Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Phylogenetic inference from conserved sites alignments.

W N Grundy¹, G J Naylor

¹Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California 95065, USA. bgrundy@cse.ucsc.edu

The Journal of Experimental Zoology

|August 10, 1999

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Are the fossil data really at odds with the molecular data? Morphological evidence for cetartiodactyla phylogeny reexamined.

Systematic biology·2002

Same author

Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences.

Systematic biology·2002

Same author

Conflicting phylogenetic patterns caused by molecular mechanisms in mitochondrial DNA sequences.

Systematic biology·2002

Same author

A high-throughput study of gene expression in preterm labor with a subtractive microarray approach.

American journal of obstetrics and gynecology·2001

Same author

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.

Bioinformatics (Oxford, England)·2001

Same author

Promoter region-based classification of genes.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2001

Same journal

Myosin expression in the developing ascidian embryo.

The Journal of experimental zoology·2012

Same journal

Regulation in the chick allantois.

The Journal of experimental zoology·2010

Same journal

A serologic study of conjugation in Paramecium bursaria.

The Journal of experimental zoology·2010

Same journal

Studies on flagellates from domesticated birds; the behavior of Trichomonas gallinarum in culture.

The Journal of experimental zoology·2010

Same journal

Experiments on the formed inclusions of the amphibian egg; the effect of pH and electrolytes on yolk and lipochondria.

The Journal of experimental zoology·2010

Same journal

Production of strophosomy in the chick embryo by local applications of colchicine.

The Journal of experimental zoology·2010

See all related articles

Conserved regions in molecular sequences improve phylogenetic tree accuracy. New methods focusing on conserved motifs or sites yield more reliable evolutionary relationships than complete alignments.

Area of Science:

Evolutionary Biology
Bioinformatics
Genomics

Background:

Phylogenetic relationships are inferred using molecular sequence data.
Accurate multiple sequence alignments are crucial for reliable phylogenetic inference.
Conserved regions, such as motifs, often contain more reliable phylogenetic signal.

Purpose of the Study:

To develop and evaluate methods for creating multiple sequence alignments enriched in conserved regions.
To improve the accuracy of phylogenetic tree reconstruction.

Main Methods:

Two novel methods for generating conserved region alignments: motif-based and site-based.
Parsimony analysis applied to mitochondrial DNA datasets.
Comparison of phylogenetic trees derived from complete alignments versus conserved region alignments.

Related Experiment Videos

Main Results:

Both conserved alignment methods produced more accurate phylogenetic trees than complete alignments for a 19-species dataset.
The motif-based method used fewer alignment sites for similar error rates.
The site-based method yielded a largely accurate tree for a 39-species dataset, suggesting novel placements.

Conclusions:

Focusing on conserved regions significantly enhances phylogenetic tree accuracy.
The developed methods offer improved approaches for phylogenetic inference from molecular sequences.
These techniques can lead to more robust evolutionary relationship reconstructions.