Genomics and the future of conservation genetics

Allendorf, Fred W.; Hohenlohe, Paul A.; Luikart, Gordon

doi:10.1038/nrg2844

Cited by 1,279 publications

(1,198 citation statements)

References 127 publications

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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%

“…Identifying geographic patterns of local adaptation, the environmental drivers of divergent selection among populations, and genes and their variants involved in local adaptation can inform conservation strategies for species at risk (Allendorf et al., 2010; Shafer et al., 2015), especially in the context of changing environmental conditions (global changes in climate or local changes in land use, fire, hydrology, and other processes altering a species’ local habitat). Genetic variants that help individuals within populations survive or reproduce more under new environmental conditions would be considered adaptive.…”

Section: Introductionmentioning

confidence: 99%

“…Minimizing adaptation to captivity: Although no examples are published to date, adaptive NGS could be used in captive breeding programs to monitor for rapid changes in allele frequencies that could be indicative of adaptation to captive conditions (Allendorf et al., 2010), which can have severe fitness consequences for reintroduced populations (Black, Seears, Hollenbeck, & Samollow, 2017). …”

Section: Introductionmentioning

confidence: 99%

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

Flanagan

Forester

Latch

et al. 2017

Evolutionary Applications

210

189

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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%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Flanagan

Forester

Latch

et al. 2017

Evolutionary Applications

210

189

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“…Recent advances in next‐generation sequencing technologies have allowed for a more thorough survey of genetic variability and differentiation across the genome (Allendorf, Hohenlohe, & Luikart, 2010). One such technique, restriction‐site‐associated DNA (RAD) sequencing, has revolutionized population genetics in nonmodel organisms by allowing discovery and genotyping of thousands of single nucleotide polymorphisms (SNPs) in multiple individuals at relatively low cost (Baird et al., 2008; Miller, Dunham, Amores, Cresko, & Johnson, 2007).…”

Section: Introductionmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction‐site‐associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation‐by‐distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low F ST marine species.

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“…Next‐generation sequencing allows the discovery of single‐nucleotide polymorphisms (SNPs) and the identification of candidate loci (outliers) involved in local adaptation, with reduced cost even in nonmodel species (Allendorf et al., 2010; De Kort et al., 2014; Funk, McKay, Hohenlohe, & Allendorf, 2012). Different approaches have been developed for detecting diversifying selection.…”

Section: Introductionmentioning

confidence: 99%

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

Brancalion

Oliveira

Zucchi

et al. 2018

Ecology and Evolution

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One of the most intriguing questions in plant ecology is which evolutionary strategy allows widely distributed species to increase their ecological range and grow in changing environmental conditions. Phenotypic plasticity and local adaptations are major processes governing species range margins, but little is known about their relative contribution for tree species distribution in tropical forest regions. We investigated the relative role of phenotypic plasticity and local adaptation in the ecological distribution of the widespread palm Euterpe edulis in the Brazilian Atlantic Forest. Genetic sampling and experiments were performed in old‐growth remnants of two forest types with higher (Seasonal Semideciduous Forests vs. Submontane Rainforest) and lower biogeographic association and environmental similarities (Submontane Rainforest vs. Restinga Forest). We first assessed the molecular genetic differentiation among populations, focusing on the group of loci potentially under selection in each forest, using single‐nucleotide polymorphism (SNPs) outliers. Further, we looked for potential adaptive divergence among populations in a common garden experiment and in reciprocal transplants for two plant development phases: seedling establishment and sapling growth. Analysis with outlier loci indicated that all individuals from the Semideciduous Forest formed a single group, while another group was formed by overlapping individuals from Submontane Rainforest and Restinga Forest. Molecular differentiation was corroborated by reciprocal transplants, which yielded strong evidence of local adaptations for seedling establishment in the biogeographically divergent Rainforest and Semideciduous Forest, but not for Restinga Forest and Submontane Rainforest. Phenotypic plasticity for palm seedling establishment favors range expansion to biogeographically related or recently colonized forest types, while persistence in the newly colonized ecosystem may be favored by local adaptations if climatic conditions diverge over time, reducing gene flow between populations. SNPs obtained by next‐generation sequencing can help exploring adaptive genetic variation in tropical trees, which impose several challenges to the use of reciprocal transplants.

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Genomics and the future of conservation genetics

Cited by 1,279 publications

References 127 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

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm

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