Call for a Paradigm Shift in the Genetic Management of Fragmented Populations

Ralls, Katherine; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D. B.; Fenster, Charles B.; Lacy, Robert C.; Sunnucks, Paul; Frankham, Richard

doi:10.1111/conl.12412

Cited by 355 publications

(374 citation statements)

References 29 publications

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“…According to population genetic theory, if inbreeding is present in a population, statistical associations will form between molecular markers and the genome (Hansson & Westerberg, ), thereby enabling the use of molecular markers to estimate GWH (see Introduction; Szulkin et al, ). Thus, using the g2 statistic to quantitatively evaluate an arguably crucial aspect of GWH, namely inbreeding (Ralls et al, ), is a valuable approach for examining the informativeness of alternative marker sets. Further, examining the expected correlations between marker heterozygosity and population inbreeding (using equations 3 and 4 from Miller et al, ) lends greater confidence to assessments of how closely our marker sets reflect GWH.…”

Section: Discussionmentioning

confidence: 99%

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

McLennan

Wright

Belov

et al. 2019

Molecular Ecology Resources

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Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions. We used a well‐studied population of Tasmanian devils (Sarcophilus harrisii) from Maria Island, Tasmania, to illustrate the issues associated with combining multiple genetic data sets and to help answer a question posed by many population managers: which data set will provide the most precise and accurate estimates of the population processes we are trying to measure? We analysed individual heterozygosity (as internal relatedness, IR) of 96 individuals, calculated using four genetic marker types (putatively neutral microsatellites, major histocompatibility complex‐linked microsatellites, reduced representation sequencing, and candidate region resequencing). We found no correlation in IR values across marker types, suggesting that various genetic markers reflect different aspects of genomic diversity. In addition, some marker types were more informative than others for conservation decision‐making. Reduced representation sequencing provided the highest precision (lowest error) for estimating population‐level genetic diversity, and most closely reflected genome‐wide heterozygosity both theoretically and empirically. Within the conservation context, our results highlight important considerations when choosing a molecular technique for wildlife genetics.

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Section: Discussionmentioning

confidence: 99%

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

McLennan

Wright

Belov

et al. 2019

Molecular Ecology Resources

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“…It has also recently been shown that the addition of foreigners does not lead to as high rates of erosion of local adaptation as originally thought (i.e., decreased rate of sweeps; Tigano & Friesen, 2016). Hence, the risks associated with outbreeding depression and foreign advantage may dissipate rapidly (Aitken & Whitlock, 2013;Harrisson et al, 2016;Ralls et al, 2017;Roitman et al, 2017;Tigano & Friesen, 2016). Hence, the risks associated with outbreeding depression and foreign advantage may dissipate rapidly (Aitken & Whitlock, 2013;Harrisson et al, 2016;Ralls et al, 2017;Roitman et al, 2017;Tigano & Friesen, 2016).…”

Section: Risks and Trade-offs Associated With Assisted Gene Flowmentioning

confidence: 95%

The active spread of adaptive variation for reef resilience

Quigley

Bay

Oppen

2019

Ecology and Evolution

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The speed at which species adapt depends partly on the rates of beneficial adaptation generation and how quickly they spread within and among populations. Natural rates of adaptation of corals may not be able to keep pace with climate warming. Several interventions have been proposed to fast‐track thermal adaptation, including the intentional translocation of warm‐adapted adults or their offspring (assisted gene flow, AGF) and the ex situ crossing of warm‐adapted corals with conspecifics from cooler reefs (hybridization or selective breeding) and field deployment of those offspring. The introgression of temperature tolerance loci into the genomic background of cooler‐environment corals aims to facilitate adaptation to warming while maintaining fitness under local conditions. Here we use research on selective sweeps and connectivity to understand the spread of adaptive variants as it applies to AGF on the Great Barrier Reef (GBR), focusing on the genus Acropora. Using larval biophysical dispersal modeling, we estimate levels of natural connectivity in warm‐adapted northern corals. We then model the spread of adaptive variants from single and multiple reefs and assess if the natural and assisted spread of adaptive variants will occur fast enough to prepare receiving central and southern populations given current rates of warming. We also estimate fixation rates and spatial extent of fixation under multiple release scenarios to inform intervention design. Our results suggest that thermal tolerance is unlikely to spread beyond northern reefs to the central and southern GBR without intervention, and if it does, 30+ generations are needed for adaptive gene variants to reach fixation even under multiple release scenarios. We argue that if translocation, breeding, and reseeding risks are managed, AGF using multiple release reefs can be beneficial for the restoration of coral populations. These interventions should be considered in addition to conventional management and accompanied by strong mitigation of CO2 emissions.

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“…Characterizing and conserving genomic variation within species is a key challenge in conservation genetics (Frankham, Ballou, & Briscoe, ; Ralls et al, ). The decreasing cost and ease with which genome‐scale data can now be produced has allowed the generation of extensive population genomic data sets that can be used to monitor and manage populations (Allendorf, Hohenlohe, & Luikart, ; Morin, Luikart, & Wayne, ).…”

Section: Introductionmentioning

confidence: 99%

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

Ewart

Johnson

Ogden

et al. 2019

Molecular Ecology Resources

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Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome‐wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red‐tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site‐associated DNA marker approach (DArTseq™). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq‐based method to produce reliable genome‐wide SNP data from traditional museum specimens.

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Call for a Paradigm Shift in the Genetic Management of Fragmented Populations

Cited by 355 publications

References 29 publications

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

The active spread of adaptive variation for reef resilience

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

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