Early Performance of Several Prunus Interspecific Hybrid Rootstocks for Redhaven Peach in Southern Ontario

A multi-year orchard experiment was established to measure the performance of Rootpac®-R, Rootpac®-20, Rootpac®-40, and Rootpac®-70 rootstocks using ‘Redhaven’ peach (Prunus persica var. persica) as the scion, and compared with the Bailey peach seedling rootstock, the current industry standard. Tree survival after five years was 79% on Rootpac-40, whereas the remaining rootstocks showed no tree mortality. Tree vigour and canopy height and width were influenced by rootstock genotype beginning the year of planting in 2016. For the first five years of production, Rootpac-70 consistently produced the largest trees based on TCSA and by year five, all rootstocks produced trees with similar TCSAs, except for Rootpac-70, which was 38% larger than Bailey. By year five, cumulative yields were greatest on Rootpac-70, which were 10% higher than Bailey; cumulative yields of Rootpac-R, Rootpac-20, and Rootpac-30 were 98%, 89%, and 84% that of Bailey, respectively. Cumulative yield efficiency was significantly influenced by rootstock although the magnitude of the differences was small and likely of insignificant commercial importance. Rootpac-40 consistently produced the largest fruit. These results are only reflective of the orchard establishment years and additional data are required before peach producers can make fully informed decisions concerning the rootstocks evaluated in this study for their orchard systems. However, at this juncture, all the Rootpac rootstocks evaluated in this study are likely to impart excessive vigour to be used in a higher density system and offer little advantage over Bailey.

The Potential to Use Variations in Tree-Ring Geometric Center to Estimate Past Wind Speed Change

Tree radial growth is characterized by not only the annual ring-width increment but also shifts in the tree-ring geometric center (TRGC) if subjected to asymmetric external forcing, such as prevailing winds. Previous dendrochronological studies have used the asymmetric growth derived from tree-ring widths to reconstruct wind speed changes. Here we propose a novel method use quantitative TRGC measurements to estimate wind speed. We investigated TRGC shifts in northeast China, where the prevailing westerly winds are strong and persistent. We found that the TRGC showed significant correlations (r = 0.64, p < 0.01) with wind speed in May-September. The higher tree geometry sensitivity to wind speed obtained with the new method compared to previous ones, suggests the possibility of reconstructing historical wind change and variability in prevailing winds using TRGC. In addition, by correcting tree-ring radius according to their TRGC shifts, the basal area increment (BAI) was calculated. Our new BAI estimation provided stronger correlations with climate than both the standard tree-ring width chronology and a traditional BAI estimation. We suggest that future dendrochronological studies should consider TRGC shifts to increase the accuracy in climate reconstructions.

An Evaluation of the Australian Coal Flotation Standards

Mining operations often send samples for testing to commercial laboratories. Unless a customised test is requested, they expect laboratories to use standard procedures, which are reproducible. A thermal coal and a metallurgical coal were sent to eight laboratories, which were requested to perform a basic flotation test (AS 4156.2.1–2004) and a sequential flotation procedure test, i.e., standard tree test (AS 4156.2.2–1998). This study compared the reports produced by the various laboratories and compared them with the requirements laid out by the Australian standards. It was found that many elements were missing in most cases, probably due to the fact that some of the requirements of the standard, such as size analysis, are offered as other services. The basic tests generally agreed with one another whilst the sequential tests presented more variations. A quantitative analysis of the variation in the yield–ash curves produced by the sequential procedure was conducted using dynamic time warping (DTW). This approach can be used to numerically compare yield–ash curves and perform statistical comparisons.

