How and why should we implement genomics into conservation?

McMahon, Barry J.; Teeling, Emma C.; Höglund, Jacob

doi:10.1111/eva.12193

Cited by 162 publications

(146 citation statements)

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“…From a practical standpoint the difference between 3 and 5 170 migrants per generation is not important, but 3 versus 500 is. Explicit formulation of the role genomics can play in achieving conservation priors -meaning a predetermined objective aimed at improving population viability -is a useful model in this regard [5]. If maintaining genetic connectivity were set as a conservation prior for example, differentiating low versus high migration scenarios with genomic data would clearly be informative.…”

Section: Increased Population Genomic Resolutionmentioning

confidence: 99%

“…Genomics further opens up the possibility to screen individuals and populations for adaptive loci, which is suggested by 80 some to be the biggest potential contribution of genomics to conservation [5]. While targeting candidate genes (presumed adaptive) or serendipitously finding neutral markers linked to adaptive loci have not been uncommon in the conservation genetics era, given the low level of linkage disequilibrium often seen in natural populations [23] and polygenic nature of many traits [24], screening the entire genome holds considerably more power.…”

Section: Scaling-up: What Can Genomics Do For Conservation Genetics?mentioning

confidence: 99%

“…The pursuit of improved resolution and adaptive loci will transform many conservation genetics labs. Additionally, as life science companies dismantle old instrumentation, discontinue software, and support only the new high-throughput instruments, many conservation genetic applications will simply be forced into using genome-wide approaches [5]. At the same time, significant gaps remain in the transfer of fundamental genomic research to end-user conservation application.…”

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Genomics and the challenging translation into conservation practice

Shafer¹,

Wolf²,

Alves³

et al. 2015

Trends in Ecology & Evolution

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460

470

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The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

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Section: Increased Population Genomic Resolutionmentioning

confidence: 99%

Section: Scaling-up: What Can Genomics Do For Conservation Genetics?mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Genomics and the challenging translation into conservation practice

Shafer¹,

Wolf²,

Alves³

et al. 2015

Trends in Ecology & Evolution

Self Cite

460

470

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show abstract

“…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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“…This is not surprising, since the knowledge regarding the population genetics of birds currently represents one of the most important sources of data considered in design strategies for the management and conservation of endangered species (Balloux and Lugon-Moulin 2002, Moritz 1994, Paetkau 1999, Paetkau et al 2004, McMahon et al 2014. Studies of behavior and/or kinship were the second most commonly identified subject, comprising 189 papers (24.4%).…”

Section: Tg Markers (N=33) Dawson Et Al 2010mentioning

confidence: 99%

The use of microsatellite markers in Neotropical studies of wild birds: a literature review

Moura

Dawson

Nogueira

2017

An. Acad. Bras. Ciênc.

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Despite extensive habitat fragmentation, the Neotropical region possesses 30% of the world´s bird species. Microsatellites have remained one of the most popular genetic markers and have been used in ecological and conservation studies since the 1990's. We conducted a literature review comparing the number of papers published from January 1990 to July 2015 that used microsatellite markers for studies of wild birds in the Neotropical region, USA and some European countries. We assigned the articles to three categories of studies: population genetics, animal behavior/kinship analysis and the development of species-specific bird microsatellite markers. We also compared the studies in the Neotropics that used heterologous versus species-specific markers and provide a list of heterologous markers of utility in multiple birds. Despite the rich bird fauna in the Neotropics, the number of articles published represents only 5.6% of that published by the USA and selected European countries. Within the Neotropical region, Brazil possessed 60.5% of the total papers published, with the remaining 39.5% shared between five countries. We conclude that the lack of specialized laboratories and resources still represents a limit to microsatellite-based genetic studies of birds within the Neotropical region. To overcome these limitations, we suggest the use of heterologous microsatellite markers as a cost-effective and time-effective tool to assist ecological studies of wild birds.

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How and why should we implement genomics into conservation?

Cited by 162 publications

References 60 publications

Genomics and the challenging translation into conservation practice

Genomics and the challenging translation into conservation practice

Recent advances in conservation and population genomics data analysis

The use of microsatellite markers in Neotropical studies of wild birds: a literature review

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