The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours.

Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found that individuals dispersed especially far when exposed to a poor environment as adults if their phenotype, or even one-third of their neighbours' phenotypes, were shaped by a poor environment as juveniles. Juvenile environment therefore shapes dispersal both directly, by influencing phenotype, as well as indirectly, by influencing the external social environment. Thus, the juvenile environment of even a minority of individuals in a group can influence the dispersal of the entire group.

Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent.

Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk (Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

Divergent maximum-likelihood-branch-support values for polytomies.

We applied simple 4-taxon simulations with 3-way character conflict or a hard polytomy to check for false positive branch support, with a focus on the bootstrap and recently introduced likelihood-based phylogenetic-inference programs. Given that there are only three possible bifurcating topologies, discrepancies among methods identified in this study should generally be restricted to factors other than topological search heuristics. Our four major conclusions are as follows. First, Bayesian MCMCMC posterior probabilities are not the only means of quantifying support that can produce dramatically inflated values when applied to cases of strong character conflict. Rapid bootstrapping with the GTRCAT model in RAxML can provide still greater support values for polytomies and we suggest that it generally be avoided. Second, the SH-like approximate likelihood-ratio test outperforms the bootstrap when applied to polytomies. We suggest that the SH-like aLRT be widely applied to likelihood-based empirical studies to complement the bootstrap by collapsing those branches with an SH-like aLRT percentage of ≤ 10, irrespective of how high the likelihood bootstrap support is. Third, the 70% bootstrap cutoff does not equate to a 5% error rate and we suggest that the idea that ≥ 70% bootstrap generally equates to 95% probability of accuracy in empirical analyses finally be abandoned. Fourth, rapid bootstrapping with the GTRCAT model in RAxML can generate values with very low precision, which reinforces our assertion that this method should be avoided, let alone be entirely relied upon for phylogenetic inference.

Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example.

A supermatrix of 272 terminals from Rubiaceae tribe Spermacoceae that were scored for up to 10 gene regions (two nrDNA, eight plastid) was used as an empirical example to quantify sources of error in heuristic parametric (Bayesian MCMC and maximum likelihood) phylogenetic analyses. The supermatrix includes dramatic disparities in which terminals were sampled for which gene regions. The sources of error examined include poor quality tree searches, requiring a single fully resolved optimal tree, undersampling-within-replicates and frequency-within-replicates bootstrap artifacts, and extrapolation from one character partition to another such that synapomorphies that would only be ambiguously optimized by parsimony are optimized with high probability by parametric methods. Four of our conclusions are as follows. (1) The resolution and support provided by parametric methods for clades that lack unambiguously optimized (by parsimony) synapomorphies are less robust to the addition of terminals and characters than those clades that have unambiguously optimized synapomorphies. (2) Those tree-search methods which can create phylogenetic artifacts (frequency-within-replicates resampling, undersampling-within-replicates resampling, requiring a single fully resolved optimal tree, non-independent resampling among replicates) provide the greatest resolution and support irrespective of whether that resolution or support is corroborated by more conservative and better justified methods. (3) Partitioning data matrices cannot be relied upon to consistently obviate potentially dubious resolution and support caused by missing-data artifacts in likelihood analyses when the models require linked branch lengths among partitions. (4) Undersampling-within-replicates and frequency-within-replicates resampling artifacts are not unique to parsimony and should be accounted for in likelihood analyses by allowing multiple equally likely trees to be saved within each resampling pseudoreplicate and applying the strict-consensus bootstrap rather than the frequency-within-replicates bootstrap.

Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support.

We used random sequences to determine which alignment methods are most susceptible to aligning sequences so as to create artifactual resolution and branch support in phylogenetic trees derived from those alignments. We compared four alignment methods (progressive pairwise alignment, simultaneous multiple alignment of sequence fragments, local pairwise alignment, and direct optimization) to determine which methods are most susceptible to creating false positives in phylogenetic trees. Implied alignments created using direct optimization provided more artifactual support than progressive pairwise alignment methods, which in turn generally provided more artifactual support than simultaneous and local alignment methods. Artifactual support derived from base pairs was generally reinforced by the incorporation of gap characters for progressive pairwise alignment, local pairwise alignment, and implied alignments. The amount of artifactual resolution and support was generally greater for simulated nucleotide sequences than for simulated amino acid sequences. In the context of direct optimization, the differences between static and dynamic approaches to calculating support were extreme, ranging from maximal to nearly minimal support. When applied to highly divergent sequences, it is important that dynamic, rather than static, characters be used whenever calculating branch support using direct optimization. In contrast to the tree-based approaches to alignment, simultaneous alignment of sequences using the similarity criterion generally does not create alignments that are biased in favor of any particular tree topology.