Tree-ring-based spring precipitation reconstruction in the Sikhote-Alin' Mountain range

Climate reconstructions provide important insight into past climate variability and help us to understand the large-scale climate drivers and impact of climate change. However, our knowledge about long-term year-to-year climate variability is still limited due to the lack of high-resolution reconstructions. Here, we present the first precipitation reconstructions based on tree rings from Pinus koraiensis (Korean pine) from three sites placed along a latitudinal (330 km) gradient in the Sikhote-Alin' mountains in the Russian Far East. The tree-ring width chronologies were built using standard tree-ring procedures. We reconstructed the April–June precipitation for the southern Sikhote-Alin' (SSA), March–June precipitation for the central Sikhote-Alin' (CSA) and March–July precipitation for the northwestern Sikhote-Alin' (NSA) over the years 1602 to 2013, 1804 to 2009 and 1858 to 2013, respectively. We found that an important limiting factor for Korean pine growth was precipitation within the period when the air current coming from the continent during the cold period is replaced with the impact of the wet ocean air current. We identified that common wet years for SSA, CSA and NSA occurred in 1805, 1853, 1877, 1903, 1906, 1927, 1983 and 2009 and common dry years occurred in 1821, 1869, 1919, 1949 and 2003. Our reconstructions have 3-, 15- and 60-year periods, which suggests the influence of the El Niño–Southern Oscillation and Pacific Decadal Oscillation on the region's climate and relevant processes. Despite the impact of various global processes, the main contribution to precipitation formation in the study area is still made by the Pacific Ocean, which determines their amount and periodicity.

The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure. We test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments: buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies, whereas solvent-exposed and helix sites had unequal numbers of sites, supporting the minority topologies. This suggests that the relatively slowly evolving buried, sheet, and coil sites are giving an accurate picture of the true species tree and the amount of conflict among gene trees. Taken as a whole, this study indicates that phylogenetic analyses using sites in different structural environments can yield different topologies for the deepest branches in the animal tree of life and that analyzing larger numbers of taxa eliminates this conflict. More broadly, our results highlight the desirability of incorporating information about protein structure into phylogenomic analyses.

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

ABSTRACT Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of ‘omic data. IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.

TPOT-NN: augmenting tree-based automated machine learning with neural network estimators

Automated machine learning (AutoML) and artificial neural networks (ANNs) have revolutionized the field of artificial intelligence by yielding incredibly high-performing models to solve a myriad of inductive learning tasks. In spite of their successes, little guidance exists on when to use one versus the other. Furthermore, relatively few tools exist that allow the integration of both AutoML and ANNs in the same analysis to yield results combining both of their strengths. Here, we present TPOT-NN—a new extension to the tree-based AutoML software TPOT—and use it to explore the behavior of automated machine learning augmented with neural network estimators (AutoML+NN), particularly when compared to non-NN AutoML in the context of simple binary classification on a number of public benchmark datasets. Our observations suggest that TPOT-NN is an effective tool that achieves greater classification accuracy than standard tree-based AutoML on some datasets, with no loss in accuracy on others. We also provide preliminary guidelines for performing AutoML+NN analyses, and recommend possible future directions for AutoML+NN methods research, especially in the context of TPOT.

Infection biology as the basis of integrated control of apple canker (Neonectria ditissima) in Northern Europe

Background European canker, caused by Neonectria ditissima, is a disease of worldwide importance in apple production, yet knowledge about it is limited, highly regional and sometimes contradictory. This is an obstacle to successful disease management. Key aspects for Northern Europe are reviewed, based on research results from Northern Germany and Norway and on international literature data. Main topics Trunk cankers developing on young trees within the first 1–3 seasons of explanting can often be traced back to latent infections initiated in the nurseries. The most important nursery infection is a lateral canker on the main trunk of ‘knip’ trees, which are the standard tree type in Northern Europe. In strongly affected batches, up to 25% of trees have to be uprooted after the first growing season due to such trunk cankers. The establishment and maintenance of healthy orchards requires clean nursery material, especially in the case of susceptible cultivars. In Northern Germany, infections within commercial orchards most often proceed through wounds caused by fruit picking or leaf fall in autumn, as shown by the appearance of cankers in the following spring and by the high efficacy of fungicide treatments at leaf fall. Ascospores, commonly thought to be relevant for long-distance spread of infections, are not released until the end of leaf fall even in wet autumn seasons in Northern Germany. Therefore, their role in the disease remains unclear. Strong nitrogen-induced vegetative growth favours apple canker. In field trials conducted under conditions of current commercial practices, autumnal sprays with copper hydroxide or copper oxide were consistently more efficacious than copper oxychloride or captan in preventing new infections. Conclusions Restricted fertilisation and other measures to curb excessive vegetative growth during the first few years of an orchard, repeated canker pruning and well-timed treatments with effective fungicides in autumn are essential for IPM of apple canker. Nonetheless, canker remains capable of severely impairing the commercial success of susceptible cultivars in regions with wet climates even if all available measures are taken. This opens up long-term perspectives for the breeding of more resistant cultivars.

