Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses.

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Abstract Text:

A L Non,A Kitchen,C J Mulligan,A L Non,A Kitchen,C J Mulligan,

Analysis of complete mitochondrial genome sequences is becoming increasingly common in genetic studies. The availability of full genome datasets enables an analysis of the information content distributed throughout the mitochondrial genome in order to optimize the research design of future evolutionary studies. The goal of our study was to identify informative regions of the human mitochondrial genome using two criteria: (1) accurate reconstruction of a phylogeny and (2) consistent estimates of time to most recent common ancestor (TMRCA). We created two series of datasets by deleting individual genes of varied length and by deleting 10 equal-size fragments throughout the coding region. Phylogenies were statistically compared to the full-coding-region tree, while coalescent methods were used to estimate the TMRCA and associated credible intervals. Individual fragments important for maintaining a phylogeny similar to the full-coding-region tree encompassed bp 577-2122 and 11,399-16,023, including all or part of 12S rRNA, 16S rRNA, ND4, ND5, ND6, and cytb. The control region only tree was the most poorly resolved with the majority of the tree manifest as an unresolved polytomy. Coalescent estimates of TMRCA were less sensitive to removal of any particular fragment(s) than reconstruction of a consistent phylogeny. Overall, we discovered that half the genome, i.e., bp 3669-11,398, could be removed with no significant change in the phylogeny (p(AU)=0.077) while still maintaining overlap of TMRCA 95% credible intervals. Thus, sequencing a contiguous fragment from bp 11,399 through the control region to bp 3668 would create a dataset that optimizes the information necessary for phylogenetic and coalescent analyses and also takes advantage of the wealth of data already available on the control region.

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Publishing Authors By Initials

AL Non,A Kitchen,CJ Mulligan,AL Non,A Kitchen,CJ Mulligan,

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Molecular phylogenetics and evolution

VOLUME: 44

Page Numbers: 1164-71

Journal Abbreviation: Mol. Phylogenet. Evol.

ISSN: 1055-7903

DAY: 31

MONTH: 12

YEAR: 2006

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9304400

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses.

AFFILIATION: Department of Anthropology, University of Florida, Gainesville, FL 32611, USA.

Country: United States

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: Mol Phylogenet Evol

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses Related Publications

• A cryoglobulin present in high concentration in the plasma of a case of multiple myeloma.
• A preschool screening program.
• A three-stage colonization model for the peopling of the americas.
• Anaerobic bioconversion of carbon dioxide to biogas in an upflow anaerobic sludge blanket reactor.
• Chronic lymphocytic leukaemia resistant to both fludarabine and alemtuzumab--double jeopardy.
• Comparison of mercurial diuretics and routes of administration with special reference to thiomerin.
• Complete correction of murine Artemis immunodeficiency by lentiviral vector-mediated gene transfer.
• Credit for unpublished case reports?
• Effect of pacing site on systolic mechanical restitution curves in the in vivo canine model.
• Exogenous control of mammalian gene expression via modulation of translational termination.
• Fetal programming of body dimensions and percentage body fat measured in prepubertal children with a 4-component model of body composition, dual-energy X-ray absorptiometry, deuterium dilution, densitometry, and skinfold thicknesses.
• Guaranteed recall of all training pairs for bidirectional associative memory.
• Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses.
• Instant electronic access to randomized controlled trials (RCT).
• Investigation of the removal of heavy metals from sediments using rhamnolipid in a continuous flow configuration.
• Leaching of heavy metals from chromated copper arsenate (CCA) treated wood after disposal.
• Linkage disequilibrium and association analysis of alpha-synuclein and alcohol and drug dependence in two American Indian populations.
• Myeloma update.
• Neoplastic diseases of dogs; mast cell sarcoma, lymphosarcoma, histiocytoma.
• Neoplastic diseases of dogs; neoplasms of melanin-forming cells.
• On multiple training for bidirectional associative memory.
• Primary liver-cell carcinoma, hepatoma, in the dog.
• Retinotopic order is surprisingly good within cell columns in the cat's lateral suprasylvian cortex.
• Testosterone replacement therapy for older men.
• The revelation effect: moderating influences of encoding conditions and type of recognition test.
• The weight of the pituitary gland of the male dog in relation to body weight and age, with a differential cell count of the anterior lobe.
• Two coding strategies for bidirectional associative memory.
• Types of neoplasms in five breeds of dogs.
• Utility of DNA viruses for studying human host history: Case study of JC virus.
• Work-related disorders of the upper limb.