Reconstructing pedigrees: Some identifiability questions for a recombination-mutation model

DOI10.1007/S00285-011-0503-8MaRDI QIDQ1937885zbMATH OpenOpenAlexWikidataFDO

Authors Bhalchandra D. Thatte

Publication date 1 February 2013

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

Full work available at URL https://arxiv.org/abs/1008.0153

zbMATH Keywords

identifiability

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) Applications of graph theory (05C90) Problems related to evolution (92D15) Directed graphs (digraphs), tournaments (05C20)

Abstract: Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.

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Cites work

• scientific article; zbMATH DE number 487720 (Why is no real title available?)
• scientific article; zbMATH DE number 1051281 (Why is no real title available?)
• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• Combinatorics of Pedigrees I: Counterexamples to a Reconstruction Question
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Mathematical and statistical methods for genetic analysis.
• Phylogenetic supertrees. Combining information to reveal the tree of life
• Probabilistic Functions of Finite State Markov Chains
• Reconstructing pedigrees: a stochastic perspective
• Reconstruction of Markov Random Fields from Samples: Some Observations and Algorithms
• Recovering a tree from the leaf colourations it generates under a Markov model
• Structuring causal trees

Cited in

(9)

• Combinatorics of Pedigrees I: Counterexamples to a Reconstruction Question
• Reconstructing pedigrees using probabilistic analysis of ISSR amplification
• Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
• Leaf-reconstructibility of phylogenetic networks
• Classes of explicit phylogenetic networks and their biological and mathematical significance
• Reconstructing pedigrees: a stochastic perspective
• Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution
• Reconstructing pedigrees: a combinatorial perspective
• The existence and abundance of ghost ancestors in biparental populations

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