Reference Tree Research Articles

Food tree selection by an arboreal marsupial: Implications for timber harvest

ContextThe Yellow-bellied Glider (Petaurus australis) is a vulnerable arboreal Australian marsupial that is threatened by logging. Trees used for sap feeding (sap trees) are a critical habitat requirement of the species, yet no harvest retention policy exists in the southern part of its range in Victoria, Australia. Yellow-bellied Gliders are extremely selective in sap tree use with some trees used far more frequently than others. AimsWe aimed to determine the tree species used and identify characteristics influencing intra-species tree selection for sap feeding by Yellow-bellied Gliders in the Highlands - Southern Fall Bioregion of Victoria. MethodsSap trees were located at each of 12 sites. We measured nine characteristics related to photosynthetic capability, microsite, and habitat for sap trees and the nearest tree of the same species without Yellow-bellied Glider incisions (reference tree). For sap trees, we measured 11 incision-related variables. Permutational Multivariate Analysis of Variance was conducted to identify distinguishing characteristics of sap trees. Generalised Linear Mixed Modelling was used to determine the influence of tree characteristics on abundance of incisions on a tree. Key resultsFive of 24 tree and tall shrub species present across the 12 sites were used for sap feeding. All five species were Eucalyptus. Within the tree species used, Yellow-bellied Gliders selected for trees that were larger, had wider crowns and occupied dominant and co-dominant canopy positions. ConclusionsYellow-bellied Gliders are highly selective of trees used for sap feeding. Although primarily selecting larger more dominant trees for sap feeding, lack of clear identifying characteristics means that identifying and retaining preferred sap trees in logging coupes must rely on site surveys for incisions on trees.

Possibilities and limits of dendrogeomorphic data as a basis for defining thresholds for landslide triggering

Dendrogeomorphic (tree-ring based) methods are an effective tool for determining the spatial and temporal activity of landslide movements. Moreover, the obtained chronological data can be used for the analysis of their potential triggers. However, the use of tree-ring based chronologies for defining trigger thresholds is very rare and has not yet been critically evaluated. Given the well-known limitations of dendrogeomorphic methods, this study aims to define the limitations and advantages of this approach for trigger threshold analysis. Thus, tree-ring based data on the activity of 26 landslides, originating from 2644 tree-ring series of disturbed trees (and 180 tree-ring series of reference trees), were used in this study. Total Water Content (TWC) as a combination of precipitation sum (PS) and snow water equivalent (SWE) was analyzed as landslide trigger. The obtained values of the range of trigger thresholds were relatively high. The considerable heterogeneity of the results seems to be largely influenced by the character of the data obtained by dendrogeomorphic methods. In the discussion section, all potential influences of the tree-ring based approach on the obtained results and the possibilities of their elimination are discussed. Among the most important ones can be considered the inertia of tree response to landslide movements, the ability of trees in general to capture landslide movements, as well as the use of the approach to define a landslide event. However, in addition to dendrogeomorphic influences, the heterogeneity of the landslides studied and their geological structure themselves must be taken into account.

Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network.

Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network's technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain.

Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution.

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].

A Novel 3D Tree-Modeling Method of Incorporating Small-Scale Spatial Structure Parameters in a Heterogeneous Forest Environment

