期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 39, 期 12, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msac215
关键词
phylogenomics; ILS; summary methods; ASTRAL; gene tree estimation error
资金
- National Science Foundation (NSF) [III-1845967, ACI-1053575]
- National Institute of health (NIH) [R35GM142725]
This paper introduces a threshold-free weighting scheme for quartet-based species tree inference, which improves the utility of summary methods and reduces incongruence with gene concatenation.
Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the unweighted ASTRAL. Our simulations show that weighting improves accuracy across many conditions and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.
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