Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

Pirmin Nietlisbach*, Lukas F. Keller, Glauco Camenisch, Frédéric Guillaume, Peter Arcese, Jane M. Reid, Erik Postma

*Corresponding author for this work

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual’s genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F. This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F. Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.

Original languageEnglish
Article number20162763
Pages (from-to)1-9
Number of pages9
JournalProceedings of the Royal Society of London. B, Biological Sciences
Volume284
Issue number1850
Early online date1 Mar 2017
DOIs
Publication statusPublished - 15 Mar 2017

Fingerprint

Inbreeding
inbreeding coefficient
Birds
wild birds
Pedigree
inbreeding
pedigree
heterozygosity
Microsatellite Repeats
genetic marker
fitness
Genes
microsatellite repeats
Sampling
bird
Population
Genetic Markers
song
genetic markers
recombination

Keywords

  • heterozygosity – fitness correlation
  • inbreeding depression
  • identity disequilibrium
  • short tandem repeats
  • Melospiza melodia

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)

Cite this

Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. / Nietlisbach, Pirmin; Keller, Lukas F.; Camenisch, Glauco; Guillaume, Frédéric; Arcese, Peter; Reid, Jane M.; Postma, Erik.

In: Proceedings of the Royal Society of London. B, Biological Sciences, Vol. 284, No. 1850, 20162763, 15.03.2017, p. 1-9.

Research output: Contribution to journalArticle

Nietlisbach, Pirmin ; Keller, Lukas F. ; Camenisch, Glauco ; Guillaume, Frédéric ; Arcese, Peter ; Reid, Jane M. ; Postma, Erik. / Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. In: Proceedings of the Royal Society of London. B, Biological Sciences. 2017 ; Vol. 284, No. 1850. pp. 1-9.
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abstract = "Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual’s genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F. This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F. Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.",
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note = "Funding Our work was supported by Swiss National Science Foundation grants (31003A-116794 to L.F.K., PP00P3_144846 to F.G.), Natural Sciences and Engineering Research Council of Canada grants to P.A., and grants by the Forschungskredit of the University of Zurich (FK-15-104), Georges und Antoine Claraz-Schenkung and Dr Joachim de Giacomi foundation to P.N. Acknowledgements We thank Thomas Bucher, Dominique Waldvogel and Franziska L{\"o}rcher for help with genotyping, Rebecca Sardell for reconstructing earlier versions of the pedigree, Patrice David, Anna Kopps, Jon Slate and anonymous reviewers for helpful comments, the Tsawout and Tseycum First Nations of Saanich, British Columbia, Canada for permission to conduct research on Mandarte Island, and to everyone involved in this long-term research project.",
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N1 - Funding Our work was supported by Swiss National Science Foundation grants (31003A-116794 to L.F.K., PP00P3_144846 to F.G.), Natural Sciences and Engineering Research Council of Canada grants to P.A., and grants by the Forschungskredit of the University of Zurich (FK-15-104), Georges und Antoine Claraz-Schenkung and Dr Joachim de Giacomi foundation to P.N. Acknowledgements We thank Thomas Bucher, Dominique Waldvogel and Franziska Lörcher for help with genotyping, Rebecca Sardell for reconstructing earlier versions of the pedigree, Patrice David, Anna Kopps, Jon Slate and anonymous reviewers for helpful comments, the Tsawout and Tseycum First Nations of Saanich, British Columbia, Canada for permission to conduct research on Mandarte Island, and to everyone involved in this long-term research project.

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