Currently, 3D tree modeling in a highly heterogeneous forest environment remains a significant challenge for the modeler. Previous research has only focused on morphological characteristics and parameters, overlooking the impact of micro-environmental factors (e.g., spatial-structural diversification and habitat heterogeneity) and providing less structural information about the individual tree and decreasing the applicability and authenticity of 3D tree models in a virtual forest. In this paper, we chose a mixed-forest conversion of Chinese fir (Cunninghamia lanceolata) plantations in a subtropical region of China as our study subject and proposed a novel 3D tree-modeling method based on a structural unit (TMSU). Our approach modified traditional rule-based tree modeling (RTM) by introducing a nonlinear mixed-effect model (NLME) to study the coupling response between the spatial structures and morphological characteristics (e.g., tree height (H), height-to-crown base (HCB), and crown width (CW)) of three dominant trees (e.g., Cunninghamia lanceolata (SM), Machilus pauhoi (BHN), and Schima superba (MH)) and develop a prediction model of the morphological characteristic by incorporating forest-based structural parameters. The results showed that: (1) The NLME model in TMSU was found to better fit the data and predict the morphological characteristics than the OLS model in RTM. As compared to the RTM morphological model, the prediction accuracy of the TMSU model of morphological features was improved by 10.4%, 3.02%, and 17.8%, for SM’s H, HCB, and CW, respectively; 6.5%, 7.6%, and 8.9% for BHN’s H, HCB, and CW, respectively; and 13.3%, 15.7%, and 13.4% for MH’s H, HCB, and CW, respectively. (2) The spatial-structural parameters of crowding (Ci), mingling (Mi), and dominance (Ui) had a significant impact on the morphological characteristics of SM, BHN, and MH in TMSU. The degree of crowding, for example, had a positive relationship with tree height, height-to-crown base, and crown width in SM, BHN, and MH; under the same crowding conditions, mingling was positively correlated with tree crown width in SM, and dominance was positively correlated with tree height but negatively correlated with height-to-crown base in BHN; under the same crowding and mingling, dominance was positively correlated with height-to-crown base in MH. (3) Using 25 scenes based on the value class of Ci,Mi for SM, 25 scenes based on the value class of Ci,Ui for BHN, and 125 scenes based on the value class of Ci,Mi,Ui for MH, we generated the model libraries for the three dominating species based on TMSU. As a result, our TSMU method outperformed the traditional 3D tree-modeling method RTM in a complex and highly heterogeneous spatial structure of a forest stand, and it provided more information concerning the spatial structure based on the neighborhood relationships than the simple morphological characteristics; a higher morphological prediction accuracy with fewer parameters; and the relationship between the spatial-structural parameters and the morphological characteristics of a reference tree.

The Impacts of Quality-Oriented Dataset Labeling on Tree Cover Segmentation Using U-Net: A Case Study in WorldView-3 Imagery

Deep learning has emerged as a prominent technique for extracting vegetation information from high-resolution satellite imagery. However, less attention has been paid to the quality of dataset labeling as compared to research into networks and models, despite data quality consistently having a high impact on final accuracies. In this work, we trained a U-Net model for tree cover segmentation in 30 cm WorldView-3 imagery and assessed the impact of training data quality on segmentation accuracy. We produced two reference tree cover masks of different qualities by labeling images accurately or roughly and trained the model on a combination of both, with varying proportions. Our results show that models trained with accurately delineated masks achieved higher accuracy (88.06%) than models trained on masks that were only roughly delineated (81.13%). When combining the accurately and roughly delineated masks at varying proportions, we found that the segmentation accuracy increased with the proportion of accurately delineated masks. Furthermore, we applied semisupervised active learning techniques to identify an efficient strategy for selecting images for labeling. This showed that semisupervised active learning saved nearly 50% of the labeling cost when applied to accurate masks, while maintaining high accuracy (88.07%). Our study suggests that accurate mask delineation and semisupervised active learning are essential for efficiently generating training datasets in the context of tree cover segmentation from high-resolution satellite imagery.

Satellite-based evidence highlights a considerable increase of urban tree cooling benefits from 2000 to 2015.

Tree planting is a prevalent strategy to mitigate urban heat. Tree cooling efficiency (TCE), defined as the temperature reduction for a 1% tree cover increase, plays an important role in urban climate as it regulates the capacity of trees to alter the surface energy and water budget. However, the spatial variation and more importantly, temporal heterogeneity of TCE in global cities are not fully explored. Here, we used Landsat-based tree cover and land surface temperature (LST) to compare TCEs at a reference air temperature and tree cover level across 806 global cities and to explore their potential drivers with a boosted regression tree (BRT) machine learning model. From the results, we found that TCE is spatially regulated by not only leaf area index (LAI) but climate variables and anthropogenic factors especially city albedo, without a specific variable dominating the others. However, such spatial difference is attenuated by the decrease of TCE with tree cover, most pronounced in midlatitude cities. During the period 2000-2015, more than 90% of analyzed cities showed an increasing trend in TCE, which is likely explained by a combined result of the increase in LAI, intensified solar radiation due to decreased aerosol content, increase in urban vapor pressure deficit (VPD) and decrease of city albedo. Concurrently, significant urban afforestation occurred across many cities showing a global city-scale mean tree cover increase of 5.3 ± 3.8% from 2000 to 2015. Over the growing season, such increases combined with an increasing TCE were estimated to on average yield a midday surface cooling of 1.5 ± 1.3°C in tree-covered urban areas. These results are offering new insights into the use of urban afforestation as an adaptation to global warming and urban planners may leverage them to provide more cooling benefits if trees are primarily planted for this purpose.

