Exploratory Multivariate Analysis by Example Using R

Husson, François; Lê, Sébastien; Pagès, Jacques

doi:10.1201/b21874

Cited by 584 publications

(542 citation statements)

References 2 publications

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“…We examined genetic population structure with STRUC-TURE version 2.3.4 (Pritchard et al 2000). To further test for genetic structure, we employed principal component analysis (PCA), with FactoMineR (Husson et al 2010) in R. STRUC-TURE and PCA were performed on both the GBS and RNAseq datasets. As our sampling design did not include the purported cytotype contact zone (shaded area in Fig.…”

Section: Demographic Analysesmentioning

confidence: 99%

Ancestral and neo‐sex chromosomes contribute to population divergence in a dioecious plant

2019

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Empirical evidence from several animal groups suggests sex chromosomes disproportionately contribute to reproductive isolation. This effect may be enhanced when sex chromosomes are associated with turnover of sex determination systems resulting from structural rearrangements to the chromosomes. We investigated these predictions in the dioecious plant Rumex hastatulus, which is composed of populations of two different sex chromosome cytotypes caused by an X‐autosome fusion. Using population genomic analyses, we investigated the demographic history of R. hastatulus and explored the contributions of ancestral and neo‐sex chromosomes to population genetic divergence. Our study revealed that the cytotypes represent genetically divergent populations with evidence for historical but not contemporary gene flow between them. In agreement with classical predictions, we found that the ancestral X chromosome was disproportionately divergent compared with the rest of the genome. Excess differentiation was also observed on the Y chromosome, even when we used measures of differentiation that control for differences in effective population size. Our estimates of the timing of the origin of neo‐sex chromosomes in R. hastatulus are coincident with cessation of gene flow, suggesting that the chromosomal fusion event that gave rise to the origin of the XYY cytotype may have also contributed to reproductive isolation.

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Section: Demographic Analysesmentioning

confidence: 99%

Ancestral and neo‐sex chromosomes contribute to population divergence in a dioecious plant

2019

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“…To assess how traits covaried, we performed a principal component analysis (PCA) on the fourteen quantitative traits using the R package 'FactoMineR' (Husson et al 2010). For each trait, we scaled the data to the unit variance.…”

Section: Trait Analysesmentioning

confidence: 99%

Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower

Moyers

Rieseberg

2016

Molecular Ecology

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Substantial intraspecific variation in life history is rare and potentially a signal of incipient ecological speciation, if variation is driven by geographically heterogenous natural selection. We present the first report of extensive life history polymorphism in Helianthus argophyllus, the silverleaf sunflower, and examine evidence for its evolution by divergent selection. In 18 populations sampled from across the species range and grown in a common garden, most quantitative traits covaried such that individuals could be assigned to two distinct life history syndromes: tall and late flowering with small initial flowerheads, or short and early flowering with larger initial flowerheads. Helianthus argophyllus exhibits regional genetic structure, but this population structure does not closely correspond with patterns of phenotypic variation. The early-flowering syndrome is primarily observed in populations from coastal barrier islands, while populations from the nearby mainland coast, although geographically and genetically close, are primarily late flowering. Additionally, several traits are more differentiated among regions than expected based on neutral genetic divergence (QST > FST ), including the first principal component score corresponding with life history syndrome. This discordance between patterns of phenotypic and genetic variation suggests that divergent selection is driving genetic differences in life history across the species range. If so, the silverleaf sunflower may be in early stages of ecological speciation.

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“…62 ] (v.test criterion) also gives an indication of whether the mean of the cluster for that variable is larger (positive sign) or smaller (negative sign) than the overall mean in the dataset. 70 Only significant variables in clusters were considered. Finally, the supplementary categories (i.e.…”

Section: Methodsmentioning

confidence: 99%

Management strategies against Drosophila suzukii: insights into Swiss grape growers choices

Knapp

Mazzi

Finger

2019

Pest Management Science

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Background In 2017, we investigated measures adopted by Swiss grape growers in response to Drosophila suzukii by conducting a survey presenting information obtained from 372 growers on 1708 vineyards. Results We found the strategies adopted to be heterogeneous and largely dependent on grape variety (table vs. wine grapes). We identified six clusters of control methods to combat D. suzukii, the most important of which involves using a combination of control methods such as insecticides, mass trapping and sanitation measures, especially pinching of foliage or mowing and mulching. Grape growers in our sample rely primarily on information from public institutions or other growers and the majority plan to continue taking sanitation measures to combat D. suzukii. Conclusion Our results suggest that strategies adopted in Switzerland differ widely, not only between growers, but also at a vineyard and regional level. Thus, policies and extension services should be targeted (e.g. to varieties and regions) and tailored to types of growers. We find that preventive measures are important when combatting D. suzukii and can reduce post‐infestation measures such as pesticide usage. In our sample, biological insecticides, such as kaolin, played a vital role in the control of D. suzukii and merit further support. © 2019 Society of Chemical Industry

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Exploratory Multivariate Analysis by Example Using R

Cited by 584 publications

References 2 publications

Ancestral and neo‐sex chromosomes contribute to population divergence in a dioecious plant

Ancestral and neo‐sex chromosomes contribute to population divergence in a dioecious plant

Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower

Management strategies against Drosophila suzukii: insights into Swiss grape growers choices

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