PMID: 12064232Jun 18, 2002Paper

On the best evolutionary rate for phylogenetic analysis

Systematic Biology
Z Yang

Abstract

The effect of the evolutionary rate of a gene on the accuracy of phylogeny reconstruction was examined by computer stimulation. The evolutionary rate is measured by the tree length, that is, the expected total number of nucleotide substitutions per site on the phylogeny. DNA sequence data were simulated using both fixed trees with specified branch lengths and random trees with branch lengths generated from a model of cladogenesis. The parsimony and likelihood methods were used for phylogeny reconstruction, and the proportion of correctly recovered branch partitions by each method was estimated. Phylogenetic methods including parsimony appear quite tolerant of multiple substitutions at the same site. The optimum levels of sequence divergence were even higher than upper limits previously suggested for saturation of substitutions, indicating that the problem of saturation may have been exaggerated. Instead, the lack of information at low levels of divergence should be seriously considered in evaluation of a gene's phylogenetic utility, especially when the gene sequence is short. The performance of parsimony, relative to that of likelihood, does not necessarily decrease with the increase of the evolutionary rate.

Citations

Jan 5, 1999·Genome Research·P Liò, N Goldman
Oct 27, 1998·Proceedings. Biological Sciences·N Goldman
Apr 26, 2000·Molecular Biology and Evolution·M J SandersonS G Brady
Jul 12, 2000·Molecular Biology and Evolution·A D Yoder, Z Yang
Mar 24, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Colin E HughestC Donovan Bailey
Jan 15, 2013·Molecular Biology and Evolution·Agnes Tóth-Petróczy, Dan S Tawfik
Nov 19, 2014·BMC Research Notes·Marie Lisandra Zepeda MendozaRute R da Fonseca
Jun 9, 2017·Systematic Biology·Seraina KlopfsteinNick Goldman
Sep 26, 2017·Systematic Biology·Caroline Parins-Fukuchi
May 3, 2019·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Omar Alazem, John Abramyan
Oct 4, 2019·PeerJ·Joseph F WalkerGregory W Stull
Oct 1, 2005·Systematic Biology·Alexandra H WortleyRobert W Scotland
Apr 28, 2007·Systematic Biology·Jeffrey P Townsend
Jul 5, 2013·BMC Plant Biology·Inês S PiresMichael D Purugganan
Mar 15, 2013·Biology & Philosophy·Eric Bapteste, John Dupré
Mar 6, 2012·Systematic Biology·Jeffrey P TownsendYonas I Tekle
Jan 16, 2014·BMC Evolutionary Biology·Per G P EricsonJohan A A Nylander
Apr 20, 2014·PLoS Computational Biology·David A RasmussenKatia Koelle
Nov 26, 2014·The New Phytologist·Elke Schaper, Maria Anisimova
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
Feb 16, 2008·Systematic Biology·Shuguang JianDouglas E Soltis
Jul 19, 2005·Proceedings. Biological Sciences·Scott V EdwardsAndrew M Shedlock
May 8, 2016·Systematic Biology·Paul O LewisDaoyuan Shi

❮ 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.