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Molecules in models: the future role of genetic data in population viability analysis

 

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Project overview

Recent years have seen huge advances in our ability to create complex individual-based models of animal and plant populations.  These models allow for nearly unlimited flexibility in the representation of organisms, and in the ways they can be used to understand how interactions among individuals mediate population processes.  One application of these models is Population Viability Analysis, which are traditionally used to determine a population’s threat of extinction given certain parameters.  In tandem with advances in computer models, advances in high-throughput sequencing and genotyping have led to an explosion in the availability of genetic data. The new opportunities that individual-based models create for incorporating detailed genetic processes, combined with the plethora of genetic data now available, creates a timely need to address several questions regarding the integration of genetics into population viability analyses.  How is genetics currently used in population viability models?  How do recent advances in modelling techniques and genomics alter the scope of what will be possible in the future?  What are the advantages and disadvantages of including genetic parameters?  We propose to assemble a working group consisting of experts in population viability analysis, population genetics, genomics, individual-based modelling, and threatened species management to address these questions.  We foresee several outcomes, including a review paper that discusses the future role of genetics in PVA and a more detailed review of the role of genetics and PVA in Australia’s threatened species recovery plans.  Importantly, we plan to provide guidelines for the researchers and managers making conservation decisions on how to best incorporate genetic processes which will lead to more informed decisions and better management of Australia’s flora and fauna.

 

Molecules in models

 

Groves, C. (2005). Wilson, D. E., & Reeder, D. M, (eds), 2005.  Mammal Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. pp. 54. OCLC 62265494. ISBN 0-801-88221-4

 

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Products and Outcomes

 

Download their final report here [910k]

 

This group published a paper in 2014.


Pierson J.C., Beissinger S.R., Bragg J.G., Coates D.J., Oostermeijer J.G.B., Sunnucks P., Schumaker N.H., Trotter M.V. and Young A.G. (2014) Incorporating evolutionary processes into population viability models. Conservation Biology. DOI: 10.1111/cobi.12431

 

http://onlinelibrary.wiley.com/doi/10.1111/cobi.12431/abstract

 

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Workshop Reports

 

  • Workshop 1 Report (19-23 March 2012)
  • Workshop 2 Report (5–9 November 2012)
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    Workshop 1 Report (19-23 March 2012)

    The first workshop was held in Brisbane and attended by 10 scientists from Australia, North America and Europe with expertise in population genetics, population viability analysis, ecological genomics, and individual-based modelling. The goals of this workshop were to broadly assess the current role of genetics in population viability models and synthesize how advances in genomics and modelling techniques alter the scope of future possibilities. In addition, time was provided during the first workshop to outline the objectives of workshop two and the schedule of activities that needed to be achieved prior to the second workshop to maximize productivity and success.

    The workshop began with all participants giving presentations on their relevant research and their thoughts on what are the most exciting new possibilities that technical advances may provide. Nathan Schumaker provided an additional talk on how genetics can now be incorporated into spatially explicit IBM (Hexsim) and Jason Bragg gave a presentation describing a population model that included phenotypes controlled by multiple loci. Participants then moved on to a group discussion of how population viability analyses are currently used, and how they can be most beneficial to conservation decision making, especially in light of increasing challenges due to anthropomorphic changes in the environment.

    The group then outlined the details for a review paper that will focus on how technological advances provide an opportunity to better incorporate genetic data and eco-evolutionary processes into estimates of population viability and at the same time greatly improve the power of PVA in delivering better conservation outcomes. This included a lengthy discussion on the genetic processes that 1) are likely important to population viability and 2) may be better understood and parameterized due to advances in ecological genomics. A table that included these processes was agreed upon and will be used as a unifying theme for the paper. Participants then split into smaller subgroups to work on individual sections of the paper and gave short presentations on these. By the conclusion of the workshop, the group had agreed on an outline for the review, a timeline for section completion and participant contribution to sections.

    A portion of the workshop was devoted to the goal of workshop 2, which is addressing the question of when genetic estimators and processes should be included in PVA and species recovery planning. The group focused this discussion on the life history parameters that play a central role in determining this and how to design a standardized tool to quantify the review of Species Recovery Plans. The goal is to have Species Recovery Plans reviewed prior to workshop two so analysis of results can be completed.

     

     

    click to enlarge
    Top l-r: David Coates, Nathan Schumaker, Jason Bragg. Middle row l-r: Meredith Trotter, Andrew Young, Jennifer Pierson Front row l-r: Steve Beissinger, Richard Frankham, Gerard Oostermeijer, Paul Sunnucks

     

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    Workshop 2 Report  (5-9 November 2012)

    A. Young and J. Pierson

    During the first workshop, we agreed on pursuing two main objectives:

     

    (i) a review paper detailing the future role of genetic data in population viability analysis,
    (ii) a review of Threatened Species Recovery Plans to assess the current use of genetic data both in the recovery process and specifically in PVA.

    The second workshop focused on completing a draft of the review paper and finalising the questionnaire to be applied to Recovery Plans as well as agreeing upon an appropriate sampling design for the assessment.

    An initial draft of the review had been written by the group in the interim between workshops. During the workshop, the group agreed on a standardized approach to recommend for including genetic data in PVA and designed an example case study to simulate to showcase the importance of including genetic processes in management decision making. The majority of the workshop was then spent drafting the paper and writing the computer simulation. A manuscript has been completed and will be submitted to a peer-reviewed journal within the next month.

    A subgroup spent the majority of the workshop focused on designing and testing a questionnaire to assess the role of genetic data in Threatened Species Recovery Plans. A questionnaire was agreed upon and tested on Plans from each of the three regions that will be included in the sample. We agreed to review 100 plans, approximately 50 plant and 50 animal, from each region for a total of 300 plans. Subsequent to workshop 2, we have completed the review of plans in Australia, the US, and Europe and plan to begin analysis soon. The outcome from this will be a manuscript assessing and comparing the consideration of genetic processes in Threatened Species Recovery Plans globally.


    click to enlarge
    Left to right: Gerard Oostermeier (University of Amsterdam), Jason Bragg (CSIRO), Jenny Pierson (CSIRO), Nathan Schumaker (United States Environmental Protection Agency), Steve Bessinger (University of California, Berkeley), David Coates (Department of Environment and Conservation, WA), Richard Frankham (Macquarie University), Andrew Young (CSIRO), Meredith Trotter (Stanford University), Paul Sunnucks (Monash University).

     

     

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    Last Updated on Sunday, 08 February 2015 16:09