Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2001 Mar;157(3):1387–1395. doi: 10.1093/genetics/157.3.1387

Determination of the number of conserved chromosomal segments between species.

S Kumar 1, S R Gadagkar 1, A Filipski 1, X Gu 1
PMCID: PMC1461575  PMID: 11238422

Abstract

Genomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 +/- 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of approximately 1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only approximately 0.74 rearrangements per million years.

Full Text

The Full Text of this article is available as a PDF (313.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aymé S., Mattei J. F., Mattei M. G., Aurran Y., Giraud F. Nonrandom distribution of chromosome breaks in cultured lymphocytes of normal subjects. Hum Genet. 1976 Feb 29;31(2):161–175. doi: 10.1007/BF00296144. [DOI] [PubMed] [Google Scholar]
  2. Bengtsson B. O., Levan K. K., Levan G. Measuring genome reorganization from synteny data. Cytogenet Cell Genet. 1993;64(3-4):198–200. doi: 10.1159/000133574. [DOI] [PubMed] [Google Scholar]
  3. Blake J. A., Eppig J. T., Richardson J. E., Davisson M. T. The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group. Nucleic Acids Res. 2000 Jan 1;28(1):108–111. doi: 10.1093/nar/28.1.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burt D. W., Bruley C., Dunn I. C., Jones C. T., Ramage A., Law A. S., Morrice D. R., Paton I. R., Smith J., Windsor D. The dynamics of chromosome evolution in birds and mammals. Nature. 1999 Nov 25;402(6760):411–413. doi: 10.1038/46555. [DOI] [PubMed] [Google Scholar]
  5. Copeland N. G., Jenkins N. A., Gilbert D. J., Eppig J. T., Maltais L. J., Miller J. C., Dietrich W. F., Weaver A., Lincoln S. E., Steen R. G. A genetic linkage map of the mouse: current applications and future prospects. Science. 1993 Oct 1;262(5130):57–66. doi: 10.1126/science.8211130. [DOI] [PubMed] [Google Scholar]
  6. Ehrlich J., Sankoff D., Nadeau J. H. Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics. 1997 Sep;147(1):289–296. doi: 10.1093/genetics/147.1.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ewing B., Green P. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet. 2000 Jun;25(2):232–234. doi: 10.1038/76115. [DOI] [PubMed] [Google Scholar]
  8. Kumar S., Hedges S. B. A molecular timescale for vertebrate evolution. Nature. 1998 Apr 30;392(6679):917–920. doi: 10.1038/31927. [DOI] [PubMed] [Google Scholar]
  9. Liang F., Holt I., Pertea G., Karamycheva S., Salzberg S. L., Quackenbush J. Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet. 2000 Jun;25(2):239–240. doi: 10.1038/76126. [DOI] [PubMed] [Google Scholar]
  10. Nadeau J. H., Sankoff D. Counting on comparative maps. Trends Genet. 1998 Dec;14(12):495–501. doi: 10.1016/s0168-9525(98)01607-2. [DOI] [PubMed] [Google Scholar]
  11. Nadeau J. H., Taylor B. A. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci U S A. 1984 Feb;81(3):814–818. doi: 10.1073/pnas.81.3.814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nusbaum C., Slonim D. K., Harris K. L., Birren B. W., Steen R. G., Stein L. D., Miller J., Dietrich W. F., Nahf R., Wang V. A YAC-based physical map of the mouse genome. Nat Genet. 1999 Aug;22(4):388–393. doi: 10.1038/11967. [DOI] [PubMed] [Google Scholar]
  13. O'Brien S. J., Menotti-Raymond M., Murphy W. J., Nash W. G., Wienberg J., Stanyon R., Copeland N. G., Jenkins N. A., Womack J. E., Marshall Graves J. A. The promise of comparative genomics in mammals. Science. 1999 Oct 15;286(5439):458-62, 479-81. doi: 10.1126/science.286.5439.458. [DOI] [PubMed] [Google Scholar]
  14. Roest Crollius H., Jaillon O., Bernot A., Dasilva C., Bouneau L., Fischer C., Fizames C., Wincker P., Brottier P., Quétier F. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet. 2000 Jun;25(2):235–238. doi: 10.1038/76118. [DOI] [PubMed] [Google Scholar]
  15. Schoen D. J. Comparative genomics, marker density and statistical analysis of chromosome rearrangements. Genetics. 2000 Feb;154(2):943–952. doi: 10.1093/genetics/154.2.943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Waddington D., Springbett A. J., Burt D. W. A chromosome-based model for estimating the number of conserved segments between pairs of species from comparative genetic maps. Genetics. 2000 Jan;154(1):323–332. doi: 10.1093/genetics/154.1.323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Zakharov I. A., Nikiforov V. S., Stepaniuk E. V. Interval'nye otsenki kombinatornykh mer skhodstva poriadkov gomologichnykh genov. Genetika. 1995 Aug;31(8):1163–1167. [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES