Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer
Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer
复制标题
DOI：
10.1093/sysbio/syr003
复制
发表时间：
2011-05-01
影响因子：
6.5
通讯作者：
Ane, Cecile
中科院分区：
文献类型：
--
作者：
Chung, Yujin;Ane, Cecile
随着人们对基因谱系之间的不一致性的认识越来越感兴趣，各种基因树/物种树协调方法已经被开发出来。我们在这里首次尝试评估和比较两种贝叶斯方法，物种树的贝叶斯估计(BEST)和BACKY(贝叶斯协调结的贝叶斯解缠)，在存在几个已知的基因树不一致性过程的情况下。DNA比对模拟在不完全谱系排序(ILS)和水平基因转移(HGT)的影响下进行。贝斯特和巴基都考虑了基因树估计中的不确定性，但他们对导致基因树不一致的原因的假设有很大不同。最好使用合并模型估计物种树，假设所有的基因树不一致都是由于ILS。巴基没有通过使用协调基因的非参数聚类来假定基因树不一致的任何特定的生物学过程。巴基估计了一个分支的协调系数(CF)，它被定义为树中真正具有该分支的基因的比例。然后，从具有最高估计CF的分支构建估计的和谐树。由于他们的假设不同，预计BEST在ILS存在的情况下表现会更好，而巴基在HGT存在的情况下表现会更好。正如预期的那样，当HGT事件不均匀地放置在物种树上时，Bucky在HGT存在的情况下更准确地重建了物种树。Bucky和Best在大多数其他情况下表现类似，包括在存在强大的ILS和均匀放置在树上的HGT事件时。然而，巴基被证明低估了CF估计的不确定性，可信度区间很短。尽管如此，巴基估计的不协调模式可以与ILS的特征进行比较。由此得到的对合并模型充分性的测试被证明具有较低的类型I误差。当HGT是不和谐的主要来源时，当HGT事件在物种树上不均匀地放置时，它是强大的。
With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed. We present here the first attempt to assess and compare two such Bayesian methods, Bayesian estimation of species trees (BEST) and BUCKy (Bayesian untangling of concordance knots), in the presence of several known processes of gene tree discordance. DNA alignments were simulated under the influence of incomplete lineage sorting (ILS) and of horizontal gene transfer (HGT). BEST and BUCKy both account for uncertainty in gene tree estimation but differ substantially in their assumptions of what caused gene tree discordance. BEST estimates a species tree using the coalescent model, assuming that all gene tree discordance is due to ILS. BUCKy does not assume any specific biological process of gene tree discordance through the use of a nonparametric clustering of concordant genes. BUCKy estimates the concordance factor (CF) of a clade, which is defined as the proportion of genes that truly have the clade in their trees. The estimated concordance tree is then built from clades with the highest estimated CFs. Because of their different assumptions, it was expected that BEST would perform better in the presence of ILS and that BUCKy would perform better in the presence of HGT. As expected, the species tree was more accurately reconstructed by BUCKy in the presence of HGT, when the HGT events were unevenly placed across the species tree. BUCKy and BEST performed similarly in most other cases, including in the presence of strong ILS and of HGT events that were evenly placed across the tree. However, BUCKy was shown to underestimate the uncertainty in CF estimation, with short credibility intervals. Despite this, the discordance pattern estimated by BUCKy could be compared with the signature of ILS. The resulting test for the adequacy of the coalescent model proved to have low Type I error. It was powerful when HGT was the major source of discordance and when HGT events were unevenly placed across the species tree.