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Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.

https://arctichealth.org/en/permalink/ahliterature130568
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Publication Type
Article
Date
Apr-2012
Author
Sanne Boessenkool
Laura S Epp
James Haile
Eva Bellemain
Mary Edwards
Eric Coissac
Eske Willerslev
Christian Brochmann
Author Affiliation
National Centre for Biosystematics, Natural History Museum, University of Oslo, Oslo, Norway. sanneboessenkool@gmail.com
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Date
Apr-2012
Language
English
Publication Type
Article
Keywords
Animals
DNA - analysis - isolation & purification
DNA Contamination
DNA Primers - genetics
Fossils
Geologic Sediments - chemistry
Humans
Ice
Perissodactyla - classification - genetics
Polymerase Chain Reaction - methods
Sequence Analysis, DNA - methods
Siberia
Abstract
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (Coelodonta antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analyses, the PCR can be biased towards the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.
PubMed ID
21988749 View in PubMed
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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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Dissimilar responses of larch stands in northern Siberia to increasing temperatures - a field and simulation based study.

https://arctichealth.org/en/permalink/ahliterature282406
Source
Ecology. 2017 May 05;
Publication Type
Article
Date
May-05-2017
Author
Mareike Wieczorek
Stefan Kruse
Laura S Epp
Alexei Kolmogorov
Anatoly N Nikolaev
Ingo Heinrich
Florian Jeltsch
Lyudmila A Pestryakova
Romy Zibulski
Ulrike Herzschuh
Source
Ecology. 2017 May 05;
Date
May-05-2017
Language
English
Publication Type
Article
Abstract
Arctic and alpine treelines worldwide differ in their reactions to climate change. A northward advance of or densification within the treeline ecotone will likely influence climate-vegetation feedback mechanisms. In our study, which was conducted in the Taimyr Depression in the North Siberian Lowlands, w present a combined field- and model-based approach helping us to better understand the population processes involved in the responses of the whole treeline ecotone, spanning from closed forest to single-tree tundra, to climate warming. Using information on stand structure, tree age, and seed quality and quantity from seven sites, we investigate effects of intra-specific competition and seed availability on the specific impact of recent climate warming on larch stands. Field data show that tree density is highest in the forest-tundra, and average tree size decreases from closed forest to single-tree tundra. Age-structure analyses indicate that the trees in the closed forest and forest-tundra have been present for at least ~240 years. At all sites except the most southerly ones, past establishment is positively correlated with regional temperature increase. In the single-tree tundra however, a change in growth form from krummholz to erect trees, beginning ~130 years ago, rather than establishment date has been recorded. Seed mass decreases from south to north, while seed quantity increases. Simulations with LAVESI (Larix Vegetation Simulator) further suggest that relative density changes strongly in response to a warming signal in the forest-tundra while intra-specific competition limits densification in the closed forest and seed limitation hinders densification in the single-tree tundra. We find striking differences in strength and timing of responses to recent climate warming. While forest-tundra stands recently densified, recruitment is almost non-existent at the southern and northern end of the ecotone due to autecological processes. Palaeo-treelines may therefore be inappropriate to infer past temperature changes at a fine scale. Moreover, a lagged treeline response to past warming will, via feedback mechanisms, influence climate change in the future. This article is protected by copyright. All rights reserved.
PubMed ID
28475233 View in PubMed
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Dissimilar responses of larch stands in northern Siberia to increasing temperatures-a field and simulation based study.

https://arctichealth.org/en/permalink/ahliterature295931
Source
Ecology. 2017 Sep; 98(9):2343-2355
Publication Type
Journal Article
Date
Sep-2017
Author
Mareike Wieczorek
Stefan Kruse
Laura S Epp
Alexei Kolmogorov
Anatoly N Nikolaev
Ingo Heinrich
Florian Jeltsch
Lyudmila A Pestryakova
Romy Zibulski
Ulrike Herzschuh
Author Affiliation
Periglacial Research Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, 14473, Germany.
Source
Ecology. 2017 Sep; 98(9):2343-2355
Date
Sep-2017
Language
English
Publication Type
Journal Article
Keywords
Arctic Regions
Climate change
Larix - physiology
Siberia
Temperature
Trees
Abstract
Arctic and alpine treelines worldwide differ in their reactions to climate change. A northward advance of or densification within the treeline ecotone will likely influence climate-vegetation feedback mechanisms. In our study, which was conducted in the Taimyr Depression in the North Siberian Lowlands, w present a combined field- and model-based approach helping us to better understand the population processes involved in the responses of the whole treeline ecotone, spanning from closed forest to single-tree tundra, to climate warming. Using information on stand structure, tree age, and seed quality and quantity from seven sites, we investigate effects of intra-specific competition and seed availability on the specific impact of recent climate warming on larch stands. Field data show that tree density is highest in the forest-tundra, and average tree size decreases from closed forest to single-tree tundra. Age-structure analyses indicate that the trees in the closed forest and forest-tundra have been present for at least ~240 yr. At all sites except the most southerly ones, past establishment is positively correlated with regional temperature increase. In the single-tree tundra, however, a change in growth form from krummholz to erect trees, beginning ~130 yr ago, rather than establishment date has been recorded. Seed mass decreases from south to north, while seed quantity increases. Simulations with LAVESI (Larix Vegetation Simulator) further suggest that relative density changes strongly in response to a warming signal in the forest-tundra while intra-specific competition limits densification in the closed forest and seed limitation hinders densification in the single-tree tundra. We find striking differences in strength and timing of responses to recent climate warming. While forest-tundra stands recently densified, recruitment is almost non-existent at the southern and northern end of the ecotone due to autecological processes. Palaeo-treelines may therefore be inappropriate to infer past temperature changes at a fine scale. Moreover, a lagged treeline response to past warming will, via feedback mechanisms, influence climate change in the future.
PubMed ID
28475233 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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6 records – page 1 of 1.