Model adequacy tests for probabilistic models of chromosome-number evolution.

The New Phytologist
Anna Rice, Itay Mayrose

Abstract

Chromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data. Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows us to determine whether the model can generate data with similar characteristics as those found in the observed ones. We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitting model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present. The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutio...Continue Reading

References

Feb 1, 1993·Journal of Molecular Evolution·N Goldman
Jun 26, 2002·Molecular Biology and Evolution·Jonathan P Bollback
Apr 26, 2008·Science·A R Leitch, I J Leitch
May 28, 2008·Cytogenetic and Genome Research·M Guerra
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Troy E WoodLoren H Rieseberg
Jun 9, 2010·Systematic Biology·Itay MayroseSarah P Otto
Aug 24, 2011·Genome Biology and Evolution·Nathaniel M Hallinan, David R Lindberg
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Jun 25, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Justin Ramsey, Tara S Ramsey
Jul 15, 2015·Molecular Biology and Evolution·David A DuchêneSimon Y W Ho
Oct 7, 2015·The New Phytologist·Michael S BarkerDonald A Levin
Oct 10, 2015·American Journal of Botany·Jonathan F Wendel
Dec 15, 2015·The American Naturalist·Matthew W PennellLuke J Harmon
May 29, 2016·American Journal of Botany·Douglas E SoltisPamela S Soltis
Jun 30, 2016·American Journal of Botany·Lior GlickItay Mayrose
Jul 29, 2016·American Journal of Botany·Shing H ZhanItay Mayrose
Aug 2, 2016·Nature Plants·Ayelet Salman-MinkovItay Mayrose
Mar 16, 2017·Evolution; International Journal of Organic Evolution·Rosana Zenil-FergusonJ Gordon Burleigh
Aug 16, 2017·Scientific Reports·Alisa O Vershinina, Vladimir A Lukhtanov
Sep 26, 2017·Systematic Biology·William A Freyman, Sebastian Höhna
Nov 15, 2017·Molecular Biology and Evolution·Sebastian HöhnaJeremy M Brown
May 8, 2018·Applications in Plant Sciences·Rosana Zenil-FergusonJosé Miguel Ponciano
Jul 17, 2018·Molecular Ecology Resources·Michal DroriItay Mayrose
Jan 29, 2019·Evolution; International Journal of Organic Evolution·Heath BlackmonEmma E Goldberg
Jan 31, 2019·Nature Ecology & Evolution·Anna RiceItay Mayrose
Feb 26, 2019·Nature Communications·Shiran AbadiItay Mayrose
Mar 19, 2019·Molecular Phylogenetics and Evolution·José Ignacio Márquez-CorroMarcial Escudero
Jun 22, 2019·BMC Bioinformatics·Wei ChenHong Gu
Oct 17, 2019·The New Phytologist·Rosana Zenil-FergusonEmma E Goldberg

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
A. Rice, Itay Mayrose
BioRxiv : the Preprint Server for Biology
Matthew PennellLuke J Harmon
BioRxiv : the Preprint Server for Biology
Orlando Schwery, B. C. O'Meara
© 2021 Meta ULC. All rights reserved