Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of<i>F</i><sub>ST</sub>

Whitlock, Michael C.; Lotterhos, Katie E.

doi:10.1086/682949

Cited by 433 publications

(515 citation statements)

References 39 publications

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“…For both sample sets, the “mahalanobis” method was used to compute the p ‐values. At last, we used OutFLANK (Whitlock & Lotterhos, 2015), which identifies outliers by comparing differentiation at each locus against a trimmed null distribution of F ST values for loci that are deemed neutral. For sample set 1, OutFLANK was run with default parameters except that LeftTrimFraction = 0.4.…”

Section: Methodsmentioning

confidence: 99%

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

Guzinski

Ballenghien

Daguin‐Thiébaut

et al. 2018

Evolutionary Applications

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Ports and farms are well‐known primary introduction hot spots for marine non‐indigenous species (NIS). The extent to which these anthropogenic habitats are sustainable sources of propagules and influence the evolution of NIS in natural habitats was examined in the edible seaweed Undaria pinnatifida, native to Asia and introduced to Europe in the 1970s. Following its deliberate introduction 40 years ago along the French coast of the English Channel, this kelp is now found in three contrasting habitat types: farms, marinas and natural rocky reefs. In the light of the continuous spread of this NIS, it is imperative to better understand the processes behind its sustainable establishment in the wild. In addition, developing effective management plans to curtail the spread of U. pinnatifida requires determining how the three types of populations interact with one another. In addition to an analysis using microsatellite markers, we developed, for the first time in a kelp, a ddRAD‐sequencing technique to genotype 738 individuals sampled in 11 rocky reefs, 12 marinas, and two farms located along ca. 1,000 km of coastline. As expected, the RAD‐seq panel showed more power than the microsatellite panel for identifying fine‐grained patterns. However, both panels demonstrated habitat‐specific properties of the study populations. In particular, farms displayed very low genetic diversity and no inbreeding conversely to populations in marinas and natural rocky reefs. In addition, strong, but chaotic regional genetic structure, was revealed, consistent with human‐mediated dispersal (e.g., leisure boating). We also uncovered a tight relationship between populations in rocky reefs and those in nearby marinas, but not with nearby farms, suggesting spillover from marinas into the wild. At last, a temporal survey spanning 20 generations showed that wild populations are now self‐sustaining, albeit there was no evidence for local adaptation to any of the three habitats. These findings highlight that limiting the spread of U. pinnatifida requires efficient management policies that also target marinas.

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Section: Methodsmentioning

confidence: 99%

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

Guzinski

Ballenghien

Daguin‐Thiébaut

et al. 2018

Evolutionary Applications

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“…Testing was conducted with 20,000 iterations, prior odds of the neutral model of 100, and a type II false discovery rate of α = 0.05. Second, OutFLANK (Whitlock & Lotterhos, 2015) was used to identify candidate loci under selection. OutFLANK estimates the distribution of F ST values at neutral, or nearly neutral, loci by fitting the empirical data to a chi‐square distribution after trimming excessively high and low F ST values, as these loci may be under diversifying or balancing selection.…”

Section: Methodsmentioning

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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“…HWE tests were applied only to the loci with no missing genotypes, and we only analyzed populations with sample size ≥ 8. We tested the outlier loci using three programs: OutFLANK [43], LOSITAN [44] and BayeScan [45]. For LOSITAN and BayeScan, the default setup was used, and for OutFLANK, q-value was set to 0.05.…”

Section: Methodsmentioning

confidence: 99%

Using NextRAD sequencing to infer movement of herbivores among host plants

Epstein

Kelley

et al. 2017

PLoS ONE

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Herbivores often move among spatially interspersed host plants, tracking high-quality resources through space and time. This dispersal is of particular interest for vectors of plant pathogens. Existing molecular tools to track such movement have yielded important insights, but often provide insufficient genetic resolution to infer spread at finer spatiotemporal scales. Here, we explore the use of Nextera-tagmented reductively-amplified DNA (NextRAD) sequencing to infer movement of a highly-mobile winged insect, the potato psyllid (Bactericera cockerelli), among host plants. The psyllid vectors the pathogen that causes zebra chip disease in potato (Solanum tuberosum), but understanding and managing the spread of this pathogen is limited by uncertainty about the insect’s host plant(s) outside of the growing season. We identified 1,978 polymorphic loci among psyllids separated spatiotemporally on potato or in patches of bittersweet nightshade (S. dulcumara), a weedy plant proposed to be the source of potato-colonizing psyllids. A subset of the psyllids on potato exhibited genetic similarity to insects on nightshade, consistent with regular movement between these two host plants. However, a second subset of potato-collected psyllids was genetically distinct from those collected on bittersweet nightshade; this suggests that a currently unrecognized source, i.e., other nightshade patches or a third host-plant species, could be contributing to psyllid populations in potato. Oftentimes, dispersal of vectors of pathogens must be tracked at a fine scale in order to understand, predict, and manage disease spread. We demonstrate that emerging sequencing technologies that detect genome-wide SNPs of a vector can be used to infer such localized movement.

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Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution ofF_ST

Cited by 433 publications

References 39 publications

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

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

Using NextRAD sequencing to infer movement of herbivores among host plants

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Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution ofFST

Cited by 433 publications

References 39 publications

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural rocky reefs

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

Using NextRAD sequencing to infer movement of herbivores among host plants

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Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution ofF_ST