Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (papaveraceae) [0.03%]
基于同源染色体的父母本基因组分配在种树推断中的应用——以紫堇属（罂粟科）为例
Yann J K Bertrand,Anne-Cathrine Scheen,Thomas Marcussen et al.
Yann J K Bertrand et al.
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of...
Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC [0.03%]
利用单一分子标记界定物种稀缺数据集：条形码差距、单倍体型网络和GMYC分析研究
Simon Dellicour,Jean-François Flot
Simon Dellicour
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that...
Daniel L Rabosky,Emma E Goldberg
Daniel L Rabosky
Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationship...
Deflating trees: improving Bayesian branch-length estimates using informed priors [0.03%]
改进分支长度的贝叶斯估计方法：使用知情先验减少系统树的偏差
Bradley J Nelson,John J Andersen,Jeremy M Brown
Bradley J Nelson
Prior distributions can have a strong effect on the results of Bayesian analyses. However, no general consensus exists for how priors should be set in all circumstances. Branch-length priors are of particular interest for phylogenetics, bec...
Paul O Lewis,Mark T Holder,David L Swofford
Paul O Lewis
Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of margin...
Age-dependent speciation can explain the shape of empirical phylogenies [0.03%]
年龄依赖性物种形成的实证系统发育树形状可以解释原因
Oskar Hagen,Klaas Hartmann,Mike Steel et al.
Oskar Hagen et al.
Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolu...
Ruchi Chaudhary,Bastien Boussau,J Gordon Burleigh et al.
Ruchi Chaudhary et al.
With the availability of genomic sequence data, there is increasing interest in using genes with a possible history of duplication and loss for species tree inference. Here we assess the performance of both nonprobabilistic and probabilisti...
Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites [0.03%]
丰度高的系统发育基因组分析揭示了生命真核生物的进化树并显示出位点抽样的力量
Laura A Katz,Jessica R Grant
Laura A Katz
Most eukaryotic lineages are microbial, and many have only recently been sampled for phylogenetic studies or remain in the "dark area" of the tree of life where there are no molecular data. To assess relationships among eukaryotic lineages,...
C Baudet,B Donati,B Sinaimeri et al.
C Baudet et al.
Despite an increasingly vast literature on cophylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Most algorithm...
Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters [0.03%]
分支系统学中形态离散性状的类间状态分布变迁模式
Luke B Harrison,Hans C E Larsson
Luke B Harrison
Likelihood-based methods are commonplace in phylogenetic systematics. Although much effort has been directed toward likelihood-based models for molecular data, comparatively less work has addressed models for discrete morphological characte...