Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships [0.03%]
对鳞足目（蜥蜴、蛇和锄足蜥）的基因组规模数据的分析不支持传统形态学关系中的关键分支结构
Frank T Burbrink,Felipe G Grazziotin,R Alexander Pyron et al.
Frank T Burbrink et al.
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the nu...
APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments [0.03%]
APPLES：有无匹配情况下的可扩展距离基础系统发育放置法
Metin Balaban,Shahab Sarmashghi,Siavash Mirarab
Metin Balaban
Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming,...
Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum [0.03%]
谱系性状数据的特征及归一化拉普拉斯光谱下的比较
Eric Lewitus,Leandro Aristide,Hélène Morlon
Eric Lewitus
The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary ...
19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology [0.03%]
计算系统发育树拓扑结构边际似然的19种可疑方法
Mathieu Fourment,Andrew F Magee,Chris Whidden et al.
Mathieu Fourment et al.
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for the posterior density, obtained by integrating the product o...
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies [0.03%]
系统探索高可能性的系统发育树拓扑结构集
Chris Whidden,Brian C Claywell,Thayer Fisher et al.
Chris Whidden et al.
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In ...
Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification [0.03%]
宏进化分析表明环境因素而非毒液装置在Terebridae海螺多样化中发挥关键作用
Maria Vittoria Modica,Juliette Gorson,Alexander E Fedosov et al.
Maria Vittoria Modica et al.
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspectiv...
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence [0.03%]
基于四倍体的计算节点 certainty 提供了稳健的系统发育不一致度量标准
Xiaofan Zhou,Sarah Lutteropp,Lucas Czech et al.
Xiaofan Zhou et al.
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of...
Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning [0.03%]
利用深度学习从多序列比对中精确推断树结构
Anton Suvorov,Joshua Hochuli,Daniel R Schrider
Anton Suvorov
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulati...
Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data [0.03%]
系统发育树和网络可以作为强大的互补方法来分析基因组数据
Christopher Blair,Cécile Ané
Christopher Blair
Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly ...