A new method to estimate relatedness from molecular markers

Molecular Ecology
J Fernández, M A Toro

Abstract

Four major problems can affect the efficiency of methods developed to estimate relatedness between individuals from information of molecular markers: (i) some of them are dependent on the knowledge of the true allelic frequencies in the base population; (ii) they assume that all loci are unlinked and in Hardy-Weinberg and linkage equilibrium; (iii) pairwise methods can lead to incongruous assignations because they take into account only two individuals at a time; (iv) most are usually constructed for particular structured populations (only consider a few relationship classes, e.g. full-sibs vs. unrelated). We have developed a new approach to estimate relatedness that is free from the above limitations. The method uses a 'blind search algorithm' (actually simulated annealing) to find the genealogy that yield a co-ancestry matrix with the highest correlation with the molecular co-ancestry matrix calculated using the markers. Thus (i and ii) it makes no direct assumptions about allelic frequencies or Hardy-Weinberg and linkage equilibrium; (iii) it always provide congruent relationships, as it considers all individuals at a time; (iv) degrees of relatedness can be as complex as desired just increasing the 'depth' (i.e. number of g...Continue Reading

References

Mar 5, 2003·Theoretical Population Biology·Anthony Almudevar
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May 13, 1983·Science·S KirkpatrickM P Vecchi

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Citations

Mar 24, 2012·Animal : an International Journal of Animal Bioscience·M A ToroA Mäki-Tanila
Mar 24, 2012·Animal : an International Journal of Animal Bioscience·J FernándezA Mäki-Tanila
Jan 24, 2008·Proceedings. Biological Sciences·Francesca D FrentiuIan P F Owens
Jan 24, 2008·Proceedings. Biological Sciences·J M Pemberton
Apr 16, 2010·Proceedings. Biological Sciences·Tim J C AndersonFrançois Nosten
Jul 17, 2012·Genetics·Markku Karhunen, Otso Ovaskainen
Feb 8, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·David CrosJesús Fernández
Mar 24, 2011·Molecular Ecology·Mikko J Sillanpää
Dec 4, 2014·Evolutionary Applications·Joseph M NorthrupGeorge Wittemyer
Feb 26, 2014·Evolutionary Applications·Aaron B A ShaferGordon B Stenhouse
Jun 14, 2006·Trends in Ecology & Evolution·Ilik Saccheri, Ilkka Hanski
Sep 24, 2016·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·V S JunqueiraP S Lopes
Jul 14, 2017·Animal : an International Journal of Animal Bioscience·R R MotaF F Cardoso
Jun 27, 2015·Journal of Animal Science·F F CardosoI Aguilar
Nov 26, 2010·Journal of Animal Science·E BömckeN Gengler
Apr 7, 2019·Heredity·Daniel Kleinman-RuizJosé A Godoy

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