DNA from soil mirrors plant taxonomic and growth form diversity.

Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13-158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies.

Norway spruce of northern Europe expanded at the end of the last glacial out of one refugium in Russia. To provide a detailed insight into how the genetic structure in the northern European lineage of this species has been shaped by postglacial migration, recurrent pollen flow and marginality, we here compare variation at seven highly variable nuclear microsatellite loci in 37 populations (1715 trees) with mitochondrial DNA variation. Microsatellite diversity was high (H(E)=0.640) and genetic differentiation was low (F(ST)=0.029). The microsatellite structure supported a mitochondrial DNA (mtDNA)-based hypothesis of two migration routes out of a single Russian refugium; one northwestern over Finland to northern Scandinavia, and one southwestern across the Baltic Sea into southern Scandinavia. Microsatellite diversity was maintained along the southwestern migration routes, whereas a significant decrease was observed towards the north. In contrast, the mtDNA diversity suggested higher amounts of historical gene flow towards the north than along the southwestern migration route. This suggests that the loss of nuclear diversity after postglacial colonization has been efficiently replenished by pollen-mediated gene flow in the south. Towards the north, smaller effective population size because of more limited seed and pollen production may have caused decreased nuclear diversity and increased inbreeding, reflecting the ecological marginality of the species in the north.

A comparison of AFLPs and microsatellites to identify the population structure of brown trout (Salmo trutta L.) populations from Hardangervidda, Norway.

A total of 495 fish from 11 Hardangervidda lakes were genotyped in order to compare amplified fragment length polymorphisms (AFLP) and microsatellites in terms of their capacity to infer population genetic structure. The 11 microsatellites used in this study gave a greater polymorphism information content and greater gene diversity, with an average of 14.8 alleles per locus, than the six AFLP primer combinations used. However, the AFLPs resulted in 178 polymorphic loci and a 3.1 times larger marker index (effective multiplex ratio multiplied with the gene diversity). Comparable population structuring, for example in terms of distinguishing fish from the different river systems, was obtained with both marker systems. An AFLP and microsatellite multilocus Bayesian assignment test with the structure program divided the fish into six groups largely concurrent with main branches on a population neighbour-joining tree. Yet, the admixture status of individuals is mostly contradictory in the AFLP and the microsatellite analyses. The results are discussed concerning migration between lake populations.