Complementarity of lacustrine pollen and sedimentary DNA in representing vegetation on the central-eastern Tibetan Plateau

Plant environmental DNA extracted from lacustrine sediments (sedimentary DNA, sedDNA) has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic resolution. However, the representation of vegetation communities surrounding the lake is still unclear. In this study, we compared plant sedDNA metabarcoding and pollen assemblages from 27 lake surface-sediment samples collected from alpine meadow on the central-eastern Tibetan Plateau to investigate the representation of sedDNA data. In general, the identified components of sedDNA are consistent with the counted pollen taxa and local plant communities. Relative to pollen identification, sedDNA data have higher taxonomic resolution, thus providing a potential approach for reconstructing past plant diversity. The sedDNA signal is strongly influenced by local plants while rarely affected by exogenous plants. Because of the overrepresentation of local plants and PCR bias, the abundance of sedDNA sequence types is very variable among sites, and should be treated with caution when investigating past vegetation cover and climate based on sedDNA data. Our finding suggests that sedDNA analysis can be a complementary approach for investigating the presence/absence of past plants and history of human land-use with higher taxonomic resolution

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era

Centennial-scale variability of the Indian Summer Monsoon during the middle to late Holocene and its links with ENSO activity

Relatively little is known about the relationship between the Indian summer monsoon (ISM) and the El Niño-Southern Oscillation (ENSO) on the centennial timescale during the Holocene. We present a well-dated high-resolution X-ray fluorescence (XRF) scanning record from a sediment core from Lake Qionghai on the southeastern Tibetan Plateau, which reveals the impact of ENSO activity on ISM variability. The results indicate a gradual drying of the regional climate on the sub-orbital timescale, which is in broad agreement with ISM changes controlled by Northern Hemisphere summer insolation. Additionally, centennial-scale drought events occurred at around 6230–5740, 4620–4250, 3820–3540, 3210–2440, 2180–1320, and 1000–615 cal yr B.P. and are consistent with enhanced ENSO activity, documenting the occurrence of ENSO-related drought events in the Holocene. Both ISM oscillations and ENSO variability show significant 350-yr, 500-yr, and 800-yr cyclicities, and there is a highly significant negative relationship between the ISM and ENSO at these cyclicities, indicating that a weak ISM was related to increased ENSO intensity, and vice versa. Our findings provide evidence for the modulation of ISM intensity by ENSO variability on the centennial timescale during the Holocene

Description of a new troglobitic Sinocyclocheilus (Pisces, Cyprinidae) species from the upper Yangtze River Basin in Guizhou, South China

Sinocyclocheilus guiyang, a new troglobitic species from a subterranean tributary of the upper Yangtze Basin in Guiyang City, Guizhou Province, China is described in the present study. The new species is distinguishable from its congeneric species by a combination of the following characters: tip of maxillary barbel reaching to posterior edge of orbit; forehead horn absent; eye absent (or highly reduced) and tip of pectoral fins not significantly extending beyond the base of the pelvic fin. Molecular evidence, based on the mitochondrial cytochrome b (cytb) gene, further supports the validity of the species and also reveals its close relationship with S. cyphotergous, S. multipunctatus, S. punctatus and S. sanxiaensis. In addition, the new species faces a high risk of extinction, underscoring the urgency for habitat protection measures within its limited range

Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high‐latitude and high‐elevation lakes in Siberia and China

Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long‐term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments. In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface‐sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores. The surface‐sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12°C and conductivity ranges between 40 and 400 μS cm−1. Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late‐glacial and Mid‐Holocene. In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation. Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake‐hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659National Natural Science Foundation of China http://dx.doi.org/10.13039/501100001809Second Tibetan Plateau Scientific Expedition and Research Programhttps://doi.pangaea.de/10.1594/PANGAEA.920866https://doi.org/10.5061/dryad.k6djh9w4

Radiocarbon dating of sediment core EN21103 from Lake Ulu, eastern Siberia

Radiocarbon dating performed on the total organic carbon content of 40 bulk sediments, measured at the MICADAS (Mini Carbon Dating System) Laboratory of AWI in Bremerhaven

Element composition of sediment core EN21103 from Lake Ulu, eastern Siberia

Element composition including total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and total nitrogen (TN), measured with a soli TOC cube (Elementar) and a rapid MAX N exceed (Elementar) at the Carbon and Nitrogen Laboratory of AWI in Potsdam. The minimum detectable concentration for natural sediment samples is 0.1% for both machines

Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China)

Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA (sedDNA) is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C and +18°C and in mean annual precipitation between 36­ and 935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying dataset was conducted by a specific plant metabarcoding approach

Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China)

Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA (sedDNA) is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C and +18°C and in mean annual precipitation between 36­ and 935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying dataset was conducted by a specific plant metabarcoding approach.We provide a large dataset of genetic plant diversity retrieved from surface sedimentary DNA from lakes in Siberia and China spanning over a large environmental gradient. Our dataset encompasses sedDNA sequence data of 259 surface lake sediments and three soil samples originating from Siberian and Chinese lakes. We used the established chloroplastidal P6 loop trnL marker for plant diversity assessment. The merged, filtered and assigned dataset includes 15,692,944 read counts resulting in 623 unique plant DNA sequence types which have a 100% match to either the EMBL or to the specific Arctic plant reference database. The underlying dataset includes a taxonomic list of identified plants and results from PCR replicates, as well as extraction blanks (BLANKs) and PCR negative controls (NTCs), which were run along with the investigated lake samples. This collection of plant metabarcoding data from modern lake sediments is still ongoing and additional data will be released in the future