Project description:Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.
Project description:This dataset include the raw sedimentary ancient DNA metabarcoding sequencing data in "Holocene rangeland characteristics on the northeastern Tibetan Plateau in relation to climate and pastoralism from sedimentary ancient DNA"
Project description:Deep Lake is a hypersaline system in Antarctica (68°33’36.8S, 78°11’48.7E) that is so saline it remains liquid at –20°C (DeMaere et al 2013). The lake is dominated by haloarchaea, comprising a low-complexity community that differs greatly to warm-hot latitude hypersaline systems, is hierarchical structured, and supports a high level of intergenera gene exchange. Metaproteomics was performed on biomass that was collected in the austral summer of 2008 by sequential size fractionation (20 – 3 µm, 3 – 0.8 µm, 0.8 – 0.1 µm). The data were integrated to obtain a systems level view of the active host-virus interactions occurring in this novel aquatic Antarctic system. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944
Project description:We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments. These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.
Project description:We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments. These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.
Project description:Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.