Screening Cotoneaster sp. for Resistance to Fire Blight Using Foliar Inoculation with Two Strains of Erwinia amylovora

The genus Cotoneaster is composed of ≈400 species with a wide variety of growth habits and forms. These hardy landscape shrubs used to be commonplace because of their low maintenance and landscape functionality. However, the interest in and sales of cotoneaster have decreased for a variety of reasons, with the greatest being its susceptibility to a bacterial disease fire blight caused by Erwinia amylovora. The resistances of 15 different genotypes of Cotoneaster to a wild-type strain of Erwinia amylovora (Ea153) and a strain LA635 that has a natural mutation in avrRpt2 that encodes for a type III secretion effector were tested separately by inoculating leaves. Fire blight resistance was assessed by calculating the percent shoot necrosis (PSN) [PSN = 100 × (lesion length ÷ total branch length)] at 6 to 8 weeks after inoculation. Across all experiments, Cotoneaster genotypes H2011-01-002 and C. ×suecicus ‘Emerald Sprite’ consistently had the lowest PSN values when inoculated with either strain. Cotoneaster ×suecicus ‘Emerald Beauty’ was significantly more resistant to Ea153 than to LA635, whereas C. splendens was significantly more susceptible to Ea153 than to LA635.

Inferring Population Size Histories using Coalescent Hidden Markov Models with TMRCA and Total Branch Length as Hidden States

Unraveling the complex demographic histories of natural populations is a central problem in population genetics. Understanding past demographic events is of general anthropological interest and is also an important step in establishing accurate null models when identifying adaptive or disease-associated genetic variation. An important class of tools for inferring past population size changes are Coalescent Hidden Markov Models (CHMMs). These models make efficient use of the linkage information in population genomic datasets by using the local genealogies relating sampled individuals as latent states that evolve across the chromosome in an HMM framework. Extending these models to large sample sizes is challenging, since the number of possible latent states increases rapidly. Here, we present our method CHIMP (CHMM History-Inference ML Procedure), a novel CHMM method for inferring the size history of a population. It can be applied to large samples (hundreds of haplotypes) and only requires unphased genomes as input. The two implementations of CHIMP that we present here use either the height of the genealogical tree (TMRCA) or the total branch length, respectively, as the latent variable at each position in the genome. The requisite transition and emission probabilities are obtained by numerically solving certain systems of differential equations derived from the ancestral process with recombination. The parameters of the population size history are subsequently inferred using an Expectation-Maximization algorithm. In addition, we implement a composite likelihood scheme to allow the method to scale to large sample sizes. We demonstrate the efficiency and accuracy of our method in a variety of benchmark tests using simulated data and present comparisons to other state-of-the-art methods. Specifically, our implementation using TMRCA as the latent variable shows comparable performance and provides accurate estimates of effective population sizes in intermediate and ancient times. Our method is agnostic to the phasing of the data, which makes it a promising alternative in scenarios where high quality data is not available, and has potential applications for pseudo-haploid data.

Patterns of variation of mutation rates of mitochondrial and nuclear genes of gastropods

Background Although mitochondrial DNA (mtDNA) of many animals tends to mutate at higher rates than nuclear DNA (nuDNA), a recent survey of mutation rates of various animal groups found that the gastropod family Bradybaenidae (suborder Helicina) shows a nearly 40-fold difference in mutation rates of mtDNA ($$\mu$$ μ m) and nuDNA ($$\mu$$ μ n), while other gastropod taxa exhibit only two to five-fold differences. To determine if Bradybaenidae represents an outlier within Gastropoda, I compared estimated values of $$\mu$$ μ m/$$\mu$$ μ n of additional gastropod groups. In particular, I reconstructed mtDNA and nuDNA gene trees of 121 datasets that include members of various clades contained within the gastropod subclasses Caenogastropoda, Heterobranchia, Patellogastropoda, and Vetigastropoda and then used total branch length estimates of these gene trees to infer $$\mu$$ μ m/$$\mu$$ μ n. Results Estimated values of $$\mu$$ μ m/$$\mu$$ μ n range from 1.4 to 91.9. Datasets that exhibit relatively large values of $$\mu$$ μ m/$$\mu$$ μ n (i.e., > 20), however, show relatively lower estimates of $$\mu$$ μ n (and not elevated $$\mu$$ μ m) in comparison to groups with lower values. These datasets also tend to contain sequences of recently diverged species. In addition, datasets with low levels of phylogenetic breadth (i.e., contain members of single genera or families) exhibit higher values of $$\mu$$ μ m/$$\mu$$ μ n than those with high levels (i.e., those that contain representatives of single superfamilies or higher taxonomic ranks). Conclusions Gastropods exhibit considerable variation in estimates of $$\mu$$ μ m/$$\mu$$ μ n. Large values of $$\mu$$ μ m/$$\mu$$ μ n that have been calculated for Bradybaenidae and other gastropod taxa may be overestimated due to possible sampling artifacts or processes that depress estimates of total molecular divergence of nuDNA in groups that recently diversified.

