| 1. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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| 2. |
- Williams, John W., et al.
(författare)
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Strengthening global-change science by integrating aeDNA with paleoecoinformatics
- 2023
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Ingår i: Trends in Ecology & Evolution. - : Elsevier. - 0169-5347 .- 1872-8383. ; 38:10, s. 946-960
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Tidskriftsartikel (refereegranskat)abstract
- Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.
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| 3. |
- Ahmed, Engy, et al.
(författare)
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Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA
- 2018
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 181, s. 19-29
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Tidskriftsartikel (refereegranskat)abstract
- The Lateglacial/early Holocene sediments from the ancient lake at Hässeldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hässeldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerød and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.
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| 4. |
- Bell, Karen L., et al.
(författare)
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Plants, pollinators and their interactions under global ecological change : The role of pollen DNA metabarcoding
- 2023
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:23, s. 6345-6362
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.
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| 5. |
- Bella, Eleni, et al.
(författare)
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Genetic insights into the hybrid origin of Abies x borisii-regis Mattf.
- 2015
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Ingår i: Plant Systematics and Evolution. - : Springer Science and Business Media LLC. - 0378-2697 .- 1615-6110 .- 2199-6881. ; 301:2, s. 749-759
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Tidskriftsartikel (refereegranskat)abstract
- Abies × borisii-regis Mattf. (King Boris fir) is a taxon endemic to the southern Balkan Peninsula, described as a hybrid between the widespread A. alba Mill. (Silver fir) and the Greek endemic A. cephalonica Loud (Greek fir). Even though A. × borisii-regis has attracted much research attention in the past, its origin, geographical distribution and taxonomic status are not fully elucidated and molecular evidence for hybridization is missing. To shed more light on this issue, we analyzed representative populations from these three Abies taxa using paternally inherited (chloroplast) and maternally inherited (mitochondrial) DNA markers. Both Silver and Greek fir could be clearly distinguished using mitochondrial markers, while we observed a mixture of maternal lineages in theA. × borisii-regis populations. In contrast, using chloroplast markers, we could not identify species-specific haplotypes, but a neighbor-joining analysis of population genetic distances revealed two separate clusters for the Silver fir and the Greek fir, while the A. × borisii-regis populations were placed in intermediate positions. Our results are in agreement with the hypothesis that the A. ×borisii-regis populations investigated are a result of hybridization between A. cephalonica and A. alba.
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| 6. |
- Bennett, Keith D., et al.
(författare)
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DNA from pollen : principles and potential
- 2006
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 16:8, s. 1031-1034
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes our recent extraction of ancient DNA (aDNA) from Holocene pollen and discusses the potential of the technique for elucidating timescales of evolutionary change. We show that plastid DNA is recoverable and usable from pollen grains of Scots pine Pinus sylvestris from 10 ka and 100 years ago. Comparison of the ancient sequences with modern sequences, obtained from an extant population, establish a first genetic link between modern and fossil samples of Scots pine, providing a genetic continuity through time. One common haplotype is present in each of the three periods investigated, suggesting that it persisted near the lake throughout the postglacial. The retrieval of aDNA from pollen has major implications for palaeoecology by allowing (i) investigation of population-level dynamics in time and space, and (ii) tracing ancestry of populations and developing phylogenetic trees that include extinct as well as extant taxa. The method should work over the last glacial oscillation, thus giving access to ancestry of populations over a crucial period of time for the understanding of the relationship between speciation and climate change.
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| 7. |
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| 8. |
- Georgolopoulos, Grigorios, et al.
(författare)
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A short phylogenetically informative cpDNA fragment for the identification of Pinus species
- 2016
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Ingår i: Biochemical Systematics and Ecology. - : Elsevier BV. - 0305-1978 .- 1873-2925. ; 66, s. 166-172
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Tidskriftsartikel (refereegranskat)abstract
- The genus Pinus L. consists of ca. 110 ecologically and economically important species extending from the arctic zone to the tropics. Nevertheless, there is little information in the literature on DNA-based methods for the identification of pine species. Here, we identified a new cpDNA fragment (trnV-H/x-h) able to differentiate among pine species and correctly depict the phylogeny within the genus. The fragment was identified based on PCR-RFLP profiles and primers designed based on the sequences of six Pinus species naturally occurring in Greece (Pinus brutia Ten., Pinus halepensis Mill., Pinus leucodermis Antoine, Pinus nigra J.F. Arnold, Pinus pinea L, and Pinus sylvestris L). We analyzed 90 highly similar pine sequences retrieved from the GenBank to investigate specificity of our marker and the haplotypes found showed to be specific to Pinus and able to differentiate among 39 different species. The phylogenetic tree constructed using these species, correctly depicted the phylogeny of the genus up to the subsection level. These characteristics together with its relatively small size (376-418 bp) make the trnV-H/x-h marker useful for pine identification even in contexts where DNA is degraded, such as in timber tracing, forensic botany and palaeobotanical investigations.
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| 9. |
- Johnson, Mark D., et al.
(författare)
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Environmental DNA as an emerging tool in botanical research
- 2023
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Ingår i: American Journal of Botany. - : John Wiley & Sons. - 0002-9122 .- 1537-2197. ; 110:2
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Forskningsöversikt (refereegranskat)abstract
- Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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| 10. |
- Källman, Thomas, et al.
(författare)
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Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:5, s. e95306-
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Tidskriftsartikel (refereegranskat)abstract
- The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce
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| 11. |
- Lendvay, Bertalan, et al.
(författare)
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Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 217:4, s. 1737-1748
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Tidskriftsartikel (refereegranskat)abstract
- Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13000yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.
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| 12. |
- MacDonald, G. M., et al.
