The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa [0.03%]
化石分类群间层位一致性对性状整合的含义
Peter J Wagner,George F Estabrook
Peter J Wagner
Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character chang...
Ikram Ullah,Joel Sjöstrand,Peter Andersson et al.
Ikram Ullah et al.
Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, ...
Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh [0.03%]
利用基因组序列探索树木状和非树木状模式：以自交植物物种拟南芥（雷尼氏）为例
Noah W M Stenz,Bret Larget,David A Baum et al.
Noah W M Stenz et al.
Genome sequence data contain abundant information about genealogical history, but methods for extracting and interpreting this information are not yet fully developed. We analyzed genome sequences for multiple accessions of the selfing plan...
Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model [0.03%]
利用Ornstein-Uhlenbeck模型在系统发育比较分析中检测适应性演化
Clayton E Cressler,Marguerite A Butler,Aaron A King
Clayton E Cressler
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and...
Vinson P Doyle,Randee E Young,Gavin J P Naylor et al.
Vinson P Doyle et al.
Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation is likely caused by systematic error in gene tree estimation. Systematic error can be mitigated by improving models of sequenc...
Andrew R Francis,Mike Steel
Andrew R Francis
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on "2-SAT") that efficiently determines wheth...
Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci [0.03%]
基于下一代测序和多基因组核位点的农杆菌克隆构建的小麦族山羊草属物种系统发育及多倍体亲缘关系研究
Jonathan Brassac,Frank R Blattner
Jonathan Brassac
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci...
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference [0.03%]
当前的多重序列比对自动过滤方法常会恶化单基因系统发育推断
Ge Tan,Matthieu Muffato,Christian Ledergerber et al.
Ge Tan et al.
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts ...
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies [0.03%]
形态学知识综合的前景：使用本体论和机器推理来提取跨研究的存在/缺失进化表型
T Alexander Dececchi,James P Balhoff,Hilmar Lapp et al.
T Alexander Dececchi et al.
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched i...
Incompatible Ages for Clearwing Butterflies Based on Alternative Secondary Calibrations [0.03%]
基于替代次要校准的清翼蝴蝶不相容的年龄估算
Ivonne J Garzón-Orduña,Karina L Silva-Brandão,Keith R Willmott et al.
Ivonne J Garzón-Orduña et al.
The recent publication of a time-tree for the plant family Solanaceae (nightshades) provides the opportunity to use independent calibrations to test divergence times previously inferred for the diverse Neotropical butterfly tribe Ithomiini....