Size correction in biology: how reliable are approaches based on (common) principal component analysis?

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 metri

Clines arc through multivariate morphospace

Evolutionary biologists typically represent clines as spatial gradients in a univariate character (or a principal-component axis) whose mean changes as a function of location along a transect spanning an environmental gradient or ecotone. This univariate approach may obscure the multivariate nature of phenotypic evolution across a landscape. Clines might instead be plotted as a series of vectors in multidimensional morphospace, connecting sequential geographic sites. We present a model showing that clines may trace nonlinear paths that arc through morphospace rather than elongating along a single major trajectory. Arcing clines arise because different characters diverge at different rates or locations along a geographic transect. We empirically confirm that some clines arc through morphospace, using morphological data from threespine stickleback sampled along eight independent transects from lakes down their respective outlet streams. In all eight clines, successive vectors of lake-stream divergence fluctuate in direction and magnitude in trait space, rather than pointing along a single phenotypic axis. Most clines exhibit surprisingly irregular directions of divergence as one moves downstream, although a few clines exhibit more directional arcs through morphospace. Our results highlight the multivariate complexity of clines that cannot be captured with the traditional graphical framework. We discuss hypotheses regarding the causes, and implications, of such arcing multivariate clines

Why and how we should join the shift from significance testing to estimation

A paradigm shift away from null hypothesis significance testing seems in progress. Based on simulations, we illustrate some of the underlying motivations. First, p‐values vary strongly from study to study, hence dichotomous inference using significance thresholds is usually unjustified. Second, ‘statistically significant’ results have overestimated effect sizes, a bias declining with increasing statistical power. Third, ‘statistically non‐significant’ results have underestimated effect sizes, and this bias gets stronger with higher statistical power. Fourth, the tested statistical hypotheses usually lack biological justification and are often uninformative. Despite these problems, a screen of 48 papers from the 2020 volume of the Journal of Evolutionary Biology exemplifies that significance testing is still used almost universally in evolutionary biology. All screened studies tested default null hypotheses of zero effect with the default significance threshold of p = 0.05, none presented a pre‐specified alternative hypothesis, pre‐study power calculation and the probability of ‘false negatives’ (beta error rate). The results sections of the papers presented 49 significance tests on average (median 23, range 0–390). Of 41 studies that contained verbal descriptions of a ‘statistically non‐significant’ result, 26 (63%) falsely claimed the absence of an effect. We conclude that studies in ecology and evolutionary biology are mostly exploratory and descriptive. We should thus shift from claiming to ‘test’ specific hypotheses statistically to describing and discussing many hypotheses (possible true effect sizes) that are most compatible with our data, given our statistical model. We already have the means for doing so, because we routinely present compatibility (‘confidence’) intervals covering these hypotheses

Stickstoffeffizienz von unterschiedlich aufbereiteten Misten in einer Ackerbaufruchtfolge auf Lösslehm

Schlussfolgerungen Unter der Einschränkung, dass die alleinige Betrachtung der N-Wirkung nur einen Teil des N-Haushaltes ausmacht (z.B. Einbau von N in den Humuskörper), können aus den vorliegenden Ergebnissen folgende Schlussfolgerungen gezogen werden: • Bei der aeroben Rotte bzw. Kompostierung von Mist wurden im Vergleich zur anaeroben Lagerung von Mist grössere N-Verluste gemessen, d.h. es wurde bei diesen Verfahren folglich weniger Stickstoff auf die Parzellen ausgebracht. • Bei der Anwendung auf dem Feld erzielten Rottemist und Mistkompost im Vergleich zu Stapelmist jedoch eine bessere N-Wirkung. Dies macht deutlich, dass bei der Beurteilung unterschiedlicher Mistformen neben N-Verlusten und N-Gehalten insbesondere die N-Wirkung (Mineralisierungseigenschaften) berücksichtigt werden muss. • Mit qualitativ hochwertigem Grünabfallkompost kombiniert mit Güllegaben konnten vergleichbare Erträge wie bei den ausschliesslich mit Hofdüngern gedüngten Parzellen erzielt werden. Die N-Wirkung ist dabei aber aufgrund des Holzanteils der Grünabfallkomposte deutlich tiefer als bei Rottemist und Mistkompost. • Mit Vollgülle wurden – bei leicht höherer N-Wirkung – ähnliche Entzüge wie mit Rottemist und Mistkompost erreicht

Feldrandkompostierung - ein Problem für das Grundwasser?

