Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests [0.03%]
层叠：利用最大同拟林进行高效树和祖先重组图的重建算法研究
David A Rasmussen,Fangfang Guo
David A Rasmussen
In the presence of recombination individuals may inherit different regions of their genome from different ancestors, resulting in a mosaic of phylogenetic histories across their genome. Ancestral recombination graphs (ARGs) can capture how ...
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors [0.03%]
良好的先验条件下的贝叶斯系统发育推理无需碱基替代模型选择
Luiza Guimarães Fabreti,Sebastian Höhna
Luiza Guimarães Fabreti
Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough not to overfit. In phylogenetics, the most commo...
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives [0.03%]
泛基因组解析揭示了早期杨柳科物种杂交及分化不均导致的系统发育冲突
Brian J Sanderson,Diksha Gambhir,Guanqiao Feng et al.
Brian J Sanderson et al.
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the gene...
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies [0.03%]
dna序列与蛋白质序列具有相同的深部系谱构建能力
Paschalia Kapli,Ioanna Kotari,Maximilian J Telford et al.
Paschalia Kapli et al.
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA seque...
Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance [0.03%]
透过基因树分歧的迷雾解决硅藻的海洋-淡水转换事件
Wade R Roberts,Elizabeth C Ruck,Kala M Downey et al.
Wade R Roberts et al.
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales,...
A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data [0.03%]
一种基于k-mer的环境基因组数据中分类单元系统发育分类方法
Julia Van Etten,Timothy G Stephens,Debashish Bhattacharya
Julia Van Etten
In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic metho...
Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data [0.03%]
基于全基因组SNP数据的鱼类物种复合体(Leporinus bahiensis)扩散及其支系间分化研究：以交错式源头溪流捕获介导的海岸盆地物种形成机制为例
Jorge L Ramirez,Carolina B Machado,Paulo Roberto Antunes de Mello Affonso et al.
Jorge L Ramirez et al.
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Acco...
Yubo Zhang,Qingjie Zhu,Yi Shao et al.
Yubo Zhang et al.
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolut...
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow [0.03%]
_phylocosimsim：一个网络多物种谱系分裂模型模拟器，包括基因流继承的新扩展_
John Fogg,Elizabeth S Allman,Cécile Ané
John Fogg
We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This ...