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Institute of Mathematical Statistics LECTURE NOTES-MONOGRAPH SERIES Statistics in Molecular Biology and Genetics Selected Proceedings of a 1997 Joint AMS-IMS-SIAM Summer Conference on Statistics in Molecular Biology Francoise Seillier-Moiseiwitsch, Editor Volume 33 Published by the Institute of Mathematical Statistics and the American Mathematical Society Institute of Mathematical Statistics LECTURE NOTES-MONOGRAPH SERIES Volume 33 Statistics in Molecular Biology and Genetics Selected Proceedings of a 1997 Joint AMS-IMS-SIAM Summer Conference on Statistics in Molecular Biology Francoise Seillier-Moiseiwitsch, Editor American Mathematical Society Providence, Rhode Island Institute of Mathematical Statistics Hayward, California Institute of Mathematical Statistics Lecture Notes-Monograph Series Editorial Board Andrew A. Barbour, Joseph Newton, and David Ruppert (Editor) The production of the IMS Lecture Notes-Monograph Series is managed by the IMS Business Office: Julia A. Norton, IMS Treasurer, and Elyse Gustafson, IMS Business Manager. This volume was co-published with the American Mathematical Society Library of Congress Catalog Card Number: 99-076060 International Standard Book Number 0-940600-47-1 Copyright © 1999 Institute of Mathematical Statistics All rights reserved Printed in the United States of America Ill TABLE OF CONTENTS Preface v F. Seillier-Moiseiwitsch Genetic Mechanisms On a Markov Model for Chromatid Interference 1 H. Zhao and T. Speed Population Genetics Some Statistical Aspects of Cytonuclear Disequilibria 21 5. Datta Diffusion Process Calculations for Mutant Genes in Nonstationary Populations R. Fan and K. Lange The Coalescent with Partial Selfing and Balancing Selection: An Application of Structured Coalescent Processes M. Nordborg 38 56 Human Genetics Statistical Aspects of the Transmission/Disequilibrium Test (TDT) W. Ewens Estimation of Conditional Multilocus Gene Identity among Relatives 77 95 E. Thompson and S. Heath Quantitative Genetics A Review of Methods for Identifying QTL's in Experimental Crosses K. Broman and T. Speed 114 Evolutionary Genetics Markov Chain Monte Carlo for the Bayesian Analysis of Evolutionary Trees from Aligned Molecular Sequences M. Newton, B. Man and B. Larget Likelihoods on Coalescents: A Monte Carlo Sampling Approach to Inferring Parameters from Population Samples of Molecular Data J. Felsenstein, M. Kuhner, J. Yamato and P. Beerli 143 163 IV Uses of Statistical Parsimony in HIV Analyses K. Crandall Linear Estimators for the Evolution of Transposable Elements P. Joyce, L. Fox, N. Casavant and H. Wichman A Conditional Approach to the Detection of Correlated Mutations M. Karnoub, F. Seillier-Moiseiwitsch and P.K. Sen Correlated Mutations in Protein Sequences: Phylogenetic and Structural Effects A. Lapedes, B. Giraud, L. Liu and G. Stormo 186 207 221 236 Sequence Motifs Compound Poisson Approximations for Occurences of Multiple Words . . . 257 G. Reinert and 5. Schbath Protein Structure Deriving Interatomic Distance Bounds from Chemical Structure M. Trosset and G. Phillips Protein Fold Class Prediction is a New Field for Statistical Classification and Regression L. Edler and J. Grassmann 276 288 PREFACE The papers in this volume were presented at one of the 1997 Summer Research Conferences in the Mathematical Sciences jointly sponsored by the Institute of Mathematical Statistics, the American Mathematical Society and the Society for Industrial and Applied Mathematics. The theme of the meeting was "Statistics in Molecular Biology and Genetics". That this volume is pub