Heyang Li

Bio: Heyang Li is an academic researcher from University of Canterbury. The author has contributed to research in topics: Tomography & Tomographic reconstruction. The author has an hindex of 6, co-authored 16 publications receiving 144 citations. Previous affiliations of Heyang Li include Monash University, Clayton campus & Monash University.

Branch Lengths on Birth–Death Trees and the Expected Loss of Phylogenetic Diversity

Abstract: Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where pendant branches leading to tips can be very short compared with branches deeper in the tree. Here, we analyze alternative and more realistic Yule and birth-death models. We show how censoring at the present both makes average branches one half what we might expect and makes pendant and interior branches roughly equal in length. Although dependent on whether we condition on the size of the tree, its age, or both, these results hold both for the Yule model and for birth-death models with moderate extinction. Importantly, the rough equivalency in interior and exterior branch lengths means that the loss of evolutionary history with loss of species can be roughly linear. Under these models, the Tree of Life may offer limited redundancy in the face of ongoing species loss.

Space-Filling X-Ray Source Trajectories for Efficient Scanning in Large-Angle Cone-Beam Computed Tomography

Abstract: We present a new family of X-ray source scanning trajectories for large-angle cone-beam computed tomography. Traditional scanning trajectories are described by continuous paths through space, e.g., circles, saddles, or helices, with a large degree of redundant information in adjacent projection images. Here, we consider discrete trajectories as a set of points that uniformly sample the entire space of possible source positions, i.e., a space-filling trajectory (SFT). We numerically demonstrate the advantageous properties of the SFT when compared with circular and helical trajectories as follows: first, the most isotropic sampling of the data, second, optimal level of mutually independent data, and third, an improved condition number of the tomographic inverse problem. The practical implications of these properties in tomography are also illustrated by simulation. We show that the SFT provides greater data acquisition efficiency, and reduced reconstruction artifacts when compared with helical trajectory. It also possesses an effective preconditioner for fast iterative tomographic reconstruction.

Optimized x-ray source scanning trajectories for iterative reconstruction in high cone-angle tomography

Abstract: With the GPU computing becoming main-stream, iterative tomographic reconstruction (IR) is becoming a com- putationally viable alternative to traditional single-shot analytical methods such as filtered back-projection. IR liberates one from the continuous X-ray source trajectories required for analytical reconstruction. We present a family of novel X-ray source trajectories for large-angle CBCT. These discrete (sparsely sampled) trajectories optimally fill the space of possible source locations by maximising the degree of mutually independent information. They satisfy a discrete equivalent of Tuy’s sufficiency condition and allow high cone-angle (high-flux) tomog- raphy. The highly isotropic nature of the trajectory has several advantages: (1) The average source distance is approximately constant throughout the reconstruction volume, thus avoiding the differential-magnification artefacts that plague high cone-angle helical computed tomography; (2) Reduced streaking artifacts due to e.g. X-ray beam-hardening; (3) Misalignment and component motion manifests as blur in the tomogram rather than double-edges, which is easier to automatically correct; (4) An approximately shift-invariant point-spread-function which enables filtering as a pre-conditioner to speed IR convergence. We describe these space-filling trajectories and demonstrate their above-mentioned properties compared with a traditional helical trajectories.

3D X-Ray Source Deblurring in High Cone-Angle Micro-CT

Abstract: High geometric magnification X-ray micro-computed tomography ( $\mu {\rm CT} $ ) is used to study many high-resolution features in insects, cellular, bones, composite and mineral materials. The resolution of lab-based $\mu {\rm CT}$ in a fine-focus geometry is limited by blurring that occurs below the spatial coherence length of the illuminating radiation: resolution can be no smaller than the size of the X-ray source spot. In cases where the source spot size cannot be reduced (e.g. due to signal-to-noise, time or cost considerations) there is a need to model and correct for this blurring. In ANU CT-lab, we use a high cone angle and high geometric magnification with transmission x-ray source spot size up to three voxels, this creates blurring in the projection. This work takes a simulation approach mimicking such source spot size, and compares systems with horizontal cone-angles (often referred to as the fan angle) of 0.06, 14.36 and 60 degrees. We aim to eliminate this blurring in the reconstruction process. Furthermore, in a high cone-angle geometry, using a reconstruction method that only deconvolves each projection image leads to non-uniform resolution in the reconstruction volume. Alternatively, iterative methods that fully model the non-point source and avoid such artefacts are computationally expensive. We propose a hybrid method that corrects the effect of the non-point source by better modelling the physics rather than just deconvolving each projection image, therefore obtains results closer to the iterative full modelling method, and while being computationally much cheaper.

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras

Abstract: In an era of accelerated biodiversity loss and limited conservation resources, systematic prioritization of species and places is essential. In terrestrial vertebrates, evolutionary distinctness has been used to identify species and locations that embody the greatest share of evolutionary history. We estimate evolutionary distinctness for a large marine vertebrate radiation on a dated taxon-complete tree for all 1,192 chondrichthyan fishes (sharks, rays and chimaeras) by augmenting a new 610-species molecular phylogeny using taxonomic constraints. Chondrichthyans are by far the most evolutionarily distinct of all major radiations of jawed vertebrates—the average species embodies 26 million years of unique evolutionary history. With this metric, we identify 21 countries with the highest richness, endemism and evolutionary distinctness of threatened species as targets for conservation prioritization. On average, threatened chondrichthyans are more evolutionarily distinct—further motivating improved conservation, fisheries management and trade regulation to avoid significant pruning of the chondrichthyan tree of life. Evolutionary distinctness is used as a metric to determine conservation priorities across all Chondrichthyes, identifying 21 countries with the highest richness, endemism and evolutionary distinctness of threatened species as targets.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

Abstract: We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.

Mammal diversity will take millions of years to recover from the current biodiversity crisis.

Abstract: The incipient sixth mass extinction that started in the Late Pleistocene has already erased over 300 mammal species and, with them, more than 2.5 billion y of unique evolutionary history. At the global scale, this lost phylogenetic diversity (PD) can only be restored with time as lineages evolve and create new evolutionary history. Given the increasing rate of extinctions however, can mammals evolve fast enough to recover their lost PD on a human time scale? We use a birth–death tree framework to show that even if extinction rates slow to preanthropogenic background levels, recovery of lost PD will likely take millions of years. These findings emphasize the severity of the potential sixth mass extinction and the need to avoid the loss of unique evolutionary history now.