Nothing Wrong with the Analysis of Clades in Comparative Evolutionary Studies: A Reply to Poe et al [0.03%]
比较进化研究中对分支的分析没有问题：对Poe等人观点的回应
Joanna Baker,Andrew Meade,Mark Pagel et al.
Joanna Baker et al.
In a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutiona...
Kristina Wicke,Arne Mooers,Mike Steel
Kristina Wicke
The extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalize this question and establish a precise mathematical condi...
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? [0.03%]
不同的序列比对和剪切方法对于系统发育基因组（UCE）分析有影响吗？
Daniel M Portik,John J Wiens
Daniel M Portik
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phyl...
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l [0.03%]
解析基因树差异的来源在系统基因组数据集中：测试Amaranthaceae广义下的古老杂交事件
Diego F Morales-Briones,Gudrun Kadereit,Delphine T Tefarikis et al.
Diego F Morales-Briones et al.
Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree est...
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy [0.03%]
肉食鱼和滤食鱼(Pirani和Pacus)(Serrasalmidae科):进化基因组学揭示了饮食趋同和平行性如何使传统形态分类复杂化
M A Kolmann,L C Hughes,L P Hernandez et al.
M A Kolmann et al.
The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every...
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction [0.03%]
UCEs的基因组特征和优化改善物种树的重建
Matthew H Van Dam,James B Henderson,Lauren Esposito et al.
Matthew H Van Dam et al.
Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly ...
Stilianos Louca
Stilianos Louca
The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example, for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion mod...
Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees [0.03%]
利用信息不和谐和贝叶斯因子调查形态复合体——以弹蜜蜂科为例
Diego S Porto,Eduardo A B Almeida,Matthew W Pennell
Diego S Porto
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morpho...
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit [0.03%]
古生物学中的贝叶斯带时标的系统发育分析：拓扑效应和地层拟合性
Benedict King
Benedict King
The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these...