Reply to Garner  et al.

Shafer, Aaron B. A.; Wolf, Jochen B. W.; Alves, Paulo C.; Bergström, Magnus; Colling, Guy; Dalén, Love; Meester, Luc De; Ekblom, Robert; Fior, Simone; Hajibabaei, Mehrdad; Hoezel, A. Rus; Höglund, Jacob; Jensen, Evelyn L.; Krützen, Michael; Norman, Anita J.; Österling, Martin; Ouborg, N. Joop; Piccolo, John; Primmer, Craig R.; Reed, Floyd A.; Roumet, Marie; Salmona, Jordi; Schwartz, Michael K.; Segelbacher, Gernot; Thaulow, Jens; Valtonen, Mia; Vergeer, Philippine; Weissensteiner, Matthias H.; Wheat, Christopher W.; Vilà, Carles; Zieliński, Piotr

doi:10.1016/j.tree.2015.11.010

Cited by 28 publications

(25 citation statements)

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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%

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: Introductionmentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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“…Without question, the ability to identify adaptive genomic variation (AGV; Table ) under selection in natural populations has made spectacular advances in the past few years, largely due to advances in sequencing technology (Brieuc & Naish, ; Hoban et al , ; see also special issue of Molecular Ecology 22, 2013). What is far less clear and has been the focus of intense debate, is how that new information can or should transfer into conservation practice (McMahon et al , ; Shafer et al , , ; Garner et al , ; see also special issue of Evolutionary Applications 7, 2014). Conservation managers have long used ecological and phenotypic variation as proxies for heritable adaptive variation in defining conservation units, which puts the focus on the adaptive environment as a whole (Dizon et al , ; Waples, ).…”

Section: The Problem: Adaptive Genomic Variation and Conservationmentioning

confidence: 99%

“…Here, a synthesis is presented of the important aspects to consider before using information from adaptive genomic variants in management and policy. While many of the topics covered here have been considered in earlier reviews with diverse viewpoints (Primmer, ; Allendorf et al , ; Ouborg et al , ; Funk et al , ; Shafer et al , , ; Garner et al , ), the goal is to consolidate the key considerations for integrating adaptive genomic data into conservation in a single document to inform policy discussions, illustrate the difficulties that must be addressed and highlight the critical role of evolutionary processes in shaping both neutral and adaptive genetic variation. This perspective will be critical in the near future as more examples of adaptive genomic variation are identified in species of conservation concern.…”

Section: The Problem: Adaptive Genomic Variation and Conservationmentioning

confidence: 99%

“…Thus, the framework of policies designed to protect biodiversity does not necessarily need to fundamentally change. Nonetheless, several recent papers have envisioned extensions to help bring AGV into applied conservation applications (Funk et al , ; Shafer et al , ). In some cases, genomic information has allowed the development of increased power in population genetic analyses, for example in the assignment of stock of origin in fisheries applications (Nielsen et al , ).…”

Section: Practical Considerations For Agv In Conservationmentioning

confidence: 99%

“…From a conservation perspective, positively identifying genomic variation that has been influenced by selection, particularly that associated with obvious fitness‐related traits, offers the potential to focus conservation efforts on the specific genomic elements that will most likely play a role in future adaptation (Allendorf et al , ). While such a reductionist approach has been immensely successful in crop and livestock improvement by identifying the genomic basis of heritable traits through quantitative trait loci (QTL) mapping and association studies and then targeting them in breeding programmes, the complexities of selection on natural biological systems make its utility in applied conservation biology unclear (Shafer et al , , ; Garner et al , ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

Pearse

2016

Journal of Fish Biology

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As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.

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Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

Çilingir

Seah

Horne

et al. 2019

Ecology and Evolution

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The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD‐seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006–2012 and identify high‐value breeders instrumental for ex‐situ management of the contemporary genetic stock of the species.

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Reply to Garner et al.

Cited by 28 publications

References 7 publications

Recent advances in conservation and population genomics data analysis

Recent advances in conservation and population genomics data analysis

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

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