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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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The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data.

https://arctichealth.org/en/permalink/ahliterature286226
Source
Genes (Basel). 2017 Oct 13;8(10)
Publication Type
Article
Date
Oct-13-2017
Author
Heike H Zimmermann
Elena Raschke
Laura S Epp
Kathleen R Stoof-Leichsenring
Lutz Schirrmeister
Georg Schwamborn
Ulrike Herzschuh
Source
Genes (Basel). 2017 Oct 13;8(10)
Date
Oct-13-2017
Language
English
Publication Type
Article
Abstract
Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.
PubMed ID
29027988 View in PubMed
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Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.

https://arctichealth.org/en/permalink/ahliterature310929
Source
Ecol Evol. 2021 Mar; 11(5):2173-2193
Publication Type
Journal Article
Date
Mar-2021
Author
Stefano Meucci
Luise Schulte
Heike H Zimmermann
Kathleen R Stoof-Leichsenring
Laura Epp
Pernille Bronken Eidesen
Ulrike Herzschuh
Author Affiliation
Polar Terrestrial Environmental Systems Research Group Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.
Source
Ecol Evol. 2021 Mar; 11(5):2173-2193
Date
Mar-2021
Language
English
Publication Type
Journal Article
Abstract
Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.
PubMed ID
33717447 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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