Andrew P. Norton

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.

Herbivory and novel weapons: no evidence for enhanced competitive ability or allelopathy induction of Centaurea diffusa by biological controls

Biological control of weeds by arthropod herbivores is thought to work by reducing the competitive ability of the weed relative to the surrounding vegetation. However, the assumption that herbivory reduces plant competitive ability has not been tested in most biological control systems, and counter to expectation, recent research on the impact of biological control agents on invasive Centaurea species suggests that this genus may respond to herbivory by increased competitive ability through enhanced plant re-growth and/or by inducing increased production of phytotoxic allelochemicals. We examined the impact of two biological control agents of the invasive plant diffuse knapweed (C. diffusa) to see if feeding by either of these insects would enhance the plant’s competitive ability or allelochemical output. Sub-lethal herbivory by either of the biological control agents significantly reduced knapweed performance when the plant was grown in competition with either of two native species. Competition with knapweed significantly reduced the performance of both native species (Artemisia frigida and Bouteloua gracilis), and herbivory by one of the biocontrol agents resulted in a small but significant increase in both native species’ performance. Diffuse knapweed’s putative allelochemical 8-hydroxyquinoline was not detected in experimental or field collected soils from knapweed-infested sites. In contrast to other studies on the impacts of biological control on other Centaurea species, these data support the premise that biological control agents may reduce invading plant competitive ability. We find no evidence for diffuse knapweed allelopathy mediated by 8-hydroxyquinoline or enhanced allelopathy in response to herbivory by biological control agents.

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.

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.

Host-plant preference of Brachypterolus pulicarius, an inadvertently introduced biological control insect of toadflaxes

Brachypterolus pulicarius (L.) (Coleoptera: Kateridae) is an inadvertently introduced biological control agent that can reduce seed set in two North American invasive species, yellow (Linaria vulgaris P. Mill.) (Scrophulariaceae) and Dalmatian toadflax (Linaria genistifolia (L.) P. Mill. ssp. dalmatica). The beetles are more common on yellow toadflax than on Dalmatian toadflax. To understand their distribution on the two host plants, we investigated whether they prefer one host to the other and whether individuals aggregate toward conspecifics. In field and laboratory experiments where beetles were presented with a choice of both toadflax species, B. pulicarius sampled from both host plants preferred yellow toadflax. However, in the laboratory experiment, beetles collected from Dalmatian toadflax showed a weaker preference for yellow toadflax than beetles collected from yellow toadflax. In the field experiment, all beetle populations sampled showed similar preferences. When given a choice between yellow toadflax plants with and without trapped adult B. pulicarius, beetles preferred plants with conspecifics, suggesting aggregation toward beetle pheromones or host‐plant volatiles induced by beetle activity. These results do not support the current practice of redistributing North American B. pulicarius onto Dalmatian toadflax because of their preference for yellow toadflax.

Restoring Competitors and Natural Enemies for Long-Term Control of Plant Invaders

Restoring Competitors and Natural Enemies for Long-Term Control of Plant Invaders DOI:10.2458/azu_rangelands_v32i1_norton

Local Environmental Context Conditions the Impact of Russian Olive in a Heterogeneous Riparian Ecosystem

Local abiotic and biotic conditions can alter the strength of exotic species impacts. To better understand the effects of exotic species on invaded ecosystems and to prioritize management efforts, it is important that exotic species impacts are put in local environmental context. We studied how differences in plant community composition, photosynthetically active radiation (PAR), and available soil N associated with Russian olive presence are conditioned by local environmental variation within a western U.S. riparian ecosystem. In four sites along the South Fork of the Republican River in Colorado, we established 200 pairs of plots (underneath and apart from Russian olive) to measure the effects of invasion across the ecosystem. We used a series of a priori mixed models to identify environmental variables that altered the effects of Russian olive. For all response variables, models that included the interaction of environmental characteristics, such as presence/absence of an existing cottonwood canopy, with the presence/absence of Russian olive canopy were stronger candidate models than those that just included Russian olive canopy presence as a factor. Compared with reference plots outside of Russian olive canopy, plots underneath Russian olive had higher relative exotic cover (exotic/total cover), lower perennial C4 grass cover, and higher perennial forb cover. These effects were reduced, however, in the presence of a cottonwood canopy. As expected, Russian olive was associated with reduced PAR and increased N, but these effects were reduced under cottonwood canopy. Our results demonstrate that local abiotic and biotic environmental factors condition the effects of Russian olive within a heterogeneous riparian ecosystem and suggest that management efforts should be focused in open areas where Russian olive impacts are strongest. Nomenclature: Cottonwood, Populus deltoides W. Bartram ex Marshall ssp. monilifera (Aiton) Eckenwalder; Russian olive, Elaeagnus angustifolia L. Management Implications: Understanding how invader impacts vary across the landscape is crucial to developing more efficient management strategies. Current strategies primarily treat landscapes as homogeneous; therefore, management efforts are often inefficient because they do not preferentially target the areas of most concern. Using a more targeted management approach, where early intervention is applied only to areas of the landscape likely to experience strong invader impacts, would be much more cost effective. Based on our results, we suggest that ideally Russian olive should be removed from all habitat types because it is associated with an increase in soil N and proportional exotic plant cover. However, when management funding is limited, we suggest prioritizing control efforts on locations where it is growing in the absence of a cottonwood canopy. In these areas, Russian olive has the largest impact on soil N and proportional exotic cover. Since Russian olive appears to cause an “invasional meltdown” by facilitating the invasion of other exotic species, particularly in open canopies, research on effects of removal is warranted to see if it reverses Russian olive impacts. If the increased soil N associated with Russian olive presence persists after the trees removal, secondary invasion after the disturbance from the removal process is likely. Additionally, favoring cottonwood establishment over Russian olive can be accomplished by promoting flood disturbance by avoiding channel stabilization (i.e., by riprap) and construction.

Native Stem-Boring Beetles (Coleoptera: Bostrichidae) Extensively and Frequently Feed on Invasive Tamarix

Abstract We initially observed native stem-boring beetles (Amphicerus bicaudatus) feeding on stems of invasive tamarisks (Tamarix) at Bonny State Park, Yuma County, in eastern Colorado. At 11 sites in Colorado, Nebraska, and Kansas, we examined tamarisks and the most common co-occurring native tree, eastern cottonwoods (Populus deltoides), for the occurrence of this beetle. We detected evidence of feeding and development of insects at nine of the sites and in 112 of 579 tamarisks. Among sites, A. bicaudatus occurred in nearly 20% of tamarisks. Only 13 of 480 eastern cottonwoods showed signs of activity by A. bicaudatus. During dissections of stems of tamarisks, nearly 90% of adult beetles were in live versus dead stems.