Literature DB >> 17169391

A graphical approach to relatedness inference.

Anthony Almudevar1.   

Abstract

The estimation of relatedness structure in natural populations using molecular marker data has become an important tool in population biology, resulting in a variety of estimation procedures for specific sampling scenarios. In this article a general approach is proposed, in which the detailed relationship structure, typically a pedigree graph or partition, is considered to be the object of inference. This makes available tools used in complex model selection theory which have demonstrated effectiveness. An important advantage of this approach is that it permits a fully Bayesian approach to the problem, providing a principled and accessible way to measure statistical error. The approach is demonstrated by applying the minimum description length principle. This technique is used in model selection to provide a rational way of comparing models of varying complexity. We show how the resulting score may be interpreted and applied as a Bayesian posterior density.

Mesh:

Year:  2006        PMID: 17169391      PMCID: PMC1995094          DOI: 10.1016/j.tpb.2006.10.005

Source DB:  PubMed          Journal:  Theor Popul Biol        ISSN: 0040-5809            Impact factor:   1.570


  18 in total

1.  A bootstrap assessment of variability in pedigree reconstruction based on genetic markers.

Authors:  A Almudevar
Journal:  Biometrics       Date:  2001-09       Impact factor: 2.571

2.  A simulated annealing algorithm for maximum likelihood pedigree reconstruction.

Authors:  Anthony Almudevar
Journal:  Theor Popul Biol       Date:  2003-03       Impact factor: 1.570

Review 3.  Methods of parentage analysis in natural populations.

Authors:  Adam G Jones; William R Ardren
Journal:  Mol Ecol       Date:  2003-10       Impact factor: 6.185

4.  Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data.

Authors:  K Butler; C Field; C M Herbinger; B R Smith
Journal:  Mol Ecol       Date:  2004-06       Impact factor: 6.185

Review 5.  The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations.

Authors:  Stuart C Thomas
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2005-07-29       Impact factor: 6.237

6.  Fractional paternity assignment: theoretical development and comparison to other methods.

Authors:  B Devlin; K Roeder; N C Ellstrand
Journal:  Theor Appl Genet       Date:  1988-09       Impact factor: 5.699

7.  Genetic analysis of male reproductive contributions in Chamaelirium luteum (L.) gray (Liliaceae).

Authors:  P E Smouse; T R Meagher
Journal:  Genetics       Date:  1994-01       Impact factor: 4.562

8.  Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale.

Authors:  R Nielsen; D K Mattila; P J Clapham; P J Palsbøll
Journal:  Genetics       Date:  2001-04       Impact factor: 4.562

9.  A bayesian framework for parentage analysis: the value of genetic and other biological data.

Authors:  B D Neff; J Repka; M R Gross
Journal:  Theor Popul Biol       Date:  2001-06       Impact factor: 1.570

10.  Statistical confidence for likelihood-based paternity inference in natural populations.

Authors:  T C Marshall; J Slate; L E Kruuk; J M Pemberton
Journal:  Mol Ecol       Date:  1998-05       Impact factor: 6.185

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  6 in total

1.  Selection of statistical thresholds in graphical models.

Authors:  Anthony Almudevar
Journal:  EURASIP J Bioinform Syst Biol       Date:  2010-03-04

2.  Fitting Boolean networks from steady state perturbation data.

Authors:  Anthony Almudevar; Matthew N McCall; Helene McMurray; Hartmut Land
Journal:  Stat Appl Genet Mol Biol       Date:  2011-10-05

3.  Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population.

Authors:  David Cros; Leopoldo Sánchez; Benoit Cochard; Patrick Samper; Marie Denis; Jean-Marc Bouvet; Jesús Fernández
Journal:  Theor Appl Genet       Date:  2014-02-07       Impact factor: 5.699

4.  On the choice of prior density for the Bayesian analysis of pedigree structure.

Authors:  Anthony Almudevar; Jason LaCombe
Journal:  Theor Popul Biol       Date:  2011-12-19       Impact factor: 1.570

5.  Maintenance of phenotypic variation: repeatability, heritability and size-dependent processes in a wild brook trout population.

Authors:  Benjamin H Letcher; Jason A Coombs; Keith H Nislow
Journal:  Evol Appl       Date:  2011-03-08       Impact factor: 5.183

6.  Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond.

Authors:  Jisca Huisman
Journal:  Mol Ecol Resour       Date:  2017-04-06       Impact factor: 7.090

  6 in total

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