Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

In the simplest phylodynamic model (the pure-birth Yule process), lineages split independently at a constant rate λ for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to 1/(2λ) as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate μ (where μ<λ), we also establish a similar result for birth--death trees, except that t/2 is replaced by t/2 x (1-μ/λ). This 'complete' tree may contain subtrees that have died out before time t; for the 'reduced tree' that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to questions concerning the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

GRMT: Generative Reconstruction of Mutation Tree From Scratch Using Single-Cell Sequencing Data

Single-cell sequencing (SCS) now promises the landscape of genetic diversity at single cell level, and is particularly useful to reconstruct the evolutionary history of tumor. There are multiple types of noise that make the SCS data notoriously error-prone, and significantly complicate tumor tree reconstruction. Existing methods for tumor phylogeny estimation suffer from either high computational intensity or low-resolution indication of clonal architecture, giving a necessity of developing new methods for efficient and accurate reconstruction of tumor trees. We introduce GRMT (Generative Reconstruction of Mutation Tree from scratch), a method for inferring tumor mutation tree from SCS data. GRMT exploits the k-Dollo parsimony model to allow each mutation to be gained once and lost at most k times. Under this constraint on mutation evolution, GRMT searches for mutation tree structures from a perspective of tree generation from scratch, and implements it to an iterative process that gradually increases the tree size by introducing a new mutation per time until a complete tree structure that contains all mutations is obtained. This enables GRMT to efficiently recover the chronological order of mutations and scale well to large datasets. Extensive evaluations on simulated and real datasets suggest GRMT outperforms the state-of-the-arts in multiple performance metrics. The GRMT software is freely available at https://github.com/qasimyu/grmt.

Dynamic visualisation of million-tip trees: the OneZoom project

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on a relatively old mobile device.The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in and supporting multiple applications including exhibition kiosks and digital art.After eight years of work, our tree of life explorer is now broadly complete, it has attracted over 1.3 million users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.

Derivation of 3D deformation fields for the 2019 Ridgecrest Earthquakes (USA) based on Sentinel-1 TOPS data

&lt;p&gt;The&lt;!-- Start of main text paraghraphs. --&gt; advances of Sentinel-1 SAR data, like its open access policy and short revisit time, gives an outstanding opportunity to conduct in-situ mapping of large scale deformations. After the requisite calibrations and corrections (radiometric, terrain), geocoding, coregistration and phase unwrapping; the unwrapped phase can be converted to Line-of-site (LOS) displacements. Although it gives a characteristic picture of the investigated phenomena only in one-dimension, but to obtain tree-dimensional (East/North/Up &amp;#8211; ENU) deformation, it requires a more complex approach.&lt;/p&gt;&lt;p&gt;To obtain the complete tree-dimensional displacement field, both ascending and descending LOS displacements shall be retrieved. As well as, the corresponding unit-vector of LOS look-vectors and its parallel, along-track azimuth vector in the direction of the azimuth offsets, from the SAR sensor to all measurements (pixel) in ENU format. This lead to four observations with different incident angles for each measurements, which can be generalized as an over-determined inverse problem. The estimated model vector of the complete tree-dimensional displacement can be obtained, if the Jacobi-matrix can be represented as the look-vectors in ENU basis and the observation vector as LOS deformations acquired from the unwrapped phase of the interferogram. Then the over-determined linear equation system can be solved in the L2 norm via the Gaussian Least Squares (LSQ) approach combined with Singular Value Decomposition (SVD).&lt;!-- OPTIONAL: if reference field exists. --&gt;&lt;/p&gt;&lt;p&gt;Demonstrating the aforementioned, we present the continuation of DInSAR results of the two strike-slip earthquakes between 2019.07.04-06. with foreshock M&lt;sub&gt;W&lt;/sub&gt; =6.5 and mainshock M&lt;sub&gt; W&lt;/sub&gt; =7.1 in the Eastern Californian Shear Zone near Ridgecrest (US).&lt;/p&gt;

The role of ecosystem services in climate and air quality in urban areas: Evaluating carbon sequestration and air pollution removal by street and park trees in Szeged (Hungary)

The evaluation of ecosystem services can provide essential help in incorporatating the multifunctionality of urban ecosystems in planning and management processes. Two important regulating services of urban trees, carbon sequestration and air pollution removal, are evaluated in this article for different types of tree stands (streets, parks) in the city centre of Szeged (Hungary). The necessary calculations were carried out by an adaptation of the targeted model (i-Tree Eco), based on a large complete tree inventory dataset. The analyses revealed the main tendencies in differences between tree species considering the tree condition, which affects the service-providing capacity to a high degree. The effects of differences in tree management on the chosen ecosystem services were investigated by comparing two pairs of tree alleys. Based on our observations, clear cuts and complete tree alley changes are not advisable from an ecosystem service point of view.

Comparative Dendrochronological and14C Dating of 15th Century Russian Icon

A 15th century Russian icon from the Novgorod region was analyzed using both dendrochronological and radiocarbon methods [liquid scintillation counting (LSC) and accelerator mass spectrometry (AMS)]. This orthodox icon represents the Mother of God (Dexiokratusa). Fine art experts attribute the icon to between the late 14th to the early 15th centuries. The last complete tree ring was dated to AD 1409. There are indications that the trees were cut down during the summer of AD 1410. Taking into account the time for seasoning (about 8 months), the icon would have been painted in AD 1411. Wiggle-matching of the six AMS samples failed. Two of six AMS dates correspond to dendrochronological dates, while four of the six AMS dates showed differences with the dendrochronological dates by 5–39 yr. This discrepancy raises the issue of a possible regional offset from the calibration curve for the 13th century AD in NW Russia.