Guidelines for standardizing the application of discriminant analysis of principal components to genotype data

Thia, Joshua A.

doi:10.1111/1755-0998.13706

Cited by 35 publications

(28 citation statements)

References 34 publications

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“…The corresponding mean fractions of total variance captured on the first two axes of our molecular spaces were more modest: a mean of 15% for JC and 18% for GTR distances (see Supporting Information Table S9). Overall, these fractions are consistent with those seen in other discrete character morphological (Hughes et al, 2013;Oyston et al, 2015) and molecular (Foote et al, 2019;Meisner & Albrechtsen, 2018;Thia, 2022) ordinations. We note that our disparity indices were calculated from all coordinate axes with nonzero eigenvalues.…”

Section: Both Morphospaces and Molecular Spaces Have High Dimensionalitysupporting

confidence: 88%

Why should we compare morphological and molecular disparity?

et al. 2023

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Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface‐based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling. Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here, we propose indices of molecular disparity analogous to those of morphological disparity. Despite numerous shortcomings discussed here, molecular sequence data can be obtained in a more objective, automated and scalable manner than morphological data. Comparisons of the morphological and molecular disparity of subclades in 16 large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. For example, within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form. Given the increasing abundance of total evidence datasets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological matrices, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.

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Section: Both Morphospaces and Molecular Spaces Have High Dimensionalitysupporting

confidence: 88%

Why should we compare morphological and molecular disparity?

et al. 2023

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“…Genetic clustering and population structure were assessed via discriminant analysis of principal components (DAPC) using the dapc function of ‘adegenet’ (Jombart et al, 2010). The xvalDapc function was implemented across 1000 replicates to determine the optimal number of principal component axes ( P‐ axes) to retain for DAPC models, with the maximum P‐ axes limited to one fewer than the number of sampling sites in order to prevent overplotting (Thia, 2022). The optimal number of genetic clusters ( K ) and individual membership of these were also explored using adegenet; the snapclust.choose.k function enabled comparisons of Akaike information criteria (AICc) across each modelled value of K , and the snapclust function performed maximum‐likelihood estimations of individual assignment probability to each cluster at given values of K , both of which are instructive in identifying the likely value of K sampled (Beugin et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

Shared and distinct patterns of genetic structure in two sympatric large decapods

Ellis

MacLeod

Jenkins

et al. 2023

Journal of Biogeography

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Aim: Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management.Location: European seas of the northeast Atlantic and Mediterranean.Taxa: European clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily fished decapods with extensive dispersal potential.Methods: By RAD-sequencing 214 H. gammarus from 32 locations and 349 P. elephas from 15 locations, we isolated 6340 and 7681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity. Results:We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region. Main Conclusions:We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographical heterogeneity at many divergent loci indicative of both neutral and adaptive processes.Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.

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“…Within the DAPC, clusters ( k ) were set a priori based on significant pairwise differences identified through post‐hoc Tukey HSD and pairwise PERMANOVA analyses (Miller et al, 2020). The number of PC's retained was set as k −1 (Thia, 2022) and 2 discriminant axes were retained in each analysis. The most influential loci were identified as those with loading scores in the 90th percentile for the two discriminant axes.…”

Section: Methodsmentioning

confidence: 99%

Relationships between phenotypic plasticity and epigenetic variation in two Caribbean Acropora corals

Hackerott,

Virdis,

Flood

et al. 2023

Molecular Ecology

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The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef‐building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes of Acropora cervicornis and A. palmata corals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent in A. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.

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Guidelines for standardizing the application of discriminant analysis of principal components to genotype data

Cited by 35 publications

References 34 publications

Why should we compare morphological and molecular disparity?

Why should we compare morphological and molecular disparity?

Shared and distinct patterns of genetic structure in two sympatric large decapods

Relationships between phenotypic plasticity and epigenetic variation in two Caribbean Acropora corals

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