Identifying parsimonious pathways of accumulation and convergent evolution from binary data [0.03%]
从二进制数据识别简约的积累和收敛进化路径
Konstantinos Giannakis,Olav N L Aga,Marcus T Moen et al.
Konstantinos Giannakis et al.
How stereotypical, and hence predictable, are evolutionary and accumulation dynamics? Here we consider processes - from genome evolution to cancer progression - involving the irreversible accumulation of binary features (characters). We see...
Phylogenomics reveals the intricate history of the most diverse group within Atyidae (Crustacea: Decapoda) [0.03%]
系基因组揭示了最多样化的_atyidae(_甲壳亚门：十足目_)类群的复杂历史
Samuel C Bernardes,Thomas von Rintelen,Adnan Moussalli et al.
Samuel C Bernardes et al.
The Atyidae is a diverse and old freshwater shrimp family distributed across all continents bar Antarctica. It is particularly speciose in the Indo-Pacific, the domain of its most diverse group, the so-called Caridella group, which includes...
Diagnosing systematic errors and incomplete lineage sorting in the deep phylogeny of Collembola [0.03%]
弹尾纲动物深部谱系系统误差和不完整分支排序的诊断
Zhihong Zhan,Daoyuan Yu,Feng Zhang
Zhihong Zhan
Resolving deep phylogeny is complicated by systematic errors and biological sources of gene tree discordance, a challenge that is clearly presented by Collembola, one of the earliest diverging hexapod lineages. To address the long-standing ...
Claudia Solís-Lemus
Claudia Solís-Lemus
Reticulate processes such as hybridization, introgression, and horizontal gene transfer cannot be fully represented by a bifurcating tree. Enter phylogenetic networks: first as split graphs to visualize tree discordance, then as explicit pr...
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...