Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference

Molecular Biology and Evolution
Neeraja M KrishnanDavid D Pollock

Abstract

Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble mo...Continue Reading

References

Jan 31, 1992·Science·D M HillisI J Molineux
Jan 17, 1995·Proceedings of the National Academy of Sciences of the United States of America·S HoraiN Takahata
Mar 1, 1994·Journal of Virology·S KarlinG A Schachtel
May 1, 1996·Molecular Biology and Evolution·X Xu, U Arnason
Feb 1, 1996·Journal of Molecular Evolution·Z Yang
Feb 1, 1996·Journal of Molecular Evolution·J M Koshi, R A Goldstein
Jan 9, 1997·Nature·W Messier, C B Stewart
Dec 1, 1996·Statistical Methods in Medical Research·A Gelman, D B Rubin
Jul 21, 1998·Molecular Phylogenetics and Evolution·M GoodmanC P Groves
Dec 16, 1998·Journal of Molecular Evolution·A Eyre-Walker
Dec 16, 1998·Journal of Molecular Evolution·U ArnasonA Janke
Mar 13, 1999·Journal of Molecular Biology·D D PollockN Goldman
Apr 26, 2000·Molecular Biology and Evolution·M J SandersonS G Brady
Jun 1, 2000·Molecular Biology and Evolution·M A Noor, J C Larkin
Aug 11, 2000·Evolution; International Journal of Organic Evolution·T H Oakley, C W Cunningham
Dec 29, 2000·Nature·M IngmanU Gyllensten
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Dec 18, 2001·Science·J P HuelsenbeckJ P Bollback
Jan 19, 2002·Proceedings. Biological Sciences·Andrea J Webster, Andy Purvis
Mar 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jianzhi Zhang, Helene F Rosenberg
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Steven A Benner
May 30, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ulfur ArnasonAxel Janke
Jun 26, 2002·Molecular Biology and Evolution·Jonathan P Bollback
Oct 25, 2002·Proceedings. Biological Sciences·David S Hibbett, Manfred Binder
Oct 25, 2002·Systematic Biology·Rasmus Nielsen
Nov 20, 2002·Cytogenetic and Genome Research·U Arnason, A Janke
Feb 25, 2003·Molecular Biology and Evolution·Christophe J DouadyEmmanuel J P Douzery
May 15, 2003·Systematic Biology·John P HuelsenbeckJonathan P Bollback
Jul 30, 2003·Molecular Biology and Evolution·Douglas M RobinsonJeffrey L Thorne
Aug 5, 2003·Evolution; International Journal of Organic Evolution·Paul M BeardsleyRichard G Olmstead
Oct 1, 2003·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·F RichardB Dutrillaux

❮ Previous
Next ❯

Citations

Jun 6, 2006·Journal of Molecular Evolution·Jiaye Yu, Jeffrey L Thorne
May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Todd A CastoeDavid D Pollock
Dec 9, 2004·DNA and Cell Biology·Neeraja M KrishnanDavid D Pollock
Apr 26, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Isaac Elias, Tamir Tuller
Jun 19, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Abdoulaye Banire DialloMathieu Blanchette
Sep 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tamir TullerEytan Ruppin
May 16, 2006·Molecular Biology and Evolution·Richard A Goldstein, David D Pollock
Sep 29, 2009·Molecular Biology and Evolution·A P Jason de KoningDavid D Pollock
Jun 5, 2012·Nucleic Acids Research·Haim AshkenazyTal Pupko
Feb 26, 2010·Cold Spring Harbor Perspectives in Biology·Eric A GaucherRyan N Randall
Dec 2, 2009·Genome Research·Tamir TullerEytan Ruppin
May 4, 2005·Genome Research·Sameer Z RainaDavid D Pollock
Feb 10, 2009·BMC Bioinformatics·José C ClementeTakashi Gojobori
Jan 14, 2011·BMC Bioinformatics·Jialiang YangStefan Grünewald
Dec 22, 2011·BMC Bioinformatics·Hadas Birin, Tamir Tuller
Oct 2, 2008·BMC Evolutionary Biology·Daniel J Gaffney, Peter D Keightley
Oct 4, 2005·Human Genomics·Yanlong O XuDavid D Pollock
Dec 19, 2008·Biology Direct·Harold S Bernhardt, Warren P Tate
Sep 14, 2004·Biological Procedures Online·Neeraja M. KrishnanDavid D. Pollock
Jun 23, 2006·PLoS Computational Biology·Paul D WilliamsRichard A Goldstein
Dec 15, 2010·PloS One·Igor V Ovchinnikov, Olga I Kholina
Feb 4, 2010·Genetics·Miguel Arenas, David Posada
Jan 2, 2013·Mathematical Biosciences·Manuela Royer-CarenziGilles Didier
Mar 20, 2010·Journal of Theoretical Biology·Hervé Seligmann
May 4, 2005·Methods in Enzymology·Zhengyuan O Wang, David D Pollock
Sep 6, 2012·Systematic Biology·Edward Susko, Andrew J Roger
Feb 8, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Hervé Seligmann, Neeraja M Krishnan
Dec 12, 2020·Ecology and Evolution·Filipe Garrett VieiraM Thomas P Gilbert

❮ 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.