Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

Gene
Jena L ChojnowskiE L Braun

Abstract

Neoaves is the most diverse major avian clade, containing ~95% of avian species, and it underwent an ancient but rapid diversification that has made resolution of relationships at the base of the clade difficult. In fact, Neoaves has been suggested to be a "hard" polytomy that cannot be resolved with any amount of data. However, this conclusion was based on slowly evolving coding sequences and ribosomal RNAs and some recent studies using more rapidly evolving intron sequences have suggested some resolution at the base of Neoaves. To further examine the utility of introns and exons for phylogenetics, we sequenced parts of two unlinked clathrin heavy chain genes (CLTC and CLTCL1). Comparisons of phylogenetic trees based upon individual partitions (i.e. introns and exons), the combined dataset, and published phylogenies using Robinson-Foulds distances (a metric of topological differences) revealed more similarity than expected by chance, suggesting there is structure at the base of Neoaves. We found that introns provided more informative sites, were subject to less homoplasy, and provided better support for well-accepted clades, suggesting that intron evolution is better suited to determining closely-spaced branching events like t...Continue Reading

References

Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Dec 29, 1998·Molecular Biology and Evolution·Z YangM Hasegawa
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Jun 25, 1999·Molecular Phylogenetics and Evolution·J G Groth, G F Barrowclough
Feb 8, 2000·Journal of Theoretical Biology·W P Maddison
Jul 28, 2001·Evolution; International Journal of Organic Evolution·E L Braun, R T Kimball
Apr 26, 2003·Trends in Biochemical Sciences·Hervé Le HirMelissa J Moore
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Apr 8, 2004·Evolution; International Journal of Organic Evolution·Steven Poe, Alison L Chubb
Dec 23, 2004·Evolution; International Journal of Organic Evolution·Matthew G Fain, Peter Houde
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Diane E WakehamFrances M Brodsky
Jun 30, 2006·Gene·Maiko WatanabeMasami Hasegawa
Dec 7, 2006·Biology Letters·Per G P EricsonGerald Mayr
Sep 12, 2008·Zoological Journal of the Linnean Society·Bradley C Livezey, Richard L Zusi

❮ Previous
Next ❯

Citations

Sep 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·John HarshmanTamaki Yuri
Jun 10, 2008·Current Opinion in Hematology·Marc H G P Raaijmakers, David T Scadden
Apr 12, 2013·Proceedings. Biological Sciences·Valérie A Olson, Samuel T Turvey
Jun 28, 2008·Science·Shannon J HackettTamaki Yuri
Dec 22, 2012·Science·Ben G HoltCarsten Rahbek
May 27, 2011·BMC Evolutionary Biology·Edward L BraunTamaki Yuri
Dec 2, 2014·BMC Bioinformatics·Pawel Górecki, Oliver Eulenstein
Sep 24, 2011·Molecular Biology and Evolution·Ning WangRebecca T Kimball
Feb 18, 2016·Molecular Phylogenetics and Evolution·Nicholas W PersonsRebecca T Kimball
Apr 20, 2010·Molecular Phylogenetics and Evolution·Amber J BonillaRebecca T Kimball
Sep 2, 2009·Molecular Phylogenetics and Evolution·Michael J Braun, Christopher J Huddleston
Sep 8, 2011·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Matthew J Greenwold, Roger H Sawyer
Nov 30, 2014·Molecular Biology and Evolution·Nicole M FoleyEmma C Teeling
Jan 1, 2015·Molecular Phylogenetics and Evolution·J Gordon BurleighEdward L Braun
Aug 15, 2014·Psychonomic Bulletin & Review·Muhammad A J Qadri, Robert G Cook
Aug 17, 2011·Molecular Phylogenetics and Evolution·Łukasz PaśkoAndrzej Elzanowski
Oct 16, 2013·Molecular Phylogenetics and Evolution·Marie AggerbeckKnud Andreas Jønsson
Jun 25, 2013·Molecular Phylogenetics and Evolution·Rebecca T KimballEdward L Braun
Oct 8, 2011·Systematic Biology·June Y LeeScott V Edwards
Jul 27, 2012·Systematic Biology·Jordan V SmithRebecca T Kimball
Jun 24, 2017·Systematic Biology·Scott V EdwardsAllan J Baker
Sep 15, 2019·Molecular Phylogenetics and Evolution·Noor D White, Michael J Braun
Jul 6, 2021·Molecular Phylogenetics and Evolution·Hernán Vázquez-Miranda, F Keith Barker

❮ 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

Evolution; International Journal of Organic Evolution
Matthew G Fain, Peter Houde
Proceedings of the National Academy of Sciences of the United States of America
John HarshmanTamaki Yuri
© 2021 Meta ULC. All rights reserved