Literature DB >> 12930771

On the use of star-shaped genealogies in inference of coalescence times.

Noah A Rosenberg1, Aaron E Hirsh.   

Abstract

Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%. Thus, the estimator is appropriate only for large populations that have grown very rapidly. The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr.

Mesh:

Year:  2003        PMID: 12930771      PMCID: PMC1462671     

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  17 in total

1.  Population growth of human Y chromosomes: a study of Y chromosome microsatellites.

Authors:  J K Pritchard; M T Seielstad; A Perez-Lezaun; M W Feldman
Journal:  Mol Biol Evol       Date:  1999-12       Impact factor: 16.240

Review 2.  Genealogical and evolutionary inference with the human Y chromosome.

Authors:  M P Stumpf; D B Goldstein
Journal:  Science       Date:  2001-03-02       Impact factor: 47.728

Review 3.  Estimating allele age.

Authors:  M Slatkin; B Rannala
Journal:  Annu Rev Genomics Hum Genet       Date:  2000       Impact factor: 8.929

Review 4.  Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.

Authors:  Noah A Rosenberg; Magnus Nordborg
Journal:  Nat Rev Genet       Date:  2002-05       Impact factor: 53.242

5.  Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition.

Authors:  Hua Tang; David O Siegmund; Peidong Shen; Peter J Oefner; Marcus W Feldman
Journal:  Genetics       Date:  2002-05       Impact factor: 4.562

6.  Consequences of recombination on traditional phylogenetic analysis.

Authors:  M H Schierup; J Hein
Journal:  Genetics       Date:  2000-10       Impact factor: 4.562

7.  Origins of Old Testament priests.

Authors:  M G Thomas; K Skorecki; H Ben-Ami; T Parfitt; N Bradman; D B Goldstein
Journal:  Nature       Date:  1998-07-09       Impact factor: 49.962

8.  The complex history of a gene proposed to participate in a sexual isolation mechanism in house mice.

Authors:  Robert C Karn; Annie Orth; François Bonhomme; Pierre Boursot
Journal:  Mol Biol Evol       Date:  2002-04       Impact factor: 16.240

Review 9.  Using linked markers to infer the age of a mutation.

Authors:  B Rannala; G Bertorelle
Journal:  Hum Mutat       Date:  2001-08       Impact factor: 4.878

10.  Bayesian analysis of haplotypes for linkage disequilibrium mapping.

Authors:  J S Liu; C Sabatti; J Teng; B J Keats; N Risch
Journal:  Genome Res       Date:  2001-10       Impact factor: 9.043

View more
  12 in total

1.  Gene genealogy and properties of test statistics of neutrality under population growth.

Authors:  Akinori Sano; Hidenori Tachida
Journal:  Genetics       Date:  2004-11-15       Impact factor: 4.562

2.  On the joint distribution of tree height and tree length under the coalescent.

Authors:  Ilana M Arbisser; Ethan M Jewett; Noah A Rosenberg
Journal:  Theor Popul Biol       Date:  2017-11-10       Impact factor: 1.570

3.  Phylogenetic analyses on the diversity of Aspergillus fumigatus sensu lato based on five orthologous loci.

Authors:  Fang Li; Bo Wang; Long Wang; Bin Cao
Journal:  Mycopathologia       Date:  2014-08-09       Impact factor: 2.574

4.  Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms.

Authors:  Yu-Chung Chiang; Kuo-Hsiang Hung; Shann-Jye Moore; Xue-Jun Ge; Shong Huang; Tsai-Wen Hsu; Barbara A Schaal; Ty Chiang
Journal:  BMC Evol Biol       Date:  2009-07-10       Impact factor: 3.260

5.  The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy.

Authors:  Martina Lari; Ermanno Rizzi; Stefano Mona; Giorgio Corti; Giulio Catalano; Kefei Chen; Cristiano Vernesi; Greger Larson; Paolo Boscato; Gianluca De Bellis; Alan Cooper; David Caramelli; Giorgio Bertorelle
Journal:  BMC Evol Biol       Date:  2011-01-31       Impact factor: 3.260

6.  Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand.

Authors:  Marcos Pérez-Losada; David V Jobes; Faruk Sinangil; Keith A Crandall; Miguel Arenas; David Posada; Phillip W Berman
Journal:  PLoS One       Date:  2011-03-10       Impact factor: 3.240

7.  Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.

Authors:  Arjun Biddanda; Matthias Steinrücken; John Novembre
Journal:  Genetics       Date:  2022-05-05       Impact factor: 4.402

8.  Matrilineal fertility inheritance detected in hunter-gatherer populations using the imbalance of gene genealogies.

Authors:  Michael G B Blum; Evelyne Heyer; Olivier François; Fréderic Austerlitz
Journal:  PLoS Genet       Date:  2006-06-21       Impact factor: 5.917

9.  Species distribution and introgressive hybridization of two Avicennia species from the Western Hemisphere unveiled by phylogeographic patterns.

Authors:  Gustavo M Mori; Maria I Zucchi; Iracilda Sampaio; Anete P Souza
Journal:  BMC Evol Biol       Date:  2015-04-10       Impact factor: 3.260

10.  Modeling the contrasting Neolithic male lineage expansions in Europe and Africa.

Authors:  Michael J Sikora; Vincenza Colonna; Yali Xue; Chris Tyler-Smith
Journal:  Investig Genet       Date:  2013-11-21
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.