Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays [0.03%]
结合物种界定、物种树和基因流测试阐明了地鸦属复杂的 speciation过程
Devon A DeRaad,John E McCormack,Nancy Chen et al.
Devon A DeRaad et al.
Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to t...
Yueyu Jiang,Metin Balaban,Qiyun Zhu et al.
Yueyu Jiang et al.
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the ref...
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem [0.03%]
标签罗宾逊-福尔DS距离问题的线性时间解决方案
Samuel Briand,Christophe Dessimoz,Nadia El-Mabrouk et al.
Samuel Briand et al.
A large variety of pairwise measures of similarity or dissimilarity have been developed for comparing phylogenetic trees, for example, species trees or gene trees. Due to its intuitive definition in terms of tree clades and bipartitions and...
Jeanne Lemant,Cécile Le Sueur,Veselin Manojlović et al.
Jeanne Lemant et al.
Balance indices that quantify the symmetry of branching events and the compactness of trees are widely used to compare evolutionary processes or tree-generating algorithms. Yet, existing indices are not defined for all rooted trees, are unr...
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index [0.03%]
灭绝面前的进化谱系多样性排名：公平比例指数的稳健性分析
Mareike Fischer,Andrew Francis,Kristina Wicke
Mareike Fischer
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness," (ED) that is, their...
Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models [0.03%]
顽固的离群值、镶嵌体以及位点特异性(CAT)混合模型对缺失数据的敏感性导致真核生物根部系统发生争议
Caesar Al Jewari,Sandra L Baldauf
Caesar Al Jewari
Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees. However, recent phylogenomic attempts...
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins [0.03%]
无脊椎动物基因组学：基于马氏毛尾螋科昆虫的磷酸化蛋白质组学研究
Carlos E Santibáñez-López,Shlomi Aharon,Jesús A Ballesteros et al.
Carlos E Santibáñez-López et al.
Scorpions constitute a charismatic lineage of arthropods and comprise more than 2500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil reco...
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support [0.03%]
用似然比比较理解系统发生支持的全基因组变化
Genevieve G Mount,Jeremy M Brown
Genevieve G Mount
Genomic data have only sometimes brought resolution to the tree of life. Large phylogenomic studies can reach conflicting conclusions about important relationships, with mutually exclusive hypotheses receiving strong support. Reconciling su...
Liliya Doronina,Charles Y Feigin,Jürgen Schmitz
Liliya Doronina
Although first posited to be of a single origin, the two superfamilies of phalangeriform marsupial possums (Phalangeroidea: brushtail possums and cuscuses and Petauroidea: possums and gliders) have long been considered, based on multiple se...
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time [0.03%]
基于全长转录组的弹尾纲长体型总科系统发育基因组学研究：久远时期从地上到地下的多次独立演化事件
Daoyuan Yu,Yinhuan Ding,Erik Tihelka et al.
Daoyuan Yu et al.
Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of paleontological data. To overcome this limitation, we conducted a genome-base...