Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.
Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily,...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22808236/?tool=EBI |
| _version_ | 1829486333194665984 |
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| author | Stéphanie Barthe Felix Gugerli Noelle A Barkley Laurent Maggia Céline Cardi Ivan Scotti |
| author_facet | Stéphanie Barthe Felix Gugerli Noelle A Barkley Laurent Maggia Céline Cardi Ivan Scotti |
| author_sort | Stéphanie Barthe |
| collection | DOAJ |
| description | Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known. |
| first_indexed | 2024-12-14T23:04:00Z |
| format | Article |
| id | doaj.art-0a9cecf38f9448a7b7baee810cdfe579 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T23:04:00Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0a9cecf38f9448a7b7baee810cdfe5792022-12-21T22:44:22ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0177e4069910.1371/journal.pone.0040699Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.Stéphanie BartheFelix GugerliNoelle A BarkleyLaurent MaggiaCéline CardiIvan ScottiSimple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22808236/?tool=EBI |
| spellingShingle | Stéphanie Barthe Felix Gugerli Noelle A Barkley Laurent Maggia Céline Cardi Ivan Scotti Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. PLoS ONE |
| title | Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. |
| title_full | Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. |
| title_fullStr | Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. |
| title_full_unstemmed | Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. |
| title_short | Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. |
| title_sort | always look on both sides phylogenetic information conveyed by simple sequence repeat allele sequences |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22808236/?tool=EBI |
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