The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

Despite the long history of using protein sequences to infer the tree of life the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure; we test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of &ldquo;strongly decisive&rdquo; sites (alignment positions that support a specific tree topology) in a dataset comprising &amp;gt;1,500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology (ctenophores sister to other animals) regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments; buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies whereas solvent exposed and helix sites had unequal numbers of sites supporting the minority topologies. Given the plausible trees equal support for minority topologies is consistent with discordance among gene trees, making it possible the relatively slowly evolving buried (and sheet and coil) sites are giving an accurate picture of the true species tree as well as the amount of conflict among gene trees. Alternatively, the apparent support could reflect currently uncharacterized processes of molecular evolution. Regardless, it is clear that analyses of the deepest branches in the animal tree of life using sites in different structural environments are associated with a subtle data type effect that results in distinct phylogenetic signals.

Sweet Orange Orchard Architecture Design, Fertilizer, and Irrigation Management Strategies under Huanglongbing-endemic Conditions in the Indian River Citrus District

The prevalence of Huanglongbing (HLB) in Florida has forced growers to search for new management strategies to optimize fruit yield in young orchards and enable earlier economic returns given the likelihood of HLB-induced yield reductions during later years. There has been considerable interest in modifying orchard architecture design and fertilizer and irrigation management practices as strategies for increasing profitability. Our objectives were to evaluate how different combinations of horticultural practices including tree density, fertilization methods, and irrigation systems affect growth, foliar nutrient content, fruit yield, and fruit quality of young ‘Valencia’ sweet orange [Citrus sinensis (L.) Osbeck] trees during the early years of production under HLB-endemic conditions. The study was conducted in Fort Pierce, FL, from 2014 to 2020 on a 1- to 7-year-old orchard and evaluated the following treatments: standard tree density (358 trees/ha) and controlled-release fertilizer with microsprinkler irrigation (STD_dry_MS), high tree density (955 trees/ha) with fertigation and microsprinkler irrigation (HDS_fert_MS), and high tree density with fertigation and double-line drip irrigation (HDS_fert_DD). Annual foliar nutrient concentrations were usually within or higher than the recommended ranges throughout the study, with a tendency for decreases in several nutrients over time regardless of treatment, suggesting all fertilization strategies adequately met the tree nutrient demand. During fruit-bearing years, canopy volume, on a per-tree basis, was higher under STD_dry_MS (6.2–7.2 m3) than HDS_fert_MS (4.3–5.3 m3) or HDS_fert_DD (4.9–5.9 m3); however, high tree density resulted in greater canopy volume on an area basis, which explained the 86% to 300% increase in fruit yield per ha that resulted in moving from standard to high tree density. Although fruit yields per ha were generally greatest under HDS_fert_MS and HDS_fert_DD, they were lower than the 10-year Florida state average (26.5 Mg·ha−1) for standard tree density orchards, possibly due to the HLB incidence and the rootstock chosen. Although tree growth parameters and foliar nutrient concentrations varied in response to treatments, management practices that included high tree density and fertigation irrespective of irrigation systems produced the highest fruit yields and highest yield of solids. Soluble solids content (SSC) and titratable acidity (TA) were lower, and the SSC-to-TA ratio was highest under STD_dry_MS in 2016–17, with no treatment effects on quality parameters detected in other years. Both drip and microsprinkler fertigation methods sufficiently met tree nutrient demand at high tree density, but additional research is needed to determine optimal fertilization rates and better rootstock cultivars in young high-density sweet orange orchards under HLB-endemic conditions in the Indian River Citrus District.