Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

Methods for inferring species trees from sets of gene trees need to account for the possibility of discordance among the gene trees. Assuming that discordance is caused by incomplete lineage sorting, species tree estimates can be obtained by finding those species trees that minimize the number of -deep- coalescence events required for a given collection of gene trees. Efficient algorithms now exist for applying the minimizing-deep-coalescence (MDC) criterion, and simulation experiments have demonstrated its promising performance. However, it has also been noted from simulation results that the MDC criterion is not always guaranteed to infer the correct species tree estimate. In this article, we investigate the consistency of the MDC criterion. Using the multipscies coalescent model, we show that there are indeed anomaly zones for the MDC criterion for asymmetric four-taxon species tree topologies, and for all species tree topologies with five or more taxa.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90434/1/cmb-2E2010-2E0102.pd

Inference of parsimonious species phylogenies from multi-locus data

The main focus of this dissertation is the inference of species phylogenies, i.e. evolutionary histories of species. Species phylogenies allow us to gain insights into the mechanisms of evolution and to hypothesize past evolutionary events. They also find applications in medicine, for example, the understanding of antibiotic resistance in bacteria. The reconstruction of species phylogenies is, therefore, of both biological and practical importance. In the traditional method for inferring species trees from genetic data, we sequence a single locus in species genomes, reconstruct a gene tree, and report it as the species tree. Biologists have long acknowledged that a gene tree can be different from a species tree, thus implying that this traditional method might infer the wrong species tree. Moreover, reticulate events such as horizontal gene transfer and hybridization make the evolution of species no longer tree-like. The availability of multi-locus data provides us with excellent opportunities to resolve those long standing problems. In this dissertation, we present parsimony-based algorithms for reconciling species/gene tree incongruence that is assumed to be due solely to lineage sorting. We also describe a unified framework for detecting hybridization despite lineage sorting. To address the first problem of species/gene tree incongruence caused by lineage sorting, we present three algorithms. In Chapter 3, we present an algorithm based on an integer-linear programming (ILP) formula to infer the species tree's topology and divergence times from multiple gene trees. In Chapter 4, we describe two methods that infer the species tree by minimizing deep coalescences (MDC), a criterion introduced by Maddison in 1997. The first method is also based on an ILP formula, but it eliminates the enumeration phase of candidate species trees of the algorithm in Chapter 3. The second algorithm further eliminates the dependence on external ILP solvers by employing dynamic programming. We ran those methods on both biological and simulated data, and experimental results demonstrate their high accuracy and speed in species tree inference, which makes them suitable for analyzing multi-locus data. The second problem this dissertation deals with is reticulation (e.g., horizontal gene transfer, hybridization) detection despite lineage sorting. The phylogeny-based approach compares the evolutionary histories of different genomic regions and test them for incongruence that would indicate hybridization. However, since species tree and gene tree incongruence can also be due to lineage sorting, phylogeny-based hybridization methods might overestimate the amount of hybridization. We present in this dissertation a framework that can handle both hybridization and lineage sorting simultaneously. In this framework, we extend the MDC criterion to phylogenetic networks, and use it to propose a heuristic to detect hybridization despite lineage sorting. Empirical results on a simulated and a yeast data set show its promising performance, as well as several directions for future research

Encouraging the Startup Spirit of Students: Implications and Solutions

Starting a business by the establishment of a new business or a new business project plays an important role in the economic development of each country. Promoting the entrepreneurial spirit of students at universities is the basis for contributing to the success of start-up countries. This study provides empirical evidence of factors affecting student entrepreneurship based on survey data of a sample of 321 students. The study results clarify the factors affecting the initial entrepreneurial intention of students, and are an important foundation for starting-up in the future. Since then, the findings from regression analysis are the basis to imply some solutions from the school and the Government to promote the entrepreneurial spirit of young people. Keywords: Entrepreneurship intention; Social-education environment; Taking risk; Student DOI: 10.7176/RJFA/11-4-07 Publication date: February 29th 202

Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions

Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of the number of HGT events, and that HGT detection methods should be designed with unresolved gene trees in mind. Second, we demonstrate, both theoretically and empirically, that based on topological comparison alone, the number of HGT scenarios that reconcile a pair of species/gene trees may be exponential. This number may be reduced when branch lengths in both trees are estimated correctly. This set of results implies that in the absence of additional biological information, and/or a biological model of how HGT occurs, multiple HGT scenarios must be sought, and efficient strategies for how to enumerate such solutions must be developed. Third, we address the issue of lineage sorting, how it confounds HGT detection, and how to incorporate it with HGT into a single stochastic framework that distinguishes between the two events by extending population genetics theories. This result is very important, particularly when analyzing closely related organisms, where coalescent effects may not be ignored when reconciling gene trees. In addition to these three confounding factors, we consider the problem of enumerating all valid coalescent scenarios that constitute plausible species/gene tree reconciliations, and develop a polynomial-time dynamic programming algorithm for solving it. This result bears great significance on reducing the search space for heuristics that seek reconciliation scenarios. Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios

Leveraging the Learnable Vertex-Vertex Relationship to Generalize Human Pose and Mesh Reconstruction for In-the-Wild Scenes

We present MeshLeTemp, a powerful method for 3D human pose and mesh reconstruction from a single image. In terms of human body priors encoding, we propose using a learnable template human mesh instead of a constant template as utilized by previous state-of-the-art methods. The proposed learnable template reflects not only vertex-vertex interactions but also the human pose and body shape, being able to adapt to diverse images. We conduct extensive experiments to show the generalizability of our method on unseen scenarios

Resolving the Steiner Point Removal Problem in Planar Graphs via Shortcut Partitions

Recently the authors [CCLMST23] introduced the notion of shortcut partition of planar graphs and obtained several results from the partition, including a tree cover with $O(1)$ trees for planar metrics and an additive embedding into small treewidth graphs. In this note, we apply the same partition to resolve the Steiner point removal (SPR) problem in planar graphs: Given any set $K$ of terminals in an arbitrary edge-weighted planar graph $G$, we construct a minor $M$ of $G$ whose vertex set is $K$, which preserves the shortest-path distances between all pairs of terminals in $G$ up to a constant factor. This resolves in the affirmative an open problem that has been asked repeatedly in literature.Comment: Manuscript not intended for publication. The results have been subsumed by arXiv:2308.00555 from the same author

Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

In vitro bioactivities of Codonopsis javanica root extract from Kon Tum province, Vietnam

Dangshen Codonopsis javanica exhibits invaluable medicinal properties in herbal remedies; however, there has currently not been much specific analysis of the phytochemicals and bioactivities of this plant. The root ethanol extract of C. javanica contains substances such as saponins, phenolic acids, terpenoids, and alkaloids. It displays an antibacterial effect against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus cereus with the IC50 values of 150, 100, 150, and 90 μg/mL, respectively. The antioxidant capacity of the root extract was also observed with an IC50 value of 46.8 ± 6.8 μg/mL. Furthermore, the extract exhibits activity on human cancer cell lines HepG2 (IC50 = 83.6 ± 2.7 μg/mL) and MCF-7 (IC50 = 95.3 ± 2.3 μg/mL). Hence, this study provides the basic data for further research on the bioactivities of natural compounds of Dangshen C. javanica for the first time