Visualizations for Genetic Assignment Analyses Using the Saddlepoint Approximation Method

McMillan, Louise; Fewster, Rachel M.

doi:10.1111/biom.12667

Cited by 18 publications

(21 citation statements)

References 23 publications

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“…Due to genetic drift and founder effects for the small island populations in our study, some loci were in linkage disequilibrium. This is unlikely to pose a problem due to the robustness of assignment analyses to moderate levels of linkage disequilibrium (McMillan & Fewster, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…These details include the extent of population overlap, patterns of subsetting and hybridization, and the variability of genetic fit within each cluster. Additionally, methods based on relative genetic fit do not distinguish between individuals that have a good fit to all populations and those with a bad fit to all populations; both can be portrayed similarly in plotted outputs (McMillan & Fewster, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…GenePlots (McMillan & Fewster, 2017), a visualization tool for genetic assignment data, were used to investigate fine‐scale population structure. The absolute fit of each individual to each given reference population is calculated.…”

Section: Methodsmentioning

confidence: 99%

“…Additionally, methods based on relative genetic fit do not distinguish between individuals that have a good fit to all populations and those with a bad fit to all populations; both can be portrayed similarly in plotted outputs (McMillan & Fewster, 2017).…”

Section: Tools For Uncovering Genetic Structurementioning

confidence: 99%

“…From a pest management perspective, it is important to (a) establish whether individuals detected after an eradication are survivors or reinvaders; (b) determine the source of potential reinvaders and (c) identify whether single or multiple incursions led to establishing a population. Here we demonstrate genetic assignment tools to assess pest origin and population connectivity, and pioneer the application of recently developed genetic visualization methods for biosecurity diagnostics (McMillan & Fewster, 2017).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity

Pichlmueller

Murphy²,

MacKay

et al. 2020

Journal of Applied Ecology

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1. Invasive species are the major threat to island biodiversity worldwide. Genetic analyses assist in identifying invasion routes as well as revealing population connectivity, which both represent crucial information for conservation management strategies and risk evaluation. Such information is critical to safeguarding vulnerable species on nearshore islands, which often serve as wildlife sanctuaries. 2. The house mouse Mus musculus has invaded islands around the world and is a model species for showcasing how genetic tools can be used to inform biosecurity management. The genetic population structure of 316 mice from 12 locations in the upper South Island of New Zealand was determined, using novel GenePlots and traditional population genetic tools based on 10 microsatellite loci, to identify gene flow and reinvasion pathways among mainland and island populations over a decade. 3. On the mainland, populations remained genetically homogeneous over landscape scales of many tens of kilometres. In contrast, historically established island populations only kilometres offshore had low genetic diversity from prolonged isolation. Two islands were potentially colonized from both the mainland and each other in a hybrid swarm. 4. Islands that had recently been invaded or reinvaded in the past decade had genetic profiles consistent with the adjacent mainland, suggesting failure of biosecurity procedures to prevent reinvasion, rather than eradication survivors. Although two islands were invaded by only a few individuals, on a third island many invaders simultaneously arrived. 5. Synthesis and applications. Assessing the genetic structure and connectivity of mainland and island populations of an invasive species, using a combination of traditional and novel visualization tools, has uncovered a spectrum of invasion mechanisms and pathways. These results have informed ongoing biosecurity measures by revealing the locations and intensities of biosecurity threats, allowing targeted management actions to reduce the likelihood of island reinvasion.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Tools For Uncovering Genetic Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity

Pichlmueller

Murphy²,

MacKay

et al. 2020

Journal of Applied Ecology

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A renewed glance at the Palearctic golden eagle: Genetic variation in space and time

Karabanina,

Lansink,

Ponnikas

et al. 2024

Ecology and Evolution

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Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re‐evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north–south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.

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A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus

et al. 2019

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Visualizations for Genetic Assignment Analyses Using the Saddlepoint Approximation Method

Cited by 18 publications

References 23 publications

Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity

Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity

A renewed glance at the Palearctic golden eagle: Genetic variation in space and time

A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus

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