A1 Refereed original research article in a scientific journal
Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome
Authors: Primmer CR, Borge T, Lindell J, Saetre GP
Publisher: BLACKWELL PUBLISHING LTD
Publication year: 2002
Journal name in source: MOLECULAR ECOLOGY
Journal acronym: MOL ECOL
Volume: 11
Issue: 3
First page : 603
Last page: 612
Number of pages: 10
ISSN: 0962-1083
DOI: https://doi.org/10.1046/j.0962-1083.2001.01452.x
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 approximate to 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 2.3-2.7x10(-3), which is approximate to 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.
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 approximate to 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 2.3-2.7x10(-3), which is approximate to 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.
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