A framework for incorporating evolutionary genomics into biodiversity conservation and management

Hoffmann, Ary A.; Griffin, Philippa C.; Dillon, Shannon; Catullo, Renee A.; Rane, Rahul; Byrne, Margaret; Jordan, Rebecca; Oakeshott, John G.; Weeks, Andrew R.; Joseph, Leo; Lockhart, Peter J.; Borevitz, Justin O.; Sgrò, Carla M.

doi:10.1186/s40665-014-0009-x

Cited by 171 publications

(186 citation statements)

References 249 publications

(258 reference statements)

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“…In particular, participants considered how and why detection rates differed between univariate and multivariate GEAs, exploring the use of latent factor mixed models (Frichot, Schoville, Bouchard, & Francois, 2013) and redundancy analysis (Forester, Jones, Joost, Landguth, & Lasky, 2016; Lasky et al., 2012), respectively. Recent work has shown that RDA is an effective means of detecting adaptive processes that result in weak, multilocus molecular signatures (Forester et al., 2018), providing a powerful tool for investigating the genetic basis of local adaptation and informing management actions to conserve evolutionary potential (Flanagan et al., 2017; Harrisson et al., 2014; Hoffmann et al., 2015). Finally, participants were encouraged to move beyond simply documenting candidate adaptive loci in their datasets, and instead focus on the ecological, evolutionary, and management‐relevant questions that can be addressed by more fully integrating a landscape genomic analytical framework.…”

Section: Improving Downstream Computational Analysesmentioning

confidence: 99%

“…Technological and analytical advances now allow us to use many thousands of loci, gene expression, or epigenetics to address basic questions of relevance for conservation, such as identifying loci associated with local adaptation or adaptive potential in species face changing environments (Bernatchez, 2016; Flanagan, Forester, Latch, Aitken, & Hoban, 2017; Harrisson et al., 2014; Hoban et al., 2016; Hoffmann et al., 2015; Jensen, Foll, & Bernatchez, 2016; Le Luyer et al., 2017; Wade et al., 2016). As conservation genomics matures, new challenges are arising.…”

Section: Introductionmentioning

confidence: 99%

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Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.

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Section: Improving Downstream Computational Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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“…In other cases, there is a failure to translate theory into practical management recommendations that managers could implement (Cook & Sgrò, 2017). For example, recommendations that managers should monitor genetic diversity are increasingly the norm (Cook & Sgrò, 2017), yet practical guidance about how this should be done and how to distinguish between neutral and adaptive diversity is largely lacking (Hoffmann et al., 2015). It has also been suggested that the slow integration of evolutionary biology into conservation practice may stem from a general failure by evolutionary biologists to engage with conservation managers (Hendry et al., 2010; Hoban et al., 2013; Mace & Purvis, 2008).…”

Section: Introductionmentioning

confidence: 99%

Understanding managers’ and scientists’ perspectives on opportunities to achieve more evolutionarily enlightened management in conservation

Cook

Sgrò

2018

Evolutionary Applications

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Despite wide acceptance that conservation could benefit from greater attention to principles and processes from evolutionary biology, little attention has been given to quantifying the degree to which relevant evolutionary concepts are being integrated into management practices. There has also been increasing discussion of the potential reasons for a lack of evolutionarily enlightened management, but no attempts to understand the challenges from the perspective of those making management decisions. In this study, we asked conservation managers and scientists for their views on the importance of a range of key evolutionary concepts, the degree to which these concepts are being integrated into management, and what would need to change to support better integration into management practices. We found that while managers recognize the importance of a wide range of evolutionary concepts for conservation outcomes, they acknowledge these concepts are rarely incorporated into management. Managers and scientists were in strong agreement about the range of barriers that need to be overcome, with a lack of knowledge reported as the most important barrier to better integration of evolutionary biology into conservation decision‐making. Although managers tended to be more focused on the need for more training in evolutionary biology, scientists reported greater engagement between managers and evolutionary biologists as most important to achieve the necessary change. Nevertheless, the challenges appear to be multifaceted, and several are outside the control of managers, suggesting solutions will need to be multidimensional.

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“…The application of genomics technologies to conservation practice has been discussed in two recent reviews (Hoffmann et al 2015;Shafer et al 2015). There has also been a focus in the recent literature on the use of genomics for investigating natural selection, with particular attention paid to the promise and pitfalls of using genomic data for identifying loci associated with environment/climate (Schoville et al 2012;Vitti et al 2013;Tiffin and RossIbarra 2014;Bragg et al 2015).…”

Section: The Genomics Era: Signatures Of Selection and Gene Expressionmentioning

confidence: 99%

Constraints to and conservation implications for climate change adaptation in plants

2015

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Contemporary climate change is having widespread impacts on plant populations. Understanding how plants respond to this change is essential to our efforts to conserve them. The key climate responses of plant populations can be categorised into one of three types: migration, in situ adaptation, or extirpation. If populations are to avoid extirpation then migration and/or in situ adaptation is essential. In this review we first articulate the current and future constraints of plant populations, but trees in particular, to the different adaptation strategies (e.g. space availability, rate of change, habitat fragmentation, niche availability). Secondly, we assess the use of the most appropriate methods (e.g. natural environmental gradients, genome and transcriptome scans) for assessing and understanding adaptive responses and the capacity to adapt to future challenges. Thirdly, we discuss the best conservation approaches (e.g. assisted migration, biodiversity corridors, ex situ strategies) to help overcome adaptive constraints in plants. Our synthesis of plant, and particularly tree, responses and constraints to climate change adaptation, combined with the identification of conservation strategies designed to overcome constraints, will help deliver effective management actions to assist adaptation in the face of current and future climate change.

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A framework for incorporating evolutionary genomics into biodiversity conservation and management

Cited by 171 publications

References 249 publications

Recent advances in conservation and population genomics data analysis

Recent advances in conservation and population genomics data analysis

Understanding managers’ and scientists’ perspectives on opportunities to achieve more evolutionarily enlightened management in conservation

Constraints to and conservation implications for climate change adaptation in plants

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