An Eigenvalue test for spatial principal component analysis

Montano, Valeria; Jombart, Thibaut

doi:10.1186/s12859-017-1988-y

Cited by 30 publications

(17 citation statements)

References 14 publications

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“…To test whether global or local structures are significantly different from the null hypothesis of alleles being randomly distributed across space, the estimated distribution of the EVs via Monte Carlo (MC) sampling was used. This test has higher statistical power than the previously suggested method based on R 2 [66,93]. We calculated the sPCA and the test procedure as implemented in the R-package "adegenet" (version 2.1.1) [94,95].…”

Section: Genetic Variation-ssr Analysesmentioning

confidence: 99%

High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands

Caré

Müller

Vornam

et al. 2018

Forests

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High elevation sites in the low mountain ranges in Germany are naturally covered by Norway spruce (Picea abies (Karst.) L.) stands. Historically, large scale anthropogenic range expansion starting in the mid to late 18th century had a huge impact on the forest composition throughout Germany. Utilisation and exploitation often led to artificial regeneration, mostly carried out using seeds from allochthonous provenances. Usually, autochthonous (natural) high elevation Norway spruce trees have narrow crown phenotypes, whereas lowland trees have broader crowns. Narrow crown phenotypes are likely the result of adaptation to heavy snow loads combined with high wind speeds. In the present study, neighbouring stand pairs of putative autochthonous and allochthonous origin with contrasting phenotypes in high elevation sites were investigated with 200 samples each. These stands are located in the Ore Mountains, the Thuringian Forest, and the Harz Mountains. Additionally, a relict population with the typical narrow high elevation phenotypes was sampled in Thuringia, known as “Schlossbergfichte”. The objective of the study was to quantify supposedly adaptive phenotypic differences in crown architecture and the genetic differentiation of 11 putatively neutral nuclear microsatellite markers (i.e., simple sequence repeats (nSSRs)). The high differentiation of morphological traits (PST = 0.952–0.989) between the neighbouring autochthonous and allochthonous stands of similar age contrasts with the very low neutral genetic differentiation (FST = 0.002–0.007; G″ST = 0.002–0.030), suggesting that directional selection at adaptive gene loci was involved in phenotypic differentiation. Comparing the regions, a small isolation by distance effect for the Harz Mountains was detected, suggesting landscape resistance restricting gene flow. Finally, the differentiation of the very old autochthonous (up to 250 years) stand “Schlossbergfichte” with typical high elevation phenotypes could cohere with the sampling of a relict genepool.

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Section: Genetic Variation-ssr Analysesmentioning

confidence: 99%

High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands

Caré

Müller

Vornam

et al. 2018

Forests

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“…Although principal component analysis (PCA) has been used as a common multivariate approach in population genetics, it does not explicitly account for spatial genetic patterns ( Montano and Jombart, 2017 ). A novel approach, sPCA, determining the spatial structure as measured by Moran’s index and eigenvalue, was conducted to further examine the genetic patterns of nipa populations.…”

Section: Resultsmentioning

confidence: 99%

Deep structured populations of geographically isolated nipa (Nypa fruticans Wurmb.) in the Indo-West Pacific revealed using microsatellite markers

Mantiquilla

Shiao²,

Lu³

et al. 2022

Front. Plant Sci.

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Nipa (Nypa fruticans Wurmb.) is an important mangrove palm species, but it is understudied due to lack of information on genetic patterns within its distribution range. In this study, we identified 18 informative microsatellite markers to assess genetic variations among local populations in the Indo-West Pacific (IWP). Results showed population stratification based on high genetic differentiation (FST = 0.22131) with the Mantel test indicating significance to isolation-by-distance. We found a pronounced differentiation between the west populations in Sri Lanka and east populations in Southeast Asia. The east populations around the South China Sea were more genetically similar than those along the Malacca Strait and Java Sea. These genetic clines were shaped by ocean circulations and seasonal monsoon reversals as plausible factors. The Malacca Strait was confirmed as both a genetic and a geographic barrier rather than a corridor according to the Monmonier plot. Simulations of directional migration indicated a statistically strong contemporary genetic connectivity from west to east where Sri Lankan immigrants were detected as far as central Philippines via long-distance dispersal. This is the first report on the recent migration patterns of nipa using microsatellites. Assignment of first-generation (F0) immigrants suggested Mainland Southeast Asia as a melting pot due to the admixture associated with excess of homozygosity. The western populations were recent expansions that emerged in rapid succession based on a phylogram as supported by footprints of genetic drift based on bottleneck tests.

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“…sPCA also allows for tests of global and local spatial structure in the genetic data. These tests were performed using the function spca_randtest from the adegenent package (Montano and Jombart 2017). Where there is global structure there is a high degree of spatial autocorrelation and individuals are likely to be genetically similar to their neighbours.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and connectivity in fragmented populations of Rhinanthus minor in two regions with contrasting land-use

et al. 2019

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Knowledge of genetic diversity and connectivity within and between populations of specialist meadow plants is crucial to developing effective conservation strategies at the landscape-scale. This study investigated levels of genetic diversity within, and gene flow between populations of a key annual species, Rhinanthus minor in protected meadows and landscape matrix sites in two contrasting regions. Possible barriers to gene flow were also analysed. Leaf material from 714 individuals in an extensively managed upland region and an intensively managed lowland region of the UK was genotyped using microsatellite markers. Genetic diversity was similar in the two regions (H e = 0.48 and 0.44). F ST values indicated population differentiation in both regions but the estimate was higher in the lowland (F ST = 0.28) than in the upland region (F ST = 0.19); evidence of global structure was revealed in a spatial principal components analysis but a maximum likelihood population effects model did not identify significant predictors of population differentiation after testing the effects of Euclidean geographic distance, land cover and elevation. Conservation strategies should aim to maintain large populations in meadows to enhance genetic diversity. At the same time the focus should be on existing and additional species-rich grassland fragments, particularly in areas of intensive land-use, if genetic connectivity is to be retained.

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An Eigenvalue test for spatial principal component analysis

Cited by 30 publications

References 14 publications

High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands

High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands

Deep structured populations of geographically isolated nipa (Nypa fruticans Wurmb.) in the Indo-West Pacific revealed using microsatellite markers

Genetic diversity and connectivity in fragmented populations of Rhinanthus minor in two regions with contrasting land-use

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