The relative performance of indel-coding methods in simulations.

We used simulations to compare the performance of 10 approaches that have been used for treating unambiguously aligned gaps in phylogenetic analyses. We examined how these approaches perform under the ideal conditions of correct alignments, as well as how robust they are to errors caused by use of inferred alignments. Our results indicate that 5th-state coding dramatically outperformed all other coding methods, which in turn all outperformed treating gaps as missing data or excluding gapped positions. Simple indel coding (SIC) and modified complex indel coding (MCIC) performed about the same, and generally outperformed the other indel-coding methods. The high performance of 5th-state coding was largely found to be a weighting artifact. We suggest that MCIC-coded gap characters be scored for all unambiguously aligned gaps in parsimony-based molecular phylogenetic analyses. When the number of terminals sampled precludes the use of MCIC, SIC may be used as an effective substitute.

Biological Control of Grape Powdery Mildew Using Mycophagous Mites.

We evaluated the efficacy of a mycophagous tydeid mite, Orthotydeus lambi, in controlling grape powdery mildew on mature vines of nine different grape cultivars and one unnamed hybrid grown in an experimental vineyard over a 3-year period. O. lambi became well established on all vines where they were released. However, some cultivars supported higher densities than others, depending on, among other factors, the presence and abundance of leaf trichomes in vein axils (domatia). The establishment of O. lambi substantially reduced powdery mildew on foliage and fruit, although the magnitude of disease suppression was greater on some grape genotypes than others, depending on mite density and innate susceptibility to grape powdery mildew. Treatments where O. lambi was used alone were as effective as fungicide. Significantly better disease control was found in treatments with both mites and fungicides. The mass of pruning material and leaf photosynthetic rates were significantly greater for vines with O. lambi, fungicide, or a combination of mites and fungicide compared with untreated vines. The combination of mites and fungicide resulted in significantly greater yield than mites or fungicide alone. Our results illustrate the potential of O. lambi for biological control of grape powdery mildew but also highlight limitations related to differences among grape genotypes in innate susceptibility to mildew and suitability for mites.

Selenium accumulation protects Brassica juncea from invertebrate herbivory and fungal infection.

• Certain plant species hyperaccumulate selenium (Se) up to 0.6% of their dry weight. It is not known whether Se hyperaccumulation offers the plants any advantage. In this study the hypothesis was tested that Se can protect plants from invertebrate herbivory or fungal infection. • Indian mustard (Brassica juncea) plants grown with or without Se were subjected to herbivory by caterpillars (Pieris rapae) and snails (Mesodon ferrissi), or to fungal infection by a root/stem pathogen (Fusarium sp.) and a leaf pathogen (Alternaria brassicicola). • When given a choice between leaves with or without Se (0.1% Se of leaf d. wt), the caterpillars strongly preferred leaves without Se (P < 0.01), while the snails preferred leaves containing Se (P < 0.015). When consumed, the Se leaves were lethal to the caterpillars. The snails showed no toxicity symptoms, even though their tissue Se concentrations were comparable with the caterpillars. Se-containing plants were less susceptible to infection by both fungi. • In conclusion, Se was shown to protect Indian mustard plants from fungal infection and from herbivory by caterpillars, but not by snails.

Host plant manipulation of natural enemies: leaf domatia protect beneficial mites from insect predators.

Acarodomatia are small tufts of hair or invaginations in the leaf surface and are frequently inhabited by several taxa of non-plant-feeding mites. For many years, ecologists have hypothesized that these structures represent a mutualistic association between mites and plants where the mites benefit the plant by reducing densities of phytophagous arthropods and epiphytic microorganisms, and domatia benefit the mite by providing protection from stressful environmental conditions, other predaceous arthropods, or both. We tested these hypothesized benefits of domatia to domatia-inhabiting mites in laboratory and growth chamber experiments. In separate experiments we examined whether domatia on the wild grape, Vitis riparia, provided protection against drying humidity conditions or predaceous arthropods to two species of beneficial mite: the mycophagous species Orthotydeus lambi, and the predaceous species Amblyseius andersoni. For both taxa of beneficial mite, domatia significantly increased mite survivorship in the presence of the predatory bug, Orius insidiosus and the coccinellids Coccinella septempunctata and Harmonia varigata. There was no evidence for a protective effect of domatia with a third species of predatory arthropod, lacewing larvae Chrysoperla rufilabris. In contrast, there was no evidence for either species of beneficial mite that domatia provided any protection against low humidity. Thus in this system the primary mechanism by which domatia benefit beneficial mites is by protecting these organisms from other predatory arthropods on the leaf surface.