Wird unter Feldrandkompostmieten mehr Nitrat ins Grundwasser ausgewaschen als unter landwirtschaftlich und gemüsebaulich genutzten Böden? Gefährden die Kompostmieten das Grundwasser? Um diese Fragen zu beantworten, wurde im Birrfeld die Nitratauswaschung unter Feldrandkompostmieten während sechs Jahren überwacht. Die Resultate sind erstaunlich

The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish

Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat-nutrient-depleted acidic lakes-based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds

On the search for the vernalization locus in caraway (Carum carvi) using genotyping by sequencing data

Kümmel (Carum carvi) kann in zweijährige und einjährige Blühtypen unterteilt werden. Zweijährige benötigen einen Kältereiz für die Blühinduktion, während Einjährige keinen Vernalisationsbedarf haben. Aufgrund der besseren Integration in die Fruchtfolge und der geringeren Produktionskosten wird der Anbau Einjähriger als vorteilhaft angesehen. Die verfügbaren einjährigen Sorten weisen jedoch ein unzureichendes Ertragspotential und einen zu geringen Ätherischölgehalt auf. Der zweijährige Genpool enthält wertvolle genetische Diversität, die durch Kreuzungen auf den einjährigen Genpool übertragen werden kann. Laut Literatur zeigen F1-Pflanzen aus Kreuzungen zwischen ein- und zweijährigen Blühtypen ein uniform einjähriges Blühverhalten. Resultierende F2-Populationen zeigen ein Mendelsches 3:1-Verhältnis zwischen einjährigen und zweijährigen Blühtypen. Dies deutet auf eine monogenetische Vererbung der Vernalisation beim Kümmel mit dominanter Einjährigkeit hin. Nach Kreuzungen zwischen ein- und zweijährigen Blühtypen kann das rezessive Allel für die zweijährige Blüte über mehrere Generationen im Zuchtmaterial verbleiben. Daher wäre ein genetischer Marker, der mit dem Vernalisations-Locus assoziiert ist, vorteilhaft, um das rezessive Allel in einem Selektionsschritt zu entfernen. Um Marker zu identifizieren, die mit dem Vernalisations-Locus assoziiert sind, wurden Genotyping by Sequencing (GBS)-Daten zu 70 zweijährigen und 67 einjährigen Blühtypen genutzt. Case-Control-Studien und populationsgenetische Studien wurden durchgeführt. Insgesamt wurden 60 gemeinsame Marker gefunden, die signifikant mit dem Vernalisationsbedarf assoziiert waren. Für 19 Marker wurden diagnostische Marker entwickelt. Diese könnten in Zukunft genutzt werden, um rezessive Allele in segregierenden Populationen zu detektieren.Caraway (Carum carvi) can be divided into biennial and annual flowering types. Biennials require a cold stimulus for initiation of flowering, whereas annuals lack any vernalization requirement. Cultivation of annuals is considered advantageous due to better integration into crop rotation and reduced production costs. However, available annual varieties lack a sufficient yield potential and essential oil content. Valuable genetic diversity exists within the biennial genepool, which can be transferred to the annual genepool by crossbreeding. According to literature, F1 plants from crosses between annual and biennial flowering types uniformly show annual flowering. Resulting F2 populations show a Mendelian 3:1 ratio between annual and biennial flowering types. This indicates a monogenetic inheritance of vernalization requirement in caraway with dominant annual flowering. After crossbreeding annual and biennial flowering types, the recessive allele for biennial flowering can remain within the breeding material over multiple generations. Thus, a genetic marker associated with the vernalization locus would be beneficial to remove the recessive allele in one selection step. To identify markers associated with vernalization requirement, we used genotyping by sequencing (GBS) data of 70 biennial and 67 annual flowering types. We conducted case-control studies and population differentiation-based tests. In total, 60 common markers were found that were significantly associated with vernalization requirement. Out of these, we developed 19 diagnostic markers. In future, these diagnostic markers might be used to detect recessive alleles in segregating populations

Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Goldmann, K., Boeddinghaus, R. S., Klemmer, S., Regan, K. M., Heintz-Buschart, A., Fischer, M., Prati, D., Piepho, H., Berner, D., Marhan, S., Kandeler, E., Buscot, F., & Wubet, T. Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot. Environmental Microbiology, 22(3),(2020): 873-888, doi:10.1111/1462-2920.14653.Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.We thank the managers of the three Exploratories, Kirsten Reichel‐Jung, Swen Renner, Katrin Hartwich, Sonja Gockel, Kerstin Wiesner, and Martin Gorke for their work in maintaining the plot and project infrastructure; Christiane Fischer and Simone Pfeiffer for giving support through the central office, Michael Owonibi and Andreas Ostrowski for managing the central data base, and Eduard Linsenmair, Dominik Hessenmöller, Jens Nieschulze, Ernst‐Detlef Schulze, Wolfgang W. Weisser and the late Elisabeth Kalko for their role in setting up the Biodiversity Exploratories project. The work has been funded by the DFG Priority Program 1374 ‘Infrastructure‐Biodiversity‐Exploratories’ (BU 941/22‐1, BU 941/22‐3, KA 1590/8‐2, KA 1590/8‐3). Field work permits were issued by the responsible state environmental office of Baden‐Württemberg (according to § 72 BbgNatSchG). Likewise, we kindly thank Beatrix Schnabel, Melanie Günther and Sigrid Härtling for 454 sequencing in Halle. AHB gratefully acknowledges the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig funded by the German Research Foundation (FZT 118). Authors declare no conflict of interests

De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7)