispersal Ability on Macroevolutionary Patterns
Huijie Qiao, Erin E. Saupe, Jorge Soberón, A. Townsend Peterson, and Corinne E. Myers
Lay summary: http://amnat.org/an/newpapers/AugQiao.html

Open Access
Including Fossils in Phylogenetic Climate Reconstructions: A Deep Time Perspective on the Climatic Niche Evolution and Diversification of Spiny Lizards (Sceloporus)
A. Michelle Lawing, P. David Polly, Diana K. Hews, and Emília P. Martins
Lay summary: http://amnat.org/an/newpapers/AugLawing.html

Open Access, Countdown to 150
Eric F. LoPresti and Marjorie G. Weber