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. 2007 Apr 3:8:115.
doi: 10.1186/1471-2105-8-115.

Dependence of paracentric inversion rate on tract length

Thomas L York  1 , Rick Durrett, Rasmus Nielsen
Affiliations

Dependence of paracentric inversion rate on tract length

Thomas L York et al. BMC Bioinformatics. .

Abstract

Background: We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths.

Results: We apply the method to data from Drosophila melanogaster and D. yakuba. We find that pericentric inversions occur at a much lower rate compared to paracentric inversions. The average paracentric inversion tract length is approx. 4.8 Mb with small inversions being more frequent than large inversions. If the two breakpoints defining a paracentric inversion tract are uniformly and independently distributed over chromosome arms there will be more short tract-length inversions than long; we find an even greater preponderance of short tract lengths than this would predict. Thus there appears to be a correlation between the positions of breakpoints which favors shorter tract lengths.

Conclusion: The method developed in this paper provides the first statistical estimator for estimating the distribution of inversion tract lengths from marker data. Application of this method for a number of data sets may help elucidate the relationship between the length of an inversion and the chance that it will get accepted.

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Figures

Figure 1
Figure 1
Position in D. melanogaster vs. position in D. yakuba for chains after filtering, chromosome 3. Lines show blocks.
Figure 2
Figure 2
Position in D. melanogaster vs. position in D. yakuba for chains after filtering, chromosome X. Lines show blocks.
Figure 3
Figure 3
Position in D. melanogaster vs. position in D. yakuba for chains after filtering, chromosome 2. Lines show blocks.
Figure 4
Figure 4
Posterior distribution of the number of inversions LI. Vertical lines indicate the 95% credible interval.
Figure 5
Figure 5
Posterior distribution of λpa. Vertical lines indicate the 95% credible interval.
Figure 6
Figure 6
Posterior distribution of exponential tract-length dependence parameter β. Vertical lines indicate the 95% credible interval.
Figure 7
Figure 7
Posterior joint distribution of λpa and β. The triangle marks the mode.
Figure 8
Figure 8
Position in D. melanogaster vs. position in D. yakuba for chains identified as on the same arm of chromosome 3 in both species.
See this image and copyright information in PMC

References

    1. Sturtevant AH, Dobzhansky T. Inversions in the third chromosome of wild races of Drosophila pseudoobscura, and their use in the study of the history of the species. Proceedings of the National Academy of Sciences USA. 1936;22:448–450. doi: 10.1073/pnas.22.7.448. - DOI - PMC - PubMed
    1. Watterson GA, Ewens WJ, Hall TE, Morgan A. The chromosome inversion problem. Journal of Theoretical Biology. 1982;99:1–7. doi: 10.1016/0022-5193(82)90384-8. - DOI
    1. Kececioglu J, Sankoff D. Exact and approximation algorithms for the inversion distance between two permutations. Algortihmica. 1995;13:180–210. doi: 10.1007/BF01188586. - DOI
    1. Hannenhalli S, Pevzner PA. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals) Proceedings of the 27th Annual ACM Symposium on the Theory of Computing. 1995. pp. 1–27.
    1. Larget B, Simon DL, Kadane JB. Bayesian phylogenetic inference from animal mitochondrial genome arrangements (with discussion) J R Stat Soc Ser B. 2002;64:681–693. doi: 10.1111/1467-9868.00356. - DOI

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