Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model [0.03%]
期望最大化方法在分类速率模型下的系统发育定年中的应用
Uyen Mai,Eduardo Charvel,Siavash Mirarab
Uyen Mai
Dating phylogenetic trees to obtain branch lengths in time unit is essential for many downstream applications but has remained challenging. Dating requires inferring substitution rates that can change across the tree. While we can assume to...
The fundamental role of character coding in Bayesian morphological phylogenetics [0.03%]
贝叶斯形态系统发育中的字符编码的基本作用
Basanta Khakurel,Courtney Grigsby,Tyler D Tran et al.
Basanta Khakurel et al.
Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic trees are estimated using a model of evolution. For molecular data, modeling evolution is often based on biochemical observat...
Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia [0.03%]
整合基因组学和生物地理学以解开一个山区生物群的起源：阿拉伯地区爬行动物特有种类热点案例研究
Bernat Burriel-Carranza,Héctor Tejero-Cicuéndez,Albert Carné et al.
Bernat Burriel-Carranza et al.
Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns ...
The influence of the number of tree searches on maximum likelihood inference in phylogenomics [0.03%]
树木搜索次数对基因组系统发育中最大似然推断的影响
Chao Liu,Xiaofan Zhou,Yuanning Li et al.
Chao Liu et al.
Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyo...
Matthew J Penn,Neil Scheidwasser,Mark P Khurana et al.
Matthew J Penn et al.
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art meth...
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria [0.03%]
随机特征映射、贝叶斯模型选择以及生物合成途径揭示了蓝藻菌栖息偏好演化的新的见解
Giorgio Bianchini,Martin Hagemann,Patricia Sánchez-Baracaldo
Giorgio Bianchini
Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dyna...
Daniele Silvestro,Thibault Latrille,Nicolas Salamin
Daniele Silvestro
Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological pro...
Towards reliable detection of introgression in the presence of among-species rate variation [0.03%]
考虑物种之间变异率差异的基因渐渗检测方法研究
Thore Koppetsch,Milan Malinsky,Michael Matschiner
Thore Koppetsch
The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchang...
Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield [0.03%]
外显子捕获古DNA测序解码九带犰狳物种复合群并鉴定盖亚那盾区特有新物种
Mathilde Barthe,Loïs Rancilhac,Maria C Arteaga et al.
Mathilde Barthe et al.
The nine-banded armadillo (Dasypus novemcinctus) is the most widespread xenarthran species across the Americas. Recent studies have suggested it is composed of four morphologically and genetically distinct lineages of uncertain taxonomic st...
Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes [0.03%]
恰逢其时：中央安第斯地区 viburnum 南部界限新物种形成的证据
Carlos A Maya-Lastra,Patrick W Sweeney,Deren A R Eaton et al.
Carlos A Maya-Lastra et al.
A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailin...