Size correction in biology: how reliable are approaches based on (common) principal component analysis?
ABSTRACT Morphological traits typically scale with the overall body size of an organism. A meaningful comparison of trait values among individuals or populations that differ in size therefore requires size correction. A frequently applied size correction method involves subjecting the set of n morphological traits of interest to (common) principal component analysis [(C)PCA], and treating the first principal component [(C)PC1] as a latent size variable. The remaining variation (PC2-PCn) is considered size-independent and interpreted biologically. I here analyze simulated data and natural datasets to demonstrate that this (C)PCA-based size correction generates systematic statistical artifacts. Artifacts arise even when all traits are tightly correlated with overall size, and they are particularly strong when the magnitude of variance is heterogeneous among the traits, and when the traits under study are few. (C)PCA-based approaches are therefore inappropriate for size correction and should be abandoned in favor of methods using univariate general linear models with an adequate independent body size metric as covariate. As I demonstrate, (C)PC1 extracted from a subset of traits, not themselves subjected to size correction, can provide such a size metric.
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ABSTRACT: Migratory divides, the boundary between adjacent bird populations that migrate in different directions, are of considerable interest to evolutionary biologists because of their alleged role in speciation of migratory birds. However, the small size of many passerines has traditionally limited the tools available to track populations and as a result, restricted our ability to study how reproductive isolation might occur across a divide. Here, we integrate multiple approaches by using genetic, geolocator, and morphological data to investigate a migratory divide in hermit thrushes (Catharus guttatus). First, high genetic divergence between migratory groups indicates the divide is a region of secondary contact between historically isolated populations. Second, despite low sample sizes, geolocators reveal dramatic differences in overwintering locations and migratory distance of individuals from either side of the divide. Third, a diagnostic genetic marker that proved useful for tracking a key population suggests a likely intermediate nonbreeding location of birds from the hybrid zone. This finding, combined with lower return rates from this region, is consistent with comparatively lower fitness of hybrids, which is possibly due to this intermediate migration pattern. We discuss our results in the context of reproductive isolating mechanisms associated with migration patterns that have long been hypothesized to promote divergence across migratory divides.Ecology and Evolution 09/2014; 4(17). DOI:10.1002/ece3.1205 · 1.66 Impact Factor
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ABSTRACT: Advances in genomic techniques are greatly facilitating the study of molecular signatures of selection in diverging natural populations. Connecting these signatures to phenotypes under selection remains challenging, but benefits from dissections of the genetic architecture of adaptive divergence. We here perform quantitative trait locus (QTL) mapping using 488 F2 individuals and 2011 single nucleotide polymorphisms (SNPs) to explore the genetic architecture of skeletal divergence in a lake-stream stickleback system from Central Europe. We find QTL for gill raker, snout, and head length, vertebral number, and the extent of lateral plating (plate number and height). Although two large-effect loci emerge, QTL effect sizes are generally small. Examining the neighborhood of the QTL-linked SNPs identifies several genes involved in bone formation, which emerge as strong candidate genes for skeletal evolution. Finally, we use SNP data from the natural source populations to demonstrate that some SNPs linked to QTL in our cross also exhibit striking allele frequency differences in the wild, suggesting a causal role of these QTL in adaptive population divergence. Our study paves the way for comparative analyses across other (lake-stream) stickleback populations, and for functional investigations of the candidate genes. This article is protected by copyright. All rights reserved.Evolution 02/2014; DOI:10.1111/evo.12390 · 4.66 Impact Factor
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ABSTRACT: 1. Intraguild predation is common in nature, but it is unclear how species that both compete and eat each other can persist together. One possibility is that intermediate predators possess inducible mor-phological defences that protect them from top predators while not compromising their ability to compete with top predators. 2. The ability of intermediate predators to develop morphological defences may be compromised in environments with a high density of conspecifics because of reduced resource availability and preda-tion risk due to the saturating functional response of top predators. Furthermore, since morphologi-cal defences take time to develop, the type and extent of morphological defences may vary during development. 3. We conducted an experiment to measure the phenotypic responses of an intermediate predator (larvae of the salamander Ambystoma opacum) to the presence of a caged top predator (larvae of the dragonfly Anax spp.) throughout ontological development in environments that differed in the den-sity of conspecifics present. We also assessed how intermediate predators, reared in the different environments, differed in their vulnerability to top predators and ability to deplete their food resources. 4. We found that Anax induced morphological defences in A. opacum, but the extent of morphological change declined with the density of conspecifics. Moreover, some morphological traits disappeared, while others appeared just prior to A. opacum metamorphosis. The change in A. opacum phenotype in response to Anax made A. opacum less vulnerable to predation by Anax but had no significant effect on the foraging ability of A. opacum. 5. Our study demonstrates that top predators can induce phenotypes in intermediate predators that reduce their vulnerability to top predators while not compromising their ability to feed on a common prey. An increase in intermediate predator density, however, could diminish the ability of intermedi-ate predators to develop the full suite of morphological defences. The inability to develop the full suite of morphological defences may reduce the probability of persistence with top predators.Freshwater Biology 01/2014; 59(1):87-99. DOI:10.1111/fwb.12248 · 2.91 Impact Factor