Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies [0.03%]
coalescent和concatenation方法以及Amborella与睡莲姐妹群关系的置信度
Zhenxiang Xi,Liang Liu,Joshua S Rest et al.
Zhenxiang Xi et al.
The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first l...
Diego Mallo,Leonardo De Oliveira Martins,David Posada
Diego Mallo
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data [0.03%]
一种新颖的贝叶斯方法，从系统发生比较数据中推断和解释适应性景观的动力学特征
Josef C Uyeda,Luke J Harmon
Josef C Uyeda
Our understanding of macroevolutionary patterns of adaptive evolution has greatly increased with the advent of large-scale phylogenetic comparative methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an adaptive process of dive...
Pablo A Goloboff,Mark P Simmons
Pablo A Goloboff
When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consis...
Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias [0.03%]
早期陆生植物线粒体系统基因组学：缓解饱和、组成异质性和密码子使用偏好效应
Yang Liu,Cymon J Cox,Wei Wang et al.
Yang Liu et al.
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to t...
Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity [0.03%]
婆罗洲和印度支那岛是东南亚生物多样性的主要进化热点地区
Mark de Bruyn,Björn Stelbrink,Robert J Morley et al.
Mark de Bruyn et al.
Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-anal...
Meta-Analysis
Systematic biology. 2014 Nov;63(6):879-901. DOI:10.1093/sysbio/syu047 2014
Gergely J Szöllősi,Eric Tannier,Vincent Daubin et al.
Gergely J Szöllősi et al.
This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequenc...
Maximum likelihood inference of small trees in the presence of long branches [0.03%]
长枝存在下的小树的最大似然推断
Sarah L Parks,Nick Goldman
Sarah L Parks
The statistical basis of maximum likelihood (ML), its robustness, and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical ...
Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences [0.03%]
下一代测序中排除缺失数据的意外后果：RAD序列模拟研究
Huateng Huang,L Lacey Knowles
Huateng Huang
There is a lack of consensus on how next-generation sequence (NGS) data should be considered for phylogenetic and phylogeographic estimates, with some studies excluding loci with missing data, whereas others include them, even when sequence...
Leonardo de Oliveira Martins,David Posada
Leonardo de Oliveira Martins