Rapid Radiation and Rampant Reticulation: Phylogenomics of South American Liolaemus Lizards [0.03%]
南美丽树蜥的谱系基因组学：快速辐射与广泛网状进化
Damien Esquerré,J Scott Keogh,Diego Demangel et al.
Damien Esquerré et al.
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn ...
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference [0.03%]
基因树中系谱间的进化率变化对物种树推断有负面影响
Mezzalina Vankan,Simon Y W Ho,David A Duchêne
Mezzalina Vankan
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals th...
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation [0.03%]
基于系统基因组的物种划分大幅减少了 Antarctician adaptive辐射中的物种多样性
Elyse Parker,Alex Dornburg,Carl D Struthers et al.
Elyse Parker et al.
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously undescribed cryptic di...
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs [0.03%]
处理不完整谱系分排的物种树推断方法对旁系同源物的存在具有鲁棒性
Zhi Yan,Megan L Smith,Peng Du et al.
Zhi Yan et al.
Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the d...
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets [0.03%]
基于一致性分析的谱系基因组数据集的关系和分子速率推断方法
Joseph F Walker,Stephen A Smith,Richard G J Hodel et al.
Joseph F Walker et al.
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species tree...
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales [0.03%]
整合分子和形态的跨时间尺度的新颖模型
Huw A Ogilvie,Fábio K Mendes,Timothy G Vaughan et al.
Huw A Ogilvie et al.
Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization pheno...
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation [0.03%]
利用数据扩充进行快速而准确的物种特异性分化率估计
Odile Maliet,Hélène Morlon
Odile Maliet
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversificatio...
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics [0.03%]
线粒体和叶绿体基因组拼接基因的界定：理论与实践在系统基因组学中的结合
Jeff J Doyle
Jeff J Doyle
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), that is, that there is free recombination between the ...
Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete [0.03%]
辐射中评估物种界定方法：克里特岛陆蜗牛Albinaria cretensis复群中的物种界定方法评估
Sonja Bamberger,Jie Xu,Bernhard Hausdorf
Sonja Bamberger
Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgressi...
Unifying Phylogenetic Birth-Death Models in Epidemiology and Macroevolution [0.03%]
传染病学和宏进化中的谱系发生模型的统一
Ailene MacPherson,Stilianos Louca,Angela McLaughlin et al.
Ailene MacPherson et al.
Birth-death stochastic processes are the foundations of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have b...