Robust expansion of phylogeny for fast-growing genome sequence data

Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm 'TIPars' by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

ORPER: a workflow for constrained SSU rRNA phylogenies

The continuous increase of sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects evermore complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow ORPER (containerized in Singularity), which allows determining the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement

Cyanobacteria are a widespread and important bacterial phylum, responsible for a significant portion of global carbon and nitrogen fixation. Unfortunately, reliable and accurate automated classification of cyanobacterial 16S rRNA gene sequences is muddled by conflicting systematic frameworks, inconsistent taxonomic definitions (including the phylum itself), and database errors. To address this, we introduce Cydrasil 3 (https://www.cydrasil.org), a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification. Cydrasil 3 contains over 1300 manually curated sequences longer than 1100 base pairs and can be used for phylogenetic placement or as a reference sequence set for de novo phylogenetic reconstructions. The web application (utilizing PaPaRA and EPA-ng) can place thousands of sequences into the reference tree and has detailed instructions on how to analyze results. While the Cydrasil web application offers no taxonomic assignments, it instead provides phylogenetic placement, as well as a searchable database with curation notes and metadata, and a mechanism for community feedback.

Structural diversity and conservation implications of Parrotia subaequalis (Hamamelidaceae), a rare and endangered tree species in China

Parrotia subaequalis (H. T. Chang) R.M. Hao & H.T. Wei is a rare and endangered Tertiary relict tree that is endemic to subtropical China. However, little is known about its growth condition and relationship with associated tree species. Here, for the first time we measured the structural diversity of P. subaequalis communities at three representative sites in eastern China using four structural indices, including mingling, tree-tree distance, and diameter and tree height differences. The results showed that: 1) Collectively, most P. subaequalis and associated tree species were small and mid-sized classes in tree height, and small-sized class in diameter; 2) There were two or more other tree species around most of P. subaequalis individuals across the three sites; 3) Overall, the mean distance between reference trees and their neighbors was mainly 1–2 m. Our results indicated that a strong interspecific competition existed between P. subaequalis and its associated tree species. Meanwhile, although the reference tree P. subaequalis had slight advantages in both horizontal and vertical planes, we think that it is necessary to take some effective measures to reduce the interspecific competition and thereby keep it at a proper successive stage. In addition, we also discuss the protection level of P. subaequalis in China, and propose to keep this species at the First-Grade State Protection.

The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters

The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as “Ocadia” kehreri and “Ocadia” messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.

A Modification of the Frechet Distance for Nonisomorphic Trees

The paper presents a modification of the Frechet distance for nonisomorphic trees. While the classical Frechet distance between nonisomorphic trees is undefined, a new measure called similarity of a tree to a reference tree is given that is defined for a wider class of trees. A polynomial-time algorithm is given to determine whether one tree’s similarity to another is less than a given number.

Automatic Tree Crown Feature Extraction from UAS Multispectral Imagery for the Detection of Bark Beetle Disturbance in an Urban Forest

<p>Multispectral imaging using unmanned aerial systems (UAS) enables rapid and accurate detection of pest insect infestations, which are an increasing threat to midlatitude natural forests. Pest detection at the level of an individual tree is of particular importance in mixed forests, where it enables a sensible forest management approach. Moreover, urban forests may be affected more seriously because an urban environment produces additional stressors. The stressors include changes in forest soil properties, tree species diversity, higher temperatures, and carbon dioxide content. The stressed trees are then optimal material for a bark beetle feeding. Therefore, it is necessary to use an appropriate method for the detection of individual infested trees.</p><p>In this contribution, we present a novel method for individual tree crown delineation (ITCD) followed by feature extraction to detect a bark beetle disturbance in a mixed urban forest using a photogrammetric point cloud (PPC) and a multispectral orthomosaic. An excess green index (ExG) threshold mask was applied before the ITCD to separate targeted coniferous trees from deciduous trees and backgrounds. The individual crowns of conifer trees were automatically delineated as (i) a full tree crown using marker-controlled watershed segmentation (MCWS), Dalponte2016, and Li 2012 region growing algorithms or (ii) a buffer around a treetop from the masked PPC.</p><p>We statistically compared selected spectral and elevation features extracted from automatically delineated crowns of each method to reference tree crowns to distinguish between the forest disturbance classes and two tree species. Moreover, the effect of PPC density on the ITCD accuracy and feature extraction was investigated. The ExG threshold mask application resulted in the excellent separability of targeted conifer trees and the increasing shape similarity of automatically delineated crowns compared to reference tree crowns. The results revealed a strong effect of PPC density on treetop detection and ITCD. If the PPC density is sufficient (> 10 points/m<sup>2</sup>), the automatically delineated crowns produced by Dalponte2016, MCWS, and Li 2012 methods are comparable, and the extracted feature statistics insignificantly differ from reference tree crowns. The buffer method is less suitable for detecting a bark beetle disturbance in the mixed forest because of the simplicity of crown delineation. It caused significant differences in extracted feature statistics compared to reference tree crowns. Therefore, the point density was found to be more significant than the algorithm used.</p><p>We conclude that the automatic methods may constitute a reliable substitute for the time-consuming manual tree crown delineation in tree-based bark beetle disturbance detection and sanitation of individual infested trees using the suggested methodology and high-density (>20 points/m<sup>2</sup>, 10 points/m<sup>2</sup> minimum) PPC.</p>

Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum. Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.