Skip to main content
Log in

PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

PedAgree is software for rapid comparison of genetically reconstructed pedigrees (RP’s). Its two primary functions are (1) to assess accuracy of a RP by comparing it to a known pedigree, and (2) to measure congruence between two RP’s. The accuracy function is used to assist in determining confidence for a RP. The congruence function is used to determine the level of agreement between two RP’s. This function determines which links within the RP’s are identical, and thus more likely to be correct. Congruence assessment between RP’s generated by sibship reconstruction (SR) and parentage assignment (PA) programs allows for implementation of the sibship constraint method. This method has been shown to increase assigned parentage accuracy by up to 53%, and to be robust to dataset characteristics that reduce conventional PA accuracies. PedAgree can compare output produced by seven SR and twelve PA programs, and is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

References

  • Almudevar A (2007) A graphical approach to relatedness inference. Theor Popul Biol 71:213–229

    Article  PubMed  Google Scholar 

  • Almudevar A, Field C (1999) Estimation of single-generation sibling relationships based on DNA markers. J Agric Biol Environ Stat 4:136–165

    Article  Google Scholar 

  • Ashley MV, Caballero IC, Chaovalitwongse W, Dasgupta B, Govindan P, Sheikh SI et al (2009) KINALYZER, a computer program for reconstructing sibling groups. Mol Ecol Resour 9:1127–1131

    Article  CAS  Google Scholar 

  • Balloux F (2001) EASYPOP (version 1.7): a computer program for population genetics simulations. J Hered 92:301–302

    Article  CAS  PubMed  Google Scholar 

  • Carvajal-Rodriguez A (2007) FAMSPHERE: a computer program for parental allocation from known genotypic pools. Mol Ecol Notes 7:213–216

    Article  CAS  Google Scholar 

  • Cercueil A, Bellemain E, Manel S (2002) PARENTE: computer program for parentage analysis. J Hered 93:458–459

    Article  CAS  PubMed  Google Scholar 

  • Charmantier A, Reale D (2005) How do misassigned paternities affect the estimation of heritability in the wild? Mol Ecol 14:2839–2850

    Article  CAS  PubMed  Google Scholar 

  • Cockburn A, Osmond HL, Double MC (2008) Swingin’ in the rain: condition dependence and sexual selection in a capricious world. Proc Biol Sci 275:605–612

    Article  PubMed  Google Scholar 

  • Coombs JA, Letcher BH, Nislow KH (2010) PEDAGOG: software for simulating eco-evolutionary population dynamics. Mol Ecol Resour. doi:10.1111/j.1755-0998.2009.02803.x

  • Coulson T, Benton TG, Lundberg P, Dall SRX, Kendall BE, Gaillard JM (2006) Estimating individual contributions to population growth: evolutionary fitness in ecological time. Proc Biol Sci 273:547–555

    Article  CAS  PubMed  Google Scholar 

  • Danzmann RG (1997) PROBMAX: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny. J Hered 88:333

    Google Scholar 

  • Duchesne P, Godbout MH, Bernatchez L (2002) PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation. Mol Ecol Notes 2:191–193

    Article  CAS  Google Scholar 

  • Duchesne P, Castric T, Bernatchez L (2005) PASOS (parental allocation of singles in open systems): a computer program for individual parental allocation with missing parents. Mol Ecol Notes 5:701–704

    Article  CAS  Google Scholar 

  • Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR (2001) Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Mol Ecol 10:1265–1278

    Article  CAS  PubMed  Google Scholar 

  • Gerber S, Chabrier P, Kremer A (2003) FAMOZ: a software for parentage analysis using dominant, codominant and uniparentally inherited markers. Mol Ecol Notes 3:479–481

    Article  CAS  Google Scholar 

  • Hedgecock D, Eichert W (1999) WHICHPARENTS (version 1.0): a windows application for determining the most likely parents of offspring using multilocus genotype data. Computer software distributed from: http://www.bml.ucdavis.edu/whichparents.html

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  • Keller LF, Reid JM, Arcese P (2008) Testing evolutionary models of senescence in a natural population: age and inbreeding effects on fitness components in song sparrows. Proc Biol Sci 275:597–604

    Article  CAS  PubMed  Google Scholar 

  • Konovalov DA, Manning C, Henshaw MT (2004) KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Mol Ecol Notes 4:779–782

    Article  Google Scholar 

  • Kruuk LEB (2004) Estimating genetic parameters in natural populations using the ‘animal model’. Philos Trans R Soc Lond B Biol Sci 359:873–890

    Article  PubMed  Google Scholar 

  • O’Connor KD, Marr AB, Arcese P, Keller LF, Jeffery KJ, Bruford MW (2006) Extra-pair fertilization and effective population size in the song sparrow Melospiza melodia. J Avian Biol 37:572–578

    Article  Google Scholar 

  • Pelletier F, Clutton-Brock T, Pemberton J, Tuljapurkar S, Coulson T (2007) The evolutionary demography of ecological change: linking trait variation and population growth. Science 315:1571–1574

    Article  CAS  PubMed  Google Scholar 

  • Pemberton JM (2008) Wild pedigrees: the way forward. Proc Biol Sci 275:613–621

    Article  CAS  PubMed  Google Scholar 

  • Smith BR, Herbinger CM, Merry HR (2001) Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics 158:1329–1338

    CAS  PubMed  Google Scholar 

  • Szulkin M, Sheldon BC (2008) Dispersal as a means of inbreeding avoidance in a wild bird population. Proc Biol Sci 275:703–711

    Article  PubMed  Google Scholar 

  • Valiere N (2002) GIMLET: a computer program for analysing genetic individual identification data. Mol Ecol Notes 2:377–379

    CAS  Google Scholar 

  • Wang JL (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963–1979

    Article  PubMed  Google Scholar 

  • Wang J (2007) Parentage and sibship exclusions: higher statistical power with more family members. Heredity 99:205–217

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Santure AW (2009) Parentage and Sibship Inference from multilocus genotype data under polygamy. Genetics 181:1579–1594

    Article  CAS  PubMed  Google Scholar 

  • Wilmer JW, Allen PJ, Pomeroy PP, Twiss SD, Amos W (1999) Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus). Mol Ecol 8:1417–1429

    Article  Google Scholar 

  • Wilson AJ, Ferguson MM (2002) Molecular pedigree analysis in natural populations of fishes: approaches, applications, and practical considerations. Can J Fish Aquat Sci 59:1696–1707

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to J. A. Coombs.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Coombs, J.A., Letcher, B.H. & Nislow, K.H. PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships. Conservation Genet Resour 2, 147–150 (2010). https://doi.org/10.1007/s12686-010-9202-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-010-9202-9

Keywords

Navigation