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Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.

Publication ,  Journal Article
Kim, A; Rosenberg, NA; Degnan, JH
Published in: Molecular biology and evolution
May 2020

A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecies coalescent are considered. A ranked tree depicts not only the topological relationship among gene lineages, as an unranked tree does, but also the sequence in which the lineages coalesce. In this article, we study how the parameters of a species tree simulated under a constant-rate birth-death process can affect the probability that the species tree lies in the anomaly zone. We find that with more than five taxa, it is possible for species trees to have both anomalous unranked and ranked gene trees. The probability of being in either type of anomaly zone increases with more taxa. The probability of anomalous gene trees also increases with higher speciation rates. We observe that the probabilities of unranked anomaly zones are higher and grow much faster than those of ranked anomaly zones as the speciation rate increases. Our simulation shows that the most probable ranked gene tree is likely to have the same unranked topology as the species tree. We design the software PRANC, which computes probabilities of ranked gene tree topologies given a species tree under the coalescent model.

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Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

May 2020

Volume

37

Issue

5

Start / End Page

1480 / 1494

Related Subject Headings

  • Software
  • Proof of Concept Study
  • Phylogeny
  • Models, Genetic
  • Evolutionary Biology
  • Computer Simulation
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology
  • 0604 Genetics
 

Citation

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Kim, A., Rosenberg, N. A., & Degnan, J. H. (2020). Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. Molecular Biology and Evolution, 37(5), 1480–1494. https://doi.org/10.1093/molbev/msz305
Kim, Anastasiia, Noah A. Rosenberg, and James H. Degnan. “Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.Molecular Biology and Evolution 37, no. 5 (May 2020): 1480–94. https://doi.org/10.1093/molbev/msz305.
Kim A, Rosenberg NA, Degnan JH. Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. Molecular biology and evolution. 2020 May;37(5):1480–94.
Kim, Anastasiia, et al. “Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.Molecular Biology and Evolution, vol. 37, no. 5, May 2020, pp. 1480–94. Epmc, doi:10.1093/molbev/msz305.
Kim A, Rosenberg NA, Degnan JH. Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. Molecular biology and evolution. 2020 May;37(5):1480–1494.
Journal cover image

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

May 2020

Volume

37

Issue

5

Start / End Page

1480 / 1494

Related Subject Headings

  • Software
  • Proof of Concept Study
  • Phylogeny
  • Models, Genetic
  • Evolutionary Biology
  • Computer Simulation
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology
  • 0604 Genetics