Applications of genetic tools for conservation intervention
Our fifth set of coordinated readings focuses on conservation interventions. As we are facing a looming biodiversity crisis, conventional conservation strategies (e.g. endangered species list, protected areas, catch limits) often seem woefully insufficient and more proactive or even radical practices are increasingly being considered. How can we use the rapidly evolving genetic and genomic toolbox to guide these conservation interventions?
This year’s papers were selected by Camille Rumberger, Mikhail Matz, and Nicolas Lou. Brendan Reid led a team (with Melissa Naugle, Lindsay Yue, and Len Aguila) that developed strategies to facilitate interactions among participants from different institutions. We are grateful to Nina Overgaard Therkildsen for coming up with this year’s theme, as well as the broader RCN community for their efforts in generating topics, discussion questions, and scientific papers.
Logistics
Forming a discussion group
We encourage you to discuss the papers with a smaller group of participants prior to joining the larger RCN reading group community on Slack. You can either form a local discussion group at your home instutition or join an online group. Your group may choose to meet either once every week or every two weeks at any time of the week. If you need helping forming or connecting to a reading group, we will provide a “looking for group” Slack thread to connect individuals who do not have an existing group at their institution. Please contact Brendan Reid or Nicolas Lou if you have any additional questions.
Once you have formed a group, have a representative create a short introductory thread for your group (including a name for the group and potentially also names of group members, physical location(s), and career stages).
Reading schedule
We divided our readings into six different topics that fall under the general theme of the applications of genetic tools in conservation intervention. For each topic, there will be two main papers and one or two supplemental papers that provide additional background to the topic. We will spend two weeks per topic, so if your group meet weekly, you can read one main paper per week and scan the supplemenal papers depending on your interest. If your group meet biweekly, we have chosen one out of the two main papers that we recommend you to focus on for each topic.
Navigating Slack
To facilitate discussions among members of the RCN, we have set up a Slack channel at evolvingseas.slack.com. To join the channel please visit this site. Then, under Channels, click the + and search for 2023-spring-readings.
For each topic, your group should choose one person to post a summary to the Slack channel that summarizes the group’s reaction to the papers and discussion questions.
All participants can use the thread feature in Slack to post additional questions, and react to comments or questions posed by other groups. We will also have a weekly thread dedicated to resolving questions that emerge from the readings. Moderators will monitor threads and respond to questions. We encourage individuals or groups to use these threads to clarify any uncertainties.
Each week will have several Slack threads for discussion:
- For each group signed up for the readings, we will create a thread entitled
Week X. Topic Name. Group Y: Post your group's discussions here.Click on the chat iconReply to threadto post a summary of your group’s discussions. You are also encouraged to read other group’s discussion summaries and reply if you have have any input or alternate perspectives raised in your group. - To ask a question about the papers, use the thread
Week X. Questions for Understanding.If you have any technical questions about the papers, post them here and the moderators will do their best to answer them!
As a “reward” for fully participating in the readings, we have some snazzy stickers emblazoned with the RCN logo that will be sent out to all groups that submit summaries for every set of readings!
Please contact Nicolas Lou if you encounter problems with Slack or accessing any of the readings.
Live discussion / RCN Happy Hour
In addition to interactions over Slack and within your discussion group, we are planning on conducting a series of RCN “happy hours” over Zoom with opportunities for larger discussions and interaction with paper authors and practitioners involved in implementing the strategies discussed in the readings. An introductory happy hour is tentatively planned for 5:30 PM EST on Feb 9, 2023. We realize that finding a single time that works for all will be difficult, and any presentations or panel discussiobs will also be recorded and made available to watch asynchronously.
Watch this space for more details as the happy hour plans develop!
Topic 1 - Introduction and Background (January 23 - February 3)
Rationale:
This week’s readings were selected to provide an overview of genetic tools for conservation intervention. Both papers explore many of the topics that will be explored more in depth in following weeks, including genetic rescue, assisted gene flow, gene editing, and de-extinction. The first paper discusses both the potential applications of genomic tools to the management of populations and questions to consider before using these methods. The second reviews strategies for genetic management and establishes common terminology for discussing such strategies. The supplemental paper is aimed at managers and conservation practitioners, and discusses the opportunities and risks of conservation interventions.
