- 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 Chakravarti, A.
- Articles by Reefer, J. E.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Chakravarti, A.
- Articles by Reefer, J. E.
Genetics, Vol 128, 175-182, Copyright © 1991
INVESTIGATIONS |
A Maximum Likelihood Method for Estimating Genome Length Using Genetic Linkage Data
A. Chakravarti, L. K. Lasher and J. E. Reefer
Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
The genetic length of a genome, in units of Morgans or centimorgans, is a fundamental characteristic of an organism. We propose a maximum likelihood method for estimating this quantity from counts of recombinants and nonrecombinants between marker locus pairs studied from a backcross linkage experiment, assuming no interference and equal chromosome lengths. This method allows the calculation of the standard deviation of the estimate and a confidence interval containing the estimate. Computer simulations have been performed to evaluate and compare the accuracy of the maximum likelihood method and a previously suggested method-of-moments estimator. Specifically, we have investigated the effects of the number of meioses, the number of marker loci, and variation in the genetic lengths of individual chromosomes on the estimate. The effect of missing data, obtained when the results of two separate linkage studies with a fraction of marker loci in common are pooled, is also investigated. The maximum likelihood estimator, in contrast to the method-of-moments estimator, is relatively insensitive to violation of the assumptions made during analysis and is the method of choice. The various methods are compared by application to partial linkage data from Xiphophorus.
This article has been cited by other articles:
 |
|
 |
|
  O. Niehuis, A. K. Judson, and J. Gadau Cytonuclear Genic Incompatibilities Cause Increased Mortality in Male F2 Hybrids of Nasonia giraulti and N. vitripennis Genetics, January 1, 2008; 178(1): 413 - 426. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. F. McDaniel, J. H. Willis, and A. J. Shaw A Linkage Map Reveals a Complex Basis for Segregation Distortion in an Interpopulation Cross in the Moss Ceratodon purpureus Genetics, August 1, 2007; 176(4): 2489 - 2500. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Mathias, L. Jacky, W. E. Bradshaw, and C. M. Holzapfel Quantitative Trait Loci Associated with Photoperiodic Response and Stage of Diapause in the Pitcher-Plant Mosquito, Wyeomyia smithii Genetics, May 1, 2007; 176(1): 391 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Sekino and M. Hara Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers Genetics, February 1, 2007; 175(2): 945 - 958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Nakazato, M.-K. Jung, E. A. Housworth, L. H. Rieseberg, and G. J. Gastony Genetic Map-Based Analysis of Genome Structure in the Homosporous Fern Ceratopteris richardii Genetics, July 1, 2006; 173(3): 1585 - 1597. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Smith, D. K. Kump, J. A. Walker, D. M. Parichy, and S. R. Voss A Comprehensive Expressed Sequence Tag Linkage Map for Tiger Salamander and Mexican Axolotl: Enabling Gene Mapping and Comparative Genomics in Ambystoma Genetics, November 1, 2005; 171(3): 1161 - 1171. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bouck, R. Peeler, M. L. Arnold, and S. R. Wessler Genetic Mapping of Species Boundaries in Louisiana Irises Using IRRE Retrotransposon Display Markers Genetics, November 1, 2005; 171(3): 1289 - 1303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Hall and J. H. Willis Transmission Ratio Distortion in Intraspecific Hybrids of Mimulus guttatus: Implications for Genomic Divergence Genetics, May 1, 2005; 170(1): 375 - 386. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hubert and D. Hedgecock Linkage Maps of Microsatellite DNA Markers for the Pacific Oyster Crassostrea gigas Genetics, September 1, 2004; 168(1): 351 - 362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Tani, T. Takahashi, H. Iwata, Y. Mukai, T. Ujino-Ihara, A. Matsumoto, K. Yoshimura, H. Yoshimaru, M. Murai, K. Nagasaka, et al. A Consensus Linkage Map for Sugi (Cryptomeria japonica) From Two Pedigrees, Based on Microsatellites and Expressed Sequence Tags Genetics, November 1, 2003; 165(3): 1551 - 1568. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Yu and X. Guo Genetic Linkage Map of the Eastern Oyster Crassostrea virginica Gmelin Biol. Bull., June 1, 2003; 204(3): 327 - 338. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Schwarz-Sommer, E. de Andrade Silva, R. Berndtgen, W.-E. Lonnig, A. Muller, I. Nindl, K. Stuber, J. Wunder, H. Saedler, T. Gubitz, et al. A Linkage Map of an F2 Hybrid Population of Antirrhinum majus and A. molle Genetics, February 1, 2003; 163(2): 699 - 710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Fishman, A. J. Kelly, E. Morgan, and J. H. Willis A Genetic Map in the Mimulus guttatus Species Complex Reveals Transmission Ratio Distortion due to Heterospecific Interactions Genetics, December 1, 2001; 159(4): 1701 - 1716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-T. Cervera, V. Storme, B. Ivens, J. Gusmao, B. H. Liu, V. Hostyn, J. Van Slycken, M. Van Montagu, and W. Boerjan Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P. trichocarpa) Based on AFLP and Microsatellite Markers Genetics, June 1, 2001; 158(2): 787 - 809. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Hurme, M. J. Sillanpää, E. Arjas, T. Repo, and O. Savolainen Genetic Basis of Climatic Adaptation in Scots Pine by Bayesian Quantitative Trait Locus Analysis Genetics, November 1, 2000; 156(3): 1309 - 1322. [Abstract] [Full Text]
|
|
|
|
|
|
S. Wickert and E. Orias Tetrahymena Micronuclear Genome Mapping: A High-Resolution Meiotic Map of Chromosome 1L Genetics, March 1, 2000; 154(3): 1141 - 1153. [Abstract] [Full Text]
|
|
|
|
|
|
D. J. Schoen Comparative Genomics, Marker Density and Statistical Analysis of Chromosome Rearrangements Genetics, February 1, 2000; 154(2): 943 - 952. [Abstract] [Full Text]
|
|
|
|
 |
|
 M. Ohtsuka, S. Makino, K. Yoda, H. Wada, K. Naruse, H. Mitani, A. Shima, K. Ozato, M. Kimura, and H. Inoko Construction of a Linkage Map of the Medaka (Oryzias latipes) and Mapping of the Da Mutant Locus Defective in Dorsoventral Patterning Genome Res., December 1, 1999; 9(12): 1277 - 1287. [Abstract] [Full Text]
|
|
|
|
|
|
M. Cáceres, A. Barbadilla, and A. Ruiz Recombination Rate Predicts Inversion Size in Diptera Genetics, September 1, 1999; 153(1): 251 - 259. [Abstract] [Full Text]
|
|
|
|
|
|
M. W. Neff, K. W. Broman, C. S. Mellersh, K. Ray, G. M. Acland, G. D. Aguirre, J. S. Ziegle, E. A. Ostrander, and J. Rine A Second-Generation Genetic Linkage Map of the Domestic Dog, Canis familiaris Genetics, February 1, 1999; 151(2): 803 - 820. [Abstract] [Full Text]
|
|