Bhalchandra D. Thatte

Reconstructing pedigrees: a stochastic perspective.

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.

Revisiting an Equivalence Between Maximum Parsimony and Maximum Likelihood Methods in Phylogenetics

Tuffley and Steel (Bull. Math. Biol. 59:581–607, 1997) proved that maximum likelihood and maximum parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suffice to make the two methods inequivalent. In particular, we analyze the case of bounded substitution probabilities as well as the molecular clock assumption. We show that in these cases, even under no common mechanism, maximum parsimony and maximum likelihood might make conflicting choices. We also show that if there is an upper bound on the substitution probabilities which is ‘sufficiently small’, every maximum likelihood tree is also a maximum parsimony tree (but not vice versa).

Maximum parsimony on subsets of taxa

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitchs maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitchs method applied to all taxa.

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

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.

On the Nash-Williams' Lemma in Graph Reconstruction Theory

A generalization of Nash-Williams? lemma is proved for the Structure of m-uniform null (m ? k)-designs. It is then applied to various graph reconstruction problems. A short combinatorial proof of the edge reconstructibility of digraphs having regular underlying undirected graphs (e.g., tournaments) is given. A type of Nash-Williams? lemma is conjectured for the vertex reconstruction problem.

A correct proof of the McMorris-Powers' theorem on the consensus of phylogenies

McMorris and Powers proved an Arrow-type theorem on phylogenies given as collections of quartets. There is an error in one of the main lemmas used to prove this theorem. However, this lemma (and thereby the theorem) is still true, and we provide a corrected proof.

A reconstruction problem related to balance equations

Abstract A modified k -deck of a graph is obtained by removing k edges in all possible ways and adding k (not necessarily new) edges in all possible ways. Krasikov and Roditty used these decks to give an independent proof of Mullers result on the edge reconstructability of graphs. They asked if a k -edge deck could be constructed from its modified k -deck. In this paper, we solve the problem when k = 1. We also offer new proofs of Lovaszs result, one describing the constructed graph explicitly (thus answering a question of Bondy), and another based on the eigenvalues of Johnson graph.

On a reconstruction problem

This note supplements an earlier paper of this author, in which the concept of a strong k-hypomorphism between two graphs was defined (Thatte, 1990, Sectin VI). For k=1, this is just a hypomorphism. Here it is proved that strongly k-hypomorphic graphs and strongly k-edge hypomorphic directed graphs are isomorphic if k>1.

Ancestries of a recombining diploid population.

We derive the exact one-step transition probabilities of the number of lineages that are ancestral to a random sample from the current generation of a bi-parental population that is evolving under the discrete Wright–Fisher model with