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 language | English |
|---|---|
| Article number | 20162763 |
| Pages (from-to) | 1-9 |
| Number of pages | 9 |
| Journal | Proceedings of the Royal Society of London. B, Biological Sciences |
| Volume | 284 |
| Issue number | 1850 |
| Early online date | 1 Mar 2017 |
| DOIs | |
| Publication status | Published - 15 Mar 2017 |
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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 journal › Article
}
TY - JOUR
T1 - Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population
AU - Nietlisbach, Pirmin
AU - Keller, Lukas F.
AU - Camenisch, Glauco
AU - Guillaume, Frédéric
AU - Arcese, Peter
AU - Reid, Jane M.
AU - Postma, Erik
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.
PY - 2017/3/15
Y1 - 2017/3/15
N2 - 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.
AB - 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.
KW - heterozygosity – fitness correlation
KW - inbreeding depression
KW - identity disequilibrium
KW - short tandem repeats
KW - Melospiza melodia
UR - http://www.scopus.com/inward/record.url?scp=85014511363&partnerID=8YFLogxK
U2 - 10.1098/rspb.2016.2763
DO - 10.1098/rspb.2016.2763
M3 - Article
AN - SCOPUS:85014511363
VL - 284
SP - 1
EP - 9
JO - Proceedings of the Royal Society of London. B, Biological Sciences
JF - Proceedings of the Royal Society of London. B, Biological Sciences
SN - 0962-8452
IS - 1850
M1 - 20162763
ER -