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Premise of the study: Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure.
Methods and Results: Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0.40 to 0.73 over four populations. The amplification rates of 10 markers (CA01– CA10) in populations of C. aculeata exceeded 85%. The markers also amplified across a range of closely related species, except for locus CA05, which did not amplify in C. australiensis and C. "panamericana," and locus CA10 which did not amplify in C. australiensis.
Conclusions: The identified microsatellite markers will be used to study the genetic diversity and phylogeographic structure in populations of C. aculeata in western Eurasia.
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
Here I analyse 23 populations of D. galeata, a large-lake cladoceran, distributed mainly across the Palaearctic. I detected high levels of clonal diversity and population differentiation using variation at six microsatellite loci across Europe. Most populations were characterised by deviations from H-W equilibrium and significant heterozygote deficiencies. Observed heterozygote deficiencies might be a consequence of simultaneous hatching of individuals produced during different times of the year or of the coexistence of ecologically and genetically differentiated subpopulations. A significant isolation by distance was only found over large geographic distances (> 700 km). This pattern is mainly due to the high genetic differentiation among neighbouring populations. My results suggest that historic populations of Daphnia were once interconnected by gene flow but current populations are now largely isolated. Thus local ecological conditions which determine the level of biparental sexual reproduction and local adaptation are the main factors mediating population structure of D. galeata. The population genetic structure and diversity in D. galeata was investigated at a European scale using six microsatellite loci and 12S rDNA sequence data to infer and compare historical and contemporary patterns of gene flow. D. galeata has the potential for long-distance dispersal via ephippial resting eggs by wind and other dispersing vectors (waterfowl), but shows in general strong population differentiation even among neighbouring populations. A total of 427 individuals were analysed for microsatellite and 85 individuals for mitochondrial (mtDNA) sequence data from 12 populations across Europe. I detected genetic differentiation among populations across Europe and locations within sampling regions for both genetic marker systems (average values: mtDNA FST = 0.574; microsatellite FST = 0.389), resulting in a lack of isolation by distance. Furthermore, several microsatellite alleles and one haplotype were shared across populations. Partitioning of molecular variance was inconsistant for both marker systems. Microsatellite variation was higher within than among populations, whereas mtDNA data yielded an inverse pattern. Relative high levels of nuclear DNA diversity were found across Europe. The amount of mitochondrial diversity was low in Spain, Hungary and Denmark. Gene flow analysis at a European scale did not reveal typical pattern of population recolonization in the light of postglacial colonization hypotheses. Populations, which recently experienced an expansion or population-bottleneck were observed both in middle and northern Europe. Since these populations revealed high genetic diversity in both marker systems, I suggest these areas to represent postglacial zones of secondary contact among divergent lineages of D. galeata. In order to reveal the relationship between population genetic structure of D. galeata and the relative contribution of environmental factors, I used a statistical framework based on canonical correspondence analysis. Although I detected no single ecological gradient mediating the genetic differentiation in either lake regions, it is noteworthy that the same ecological factors were significantly correlated with intra- and interspecific genetic variation of D. galeata. For example, I found a relationship between genetic variation of D. galeata and differentiation with higher and lower trophic levels (phytoplankton, submerged macrophytes and fish) and a relationship between clonal variation and species diversity within Cladocera. Variance partitioning had only a minor contribution of each environmental category (abiotic, biomass/density and diversity) to genetic diversity of D. galeata, while the largest proportion of variation was explained by shared components. My work illustrates the important role of ecological differentiation and adaptation in structuring genetic variation, and it highlights the need for approaches incorporating a landscape context for population divergence.
Length variations of repetitive sequences in different AT-rich loop-coding regions of mitochondrial 16S rDNA in two gastropod species were discovered during intraspecific haplotype surveys. Examination of the discrete length variation of the basic repeat unit in a phylogenetic framework led to the conclusion of a microsatellite-like mutational dynamic. The observations suggest that the presence of a repetitive sequence structure alone is sufficient to trigger this dynamic.