Paper 1:
New developments in the field of genomic technologies and their relevance to conservation management (recommended for bi-weekly groups)
Authors: Gernot Segelbacher, Mirte Bosse, Pamela Burger, Peter Galbusera, José A. Godoy, Philippe Helsen, Christina Hvilsom, Laura Iacolina, Adla Kahric, Chiara Manfrin, Marina Nonic, Delphine Thizy, Ivaylo Tsvetkov, Nevena Veličković, Carles Vilà, Samantha M. Wisely, Elena Buzan
Paper 2:
Genetic mixing for population management: From genetic rescue to provenancing
Authors: Ary A. Hoffmann, Adam D. Miller, Andrew R. Weeks
Optional Supplemental Paper:
Authors: Juan D. Gaitán-Espitia, Alistair J. Hobday
Topic 2 - The Debate Surrounding Genetic Rescue (February 6 - February 17)
Rationale: Genetic rescue is one of the few conservation intervention strategies that have already been implemented in multiple systems and it has enjoyed considerable success. However, it is also a topic of great controversy. The debate surrounding genetic rescue often centers around the benifit of genome-wide genetic diversity versus the cost of introduced deleterious mutations. This week’s readings were selected to provide you with perspectives from both sides of this debate.
Paper 1:
Authors: Christopher C. Kyriazis, Robert K. Wayne, Kirk E. Lohmueller
Paper 2:
The crucial role of genome-wide genetic variation in conservation (recommended for bi-weekly groups)
Authors: Marty Kardos, Ellie E. Armstrong, Sarah W. Fitzpatric, Samantha Hauser, Philip W. Hedrick, Joshua M. Miller, David A. Tallmon, W. Chris Funk
Optional Supplemental Papers:
Authors: Katherine Ralls, Paul Sunnucks, Robert C. Lacy, Richard Frankham
The inflated significance of neutral genetic diversity in conservation genetics
Authors: João C. Teixeira, Christian D. Huber
Topic 3 - Genetic Rescue in Action (February 20 - March 3)
Rationale: Following up on our last week’s discussion on the theoretical pros and cons of genetic rescue, we will dive into several case studies this week to learn how genetic tools can be used to monitor and assess the result of real-life genetic rescue efforts. Based on this evidence, we can further discuss the key factors that may contribute to the success of genetic rescue programs.
Paper 1:
Genomic erosion in a demographically recovered bird species during conservation rescue (recommended for bi-weekly groups)
Authors: Hazel A. Jackson, Lawrence Percival-Alwyn, Camilla Ryan, Mohammed F. Albeshr, Luca Venturi, Hernán E. Morales, Thomas C. Mathers, Jonathan Cocker, Samuel A. Speak, Gonzalo G. Accinelli, Tom Barker, Darren Heavens, Faye Willman, Deborah Dawson, Lauren Ward, Vikash Tatayah, Nicholas Zuël, Richard Young, Lianne Concannon, Harriet Whitford, Bernardo Clavijo, Nancy Bunbury, Kevin M. Tyler, Kevin Ruhomaun, Molly K. Grace, Michael W. Bruford, Carl G. Jones, Simon Tollington, Diana J. Bell, Jim J. Groombridge, Matt Clark, Cock Van Oosterhout
Paper 2:
Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers
Authors: Alexander Ochoa, David P. Onorato, Melody E. Roelke-Parker, Melanie Culver, Robert R. Fitak
Optional Supplemental Papers:
Genomic and fitness consequences of genetic rescue in wild populations
Authors: Sarah W. Fitzpatrick, Gideon S. Bradburd, Colin T. Kremer, Patricia E. Salerno, Lisa M. Angeloni, W. Chris Funk
Genetic rescue increases fitness and aids rapid recovery of an endangered marsupial population
Authors: Andrew R. Weeks, Dean Heinze, Louise Perrin, Jakub Stoklosa, Ary A. Hoffmann, Anthony van Rooyen, Tom Kelly, Ian Mansergh
Topic 4 - Assisted Gene Flow (March 6 - March 17)
Rationale:
This week’s readings were selected to provide a comprehensive overview of assisted gene flow. The first paper uses simulations to explore assisted gene flow outcomes on population-level fitness and thus determine scenarios in which assisted gene flow may be an appropriate intervention. The second is a case study of genome-informed assisted gene flow in the valley oak Quercis lobata. Supplemental papers include an experimental study of assisted gene flow for forest management and another paper using models to assess assisted migration outcomes, respectively.
