Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs.

BMC Genetics
U HanneliusJ Kere

Abstract

Despite several thousands of years of close contacts, there are genetic differences between the neighbouring countries of Finland and Sweden. Within Finland, signs of an east-west duality have been observed, whereas the population structure within Sweden has been suggested to be more subtle. With a fine-scale substructure like this, inferring the cluster membership of individuals requires a large number of markers. However, some studies have suggested that this number could be reduced if the individual spatial coordinates are taken into account in the analysis. We genotyped 34 unlinked autosomal single nucleotide polymorphisms (SNPs), originally designed for zygosity testing, from 2044 samples from Sweden and 657 samples from Finland, and 30 short tandem repeats (STRs) from 465 Finnish samples. We saw significant population structure within Finland but not between the countries or within Sweden, and isolation by distance within Finland and between the countries. In Sweden, we found a deficit of heterozygotes that we could explain by simulation studies to be due to both a small non-random genotyping error and hidden substructure caused by immigration. Geneland, a model-based Bayesian clustering algorithm, clustered the individua...Continue Reading

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Citations

Apr 16, 2009·European Journal of Human Genetics : EJHG·Jukka U PaloAntti Sajantila
Oct 20, 2012·BMC Evolutionary Biology·Ivania Cerón-SouzaFrank Andrew Jones
Aug 11, 2011·PloS One·Keith HumphreysPatrik K E Magnusson
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Jul 8, 2016·Scientific Reports·Tea KaartokallioHannele Laivuori
Mar 9, 2012·Systematic Biology·Gilles GuillotJulien Claude
Oct 9, 2019·Clinical Obesity·Heli ViljakainenElisabete Weiderpass
Dec 16, 2019·Acta Neurologica Scandinavica·Annukka Murtonen, Marja-Liisa Sumelahti
Jun 6, 2020·Acta Neurologica Scandinavica·Anna-Leena PirttisaloJussi O T Sipilä
Apr 12, 2019·The Pharmacogenomics Journal·Frank R WendtBruce Budowle
May 23, 2018·Multidisciplinary Respiratory Medicine·Ida PesonenGiovanni Ferrara

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Methods Mentioned

BETA
genotyping
electrophoresis
Profiler
PCA

Software Mentioned

R package GenABEL
PowerMarker
R package ade4
Geneland
MegaBACE
CONVERT
Structure
Arlequin
R package Hierfstat
Spectro Typer

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