Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent [0.03%]
多物种顺序合并的谱系基因组统计推断
Patrick F McKenzie,Deren A R Eaton
Patrick F McKenzie
Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. G...
Sean A S Anderson,Sachin Kaushik,Daniel R Matute
Sean A S Anderson
For many questions in ecology and evolution, the most relevant data to consider are attributes of lineage pairs. Comparative tests for causal relationships among traits like 'diet niche overlap', 'divergence time', and 'strength of reproduc...
Parameter Estimation from Phylogenetic Trees Using Neural Networks and Ensemble Learning [0.03%]
基于神经网络和集成学习的系统发生树参数估计方法研究
Tianjian Qin,Koen J van Benthem,Luis Valente et al.
Tianjian Qin et al.
Species diversification is characterized by speciation and extinction, the rates of which can, under some assumptions, be estimated from time-calibrated phylogenies. However, maximum likelihood estimation methods (MLE) for inferring rates a...
New perspectives in phylogenetic support assessment: using the new Relative Contradiction Index to investigate the phylogenetic controversies in Crocodylia [0.03%]
新的系统发育支持度评估视角——以Relative Contradiction Index探讨鼍总目分类争议
Paul Aubier,Valentin Rineau,Jorge Cubo et al.
Paul Aubier et al.
Numerous tools have been developed since the advent of phylogenetic methods to assess tree robustness. Identifying the degree of contradiction in a phylogenetic matrix, as well as the specific contribution of each taxon and character, is es...
Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae [0.03%]
物种丰富的被子植物豆科的系谱解析与分歧冲突研究
Rong Zhang,Gregory W Stull,Jian-Jun Jin et al.
Rong Zhang et al.
The Tree of Life is central to evolutionary biology, yet resolving deep, recalcitrant phylogenetic relationships remains challenging due to complex processes such as incomplete lineage sorting (ILS), hybridization, and polyploidization. Alt...
Liam U Taylor,Josef C Uyeda,Richard O Prum
Liam U Taylor
One puzzling feature of avian life histories is that individuals in many different lineages delay reproduction for several years after they finish growing. Intraspecific field studies suggest that various complex social environments-such as...
ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing [0.03%]
凸ML：在不可逆突变模型下进行快速且准确的分支长度估计，并通过CRISPR/Cas9系谱追踪的应用进行说明
Sebastian Prillo,Akshay Ravoor,Nir Yosef et al.
Sebastian Prillo et al.
Branch length estimation is a fundamental problem in Statistical Phylogenetics and a core component of tree reconstruction algorithms. Traditionally, general time-reversible mutation models are employed, and many software tools exist for th...
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating [0.03%]
但时钟Tick-Tock来了：实证案例研究强调了在总证据 dating中放松 clock模型的优越性
Nicolás Mongiardino Koch,Jeffrey R Thompson,Rich Mooi et al.
Nicolás Mongiardino Koch et al.
Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed-clock models, wh...
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments using AIC [0.03%]
利用AIC选择全基因组比对的系统基因组分析窗口大小
Jeremias Ivan,Paul Frandsen,Robert Lanfear
Jeremias Ivan
Gene tree discordance along a set of aligned genomes presents a challenge for phylogenomic methods to identify the non-recombining regions and reconstruct the phylogenetic tree for each region. To address this problem, many studies used the...
Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression and Demographic Analyses of Asian Shrew Moles [0.03%]
基于基因组、渐渗和人口遗传分析揭示的中国西南天岛地区亚洲隐 mole 物种分化
Yi-Xian Li,Zhong-Zheng Chen,Quan Li et al.
Yi-Xian Li et al.
The Mountains of Southwest China, a global biodiversity hotspot, have a unique "sky island" landscape with high diversity of both ancient and recent-formed species. While their distribution patterns offer significant insights into diversifi...