A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution [0.03%]
高维谱系比较方法的惩罚似然框架及在新世界猴脑进化中的应用
Julien Clavel,Leandro Aristide,Hélène Morlon
Julien Clavel
Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and be...
Analyzing Contentious Relationships and Outlier Genes in Phylogenomics [0.03%]
从基因组系统发育分析争论不休的关系和离群基因
Joseph F Walker,Joseph W Brown,Stephen A Smith
Joseph F Walker
Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Herein, we examined two data set...
The Increasing Disconnection of Primary Biodiversity Data from Specimens: How Does It Happen and How to Handle It? [0.03%]
生物多样性数据与其载体标本相脱离的现象日益严重，原因是什么，如何应对？
Julien Troudet,Régine Vignes-Lebbe,Philippe Grandcolas et al.
Julien Troudet et al.
Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based (OB) occurrences is overthrowing t...
James H Degnan
James H Degnan
Simultaneously modeling hybridization and the multispecies coalescent is becoming increasingly common, and inference of species networks in this context is now implemented in several software packages. This article addresses some of the con...
Divergence Estimation in the Presence of Incomplete Lineage Sorting and Migration [0.03%]
存在不完全谱系排序和基因流时的分歧时间估计问题研究
Graham R Jones
Graham R Jones
This article focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. I develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary proce...
Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa [0.03%]
分辨三 taxa 的收敛演化和分子钟失效事件
Jonathan D Mitchell,Jeremy G Sumner,Barbara R Holland
Jonathan D Mitchell
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become ...
Jonathan S Mitchell,Rampal S Etienne,Daniel L Rabosky
Jonathan S Mitchell
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can b...
Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements [0.03%]
相位分型极大地提高了超保守元件的系统基因组学效用
Tobias Andermann,Alexandre M Fernandes,Urban Olsson et al.
Tobias Andermann et al.
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts ...
Haim Ashkenazy,Itamar Sela,Eli Levy Karin et al.
Haim Ashkenazy et al.
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were...
Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation [0.03%]
正向选择对基于谱系树的物种树估计和物种界定的影响评估
Richard H Adams,Drew R Schield,Daren C Card et al.
Richard H Adams et al.
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct compu...