Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data [0.03%]
目标取样与目标捕获：利用全基因组数据评估谱系地理学一致性
Lisa N Barrow,Alan R Lemmon,Emily Moriarty Lemmon
Lisa N Barrow
Comparative phylogeography provides the necessary framework to examine the factors influencing population divergence, persistence, and change over time. Avise (2000) outlined four aspects of concordance that result when data exhibit signifi...
Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets [0.03%]
统计多序列比对在蛋白质数据集上的评估及其与其他比对方法的比较
Michael Nute,Ehsan Saleh,Tandy Warnow
Michael Nute
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical coestimation ...
Daisy A Shepherd,Steffen Klaere
Daisy A Shepherd
The test for model-to-data fitness is a fundamental principle within the statistical sciences. The purpose of such a test is to assess whether the selected best-fitting model adequately describes the behavior in the data. Despite their broa...
D S Caetano,L J Harmon
D S Caetano
Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration ...
Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty [0.03%]
整合序列比对不确定性的蛋白质系统发生分析的广义自举支持法
Maria Chatzou,Evan W Floden,Paolo Di Tommaso et al.
Maria Chatzou et al.
Phylogenetic reconstructions are essential in genomics data analyses and depend on accurate multiple sequence alignment (MSA) models. We show that all currently available large-scale progressive multiple alignment methods are numerically un...
Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data [0.03%]
基于系统发育树和性状数据检测分化对多个性状的依赖性
Leonel Herrera-Alsina,Paul van Els,Rampal S Etienne
Leonel Herrera-Alsina
Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The state-dependent speciation and extinction (SSE) framework contains methods to detect the dependence of diversifica...
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods [0.03%]
物种树估计中的长枝吸引问题：分区似然和拓扑总结方法的不一致性
Sebastien Roch,Michael Nute,Tandy Warnow
Sebastien Roch
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when differ...
Mitochondrial Genome Fragmentation Unites the Parasitic Lice of Eutherian Mammals [0.03%]
线粒体基因组分割联合有胎盘哺乳动物的寄生虱子
Fan Song,Hu Li,Guo-Hua Liu et al.
Fan Song et al.
Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the...
R$^{2}$s for Correlated Data: Phylogenetic Models, LMMs, and GLMMs [0.03%]
相关数据的R²：系统发育模型、线性混合模型和广义线性混合模型
Anthony R Ives
Anthony R Ives
Many researchers want to report an $R^{2}$ to measure the variance explained by a model. When the model includes correlation among data, such as phylogenetic models and mixed models, defining an $R^{2}$ faces two conceptual problems. (i) It...
Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis [0.03%]
基于贝叶斯形态钟分析的树懒的系统发育、宏进化趋势和历史生物地理学研究
Luciano Varela,P Sebastián Tambusso,H Gregory McDonald et al.
Luciano Varela et al.
Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America durin...