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A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.

https://arctichealth.org/en/permalink/ahliterature292509
Source
Mol Ecol Resour. 2017 Nov; 17(6):e46-e62
Publication Type
Comparative Study
Evaluation Studies
Journal Article
Date
Nov-2017
Author
Bastian Niemeyer
Laura S Epp
Kathleen R Stoof-Leichsenring
Luidmila A Pestryakova
Ulrike Herzschuh
Author Affiliation
Periglacial Research Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
Source
Mol Ecol Resour. 2017 Nov; 17(6):e46-e62
Date
Nov-2017
Language
English
Publication Type
Comparative Study
Evaluation Studies
Journal Article
Keywords
Biodiversity
DNA Barcoding, Taxonomic - methods
DNA, Plant - genetics - isolation & purification
Geologic sediments
Lakes
Metagenomics - methods
Plants - classification - genetics
Pollen - classification
Siberia
Abstract
Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.
PubMed ID
28488798 View in PubMed
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Genetic data from algae sedimentary DNA reflect the influence of environment over geography.

https://arctichealth.org/en/permalink/ahliterature265299
Source
Sci Rep. 2015;5:12924
Publication Type
Article
Date
2015
Author
Kathleen R Stoof-Leichsenring
Ulrike Herzschuh
Luidmila A Pestryakova
Juliane Klemm
Laura S Epp
Ralph Tiedemann
Source
Sci Rep. 2015;5:12924
Date
2015
Language
English
Publication Type
Article
Abstract
Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur in similar environments and less-related lineages in dissimilar environments, in our case different vegetation and co-varying climatic and limnic variables across treeline transects. Thus our study reveals that environmental conditions rather than geographic distance is reflected by diatom-relatedness patterns in space and time. We tentatively speculate that the detected relatedness pattern in Staurosira across the treeline could be a result of adaptation to diverse environmental conditions across the arctic boreal treeline, however, a geographically-driven divergence and subsequent repopulation of ecologically different habitats might also be a potential explanation for the observed pattern.
PubMed ID
26261899 View in PubMed
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Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia.

https://arctichealth.org/en/permalink/ahliterature306219
Source
PLoS One. 2020; 15(4):e0230284
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
2020
Author
Kathleen R Stoof-Leichsenring
Katharina Dulias
Boris K Biskaborn
Luidmila A Pestryakova
Ulrike Herzschuh
Author Affiliation
Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
Source
PLoS One. 2020; 15(4):e0230284
Date
2020
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Biodiversity
Diatoms - classification - genetics
Lakes - microbiology
Phylogeny
Siberia
Abstract
Large, old and heterogenous lake systems are valuable sources of biodiversity. The analysis of current spatial variability within such lakes increases our understanding of the origin and establishment of biodiversity. The environmental sensitivity and the high taxonomic richness of diatoms make them ideal organisms to investigate intra-lake variability. We investigated modern intra-lake diatom diversity in the large and old sub-arctic Lake Bolshoe Toko in Siberia. Our study uses diatom-specific metabarcoding, applying a short rbcL marker combined with next-generation sequencing and morphological identification to analyse the diatom diversity in modern sediment samples of 17 intra-lake sites. We analysed abundance-based compositional taxonomic diversity and generic phylogenetic diversity to investigate the relationship of diatom diversity changes with water depth. The two approaches show differences in taxonomic identification and alpha diversity, revealing a generally higher diversity with the genetic approach. With respect to beta diversity and ordination analyses, both approaches result in similar patterns. Water depth or related lake environmental conditions are significant factors influencing intra-lake diatom patterns, showing many significant negative correlations between alpha and beta diversity and water depth. Further, one near-shore and two lagoon lake sites characterized by low (0-10m) and medium (10-30m) water depth are unusual with unique taxonomic compositions. At deeper (>30m) water sites we identified strongest phylogenetic clustering in Aulacoseira, but generally much less in Staurosira, which supports that water depth is a strong environmental filter on the Aulacoseira communities. Our study demonstrates the utility of combining analyses of genetic and morphological as well as phylogenetic diversity to decipher compositional and generic phylogenetic patterns, which are relevant in understanding intra-lake heterogeneity as a source of biodiversity in the sub-arctic glacial Lake Bolshoe Toko.
PubMed ID
32294095 View in PubMed
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Long-lived larch clones may conserve adaptations that could restrict treeline migration in northern Siberia.

https://arctichealth.org/en/permalink/ahliterature304690
Source
Ecol Evol. 2020 Sep; 10(18):10017-10030
Publication Type
Journal Article
Date
Sep-2020
Author
Stefan Kruse
Aleksey I Kolmogorov
Luidmila A Pestryakova
Ulrike Herzschuh
Author Affiliation
Polar Terrestrial Environmental Systems Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research Potsdam Germany.
Source
Ecol Evol. 2020 Sep; 10(18):10017-10030
Date
Sep-2020
Language
English
Publication Type
Journal Article
Abstract
The occurrence of refugia beyond the arctic treeline and genetic adaptation therein play a crucial role of largely unknown effect size. While refugia have potential for rapidly colonizing the tundra under global warming, the taxa may be maladapted to the new environmental conditions. Understanding the genetic composition and age of refugia is thus crucial for predicting any migration response. Here, we genotype 194 larch individuals from an ~1.8 km2 area in northcentral Siberia on the southern Taimyr Peninsula by applying an assay of 16 nuclear microsatellite markers. For estimating the age of clonal individuals, we counted tree rings at sections along branches to establish a lateral growth rate that was then combined with geographic distance. Findings reveal that the predominant reproduction type is clonal (58.76%) by short distance spreading of ramets. One outlier of clones 1 km apart could have been dispersed by reindeer. In clonal groups and within individuals, we find that somatic mutations accumulate with geographic distance. Clonal groups of two or more individuals are observed. Clonal age estimates regularly suggest individuals as old as 2,200 years, which coincides with a major environmental change that forced a treeline retreat in the region. We conclude that individuals with clonal growth mode were naturally selected as it lowers the likely risk of extinction under a harsh environment. We discuss this legacy from the past that might now be a maladaptation and hinder expansion under currently strongly increasing temperatures.
PubMed ID
33005360 View in PubMed
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Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China).

https://arctichealth.org/en/permalink/ahliterature303896
Source
Biodivers Data J. 2020; 8:e57089
Publication Type
Journal Article
Date
2020
Author
Kathleen Rosmarie Stoof-Leichsenring
Sisi Liu
Weihan Jia
Kai Li
Luidmila A Pestryakova
Steffen Mischke
Xianyong Cao
Xingqi Liu
Jian Ni
Stefan Neuhaus
Ulrike Herzschuh
Author Affiliation
Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.
Source
Biodivers Data J. 2020; 8:e57089
Date
2020
Language
English
Publication Type
Journal Article
Abstract
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.
PubMed ID
33364896 View in PubMed
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