Chloroplast microsatellites: new tools for studies in plant ecology and systematics

The nonrecombinant, uniparentally inherited nature of organelle genomes
makes them useful tools for evolutionary studies. However, in plants, detecting
useful polymorphism at the population level is often difficult because of the
low level of substitutions in the chloroplast genome, and because of the slow
substitution rates and intramolecular recombination of mtDNA. Chloroplast
microsatellites represent potentially useful markers to circumvent this problem
and, to date, studies have demonstrated high levels of intraspecific variability.
Here,we discuss the use of these markers in ecological and evolutionary
studies of plants, as well as highlighting some of the potential problems
associated with such use.

Complex sociogenetic organization and reproductive skew in a primitively eusocial sweat bee, Lasioglossum malachurum, as revealed by microsatellites

The sweat bees (Family Halictidae) are a socially diverse taxon in which eusociality has arisen independently numerous times. The obligate, primitively eusocial Lasioglossum malachurum, distributed widely throughout Europe, has been considered the zenith of sociality within halictids. A single queen heads a colony of smaller daughter workers which, by mid-summer, produce new sexuals (males and gynes), of which only the mated gynes overwinter to found new colonies the following spring. We excavated successfully 18 nests during the worker- and gyne-producing phases of the colony cycle and analysed each nest's queen and either all workers or all gynes using highly variable microsatellite loci developed specifically for this species. Three important points arise from our analyses. First, queens are facultatively polyandrous (queen effective mating frequency: range 1–3, harmonic mean 1.13). Second, queens may head colonies containing unrelated individuals (n = 6 of 18 nests), most probably a consequence of colony usurpation during the early phase of the colony cycle before worker emergence. Third, nonqueen's workers may, but the queen's own workers do not, lay fertilized eggs in the presence of the queen that successfully develop into gynes, in agreement with so-called 'concession' models of reproductive skew

A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.

Expressed sequence tag-derived microsatellites for the cool-water marine copepod Calanus finmarchicus

The copepod Calanus finmarchicus is the major contributor to zooplankton biomass in the North Atlantic and Norwegian Sea, but recent studies have shown a 70% decrease in abundance as well as a northward shift in the species' range. Insights into dispersal capabilities gained from population genetic studies will be crucial in predicting the response of C. finmarchicus communities to climate change and, consequently, we have developed a set of expressed sequence tag-derived microsatellite markers to allow fine-scale elucidation of population structuring and dispersal. Ten polymorphic markers displayed between two and 19 alleles, with levels of expected heterozygosity ranging from 0.044 to 0.924.

Development of microsatellites for the invasive riparian plant Impatiens glandulifera (Himalayan balsam) using intersimple sequence repeat cloning

Impatiens glandulifera (Himalayan balsam) is an invasive riparian plant species that can outcompete native perennials. Population genetic data on dispersal may aid in the management of invasive species, so we have developed microsatellite markers for this significant invader using an intersimple sequence repeat (ISSR)-based cloning method. Eight polymorphic markers displayed between two and five alleles, with overall levels of observed and expected heterozygosities ranging from 0.0500 to 0.7500 and from 0.1449 to 0.7692, respectively.

Development of microsatellites for the peat moss Sphagnum capillifolium using ISSR cloning

Sphagnum mosses are major components of peat bogs but populations of many species are under threat due to habitat fragmentation resulting from the cutting of peat for fuel. We have used an intersimple sequence repeat (ISSR)-based cloning method to develop nine polymorphic nuclear microsatellites for the peat moss species Sphagnum capillifolium. Between three and seven alleles per locus were detected in a sample of 48 haploid gametophytes and levels of gene diversity ranged from 0.5391 to 0.7960. These represent the first microsatellite markers developed for this important genus and most also exhibited cross-species amplification across a range of common Sphagnum species.

Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae)

Attempts to design truly universal primers to amplify chloroplast microsatellites have met with limited success due to nonconservation of repeat loci across widely divergent taxa. We have used the complete chloroplast genome sequences of rice, maize and wheat to design five pairs of primers that amplify homologous mononucleotide repeats across the Poaceae (grasses). Sequencing confirmed conservation of repeat motifs across subfamilies and a preliminary study in Anthoxanthum odoratum revealed polymorphism at two loci with a haplotype diversity value of 0.495. These primers provide a valuable tool to study cytoplasmic diversity in this extensively studied and economically important range of taxa.

