Reconstructing sibling relationships in wild populations.

Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
Bioinformatics (Impact Factor: 5.47). 08/2007; 23(13):i49-56. DOI: 10.1093/bioinformatics/btm219
Source: PubMed

ABSTRACT Reconstruction of sibling relationships from genetic data is an important component of many biological applications. In particular, the growing application of molecular markers (microsatellites) to study wild populations of plant and animals has created the need for new computational methods of establishing pedigree relationships, such as sibgroups, among individuals in these populations. Most current methods for sibship reconstruction from microsatellite data use statistical and heuristic techniques that rely on a priori knowledge about various parameter distributions. Moreover, these methods are designed for data with large number of sampled loci and small family groups, both of which typically do not hold for wild populations. We present a deterministic technique that parsimoniously reconstructs sibling groups using only Mendelian laws of inheritance. We validate our approach using both simulated and real biological data and compare it to other methods. Our method is highly accurate on real data and compares favorably with other methods on simulated data with few loci and large family groups. It is the only method that does not rely on a priori knowledge about the population under study. Thus, our method is particularly appropriate for reconstructing sibling groups in wild populations.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Studying associations between mating system parameters and fitness in natural populations of trees advances our understanding of how local environments affect seed quality, and thereby helps to predict when inbreeding or multiple paternities should impact on fitness. Indeed, for species that demonstrate inbreeding avoidance, multiple paternities (i.e. the number of male parents per half-sib family) should still vary and regulate fitness more than inbreeding - named here as the 'constrained inbreeding hypothesis'. We test this hypothesis in Eucalyptus gracilis, a predominantly insect-pollinated tree. Fifty-eight open-pollinated progeny arrays were collected from trees in three populations. Progeny were planted in a reciprocal transplant trial. Fitness was measured by family establishment rates. We genotyped all trees and their progeny at eight microsatellite loci. Planting site had a strong effect on fitness, but seed provenance and seed provenance × planting site did not. Populations had comparable mating system parameters and were generally outcrossed, experienced low biparental inbreeding and high levels of multiple paternity. As predicted, seed families that had more multiple paternities also had higher fitness, and no fitness-inbreeding correlations were detected. Demonstrating that fitness was most affected by multiple paternities rather than inbreeding, we provide evidence supporting the constrained inbreeding hypothesis; i.e. that multiple paternity may impact on fitness over and above that of inbreeding, particularly for preferentially outcrossing trees at life stages beyond seed development.
    PLoS ONE 01/2014; 9(2):e90478. · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Present broodstocks of large yellow croaker are borne from extremely small numbers of base population. Thus, it is necessary to analyze kinship of broodstocks in order to avoid inbreeding that will bring out the reduction of individual survival and growth. This paper reports kinship reconstruction and genetic diversity in 103 broodstocks of large yellow croaker by utilizing 23 microsatellite markers. Genetic diversities of 103 croakers at 23 loci pronounce that there are 134 alleles in total and an average of 5.82, and the observed average heterozygosity of 0.599 3, demonstrating that these broodstocks still maintain genetic variability to some extent. The results of sibling groups reconstructed are not identical using two methods of Likelihood and 2-allele recombinatorial optimization. However, the evidence of close relationship between broodstocks is confirmed. The mating combinations are compared between these two methods, as a result of 85% identity and a final selection of 2-allele method. This study aims at finding a better way to avoid inbreeding occurred in broodstocks, and facilitating the aquaculture market of large yellow croaker, meanwhile, offering methods and statistical models to artificial propagation in other marine fish species.
    Zoological Research. 01/2010; 30(6):620-626.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: New technologies for collecting genotypic data from natural populations open the possibilities of investigating many fundamental biological phenomena, including be- havior, mating systems, heritabilities of adaptive traits , kin selection, and dispersal patterns. The power and potential of genotypic information often rests in the ability to reconstruct genealogical relationships among individuals. These relationships include parentage, full and half-sibships, and higher order aspect s of pedigrees. Some areas of genealogical inference, such as parentage, have been studied extensively. Although methods for pedigree inference and kinship analysis exist, most make assumptions that do not hold for wild populations of animals and plants. In this chapter, we focus on the full sibling relationship an d first review existing methods for full sibship reconstructions from microsatell ite genetic markers. We then describe our new combinatorial methods for sibling reconstruction based on simple

Full-text (2 Sources)

Available from
May 27, 2014