A novel phylogenomics pipeline reveals extensive topological conflict in the evolution of the angiosperm order Cucurbitales [0.03%]
一种新型的系统基因组学管通揭示了被子植物目的葫芦目演化中的大量拓扑冲突
Edgardo M Ortiz,Alina Höwener,Gentaro Shigita et al.
Edgardo M Ortiz et al.
High-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are used for phylogenomic analyses. Integrating these mixed data types into a single phylogenomic dataset requires se...
Christine E Thacker,W Tyler McCraney,Michael E Alfaro
Christine E Thacker
The pace of evolutionary diversification varies among groups, between environments, and over geologic timescales. Radiations may be linked to phenotypic innovations and ecological opportunity but for highly diverse groups the factors contri...
Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae) [0.03%]
多倍体丰富的类群中的系统基因组挑战——来自复杂属Packera（菊科）同源处理和网状进化方法的启示
Erika R Moore-Pollard,Paige A Ellestad,Jennifer R Mandel
Erika R Moore-Pollard
Phylogenomic discordance is pervasive and cannot always be resolved by increasing the amount of sequencing data alone. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are major contributors to discorda...
Michael J Landis,Joel L Cracraft,Isabel Sanmartín
Michael J Landis
Biogeography is intrinsically linked to evolution as a process and to systematics as a practice. Phylogenetic biogeography, in particular, studies the distribution of life in space over time through the lens of common ancestry. Over the pas...
Charley G P McCarthy,Edward Susko,Ryo Harada et al.
Charley G P McCarthy et al.
Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino acid sequences may be heterogeneous across both sites and branches, particularly if deep phyloge...
Coalescent-based branch length estimation improves dating of species trees [0.03%]
基于分支长度的估计可改善物种树的定年结果
Yasamin Tabatabaee,Santiago Claramunt,Siavash Mirarab
Yasamin Tabatabaee
Species trees need to be dated for many downstream applications. Some scalable molecular dating methods take a phylogenetic tree with branch lengths in substitution units, as well as a set of calibrations, as input and convert the branch le...
Tomomi Parins-Fukuchi
Tomomi Parins-Fukuchi
One of the most transformative advances in molecular systematics over the past several decades has been our understanding of how population processes like incomplete lineage sorting (ILS) give rise to phylogenetic discordance. Fossil clades...
Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity [0.03%]
离散化Γ速率异质性模型导致的系统发育分支长度估计偏差
Luca Ferretti,Tanya Golubchik,Francesco Di Lauro et al.
Luca Ferretti et al.
A standard method in phylogenetic reconstruction for representing variation in substitution rates between sites in the genome is the discrete Gamma model (DGM). Relative rates are assumed to be distributed according to a discretised Gamma d...
Cold Origins Limit the Establishment of Northern Temperate Plants in the Southern Hemisphere [0.03%]
北方温带植物在南半球的建立受限于其冷起源
William H Brightly,Siri Fjellheim,Thomas Lux et al.
William H Brightly et al.
Plants with amphitropical distributions have closely related populations in both Northern and Southern Hemispheres, but are absent from the intervening tropics. They provide a unique opportunity to study the constraints shaping the distribu...