MBE Advance Access originally published online on November 21, 2005
Molecular Biology and Evolution 2006 23(3):598-607; doi:10.1093/molbev/msj065
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
Quantifying Ascertainment Bias and Species-Specific Length Differences in Human and Chimpanzee Microsatellites Using Genome Sequences
Department of Zoology, University of Cambridge, Cambridge, United Kingdom
E-mail: ejv22{at}cam.ac.uk.
Surveys of variability of homologous microsatellite loci among species reveal an ascertainment bias for microsatellite length where microsatellite loci isolated in one species tend to be longer than homologous loci in related species. Here, we take advantage of the availability of aligned human and chimpanzee genome sequences to compare length difference of homologous microsatellites for loci identified in humans to length difference for loci identified in chimpanzees. We are able to quantify ascertainment bias for a range of motifs and microsatellite lengths. Because ascertainment bias should not exist if a microsatellite selected in one species is as likely to be longer as it is to be shorter than its homologue, we propose that the nature of ascertainment bias can provide evidence for understanding how microsatellites evolve. We show that bias is greater for longer microsatellites but also that many long microsatellites have short homologues. These results are consistent with the notion that growth of long microsatellites is constrained by an upper length boundary that, when reached, sometimes results in large deletions. By evaluating ascertainment bias separately for interrupted and uninterrupted repeats we also show that long microsatellites tend to become interrupted, thereby contributing a second component of ascertainment bias. Having accounted for ascertainment bias, in agreement with results published elsewhere, we find that microsatellites in humans are longer on average than those in chimpanzees. This length difference is similar among repeat motifs but surprisingly comprises two roughly equal components, one associated with the repeats themselves and one with the flanking sequences. The differences we find can only be explained if microsatellites are both evolving directionally under a biased mutation process and are doing so at different rates in different closely related species.
Key Words: microsatellite • short tandem repeat • ascertainment bias • human • chimpanzee
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Brandstrom and H. Ellegren Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias Genome Res., June 1, 2008; 18(6): 881 - 887. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. D. Kelkar, S. Tyekucheva, F. Chiaromonte, and K. D. Makova The genome-wide determinants of human and chimpanzee microsatellite evolution Genome Res., January 1, 2008; 18(1): 30 - 38. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Laidlaw, Y. Gelfand, K.-W. Ng, H. R. Garner, R. Ranganathan, G. Benson, and J. W. Fondon III Elevated Basal Slippage Mutation Rates among the Canidae J. Hered., August 3, 2007; (2007) esm017v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Kayser, E. J. Vowles, D. Kappei, and W. Amos Microsatellite Length Differences Between Humans and Chimpanzees at Autosomal Loci Are Not Found at Equivalent Haploid Y Chromosomal Loci Genetics, August 1, 2006; 173(4): 2179 - 2186. [Abstract] [Full Text] [PDF]
|
|