Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

Garner, Brittany A.; Hand, Brian K.; Amish, Stephen J.; Bernatchez, Louis; Foster, Jeffrey T.; Miller, Kristina M.; Morin, Philip A; Narum, Shawn R.; O’Brien, Stephen J.; Roffler, Gretchen H.; Templin, William D.; Sunnucks, Paul; Strait, Jeffrey; Warheit, Kenneth I.; Seamons, Todd R.; Wenburg, John K.; Olsen, Jeffrey B.; Luikart, Gordon

doi:10.1016/j.tree.2015.10.009

Cited by 163 publications

(170 citation statements)

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“…Genomic: A loosely defined term that can refer to the use of large numbers of anonymous genetic markers (thousands to millions), the use of targeted gene sequences, or analyses that account for genomic context such as linkage, recombination, or gene function (Allendorf et al., 2010; Garner et al., 2016). The distinction between “genetic” and “genomic” studies varies across the literature.…”

Section: Introductionmentioning

confidence: 99%

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Flanagan

Forester

Latch

et al. 2017

Evolutionary Applications

197

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Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives. Studies of adaptive variation using genomic tools will inform conservation actions in many cases, including applications such as assisted gene flow and identifying conservation units. In others, assessing genetic diversity, inbreeding, and demographics using selectively neutral genetic markers may be most useful. And in some cases, local adaptation may be assessed more efficiently using alternative approaches such as common garden experiments. Here, we identify key considerations of genomics studies of locally adaptive variation, provide a road map for successful collaborations with genomics experts including key issues for study design and data analysis, and offer guidelines for interpreting and using results from genomic assessments to inform monitoring programs and conservation actions.

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Section: Introductionmentioning

confidence: 99%

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Flanagan

Forester

Latch

et al. 2017

Evolutionary Applications

197

189

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“…At this time, conservation and evolutionary geneticists can employ the power of genomic tools to answer questions in conservation that could not be answered using traditional genetics approaches (Allendorf, Hohenlohe, & Luikart, 2010; Bernatchez et al., 2017; Garner et al., 2016; Harrisson, Pavlova, Telonis‐Scott, & Sunnucks, 2014; McMahon, Teeling, & Höglund, 2014; Shafer et al., 2015a, 2015b). 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).…”

Section: Introductionmentioning

confidence: 99%

“…Interestingly, of the 30 attendees at ConGen just 4 years ago, only a few students had RAD‐seq data, only one had sequence capture data, and none had WGS data. The main focus of the 15 experts was on narrow‐sense conservation genomics applications, which require use of conceptually novel approaches (Garner et al., 2016). …”

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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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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“…For example, both Sanger (first generation) and later platforms such as Roche 454, SOLiD, and Illumina (second generation) may be referred to as next generation sequencing (NGS) in the literature, and both second and third-generation (PacBio, Ion Torrent, Oxford Nanopore) may be referred to as massively parallel or high-throughput sequencing (HTS). Other examples of terms with ambiguous usage include: conservation genomics (Garner et al, 2016), genetic fingerprinting, tag sequencing, targeted metagenomics, metabarcoding (Mendoza et al, 2015), and community analysis. With continued modifications to technology, expanding applications, and development of bioinformatic tools, terminology is expected to remain a challenge.…”

Section: Dna Sequencing Applied To Marine Monitoring Technical Contextmentioning

confidence: 99%

DNA Sequencing as a Tool to Monitor Marine Ecological Status

et al. 2017

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Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.

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Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

Cited by 163 publications

References 10 publications

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Recent advances in conservation and population genomics data analysis

DNA Sequencing as a Tool to Monitor Marine Ecological Status

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