Standardizing for microsatellite length in comparisons of genetic diversity (original) (raw)
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Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy
Molecular Ecology, 2009
Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed.
Current Biology, 1995
The study of plant populations is greatly facilitated by the deployment of chloroplast DNA markers. Asymmetric inheritance, lower effective population sizes and perceived lower mutation rates indicate that the chloroplast genome may have different patterns of genetic diversity compared to nuclear genomes. Convenient assays that would allow intraspecific chloroplast variability to be detected-are required. Results: Eukaryote nuclear genomes contain ubiquitous simple sequence repeat (microsatellite) loci that are highly polymorphic in length; these polymorphisms can be rapidly typed by the polymerase chain reaction (PCR). Using primers flanking simple mononucleotide repeat motifs in the chloroplast DNA of annual and perennial soybean species, we demonstrate that microsatellites in the chloroplast genome also exhibit length variation, and that this polymorphism is due to changes in the repeat region. Furthermore, we have observed a nonrandom geographic distribution of variations at these loci, and have examined the number and location of such repeats within the chloroplast genomes of other species. Conclusions: PCR-based analysis of mononucleotide repeats may be used to detect both intraspecific and interspecific variability in the chloroplast genomes of seed plants. The analysis of polymorphic microsatellites thus provides an important experimental tool to examine a range of issues in plant genetics.
PLoS ONE, 2013
Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.
Theoretical and Applied Genetics, 2002
We employed a novel set of six highly polymophic chloroplastic simple sequence repeat (cpSSR) loci to investigate the phylogeography of lodgepole pine (Pinus contorta Dougl. Ex. Loud.), and to examine aspects of the evolutionary process operating on these repetitive DNA sequences. Chloroplast haplotypes of 500 trees, sampled throughout the range of lodgepole pine, were determined. We found a marked association of genetic distance with physical distance within the scale of 0 to 1,000 km, but no association beyond that range. Likewise, geographic clustering was observed only among recent clades in a dendrogram. These phylogeographic patterns are consistant with a rapid rangewide expansion ("big-bang") followed by recent, local population differentiation ("galaxy formation"). In support of this expansion, coalescent simulations of the genealogical process gave a long-term effective population size in the low thousands, and a time to common ancestry of about 1,500 generations (12,000 years), consistent with a post-Pleistocene population expansion as documented by previous pollen-sediment analyses. Two lines of evidence (mapping mutational events onto a phylogeny, and evaluation of observed versus expected gene diversity) suggest that five of the cpSSR loci evolve primarily by a stepwise model of evolution of single repeat changes (but with a small proportion of changes involving two or more repeats), and the coalescent simulations point to a mutation rate of about 10-3 .
Microsatellite DNA as shared genetic markers among conifer species
Canadian Journal of Forest Research, 1999
Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC) n loci that were polymorphic in P. strobus also amplified SSR loci in two other soft pines of the subgenus Strobus but not in seven hard pines of the subgenus Pinus, nor in Picea glauca (Moench) Voss or Pseudotsuga menziesii (Mirb.) Franco. The six P. strobus SSR primer pairs that did amplify loci from conifers other than soft pines were those that were specific to loci monomorphic within P. strobus. These six loci were also monomorphic within seven other species tested, but four of the loci were polymorphic among species. A comparison of allelic variation among the three soft pine species found only 25 shared alleles among a total of 122 alleles at eight loci. Primer pairs for dinucleotide SSR loci that were polymorphic in Pinus radiata also specifically amplified loci from various other hard pines but not from the soft pines or from the other conifers tested.
Chloroplast microsatellites: new tools for studies in plant ecology and evolution
Trends in Ecology & Evolution, 2001
Over the past 25 years, powerful insights have been gained into the ecology, history and evolution of animal populations from the analysis of organelle DNA (Ref. 1). Organelle genomes are typically nonrecombinant, uniparentally inherited and effectively haploid 2 . In animals, the small size, high copy number, relatively conserved gene order, easy availability of primers and rapid substitution rates associated with mtDNA have led to its extensive use in a variety of studies. These studies have provided insights into many aspects of evolutionary population biology, including patterns of migration, population histories and levels of differentiation 1 .
High level of variation at Abies alba chloroplast microsatellite loci in Europe
Molecular Ecology, 1999
Based on two polymorphic chloroplast microsatellites that had been previously identified and sequence characterized in the genus Abies , genetic variation was studied in a total of 714 individuals from 17 European silver fir ( Abies alba Mill.) populations distributed all over the natural range. We found eight and 18 different length variants at each locus, respectively, which combined into 90 different haplotypes. Genetic distances between most populations were high and significant. There is also evidence for spatial organization of the distribution of haplotypes, as shown by permutation tests, which demonstrate that genetic distances increase with spatial distances. A large heterogeneity in levels of diversity across populations was observed. Furthermore, there is good congruence in the levels of allelic richness of the two loci across populations. The present organization of levels of allelic richness across the range of the species is likely to have been shaped by the distribution of refugia during the last glaciation and the subsequent recolonization processes.
Cross-specific amplification of microsatellite loci greatly enhances the effectiveness of this marker system. This shortcut would greatly enhance our examination of the gene flow and population structure of trees in diverse tropical rainforests. To explore the effectiveness and limitations of this approach, we examined allelic diversity at six microsatellite loci, originally developed in a congeneric species, in three populations of Shorea platyclados from Peninsular Malaysia. Fragment sizing was performed by an efficient and sensitive (1 bp resolution) technique using capillary electrophoresis, ethidium bromide detection, and minimal clean-up. Fragment size ranges were conserved between species and null allele frequencies were low. Higher overall levels of genetic diversity were detected in our study. Variation among populations was directly related to geographic distance. Fragment size class distributions suggest that each locus should be studied using different evolutionary models. Direct sequencing of SSR fragments revealed that size differences were due to changes in both the flanking regions and repeat motifs. Several clear examples of size homoplasy were observed, along with the disruption of perfect repeats, suggesting that cross-specific amplification of microsatellite loci requires an additional level of confirmation at the DNA sequence level before the influence of size homoplasy and changes in repeat structure can be assessed. Simulation studies demonstrate that the increasing intensity of timber harvest leads to higher variability in levels of potential heterozygosity and decreasing total number of alleles in the remnant "mother trees" The careful selection of "mother" trees can greatly enhance the future genetic diversity of populations. R e f e r e n c e s Adams R.I., Brown K.M., Hamilton M.B. (2004): The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Molecular Ecology, 13: 2579-2588.
Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait
Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were found among 159 individuals surveyed in seven widely separated populations. The total genetic diversity, H T , was 0.618, but haplotype differentiation among populations was low (G ST = 0.121). All populations were distinguished from each other by their haplotype compositions, and only one haplotype was common among all populations. Based on average squared composite cpSSR length differences (stepwise haplotypes), within-population diversity was relatively high for only one population (D 2 SH = 0.443). Frequency distributions of pairwise SSR differences among individuals within different populations, as well as branch length differences in neighbour-joining dendrograms, indicated recovery from one or more population bottlenecks, and may be explained by metapopulation dynamics.