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Amplified fragment length homoplasy: in silico analysis for model and non-model species.

Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L - BMC Genomics (2010)

Bottom Line: In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus).Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti.These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France. margotparis1@gmail.com

ABSTRACT

Background: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

Results: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

Conclusions: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

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In silico AFLPs obtained on model species vs. empirical AFLPs obtained on related non-model species. A) Comparison between numbers of peaks per profile obtained for model and non-model species. B) AFLP peak length distribution obtained in silico and empirically. Peaks were grouped by classes of 20 bp-length. Symbols ● corresponded to bacteria species, ◆ to plant species and ▲ to insect species.
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Figure 3: In silico AFLPs obtained on model species vs. empirical AFLPs obtained on related non-model species. A) Comparison between numbers of peaks per profile obtained for model and non-model species. B) AFLP peak length distribution obtained in silico and empirically. Peaks were grouped by classes of 20 bp-length. Symbols ● corresponded to bacteria species, ◆ to plant species and ▲ to insect species.

Mentions: The number of fragments obtained in silico for three model species, the bacterium B. thuringiensis ser. konkukian, the plant A. thaliana and the insect Ae. aegypti, was compared with that obtained for closely related species, B. thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus, for which no full genome sequences were available (Figure 3A). The details for each model/non-model species pair and each primer combination are presented in Additional file 2.


Amplified fragment length homoplasy: in silico analysis for model and non-model species.

Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L - BMC Genomics (2010)

In silico AFLPs obtained on model species vs. empirical AFLPs obtained on related non-model species. A) Comparison between numbers of peaks per profile obtained for model and non-model species. B) AFLP peak length distribution obtained in silico and empirically. Peaks were grouped by classes of 20 bp-length. Symbols ● corresponded to bacteria species, ◆ to plant species and ▲ to insect species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875239&req=5

Figure 3: In silico AFLPs obtained on model species vs. empirical AFLPs obtained on related non-model species. A) Comparison between numbers of peaks per profile obtained for model and non-model species. B) AFLP peak length distribution obtained in silico and empirically. Peaks were grouped by classes of 20 bp-length. Symbols ● corresponded to bacteria species, ◆ to plant species and ▲ to insect species.
Mentions: The number of fragments obtained in silico for three model species, the bacterium B. thuringiensis ser. konkukian, the plant A. thaliana and the insect Ae. aegypti, was compared with that obtained for closely related species, B. thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus, for which no full genome sequences were available (Figure 3A). The details for each model/non-model species pair and each primer combination are presented in Additional file 2.

Bottom Line: In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus).Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti.These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France. margotparis1@gmail.com

ABSTRACT

Background: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

Results: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

Conclusions: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

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