Reconstructing pedigrees: a stochastic perspective

DOI10.1016/J.JTBI.2007.12.004MaRDI QIDQ1788666zbMATH OpenOpenAlexWikidataFDO

Authors Bhalchandra D. Thatte, Mike Steel

Publication date 8 October 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0706.2516

zbMATH Keywords

hidden Markov modelsequencesgraph reconstructionpedigree digraphs

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Problems related to evolution (92D15) Directed graphs (digraphs), tournaments (05C20)

Abstract: A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data for present day individuals. This is motivated by the increasing availability of genomic sequences, but in this paper we take a more theoretical approach and consider what models of sequence evolution might allow pedigree reconstruction (given sufficiently long sequences). Our results complement recent work that showed that pedigree reconstruction may be fundamentally impossible if one uses just the degrees of relatedness between different extant individuals. We find that for certain stochastic processes, pedigrees can be recovered up to isomorphism from sufficiently long sequences.

Recommendations

• Reconstructing pedigrees: a combinatorial perspective
• Reconstructing pedigrees: Some identifiability questions for a recombination-mutation model
• Combinatorics of Pedigrees I: Counterexamples to a Reconstruction Question
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Cites work

• Probability and random processes.
• Reconstructing pedigrees: a combinatorial perspective
• Statistical inference from genetic data on pedigrees
• Topics in Intersection Graph Theory

Cited in

(9)

• Combinatorics of Pedigrees I: Counterexamples to a Reconstruction Question
• Reconstructing pedigrees using probabilistic analysis of ISSR amplification
• scientific article; zbMATH DE number 4066687 (Why is no real title available?)
• Leaf-reconstructibility of phylogenetic networks
• Pedigree in the biparental Moran model
• Reconstructing pedigrees: Some identifiability questions for a recombination-mutation model
• Reconstructing pedigrees: a combinatorial perspective
• A simulated annealing algorithm for maximum likelihood pedigree reconstruction
• The existence and abundance of ghost ancestors in biparental populations

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