Reconstructing sibling relationships in wild populations

Department of Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States
Bioinformatics (Impact Factor: 4.98). 08/2007; 23(13):i49-56. DOI: 10.1093/bioinformatics/btm219
Source: PubMed


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.

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Available from: Bhaskar Dasgupta
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    • "Specifically, in bioinformatics a great deal of attention is being paid to measuring the distance between clusterings of populations, either natural or experimental, for sibling relationship reconstruction. In practice, thus far the focus has been placed almost exclusively on a unique distance measure (see [17], [6], [31], [19], [18], [30], [2], [8], [5], [10], [3]), namely one relying on maximum matching and denoted MMD in the sequel. After its first appearance [4], this measure was subsequently shown [15] to be computable via the assignment problem (see [20, p. 236] and [12, subsection 4.1]). "
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    • "The likelihood methods estimate the probability of the data under different partitions and assign individuals to maximum likelihood sibling groups in a population (Smith et al. 2001; Butler et al. 2004; Konovalov et al. 2004; Jones and Wang 2010). The combinatorial approaches use Mendelian laws of inheritance to reconstruct sibling groups to find the smallest number of full-sibling groups (Almudevar and Field 1999; Berger-Wolf et al. 2007). For example, the minimum 2-Allele Set Cover approach, based on Mendelian inheritance rules, does not require population allele frequencies and makes no assumptions about a species' mating system (Berger-Wolf et al. 2007). "
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    • "Family-level mating system parameters were estimated in the same way except that individuals within families were bootstrapped 1000 times to calculate variance estimates. To further investigate the role of the multiple paternities, we estimated the number of full-sib groups within progeny arrays using KINALYZER [57], [58], implementing the 2-allele algorithm, and scaled this value to the size of progeny arrays (kn). Selfed offspring were excluded from this analysis. "
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