Resolution of phylogenetic relationships among recently evolved species as a function of amount of DNA sequence

An empirical study based on woodpeckers (Aves: Picidae)

Victor De Filippis, William S. Moore

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

Synonymous substitutions in the 13 mitochondrial encoded protein genes form a large pool of characters that should approach the ideal for phylogenetic analysis of being independently and identically distributed. Pooling sequences from multiple mitochondrial protein-coding genes should result in statistically more powerful estimates of relationships among species that diverged sufficiently recently that most nucleotide substitutions are synonymous. Cytochrome oxidase I (COI) was sequenced for woodpecker species for which cytochrome b (cyt b) sequences were available. A pairing-design test based on the normal distribution indicated that cyt b evolves more rapidly than COI when all nucleotides are compared but their rates are equal for synonymous substitutions. Nearly all of the phylogenetically informative substitutions among woodpeckers are synonymous. Statistical support for relationships, as measured by bootstrap proportions, increased as the number of nucleotides increased from 1047 (cyt b) to 1512 (COI) to 2559 nucleotides (aggregate data set). Pseudo-bootstrap replicates showed the same trend and increasing the amount of sequence beyond the actual length of 2559 nucleotides to 5120 (2x) resulted in stronger bootstrap support, even though the amount phylogenetic information was the same. However, the amount of sequence required to resolve an internode depends on the length of the internode and its depth in the phylogeny. (C) 2000 Academic Press.

Original languageEnglish (US)
Pages (from-to)143-160
Number of pages18
JournalMolecular Phylogenetics and Evolution
Volume16
Issue number1
DOIs
StatePublished - Jul 2000
Externally publishedYes

Fingerprint

Picidae
woodpeckers
Aves
Birds
cytochrome
Nucleotides
nucleotides
Cytochromes b
phylogenetics
nucleotide sequences
DNA
Electron Transport Complex IV
cytochrome b
cytochrome-c oxidase
phylogeny
substitution
Mitochondrial Proteins
internodes
Normal Distribution
protein aggregates

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

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abstract = "Synonymous substitutions in the 13 mitochondrial encoded protein genes form a large pool of characters that should approach the ideal for phylogenetic analysis of being independently and identically distributed. Pooling sequences from multiple mitochondrial protein-coding genes should result in statistically more powerful estimates of relationships among species that diverged sufficiently recently that most nucleotide substitutions are synonymous. Cytochrome oxidase I (COI) was sequenced for woodpecker species for which cytochrome b (cyt b) sequences were available. A pairing-design test based on the normal distribution indicated that cyt b evolves more rapidly than COI when all nucleotides are compared but their rates are equal for synonymous substitutions. Nearly all of the phylogenetically informative substitutions among woodpeckers are synonymous. Statistical support for relationships, as measured by bootstrap proportions, increased as the number of nucleotides increased from 1047 (cyt b) to 1512 (COI) to 2559 nucleotides (aggregate data set). Pseudo-bootstrap replicates showed the same trend and increasing the amount of sequence beyond the actual length of 2559 nucleotides to 5120 (2x) resulted in stronger bootstrap support, even though the amount phylogenetic information was the same. However, the amount of sequence required to resolve an internode depends on the length of the internode and its depth in the phylogeny. (C) 2000 Academic Press.",
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