Patterns of cytoplasmic variation in Arabidopsis thaliana (Brassicaceae) revealed by polymorphic chloroplast microsatellites

Despite being the model organism for plant molecular genetic studies, little is known about the origins and evolutionary history of extant natural populations of Arabidopsis thaliana. We have analysed phylogenetic relationships between worldwide populations of Arabidopsis using polymorphic chloroplast microsatellites. These highly variable markers have revealed previously undetected levels of cytoplasmic variation and confirm previous hypotheses of a recent and rapid expansion of the species from its centre of origin. Furthermore, the results seem to verify previous nuclear analyses that call into question the true origin of several individual Arabidopsis ecotypes.

Characterization of polymorphic microsatellites for the periwinkle gastropod, Littorina littorea (Linnaeus, 1758) and their cross-amplification in four congeners

Eight polymorphic microsatellite loci are described for Littorina littorea (Linnaeus, 1758). Data on allelic variation in Irish and Celtic Sea samples are reported. The average number of alleles per locus was 11 (range 4-29), and observed and expected heterozygosities ranged from 6.9 to 84.3% and from 9.4 to 95.2%, respectively. Loci did not deviate from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci pairs was detected. Microsatellites were not highly conserved in the congeners, L. fabalis, L. saxatilis, L. compressa and L. obtusata as evidenced by a low rate of cross-amplification. These microsatellites should prove useful in population genetic studies.

Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners.

Eight new microsatellite loci were characterized for Littorina saxatilis (Olivi, 1792) and tested for their cross-hybridization in congeners. All loci were polymorphic in Irish and Celtic Sea samples, with an average number of alleles per locus of 15 (range, 6–31). Observed and expected locus heterozygosities ranged from 26 to 85% and from 53 to 92%, respectively. Three loci showed excess homozygosity and significant departures from Hardy–Weinberg expectations in one sample, possibly due to null alleles, population structuring or inbreeding. No linkage disequilibrium was detected among loci within samples. A high degree of cross-hybridization was observed in closely related congeners and most loci were polymorphic. These markers will be useful for investigating population genetic diversity and connectivity in coastal populations, especially for marine reserve design.

Levels and patterns of population genetic diversity in the red seaweed Chondrus crispus (Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites

Single nucleotide polymorphisms (SNPs) are predicted to supersede microsatellites as the marker of choice for population genetic studies in the near future. To date, however, very few studies have directly compared both marker systems in natural populations, particularly in non-model organisms. In the present study, we compared the utility of SNPs and microsatellites for population genetic analysis of the red seaweed Chondrus crispus (Florideophyceae). Six SNP loci yielded very different patterns of intrapopulation genetic diversity compared to those obtained using seven moderately (mean 5.2 alleles) polymorphic microsatellite loci, although Bayesian clustering analysis gave largely congruent results between the two marker classes. A weak but significant pattern of isolation-by-distance was observed across scales from a few hundred metres to approximately 200?km using the combined SNP and microsatellite data set of 13 loci. Over larger scales, however, there was little correlation between genetic divergence and geographical distance. Our findings suggest that even a moderate number of SNPs is sufficient to determine patterns of genetic diversity across natural populations, and also highlight the fact that patterns of genetic variation in seaweeds arise through a complex interplay of short- and long-term natural processes, as well as anthropogenic influence.

Reproductive isolation and genetic differentiation of ferox trout from sympatric brown trout in Loch Aweand Loch Laggan, Scotland

Molecular marker studies reported here, involving allozymes, mitochondrial DNA and microsatellites, demonstrate that ferox brown trout Salmo trutta in Lochs Awe and Laggan, Scotland, are reproductively isolated and genetically distinct from co-occurring brown trout. Ferox were shown to spawn primarily, and possibly solely, in a single large river in each lake system making them particularly vulnerable to environmental changes. Although a low level of introgression seems to have occurred with sympatric brown trout, possibly as a result of human-induced habitat alterations and stocking, ferox trout in these two lakes meet the requirements for classification as a distinct biological, phylogenetic and morphological species. It is proposed that the scientific name Salmo ferox Jardine, 1835, as already applied to Lough Melvin (Ireland) ferox, should be extended to Awe and Laggan ferox.