- THIS ARTICLE
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Slatkin, M.
- Articles by Maddison, W. P.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Slatkin, M.
- Articles by Maddison, W. P.
Genetics, Vol 126, 249-260, Copyright © 1990
INVESTIGATIONS |
Detecting Isolation by Distance Using Phylogenies of Genes
M. Slatkin and W. P. Maddison
Department of Zoology, University of California, Berkeley, California 94720
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)(2) in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.
This article has been cited by other articles:
 |
|
 |
|
  P. D. Schloss and J. Handelsman Introducing TreeClimber, a Test To Compare Microbial Community Structures Appl. Envir. Microbiol., April 1, 2006; 72(4): 2379 - 2384. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. F. Wilkins A Separation-of-Timescales Approach to the Coalescent in a Continuous Population Genetics, December 1, 2004; 168(4): 2227 - 2244. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. P. Anderson, G. H. Learn, A. G. Rodrigo, X. He, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins Predicting Demographic Group Structures Based on DNA Sequence Data Mol. Biol. Evol., July 1, 2003; 20(7): 1168 - 1180. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. C. Nickle, M. A. Jensen, D. Shriner, S. J. Brodie, L. M. Frenkel, J. E. Mittler, and J. I. Mullins Evolutionary Indicators of Human Immunodeficiency Virus Type 1 Reservoirs and Compartments J. Virol., May 1, 2003; 77(9): 5540 - 5546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Collins, M. E. Quinones-Mateu, M. Wu, H. Luzze, J. L. Johnson, C. Hirsch, Z. Toossi, and E. J. Arts Human Immunodeficiency Virus Type 1 (HIV-1) Quasispecies at the Sites of Mycobacterium tuberculosis Infection Contribute to Systemic HIV-1 Heterogeneity J. Virol., February 15, 2002; 76(4): 1697 - 1706. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kudoh and D. F. Whigham A genetic analysis of hydrologically dispersed seeds of Hibiscus moscheutos (Malvaceae) Am. J. Botany, April 1, 2001; 88(4): 588 - 593. [Abstract] [Full Text]
|
|
|
|
 |
|
 A. G. Rodrigo, E. G. Shpaer, E. L. Delwart, A. K. N. Iversen, M. V. Gallo, J. Brojatsch, M. S. Hirsch, B. D. Walker, and J. I. Mullins Coalescent estimates of HIV-1 generation time in vivo PNAS, March 2, 1999; 96(5): 2187 - 2191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Poss, A. G. Rodrigo, J. J. Gosink, G. H. Learn, D. de Vange Panteleeff, H. L. Martin Jr., J. Bwayo, J. K. Kreiss, and J. Overbaugh Evolution of Envelope Sequences from the Genital Tract and Peripheral Blood of Women Infected with Clade A Human Immunodeficiency Virus Type 1 J. Virol., October 1, 1998; 72(10): 8240 - 8251. [Abstract] [Full Text] [PDF]
|
|