PMID- 22808236
OWN - NLM
STAT- MEDLINE
DCOM- 20130110
LR  - 20220330
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 7
IP  - 7
DP  - 2012
TI  - Always look on both sides: phylogenetic information conveyed by simple sequence 
      repeat allele sequences.
PG  - e40699
LID - 10.1371/journal.pone.0040699 [doi]
LID - e40699
AB  - 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.
FAU - Barthe, Stephanie
AU  - Barthe S
AD  - Unite Mixte de Recherche Ecologie des forets de Guyane, University of French West 
      Indies and French Guiana, Kourou, French Guiana.
FAU - Gugerli, Felix
AU  - Gugerli F
FAU - Barkley, Noelle A
AU  - Barkley NA
FAU - Maggia, Laurent
AU  - Maggia L
FAU - Cardi, Celine
AU  - Cardi C
FAU - Scotti, Ivan
AU  - Scotti I
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120713
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - *Alleles
MH  - Base Sequence
MH  - Genetic Loci/genetics
MH  - Genetics, Population
MH  - Linkage Disequilibrium/genetics
MH  - Microsatellite Repeats/*genetics
MH  - Molecular Sequence Data
MH  - *Phylogeny
MH  - Plants/genetics
MH  - Polymorphism, Genetic
MH  - Sequence Alignment
PMC - PMC3396589
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2012/07/19 06:00
MHDA- 2013/01/11 06:00
PMCR- 2012/07/13
CRDT- 2012/07/19 06:00
PHST- 2012/02/07 00:00 [received]
PHST- 2012/06/12 00:00 [accepted]
PHST- 2012/07/19 06:00 [entrez]
PHST- 2012/07/19 06:00 [pubmed]
PHST- 2013/01/11 06:00 [medline]
PHST- 2012/07/13 00:00 [pmc-release]
AID - PONE-D-12-04240 [pii]
AID - 10.1371/journal.pone.0040699 [doi]
PST - ppublish
SO  - PLoS One. 2012;7(7):e40699. doi: 10.1371/journal.pone.0040699. Epub 2012 Jul 13.