Distribution of epicormic branches and foliage on Douglas-fir as influenced by adjacent canopy gaps

The influence of adjacent canopy gaps on spatial distribution of epicormic branches and delayed foliage (originating from dormant buds) was investigated in 65-year-old coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco). Sample trees were selected across a broad range of local densities (adjacent canopy gap sizes) from a repeatedly thinned stand in which gaps had been created 12 years prior to our study. Lengths and stem locations of original and epicormic branches were measured within the south-facing crown quadrant, along with extents to which branches were occupied by sequential (produced in association with terminal bud elongation) and (or) delayed foliage. Epicormic branches, while prevalent throughout crowns, contributed only 10% of total branch length and 2% of total foliage mass. In contrast, delayed foliage occupied over 75% of total branch length, accounted for nearly 39% of total foliage mass, and often overlapped with sequential foliage. Canopy gap size did not influence original or epicormic branch length or location. On original branches, larger gaps may have modestly negatively influenced the relative extent of sequential foliage on branches and (or) slightly positively influenced delayed foliage mass. Delayed foliage appears to contribute substantially to Douglas-fir crown maintenance at this tree age, but canopy gap size had a minor influence, at least in the short term.

The Total External Branch Length of Beta-Coalescents

For 1 < α < 2 we derive the asymptotic distribution of the total length of external branches of a Beta(2 − α, α)-coalescent as the number n of leaves becomes large. It turns out that the fluctuations of the external branch length follow those of τn2−α over the entire parameter regime, where τn denotes the random number of coalescences that bring the n lineages down to one. This is in contrast to the fluctuation behaviour of the total branch length, which exhibits a transition at $\alpha_0 = (1+\sqrt 5)/2$ ([18]).

On Asymptotics of the Beta Coalescents

We show that the total number of collisions in the exchangeable coalescent process driven by the beta (1, b) measure converges in distribution to a 1-stable law, as the initial number of particles goes to ∞. The stable limit law is also shown for the total branch length of the coalescent tree. These results were known previously for the instance b = 1, which corresponds to the Bolthausen-Sznitman coalescent. The approach we take is based on estimating the quality of a renewal approximation to the coalescent in terms of a suitable Wasserstein distance. Application of the method to beta (a, b)-coalescents with 0 < a < 1 leads to a simplified derivation of the known (2 - a)-stable limit. We furthermore derive asymptotic expansions for the moments of the number of collisions and of the total branch length for the beta (1, b)-coalescent by exploiting the method of sequential approximations.

On Asymptotics of the Beta Coalescents

We show that the total number of collisions in the exchangeable coalescent process driven by the beta (1,b) measure converges in distribution to a 1-stable law, as the initial number of particles goes to ∞. The stable limit law is also shown for the total branch length of the coalescent tree. These results were known previously for the instanceb= 1, which corresponds to the Bolthausen-Sznitman coalescent. The approach we take is based on estimating the quality of a renewal approximation to the coalescent in terms of a suitable Wasserstein distance. Application of the method to beta (a,b)-coalescents with 0 &lt;a&lt; 1 leads to a simplified derivation of the known (2 -a)-stable limit. We furthermore derive asymptotic expansions for the moments of the number of collisions and of the total branch length for the beta (1,b)-coalescent by exploiting the method of sequential approximations.

Cyclanilide Differentially Affects Branching in Red Maple Cultivars and Hybrids

Development of the canopy is an important aspect of ornamental shade tree production. Branching can be induced by pruning the apical meristem, but this process is time consuming and costly to growers. Cyclanilide is an auxin transport inhibitor that has been successfully used to eliminate apical dominance and increase branching in a number of tree species. In this study, we tested the effects of cyclanilide application in two years on branching, canopy form, and trunk diameter. Cyclanilide did not cause phytotoxicity symptoms in any cultivar at any rate. Two cultivars, Celebration® (Acer × freemanii A.E. Murray ‘Celzam’) and Sienna Glen® (Acer × freemanii ‘Sienna’) Freeman maples responded to cyclanilide treatments with increased primary and secondary shoots, whereas Red Sunset® red maple (Acer rubrum L. ‘Franksred’) and Autumn Blaze® Freeman maple (Acer × freemanii A.E. Murray ‘Jeffersred’) did not respond to any treatments. Responsive cultivars had approximately double the number of growing points and larger total branch length after second year applications, but this did not result in an increase in trunk caliper. Despite the increased number of shoots produced, overall canopy ratings did not differ among treatments. Cyclanilide had a limited affect on branching in red and Freeman maple whips. Furthermore, if growers choose to utilize this product, they should be aware that cultivar response is likely to vary, and initial testing should be done before making large-scale applications.