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Cited by 607Genomics and Phylogenetic StudiesGenetic diversity and population structureEvolution and Paleontology Studies

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

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Liu, Liang, Yu, Lili, Edwards, Scott V·2010·BMC Evolutionary Biology
DOI 10.1186/1471-2148-10-302PMC PMC2976751
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Abstract

BACKGROUND: Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units. RESULTS: We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals. CONCLUSIONS: MP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.

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  • Comparative genomics analyses (species-tree inference, comparative annotation, selection detection) require genome alignments.

    “Comparative genomics analyses, including species-tree inference7,8, comparative annotation9,10, and selection detection11,12, require genome alignments.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [7]

    The Methods section (page not available) describes estimating gene trees from multilocus sequences and resampling sites in aligned sequences, supporting the use of alignments for species-tree inference. But it says MP-EST constructs a species tree from rooted gene trees; it does not establish that genome alignments are required. This citation supports the species-tree portion of the sentence, not the separately cited annotation and selection examples. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Liu, L., Yu, L., & Edwards, S. V.
Affiliations
  • Delaware State University (US)
  • Georgia Southern University (US)
  • Harvard University (US)
Corresponding author
Liu, Liang
ORCID
Venue
BMC Evolutionary Biology
Publisher
Springer Science and Business Media LLC
Published
2010
Volume
10
Issue
1
Pages
302
ISSN
1471-2148 (ISSN-L)
DOI
10.1186/1471-2148-10-302
PMC
PMC2976751
OpenAlex
W2125024684
Cited by
607
References
3
Citations by year
2026: 17 · 2025: 26 · 2024: 21 · 2023: 29 · 2022: 37 · 2021: 48 · 2020: 41 · 2019: 62 · 2018: 60 · 2017: 53 · 2016: 61 · 2015: 55 · 2014: 58 · 2013: 24 · 2012: 11
FWCI
4.73
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • BMC Evolutionary Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Science Foundation (0743616)
  • Division of Environmental Biology
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
species tree estimation, multispecies coalescent, gene trees, statistical consistency, placental mammals, horizontal gene transfer, bootstrap support, gene flow
MeSH terms
Models, Theoretical, Phylogeny, Likelihood Functions, Gene Transfer, Horizontal

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