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PMID: 11918793 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome.

Molecular ecology ·Vol. 11 ·No. 3 ·2002-03-00 ·Pages 603-12

Primmer CR, Borge T, Lindell J, Saetre GP

Abstract

As a case study for single-nucleotide polymorphism (SNP) identification in species for which little or no sequence information is available, we investigated several approaches to identifying SNPs in two passerine bird species: pied and collared flycatchers (Ficedula hypoleuca and F. albicollis). All approaches were successful in identifying sequence polymorphism and over 50 candidate SNPs per species were identified from approximately 9.1 kb of sequence. In addition, 17 sites were identified in which the frequency of alternative bases differed by > 50% between species (termed interspecific SNPs). Interestingly, polymorphism of microsatellite/intron loci in the source species appeared to be a positive predictor of nucleotide diversity in homologous flycatcher sequences. The overall nucleotide diversity of flycatchers was 2.3-2.7 x 10(-3), which is approximately 3-6 times higher than observed in recent studies of human SNPs. Higher nucleotide diversity in the avian genome could be due to the relatively older age of flycatcher populations, compared with humans, and/or a higher long-term effective population size.

MeSH Terms

Animals Humans Microsatellite Repeats Molecular Sequence Data Polymerase Chain Reaction Polymorphism, Single Nucleotide Sequence Analysis, DNA Songbirds/genetics

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Primmer C R

Division of Population Biology, Department of Ecology and Systematics, University of Helsinki, PO Box 65, 00014, Helsinki, Finland. [email protected]

Borge T

Lindell J

Saetre G-P

Article Info

Journal

Molecular ecology

Abbr.

Mol Ecol

ISSN

0962-1083

DOI

10.1046/j.0962-1083.2001.01452.x

[email protected]

Published

2002-03-00

Pages

603-12

Language

English

Region

England

NLM ID

9214478

Subset

Databases

GENBANK

AF454198, AF454199, AF454200, AF454201, AF454202, AF454203, AF454204, AF454205, AF454206, AF454207, AF454208, AF454209, AF454210, AF454211, AF454212, AF454213, AF454214, AF454215, AF454216, AF454217, AF454218, AF454219, AF454220, AF454221, AF454222, AF454223, AF454224, AF454225, AF454226, AF454227, AF454228, AF454229, AF454230, AF454231, AF454232, AF454233, AF454234, AF454235, AF454236, AF454237, AF454238, AF454239, AF454240, AF454241, AF454242, AF454243, AF454244, AF454245, AF454246, AF454247, AF454248, AF454249, AF454250, AF454251, AF454252, AF454253, AF454254, AF454255, AF454256, AF454257, AF454258, AF454259, AF454260, AF454261, AF454262, AF454263, AF454264, AF454265, AF454266, AF454267, AF454268, AF454269, AF454270, AF454271, AF454272, AF454273, AF454274, AF454275, AF454276, AF454277, AF454278, AF454279, AF454280, AF454281, AF454282, AJ299592, AJ299593, AJ299594, AJ299595, AJ299596, AJ299597, AJ299598, AJ299604, AJ299605, AJ299612, AJ299613, AJ299614, AJ299615, AJ299616, AJ299617, AJ299624, AJ299625, AJ299626, AJ299627, AJ299628, AJ299629, AJ299630, AJ299631, AJ299632, AJ299633, AJ299640, AJ299641, AJ299642, AJ299643, AJ299644, AJ299645, AJ299646, AJ299651, AJ299652, AJ299653, AJ299654, AJ299655, AJ299656, AJ299657, AJ299664, AJ299665, AJ299666, AJ299667, AJ299668, AJ299675, AJ299676, AJ299677, AJ299678, AJ299691, AJ299692, AJ299693, AJ299694, AJ299698, AJ299699, AJ299700, AJ299701, AJ299702, AJ299703, AJ299704, AJ299705, AJ299706, AY069952

External Links

PubMed source DOI: 10.1046/j.0962-1083.2001.01452.x View journal details

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Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome.

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