Assessing the Performance of a Handheld Laser Scanning System for Individual Tree Mapping—A Mixed Forests Showcase in Spain

The use of mobile laser scanning to survey forest ecosystems is a promising, scalable technology to describe the 3D structure of forests at a high resolution. We use a structurally complex, mixed-species Mediterranean forest to test the performance of a mobile Handheld Laser Scanning (HLS) system to estimate tree attributes within a forest patch in central Spain. We describe the different stages of the HLS approach: field position, ground data collection, scanning path design, point cloud processing, alignment between detected trees and measured reference trees, and finally, the assessment of main tree structural attributes diameter at breast height (DBH) and tree height considering species and tree size as control factors. We surveyed 418 reference trees to account for omission and commission error rates over a 1 ha plot divided into 16 sections and scanned using two different scanning paths. The HLS-based approach reached a high of 88 and 92% tree detection rate for the best combination of scanning path and point cloud processing modes for the HLS system. The root mean squared errors for DBH estimates varied between species: errors for Pinus pinaster were below 2 cm for Scan 02. Quercus pyrenaica, and Alnus glutinosa showed higher error rates. We observed good agreement between ALS and HLS estimates for tree height, highlighting differences to field measurements. Despite the complexity of the mixed forest area surveyed, our results show that HLS is highly efficient at detecting tree locations, estimating DBH, and supporting tree height measurements as confirmed with airborne laser data used for validation. This study is one of the first HLS-based studies conducted in the Mediterranean mixed forest region, where variability in tree allometries and spacing and the presence of natural regeneration pose challenges for the HLS approach. HLS is a feasible, time-efficient, scalable technology for tree mapping in mixed forests with potential to support forest monitoring programmes such as national forest inventories lacking three-dimensional, remote sensing data to support field measurements.

Generalizations of the genomic rank distance to indels.

The rank distance model represents genome rearrangements in multi-chromosomal genomes as matrix operations, which allows the reconstruction of parsimonious histories of evolution by rearrangements. We seek to generalize this model by allowing for genomes with different gene content, to accommodate a broader range of biological contexts. We approach this generalization by using a matrix representation of genomes. This leads to simple distance formulas and sorting algorithms for genomes with different gene contents, but without duplications. We generalize the rank distance to genomes with different gene content in two different ways. The first approach adds insertions, deletions and the substitution of a single extremity to the basic operations. We show how to efficiently compute this distance. To avoid genomes with incomplete markers, our alternative distance, the rank-indel distance, only uses insertions and deletions of entire chromosomes. We construct phylogenetic trees with our distances and the DCJ-Indel distance for simulated data and real prokaryotic genomes, and compare them against reference trees. For simulated data, our distances outperform the DCJ-Indel distance using the Quartet metric as baseline. This suggests that rank distances are more robust for comparing distantly related species. For real prokaryotic genomes, all rearrangement-based distances yield phylogenetic trees that are topologically distant from the reference (65% similarity with Quartet metric), but are able to cluster related species within their respective clades and distinguish the Shigella strains as the farthest relative of the Escherichia coli strains, a feature not seen in the reference tree. Code and instructions are available at https://github.com/meidanis-lab/rank-indel. Supplementary data are available at Bioinformatics online.

Associational protection of urban ash trees treated with systemic insecticides against emerald ash borer.

Emerald ash borer (EAB), Agrilus plannipenis Fairmaire, is an invasive insect accidentally introduced to North America from Asia that attacks and kills ash trees (Fraxinus spp.). A common control strategy in urban centers has been the injection of systemic insecticides into mature trees, which can be costly at large scales. This study investigated whether treating a subset of a susceptible urban ash population could confer associational protection to untreated trees; i.e. improving or maintaining crown health of the latter. We selected approximately 100 mature ash trees along city streets in each of 12 sites in central and southeastern Minnesota in 2017. Each site had low but growing infestations of EAB such that canopy decline was not yet widespread. We treated 50% of trees with emamectin benzoate in eight sites and 50% of trees in four sites with azadirachtin in site-wide spatial gradients, such that the remaining 50% of trees at all sites were left untreated. Crown health of all trees was monitored for five years (2017 to 2021). Across all sites, we noted an overall maintenance or increase in crown health of both treated and untreated trees, while groups of untreated reference trees approximately three km distant from each site to monitor general tree health and EAB pressure declined quickly. These results suggested that protective benefits were conferred by treated trees to untreated trees within sites. Quantifying the spatial scale of canopy preservation of untreated trees within sites proved challenging due to the lack of variation in crown condition between treated and untreated trees. In two of the twelve sites treated with emamectin benzoate, we noted statistical evidence of improvements in crown condition of untreated trees when located within 100m of treated trees. Treating a subset of a susceptible ash population may aid in preserving untreated trees and provides a basis for developing a more cost-effective and environmentally favorable treatment regimen against EAB.

