Evidence map›Paper›PMID 35652926›Full record

ReviewJournal of molecular evolution2022

Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies.

Simon Laurin-Lemay, Kassandra Dickson, Nicolas Rodrigue

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Journal of molecular evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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.

Simon Laurin-LemayDepartment of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
Kassandra DicksonDepartment of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
Nicolas RodrigueDepartment of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. nicolas.rodrigue@carleton.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We draw attention to an under-appreciated simulation method for generating artificial data in a phylogenetic context. The approach, which we refer to as jump-chain simulation, can invoke rich models of molecular evolution having intractable likelihood functions. As an example, we simulate data under a context-dependent model allowing for CpG hypermutability and show how such a feature can mislead common codon models used for detecting positive selection. We discuss more generally how this method can serve to elucidate the ways by which currently used models for inference are susceptible to violations of their underlying assumptions. Finally, we show how the method could serve as an inference engine in the Approximate Bayesian Computation framework.

Indexed as

AlgorithmsModels, GeneticBayes TheoremComputer SimulationEvolution, MolecularLikelihood FunctionsMarkov ChainsPhylogenyApproximate Bayesian ComputationCpG hypermutabilityLikelihood ratio testModel violationsPositive selectionSite-interdependent modelsSubstitution models

Identifiers

PMID35652926
PMCPMC9233627

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.