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PMID: 10688128 Published · ppublish English Journal Article Review

Evolution of genes and taxa: a primer.

Plant molecular biology ·Vol. 42 ·No. 1 ·2000-01-00 ·Pages 1-23

Doyle JJ, Gaut BS

Abstract

The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction--parsimony, distance and maximum likelihood--differ in their use of these models. All three face similar problems in finding optimal--and reliable--solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.

MeSH Terms
Base Sequence Evolution, Molecular Genes, Plant/genetics Phylogeny Plants/classification,genetics Sequence Homology, Nucleic Acid
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Doyle J J
L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA. [email protected]
Gaut B S
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Article Info
Journal
Plant molecular biology
Abbr.
Plant Mol Biol
ISSN
0167-4412
Email
[email protected]
Published
2000-01-00
Pages
1-23
Language
English
Region
Netherlands
NLM ID
9106343
Subset
IM
External Links
PubMed source View journal details
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