On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

Molecular Ecology
Anna W SantureJon Slate


In recent years there has been a dramatic increase in the availability of high density genetic marker data for both model and non-model organisms. A potential application of these data is to infer relatedness in the absence of a complete pedigree. Using a marker panel of 771 SNPs genotyped in three generations of an extensive zebra finch pedigree, correlations between pedigree relatedness and seven marker-based estimates of relatedness were examined, as was the relationship between heterozygosity and inbreeding. Although marker-based and pedigree relatedness were highly correlated, the variance in estimated relatedness was high. Further, the correlation between heterozygosity and inbreeding was weak, even though mean inbreeding coefficient is typical of that seen in wild vertebrate pedigrees; the weak relationship was in part due to the small variance in inbreeding in the pedigree. Our data suggest that using marker information to reconstruct the pedigree, and then calculating relatedness from the pedigree, is likely to give more accurate relatedness estimates than using marker-based estimators directly.


Oct 4, 2013·Genetics, Selection, Evolution : GSE·Fernando Gómez-RomanoJ Fernández
Nov 2, 2011·BMC Evolutionary Biology·Craig A WallingJosephine M Pemberton
Sep 26, 2013·BMC Genetics·Marcos S LopesEgbert F Knol
Mar 4, 2014·Proceedings of the National Academy of Sciences of the United States of America·Joseph I HoffmanKanchon K Dasmahapatra
May 14, 2011·Molecular Ecology Resources·E GuichouxR J Petit
Nov 9, 2011·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M A R de CaraB Villanueva
Jan 30, 2013·Molecular Ecology Resources·Jacquelin DeFaveriJuha Merilä
Apr 1, 2011·Molecular Ecology Resources·Robin S Waples, Ryan K Waples
Sep 22, 2012·Molecular Ecology·O PueblaW O McMillan
Oct 29, 2011·Evolutionary Anthropology·Brenda J Bradley, Richard R Lawler
Mar 24, 2011·Molecular Ecology·Mikko J Sillanpää
Jul 31, 2013·Evolution; International Journal of Organic Evolution·Sheena M Townsend, Ian G Jamieson
Oct 1, 2013·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·L SilióA Fernández
Feb 1, 2012·Evolutionary Applications·Francesco AngeloniJoop Ouborg
Dec 30, 2014·Ecology and Evolution·Alexander I Putman, Ignazio Carbone
Mar 7, 2014·Animal Genetics·A I FernándezB Villanueva
May 12, 2010·Molecular Ecology·Peter E Smouse
Oct 28, 2014·Evolution; International Journal of Organic Evolution·Jane M ReidPirmin Nietlisbach
Nov 19, 2014·Nature Reviews. Genetics·Doug Speed, David J Balding
May 22, 2016·The Journal of Heredity·Jamie A IvyOliver A Ryder
Sep 21, 2016·Ecology and Evolution·Veronika Städele, Linda Vigilant


Jan 1, 1993·Human Heredity·C C LiA Chakravarti
Jan 1, 1995·Annual Review of Genetics·R Frankham
Jun 20, 1998·Molecular Ecology·Tristan C MarshallJosephine M Pemberton
Jun 20, 2001·Molecular Ecology·T Van de CasteeleE Matthysen
Sep 26, 2001·Proceedings. Biological Sciences·W AmosT Coulson
Aug 7, 2004·Bioinformatics·J C BarrettM J Daly
Aug 13, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Loeske E B Kruuk
May 25, 2005·Molecular Ecology·Dany Garant, Loeske E B Kruuk
Oct 15, 2005·Human Heredity·Suzanne M LealBertram Müller-Myhsok
Jan 4, 2006·Theoretical Population Biology·Jinliang Wang
Apr 25, 2006·Molecular Ecology·J Fernández, M A Toro
Sep 20, 2006·Nature Reviews. Genetics·Bruce S WeirAmanda B Hepler
Nov 17, 2006·Molecular Ecology·J M AparicioP J Cordero
Aug 8, 2007·Theoretical Population Biology·Dario GasbarraElja Arjas
Sep 27, 2007·Molecular Ecology·Wolfgang ForstmeierBart Kempenaers
Oct 27, 2007·BMC Bioinformatics·Dario GasbarraElja Arjas
Jan 24, 2008·Proceedings. Biological Sciences·Josephine M Pemberton
Aug 1, 2008·Genetica·Peter M Visscher
Sep 10, 2008·Genetica·Jon SlateJosephine M Pemberton
Feb 18, 2009·Genetics·Jinliang Wang, Anna W Santure
Mar 1, 1989·Evolution; International Journal of Organic Evolution·David C Queller, Keith F Goodnight

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