| 软冲突(假冲突) Soft incongruence | | |
| 人为因素 Artificial factors | 数据不足 Insufficient data | 下一代测序技术; 系统发育基因组学; 取样代表性; 基因选择; 进化模型的选择
Next-generation sequencing technologies; phylogenomics; Taxon sampling; DNA regions selection; selection of substitution models |
| 取样偏差 Biased sampling |
| 基因选择不当 Sub-optimized gene selection |
| 测序错误 Sequencing errors |
| 序列因素 Sequencing factors | 碱基组成成分偏差 Compositional bias | 第三密码子排除; 氨基酸序列建树; RY编码; 快速进化位点移除; 一致网络分析法
3rd codon position exclusion; amino acid tree; RY coding; removing fast-evolving nucleotide sites; consensus networks |
| 长枝吸引 Long-branch attraction |
| 进化速率异质性 Evolutionary rate heterogeneity |
| 进化饱和 Evolutionary saturation |
| 硬冲突 Hard incongruence | | |
| 生物过程 Biological factors | 快速辐射分化 Rapid diversification | 最小遗传距离法; 融合法; 基因树简约法; 网状进化网络分析法
Minimum genetic distance method; coalescence-based methods; gene tree parsimony; reticulation networks |
| 杂交/渐渗 Hybridization/Introgression |
| 不完全谱系筛选 Incomplete lineage sorting |
| 基因水平转移 Horizontal gene transfer |
| 并系基因 Paralogous genes |
| 基因重复和/或丢失 Gene duplication and/or gene loss |
| 基因重组 Gene recombination | |