The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Estimating Species Trees from Unrooted Gene Trees
Open accessAbstract
In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.
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Cites
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Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
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The Rooting of the Universal Tree of Life Is Not Reliable
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OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2129-y · Cited by 2,471
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015) · Nature · doi:10.1038/nature15697 · Cited by 1,668
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
Sayyari, E., & Mirarab, S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw079 · Cited by 869
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012) · Systematic Biology · doi:10.1093/sysbio/sys049 · Cited by 833
Metadata
- Authors
- Liu, L., & Yu, L.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-03-28
- Volume
- 60
- Issue
- 5
- Pages
- 661-667
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2108039804
- Cited by
- 252
- References
- 7
- FWCI
- 3.29
- Type
- journal article
- Language
- en
- Open access
- bronze
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