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Home / Equine Research Bank / Genet Sel Evol / Methods to estimate effective population size using pedigree...
Genetics, selection, evolution : GSE2013; 45(1); 1; doi: 10.1186/1297-9686-45-1

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse.

Abstract: Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results: Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions: When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.
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Publication Date: 2013-01-02 PubMed ID: 23281913PubMed Central: PMC3599586DOI: 10.1186/1297-9686-45-1Google Scholar: Lookup
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Summary

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This study aims to understand effective population sizes across different domesticated animal breeds using six various computation methods based on pedigree data. Their findings highlight significant differences in the estimated population sizes depending on the breed, computation method, species, breeding practices, and genetic substructure. The researchers suggest taking these factors into consideration when calculating effective population sizes.

Research methodology

  • The researchers analyzed the effective population sizes of 140 populations, including 60 dog breeds, 40 sheep breeds, 20 cattle breeds, and 20 horse breeds.
  • Data was extracted from pedigree information and subjected to six different computation methods. These methods accounted for various factors, including the number of breeding males and females, variance of progeny size, and evolution of identity by descent probabilities based on coancestry or inbreeding.
  • Additionally, the researchers used the identity by descent rate between two successive generations and individual identity by descent rate as part of the calculation.

Key findings

  • They found that effective population sizes varied greatly, ranging from 15 to 133,056, depending on the breed and computation method used.
  • Computation method and interaction between computation method and species were identified as significant factors influencing effective population size.
  • On average, methods based on the number of breeding males and females and variance of progeny size led to larger values (4425 and 356, respectively) as compared to methods based on identity by descent probabilities.
  • Breeding practices and genetic substructure within dog breeds were observed to increase inbreeding, leading to lower effective population sizes in these breeds.
  • The researchers found that the correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusion

  • The researchers concluded that when choosing a method to compute effective population size, attention should be paid to the species and the specific genetic structure of the population under study.
  • Therefore, this implies that there is no ‘one size fits all’ method in population size computation. Instead, the method chosen should suit the species, its breeding practices, and genetic substructure among other variables.

Cite This Article

APA
Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C. (2013). Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genet Sel Evol, 45(1), 1. https://doi.org/10.1186/1297-9686-45-1

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 45
Issue: 1
Pages: 1

Researcher Affiliations

Leroy, Grégoire
  • AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, 16 rue Claude Bernard, F-75321, Paris 05, France. gregoire.leroy@agroparistech.fr
Mary-Huard, Tristan
    Verrier, Etienne
      Danvy, Sophie
        Charvolin, Eleonore
          Danchin-Burge, Coralie

            MeSH Terms

            • Animals
            • Animals, Inbred Strains
            • Breeding
            • Cattle
            • Dogs
            • Evolution, Molecular
            • Female
            • Genetic Variation
            • Genetics, Population / methods
            • Horses
            • Inbreeding
            • Male
            • Models, Genetic
            • Models, Statistical
            • Pedigree
            • Population / genetics
            • Sex Ratio
            • Sheep

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            Citations

            This article has been cited 68 times.
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