Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model.

Elizabeth S Allman, James H Degnan, John A Rhodes

Abstract read

In one paragraph

Article in Bulletin of mathematical biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

Algebraic Methods in Phylogenetics.Bulletin of mathematical biology · 2019
Article
OCTAL: Optimal Completion of gene trees in polynomial time.Algorithms for molecular biology : AMB · 2018
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Elizabeth S AllmanDepartment of Mathematics and Statistics, University of Alaska Fairbanks, P.O. Box 756660, Fairbanks, AK, 99775, USA.

James H DegnanDepartment of Mathematics and Statistics, The University of New Mexico, Albuquerque, NM, 87131, USA.

John A RhodesDepartment of Mathematics and Statistics, University of Alaska Fairbanks, P.O. Box 756660, Fairbanks, AK, 99775, USA. j.rhodes@alaska.edu.ORCID 0000-0001-9921-1091

Funding

Mathematical and computational analysis for species tree inferenceR01GM117590 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI RHODES, JOHN · 2015 to 2018

$1.5M

NIGMS NIH HHS R01 GM117590NIH HHS R01 GM117590

6 · The paper itself

Abstract

Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the probabilities of splits on gene trees under the multispecies coalescent model, and how their features might inform species tree inference. After investigating the behavior of split consensus methods, we investigate split invariants-that is, polynomial relationships between split probabilities. These invariants are then used to show that, even though a split is an unrooted notion, split probabilities retain enough information to identify the rooted species tree topology for trees of 5 or more taxa, with one possible 6-taxon exception.

Indexed as

Models, GeneticPhylogenyEvolution, MolecularGenetic SpeciationLinear ModelsMathematical ConceptsProbabilityMultispecies coalescent modelSpecies tree identifiabilitySplit probability

Identifiers

PMID29127546

DOI10.1007/s11538-017-0363-5

PMCPMC5766424

What OpenQuestion holds

Textmetadata

LicenceTDM

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.