Paper 1:
The genetics of assisted gene flow: immediate costs and long-term benefits (recommended for bi-weekly groups)
Authors: Jared A. Grummer, Tom R. Booker, Remi Matthey-Doret, Pirmin Nietlisbach, Andréa T. Thomaz, Michael C. Whitlock
Paper 2:
Authors: Luke Browne, Jessica W. Wright, Sorel Fitz-Gibbon, Paul F. Gugger, Victoria L. Sork
Optional Supplemental Papers:
Assisted gene flow in the context of large-scale forest management in California, USA
Authors: Derek J. N. Young, Thomas D. Blush, Michael Landram, Jessica W. Wright, Andrew M. Latimer, Hugh D. Safford
Identifying robust strategies for assisted migration in a competitive stochastic metacommunity
Authors: Gregory A. Backus, Marissa L. Baskett
Topic 5 - Artificial Breeding and Restoration (March 20 - March 31)
Rationale: For populations that have experienced local extinction, reintroduction/restoration efforts using captively bred individuals can be an effective conservation intervention strategy, and genetic tools can often be used to guide such efforts. The first paper of this week gives us an example of using temporal genetic data to monitor a captive breeding program, and the second paper demonstrates the power of genomics in screening the individuals selected for breeding. The two supplemental papers provide some extra background on the roles of genetic tools in captive breeding and restoration.
Paper 1:
Temporal monitoring of the Floreana Island Galapagos giant tortoise captive breeding program
Authors: Rachel Gray, Nicole Fusco, Joshua M Miller, Washington Tapia, Carol Mariani, Adalgisa Caccone, Evelyn L Jensen
Paper 2:
Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch) (recommended for bi-weekly groups)
Authors: Rebekah L. Horn, Cory Kamphaus, Keely Murdoch & Shawn R. Narum
Optional Supplemental Papers:
A novel holistic framework for genetic-based captive-breeding and reintroduction programs
Authors: C.R.M. Attard, L.M. Möller, M. Sasaki, M.P. Hammer, C.M. Bice, C.J. Brauer, D.C. Carvalho, J.O. Harris, L.B. Beheregaray
Molecular tools for coral reef restoration: Beyond biomarker discovery
Authors: John Everett Parkinson, Andrew C. Baker, Iliana B. Baums, Sarah W. Davies, Andréa G. Grottoli, Sheila A. Kitchen, Mikhail V. Matz, Margaret W. Miller, Andrew A. Shantz, Carly D. Kenke
Topic 6 - Population Control and De-extinction through Genome Editing (April 3 - April 14)
Rationale: Using genome editing for population control and de-extinction are radical ideas that were once so far-fetched that they can only appear in scientic fictions, but with recent development in genome editing, they may soon become realities. Although this may sound exciting to many, there are many technical limitations as well as ethical considerations that still need to be addressed. For this week, we will read two papers that tackled some of the technical aspects of this discussion, whereas the two supplemental papers provide more context on the use of genome editing in conservation.
Paper 1:
Gene drives for vertebrate pest control: Realistic spatial modelling of eradication probabilities and times for island mouse populations (recommended for bi-weekly groups)
Authors: Aysegul Birand, Phillip Cassey, Joshua V. Ross, James C. Russell, Paul Thomas, Thomas A. A. Prowse
Paper 2:
Probing the genomic limits of de-extinction in the Christmas Island rat
Authors: Jianqing Lin, David Duchêne, Christian Carøe, Oliver Smith, Marta Maria Ciucani, Jonas Niemann, Douglas Richmond, Alex D. Greenwood, Ross MacPhee, Guojie Zhang, Shyam Gopalakrishnan, M. Thomas P. Gilbert
Optional Supplemental Papers:
Transforming ecology and conservation biology through genome editing
Authors: Michael P. Phelps, Lisa W. Seeb, James E. Seeb
Pathways to de-extinction: how close can we get to resurrection of an extinct species?
Author: Beth Shapiro
Synthesis (April 17 - April 28)
Rationale: As always, a central goal of the RCN-ECS is to synthesize and integrate ideas about evolution in changing seas. Therefore, the final week is for groups to gather together and synthesize previous discussions. Your group are also welcome to discuss any additional papers that you find interesting, or have several blitz presentations with each participant choosing one paper to present in 5-10 minutes.