Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans

Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans

Bradly J Alicea

Demographic inference under the coalescent in a spatial continuum

Demographic inference under the coalescent in a spatial continuum

Stephane Guindon, Hongbin Guo, David Welch

Genotyping Allelic and Copy Number Variation in the Immunoglobulin Heavy Chain Locus

Genotyping Allelic and Copy Number Variation in the Immunoglobulin Heavy Chain Locus

Shishi Luo, Jane A Yu, Yun S. Song

The regulator-executor-phenotype architecture shaped by natural selection

The regulator-executor-phenotype architecture shaped by natural selection

Han Chen, Chung-I Wu, Xionglei He

Powerful decomposition of complex traits in a diploid model using Phased Outbred Lines

Powerful decomposition of complex traits in a diploid model using Phased Outbred Lines

Johan Hallin, Kaspar Martens, Alexander Young, Martin Zackrisson, Francisco Salinas, Leopold Parts, Jonas Warringer, Gianni Liti

Transposable Element Evolution in the Allotetraploid Capsella bursa-pastoris and the Perfect Storm Hypothesis

Transposable Element Evolution in the Allotetraploid Capsella bursa-pastoris and the Perfect Storm Hypothesis

J Arvid Agren, Hui-Run Huang, Stephen I Wright

The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes

The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes

Václav Janoušek, Christina M Laukaitis, Alexey Yanchukov, Robert Karn

Plant root pathogens over 120,000 years of temperate rainforest ecosystem development

Plant root pathogens over 120,000 years of temperate rainforest ecosystem development

Ian A. Dickie, Angela Wakelin, Laura Martinez-Garcia, Sarah J. Richardson, Andreas Makiola, Jason M. Tylianakis

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences

Alexey M Kozlov, Jiajie Zhang, Pelin Yilmaz, Frank Oliver Glockner, Alexandros Stamatakis

Non-Identifiable Pedigrees and a Bayesian Solution

Non-Identifiable Pedigrees and a Bayesian Solution
B. Kirkpatrick

Some methods aim to correct or test for relationships or to reconstruct the pedigree, or family tree. We show that these methods cannot resolve ties for correct relationships due to identifiability of the pedigree likelihood which is the probability of inheriting the data under the pedigree model. This means that no likelihood-based method can produce a correct pedigree inference with high probability. This lack of reliability is critical both for health and forensics applications.
In this paper we present the first discussion of multiple typed individuals in non-isomorphic pedigrees, P and Q, where the likelihoods are non-identifiable, Pr[G | P,θ]=Pr[G | Q,θ], for all input data G and all recombination rate parameters θ. While there were previously known non-identifiable pairs, we give an example having data for multiple individuals.
Additionally, deeper understanding of the general discrete structures driving these non-identifiability examples has been provided, as well as results to guide algorithms that wish to examine only identifiable pedigrees. This paper introduces a general criteria for establishing whether a pair of pedigrees is non-identifiable and two easy-to-compute criteria guaranteeing identifiability. Finally, we suggest a method for dealing with non-identifiable likelihoods: use Bayes rule to obtain the posterior from the likelihood and prior. We propose a prior guaranteeing that the posterior distinguishes all pairs of pedigrees.
Shortened version published as: B. Kirkpatrick. Non-identifiable pedigrees and a Bayesian solution. Int. Symp. on Bioinformatics Res. and Appl. (ISBRA), 7292:139-152 2012.