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.

δ13C and Intrinsic Water Use Efficiency for Trees in Various Health Conditions – Case Study for Świerklaniec Forest District Forest District

Abstract The study included a comparative analysis of two Pinus sylvestris L. trees growing next to each other, but in a different health condition, and the reference trees growing in the same area in Poland. The declining tree, although it was a more difficult research material, was subjected to the same analyses as healthy trees, including: creating a ring width index (RWI) record, a δ13C record, an intrinsic water use efficiency (iWUE) record and checking for the following correlations: δ13C-temperature, δ13C-precipitation, δ13C-SO2, and iWUE-SO2. Our study found that trees with different health conditions may have comparable growth patterns, but different carbon isotopic compositions and iWUE. Differences between individual trees were also observed in sensitivity to changes in temperature and SO2 emissions. The declining tree showed more significant correlations with summer temperatures, than the healthy tree and the reference trees, where significant correlations occurred in single months. Only in the instance of the declining tree, correlations were found between δ13C and SO2. iWUE of all trees did not show sensitivity to SO2 emitted in high concentrations; however, we observed the sensitivity of iWUE from the reference trees to low SO2 concentrations.

Some of the Mechanisms for Coexistence of Tree Species Diversity in Tropical Forests: A Review of Effects of Tree Density Dependence

Tree communities contribute to maintenance of species diversity in tropical forests. Coexistence of many tree species is not without competition. Therefore, coexistence of tree species and size diversities occur sequentially or simultaneously in tropical natural forests. Understanding coexistence and competition mechanisms of tree species requires knowledge of interactions within and between species. However, many conservation efforts and strategies failed due to inability to identify and maintain functional coexistence mechanisms among tree species in the forest. Also, most trees died because of pressure on their habitats and not because of limiting growth resources. Hence, species identity, minimum distance and size of the neighbouring trees which are responsible for coexistence of competing trees in most tropical forests have not been explicitly reviewed. Therefore, this review evaluated some of the density dependent mechanisms for coexistence of tree species alpha diversity in tropical forests. Many interactive mechanisms are responsible for coexistence tree species in tropical forests. Inter- and intra-specific competitions are the most significant and both facilitate positive and negative density dependence. Therefore, switching from negative to positive density dependence may occur in some situations. Positive and negative density effects regulate species abundance and coexistence through conspecific and heterospecific structures. Aggregates of conspecific and heterospecific neighbours constitute forest spatial structure. Negative density interactions are mutually exclusive and basically ranged from effect of species identity of neighbours, distance to neighbours and tree size of the neighbours to reference trees in the community structures. Some mechanisms shorten distances for heterospecific than conspecific interactions. Conspecific structures improved survival and growth of rare tree species. Interactive mechanisms in tree community and population structures facilitate species diversity and size inequality, respectively.

3D Graph-Based Individual-Tree Isolation (Treeiso) from Terrestrial Laser Scanning Point Clouds

Using terrestrial laser scanning (TLS) technology, forests can be digitized at the centimeter-level to enable fine-scale forest management. However, there are technical barriers to converting point clouds into individual-tree features or objects aligned with forest inventory standards due to noise, redundancy, and geometric complexity. A practical model treeiso based on the cut-pursuit graph algorithm was proposed to isolate individual-tree points from plot-level TLS scans. The treeiso followed the local-to-global segmentation scheme, which grouped points into small clusters, large segments, and final trees in a hierarchical manner. Seven tree attributes were investigated to understand the underlying determinants of isolation accuracy. Sensitivity analysis based on the PAWN index was performed using 10,000 parameter combinations to understand the treeiso’s parameter importance and model robustness. With sixteen reference TLS plot scans from various species, an average of 86% of all trees were detected. The mean intersection-over-union (mIoU) between isolated trees and reference trees was 0.82, which increased to 0.92 within the detected trees. Sensitivity analysis showed that only three parameters were needed for treeiso optimization, and it was robust against parameter variations. This new treeiso method is operationally simple and addresses the growing need for practical 3D tree segmentation tools.

