Thomas Mitchell-Olds

Regression analysis of natural selection statistical inference and biological interpretation

Recent theoretical work in quantitative genetics has fueled interest in measuring natural selection in the wild. We discuss statistical and biological issues that may arise in applications of Lande and Arnolds (1983) multiple‐regression approach to measuring selection. We review assumptions involved in estimation and hypothesis testing in regression problems, and we note difficulties that frequently arise as a result of violation of these assumptions. In particular, multicollinearity (extreme intercorrelation of characters) and extrinsic, unmeasured factors affecting fitness may seriously complicate inference regarding selection. Further, violation of the assumption that residuals are normally distributed vitiates tests of significance. For this situation, we suggest applications of recently developed jackknife tests of significance. While fitness regression permits direct assessment of selection in a form suitable for predicting selection response, we suggest that the aim of inferring causal relationships about the effects of phenotypic characters on fitness is greatly facilitated by manipulative experiments. Finally, we discuss alternative definitions of stabilizing and disruptive selection.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.

Disarming the mustard oil bomb

Plants are attacked by a broad array of herbivores and pathogens. In response, plants deploy an arsenal of defensive traits. In Brassicaceae, the glucosinolate–myrosinase complex is a sophisticated two-component system to ward off opponents. However, this so-called “mustard oil bomb” is disarmed by a glucosinolate sulfatase of a crucifer specialist insect, diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Sulfatase activity of this enzyme largely prevents the formation of toxic hydrolysis products arising from this plant defense system. Importantly, the enzyme acts on all major classes of glucosinolates, thus enabling diamondback moths to use a broad range of cruciferous host plants.

Anova for Unbalanced Data: An Overview

Ecological studies typically involve comparison of biological responses among a variety of environmental conditions. When the response variables have continuous distributions and the conditions are discrete, whether inherently or by design, then it is appropriate to analyze the data using analysis of variance (ANOVA). When data conform to a complete, balanced design (equal numbers of observations in each experimental treatment), it is straightforward to conduct an ANOVA, particularly with the aid of the numerous statistical computing packages that are available. Interpretation of an ANOVA of balanced data is also unambiguous. Unfortunately, for a variety of reasons, it is rare that a practicing ecologist embarks on an analysis of data that are completely balanced. Regardless of its cause, lack of balance necessitates care in the analysis and interpretation. In this paper, our aims is to provide an overview of the consequences of lack of balance and to give some guidelines to analyzing unbalanced data for models involving fixed effects. Our treatment is necessarily cursory and will not substitute for training available from a sequence of courses in mathematical statistics and linear models. It is intended to introduce the reader to the main issues and to the extensive statistical literature that deals with them.

Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences

Phylogenetic relationships were inferred using nucleotide sequence variation of the nuclear-encoded chalcone synthase gene (Chs) and the chloroplast gene matK for members of five tribes from the family Brassicaceae to analyze tribal and subtribal structures. Phylogenetic trees from individual data sets are mostly in congruence with the results from a combined matK-Chs analysis with a total of 2721 base pairs, but with greater resolution and higher statistical support for deeper branching patterns. The analysis indicates that tribes Lepidieae, Arabideae, and Sisymbrieae are not monophyletic. Among taxa under study four different lineages each were detected in tribes Arabideae and Lepidieae, interspersed with taxa from tribes Sisymbrieae, Hesperideae, and Brassiceae. It is concluded that tribe Brassiceae might be the only monophyletic group of the traditional tribes. From our data we estimated several divergence times for different lineages among cruciferous plants: 5.8 mya (million years ago) for the Arabidopsis-Cardaminopsis split, 20 mya for the Brassica-Arabidopsis split, and ∼40 mya for the age of the deepest split between the most basal crucifer Aethionema and remaining cruciferous taxa.

Evolutionary and ecological functional genomics

A unique combination of disciplines is emerging — evolutionary and ecological functional genomics — which focuses on the genes that affect ecological success and evolutionary fitness in natural environments and populations. Already this approach has provided new insights that were not available from its disciplinary components in isolation. However, future advances will necessitate the re-engineering of scientific attitudes, training and institutions, to achieve extensive multidisciplinarity.

Gene Duplication in the Diversification of Secondary Metabolism: Tandem 2-Oxoglutarate–Dependent Dioxygenases Control Glucosinolate Biosynthesis in Arabidopsis

Secondary metabolites are a diverse set of plant compounds believed to have numerous functions in plant–environment interactions. The large chemical diversity of secondary metabolites undoubtedly arises from an equally diverse set of enzymes responsible for their biosynthesis. However, little is known about the evolution of enzymes involved in secondary metabolism. We are studying the biosynthesis of glucosinolates, a large group of secondary metabolites, in Arabidopsis to investigate the evolution of enzymes involved in secondary metabolism. Arabidopsis contains natural variations in the presence of methylsulfinylalkyl, alkenyl, and hydroxyalkyl glucosinolates. In this article, we report the identification of genes encoding two 2-oxoglutarate–dependent dioxygenases that are responsible for this variation. These genes, AOP2 and AOP3, which map to the same position on chromosome IV, result from an apparent gene duplication and control the conversion of methylsulfinylalkyl glucosinolate to either the alkenyl or the hydroxyalkyl form. By heterologous expression in Escherichia and the correlation of gene expression patterns to the glucosinolate phenotype, we show that AOP2 catalyzes the conversion of methylsulfinylalkyl glucosinolates to alkenyl glucosinolates. Conversely, AOP3 directs the formation of hydroxyalkyl glucosinolates from methylsulfinylalkyl glucosinolates. No ecotype coexpressed both genes. Furthermore, the absence of functional AOP2 and AOP3 leads to the accumulation of the precursor methylsulfinylalkyl glucosinolates. A third member of this gene family, AOP1, is present in at least two forms and found in all ecotypes examined. However, its catalytic role is still uncertain.

Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis

Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.

Which evolutionary processes influence natural genetic variation for phenotypic traits

Although many studies provide examples of evolutionary processes such as adaptive evolution, balancing selection, deleterious variation and genetic drift, the relative importance of these selective and stochastic processes for phenotypic variation within and among populations is unclear. Theoretical and empirical studies from humans as well as natural animal and plant populations have made progress in examining the role of these evolutionary forces within species. Tentative generalizations about evolutionary processes across species are beginning to emerge, as well as contrasting patterns that characterize different groups of organisms. Furthermore, recent technical advances now allow the combination of ecological measurements of selection in natural environments with population genetic analysis of cloned QTLs, promising advances in identifying the evolutionary processes that influence natural genetic variation.

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species’ native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush‐like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree‐like, bifurcating pattern of evolution – there is no ‘ecotype phylogeny.’ Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.