StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent [0.03%]
星兽3：多重物种合并情形下的自适应并行贝叶斯推理
Jordan Douglas,Cinthy L Jiménez-Silva,Remco Bouckaert
Jordan Douglas
As genomic sequence data become increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rate...
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial [0.03%]
基于树晶格坐标系和图多项式的系统发育树分析方法研究
Pengyu Liu,Priscila Biller,Matthew Gould et al.
Pengyu Liu et al.
Phylogenetic trees are a central tool in many areas of life science and medicine. They demonstrate evolutionary patterns among species, genes, and patterns of ancestry among sets of individuals. The tree shapes and branch lengths of phyloge...
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies [0.03%]
全似然基因组分析阐明了物种分化和杂交的复杂历史：Heliconius蝴蝶erato-sara类群为例
Yuttapong Thawornwattana,Fernando A Seixas,Ziheng Yang et al.
Yuttapong Thawornwattana et al.
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key populat...
Théo Tricou,Eric Tannier,Damien M de Vienne
Théo Tricou
Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, intr...
The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation [0.03%]
基因树与物种树拓扑不一致对分化时间估算的影响
Tom Carruthers,Miao Sun,William J Baker et al.
Tom Carruthers et al.
Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies...
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models [0.03%]
nQMaker：估计不可逆氨基酸替代模型的时间
Cuong Cao Dang,Bui Quang Minh,Hanon McShea et al.
Cuong Cao Dang et al.
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for bi...
Corrigendum to: A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process retained in Recoded DNA? [0.03%]
文章修正案：谱系数据的聚集似然比检验：进化过程中DNA编码减少后的马尔可夫性是否保留？
Published Erratum
Systematic biology. 2022 Apr 19;71(3):774. DOI:10.1093/sysbio/syac004 2022
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi [0.03%]
进退维谷：马拉维湖丽鱼科裂唇鱼属的种系基因组学研究
Mark D Scherz,Paul Masonick,Axel Meyer et al.
Mark D Scherz et al.
Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete li...
Robert C Thomson,Jeremy M Brown
Robert C Thomson
The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches...
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex) [0.03%]
近ctic奶蛇（Lampropeltis triangulum复合体）的生态分化和基因流历史
Frank T Burbrink,Justin M Bernstein,Arianna Kuhn et al.
Frank T Burbrink et al.
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contempor...