Soil faunal communities in mass outbreak areas of the great web-spinning sawfly Acantholyda posticalis (Mats.) are impoverished compared to pest-free Scots pine forests

Mass outbreaks of pests defoliating Scots pine monocultures are of constant concern to foresters, and the increase in their frequency under conditions of a warming climate is expected. Repeated mass outbreaks usually involve the same areas, which suggests that predispositions to pest attack are shaped by certain stand characteristics or their habitat conditions. The aim of the study was to examine whether the soil invertebrate communities of pine forests with A. posticalis mass outbreaks differ from those of stands with no mass occurrence of this pest, despite analogous stand-habitat conditions and close proximity. Pine monocultures in two regions of Poland differing in the timing of the pest's mass occurrence were selected for the study. The soils of the studied monocultures, both in outbreak areas and reference tree stands, were characterized by strong acidity and low nutrient status. A lower (soil invertebrate communities) and a higher (Collembola communities) taxonomic resolution were used to assess the differences between the soil fauna of infected and reference stands. We show that soil invertebrate communities of the mass outbreak areas were characterized by impoverishment compared to those of reference forests. However, both invertebrate and Collembola communities, which in outbreak areas consisted of fewer taxa, did not differ significantly in density from reference tree stands. Nonmetric multidimensional scaling (NMDS) ordination of the collembolan communities revealed that not only their composition but also their structure in the mass outbreak areas differed significantly from those of uninfected tree stands. Further research is needed to clarify whether the depletion of soil invertebrates is a result of foliar insect feeding, or is rather a manifestation of weakened stands increasing their predisposition to attacks by pest insects.

On forest expansions for two-body partition functions on tree-like interaction graphs

We study tree approximations to classical two-body partition functions on sparse and loopy graphs via the Brydges–Kennedy–Abdessalam–Rivasseau forest expansion. We show that for sparse graphs (with large cycles), the partition function above a certain temperature T∗ can be approximated by a graph polynomial expansion over forests of the interaction graph. Within this region, we show that the approximation can be written in terms of a reference tree T on the interaction graph, with corrections due to cycles. From this point of view, this implies that high-temperature models are easy to solve on sparse graphs, as one can evaluate the partition function using belief propagation. We also show that there exist a high- and low-temperature regime, in which T can be obtained via a maximal spanning tree algorithm on a (given) weighted graph. We study the algebra of these corrections and provide first- and second-order approximation to the tree Ansatz, and give explicit examples for the first-order approximation.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns.

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

GTDB-Tk v2: memory friendly classification with the genome taxonomy database.

The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary data are available at Bioinformatics online.

Approach for graph-based individual branch modelling of meadow orchard trees with 3D point clouds

The cultivation of meadow orchards provides an ecological benefit for biodiversity, which is significantly higher than in intensively cultivated orchards. However, the maintenance of meadow orchards is not economically profitable. The use of automation for pruning would reduce labour costs and avoid accidents. The goal of this research was, using photogrammetric point clouds, to automatically calculate tree models, without additional human input, as basis to estimate pruning points for meadow orchard trees. Pruning estimates require a knowledge of the major tree structure, containing the branch position, the growth direction and their topological connection. Therefore, nine apple trees were captured photogrammetrically as 3D point clouds using an RGB camera. To extract the tree models, the point clouds got filtered with a random forest algorithm, the trunk was extracted and the resulting point clouds were divided into numerous K-means clusters. The cluster centres were used to create skeleton models using methods of graph theory. For evaluation, the nodes and edges of the calculated and the manually created reference tree models were compared. The calculated models achieved a producer’s accuracy of 73.67% and a user's accuracy of 74.30% of the compared edges. These models now contain the geometric and topological structure of the trees and an assignment of their point clouds, from which further information, such as branch thickness, can be derived on a branch-specific basis. This is necessary information for the calculation of pruning areas and for the actual pruning planning, needed for the automation of tree pruning.

Comparison of single tree detection methods to extract support trees for cable road planning

For the provision of various ecosystem services in steep terrain, such as protection against natural hazards, a forest must be managed, which often requires the use of cable yarders. The design of a cable road is a complex and demanding task that also includes the search for appropriate support and anchor trees. The aim of this study was to evaluate whether and with what reliability potential support trees for cable yarding can be detected using remote sensing data. The detection of potential support trees was tested using 48 method combinations on 10 test plots of the Experimental Forest Management project in cable yarder terrain in the Swiss Alps in the Canton of Grisons. The most suitable method combinations used a Gaussian filter and a local maxima algorithm. On average, they had an extraction rate of 108.9–124.5% (root mean square, RMS) and a mean commission error of 66.0–67.2% (RMS). The correctly detected trees deviated horizontally by an average of 1.8 to 1.9 m from the position of the reference trees. The difference in tree heights was 1.1 to 1.6 m. However, for the application of single tree detection to support cable road planning in steep and complex terrain, too few potential support trees were detected. Nonetheless, the accuracy of the extracted tree parameters would already be sufficient for cable road planning.