A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse ( Lagopus lagopus )

• Published in: BMC Genetics
• Main Authors: Quintela Maria, Berlin Sofia, Höglund Jacob
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2008
• Subjects: Genetics; QH426-470; Greenland; North Atlantic; Tundra
• Online Access: https://doi.org/10.1186/1471-2156-9-89; https://doaj.org/article/111e7dac88cf48d38a97a3c4c030e2f5

Abstract Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10 -3 ) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse ( Lagopus lagopus ) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity ( π t ) was between 1.30 × 10 -4 and 7.66 × 10 -3 (average π t = 2.72 × 10 -3 ± 2.06 × 10 -3 ) and silent nucleotide diversity varied between 4.20 × 10 -4 and 2.76 × 10 -2 (average π S = 9.22 × 10 -3 ± 7.43 × 10 -4 ). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10 -3 (average π a = 5.08 × 10 -4 ± 7.43 × 10 3 ), which suggest that purifying selection is strong in these genes. F ST values based on synonymous SNP's varied between -5.60 × 10 -4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of F ST = 0.03 (95% CI: 0.006 – 0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within ...