(författare)
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Impacts of climate change on species, populations and communities : palaeobiogeographical insights and frontiers
- 2008
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Ingår i: Progress in physical geography. - : SAGE Publications. - 0309-1333 .- 1477-0296. ; 32:2, s. 139-172
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Forskningsöversikt (refereegranskat)abstract
- Understanding climate change and its potential impact on species, populations and communities is one of the most pressing questions of twenty-first-century conservation planning. Palaeobiogeographers working on Cenozoic fossil records and other lines of evidence are producing important insights into the dynamic nature of climate and the equally dynamic response of species, populations and communities. Climatic variations ranging in length from multimillennia to decades run throughout the palaeo-records of the Quaternary and earlier Cenozoic and have been shown to have had impacts ranging from changes in the genetic structure and morphology of individual species, population sizes and distributions, community composition to large-scale bio-diversity gradients. The biogeographical impacts of climate change may be due directly to the effects of alterations in temperature and moisture on species, or they may arise due to changes in factors such as disturbance regimes. Much of the recent progress in the application of palaeobiogegraphy to issues of climate change and its impacts can be attributed to developments along a number of still advancing methodological frontiers. These include increasingly finely resolved chronological resolution, more refined atmosphere-biosphere modelling, new biological and chemical techniques in reconstructing past species distributions and past climates, the development of large and readily accessible geo-referenced databases of biogeographical and climatic information, and new approaches in fossil morphological analysis and new molecular DNA techniques.
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| 13. |
- Magyari, Eniko K., et al.
(författare)
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Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 66-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect. This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
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| 14. |
- Mahmoudi Shamsabad, M, et al.
(författare)
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Impact of climate change implies the northward shift in distribution of the Irano-Turanian subalpine species complex Acanthophyllum squarrosum
- 2018
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Ingår i: Journal of Asia-Pacific Biodiversity. - : Elsevier BV. - 2287-884X. ; 11:4, s. 566-572
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we used maximum entropy modeling to predict the climate changeeffects on the distribution range of a subalpine steppe flora species complex, Acanthophyllum squarrosum (Caryophyllaceae). We used data from four different models, with two representative concentration pathways of climate scenarios in modern time, 2030, 2070 and 2080. Our results showed that A. squarrosum has a suitable habitat in ca. 1 million km² (33% of our study area) and will likely experience a northward shift, gaining new habitat in Azerbaijan, Armenia and North of Afghanistan in the near decades. Maxent model predicts A. squarrosum complex populations from southern Iran to be under treat of extinction, especially at lower altitudes regions and this prediction may concern other subalpine species found in the same region. Among the climatic variables investigated, annual mean temperature, and precipitation of warmest and coldest quarter were those that mostly affected A. squarrosum complex distribution.
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| 15. |
- Michel, Alice, et al.
(författare)
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Isolated Grauer's gorilla populations differ in diet and gut microbiome
- 2023
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:23, s. 6523-6542
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Tidskriftsartikel (refereegranskat)abstract
- The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.
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| 16. |
- Nota, Kevin, 1993-, et al.
(författare)
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Norway spruce postglacial recolonization of Fennoscandia
- 2022
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
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| 17. |
- Nota, Kevin, 1993-
(författare)
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Palaeoenvironmental reconstructions from modern and ancient plant DNA
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Palaeoecological studies on lake sediments and peat archives have provided fundamental knowledge about past environments, nevertheless, a lot remains to be learned. In this thesis, I focussed on plant ancient DNA extracted from sedimentary archives (sedaDNA), in combination with DNA from living trees with the aims of: (1) investigating different extraction methods and levels of inhibition in sediments, (2) investigating postglacial recolonisation history of Norway spruce in Fennoscandia, (3) comparing different sequencing and bioinformatic approaches to investigate past flora changes using sedaDNA and investigating past flora change in contrasting environments (southern Italy versus southern Sweden), and (4) communicating my work more broadly using art.Based on seven original methodological case studies investigating enzyme inhibition, the effect of freeze-thaw and oxygen exposure on microbial composition, and the effects of DNA extraction methods on biological diversity, we formulated guidelines and recommendations for future sedaDNA analyses. We analysed DNA traces of spruce in multiple sediments from northern Europe and confirmed that the species was present in central Sweden already at the beginning of the Holocene and, more controversially, at the end of the last glaciation in southern Sweden. Moreover, genetic ancestry of spruce trees still growing today in central Sweden suggested eastern origin of early spruce colonisers. We further demonstrated that, when sedaDNA reads are mapped to a large and high-quality nuclear plant DNA database, shotgun metagenomic analysis outperforms metabarcoding for reconstructing flora in degraded samples. However, metabarcoding remains a powerful tool to investigate past flora, because our metabarcoding analysis on southern Italian lake sediment, showed woody taxa replacement in the Holocene in good agreement with previous pollen analysis. Despite several methodological issues which complicated our floristic interpretations, at this site we also recovered a rich herbaceous flora and many aquatics. Similar methodological issues and complications, however, were also observed at higher latitudes in southern Sweden during the transition from full Glacial to the Holocene, indicating that sedaDNA from temperate environments is a comparable source of information for floral reconstruction as from high-latitude lakes. Finally, during the work of my thesis, we produced five original paintings through a long collaboration with the scientist and artist Jill Pelto, which I used in this thesis and on many other occasions to illustrate and communicate our work to a broader audience.
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| 18. |
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| 19. |
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| 20. |
- Parducci, Laura, et al.
(författare)
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Ancient DNA research
- 2004
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Ingår i: Bioscience-explained.
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 21. |
- Parducci, Laura, et al.
(författare)
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Ancient DNA studies in plant populations
- 2010
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Ingår i: Molecular markers, PCR, bioinformatics and ancient DNA-technology, troubleshooting and applications. - Cordoba : Cordoba University.
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Bokkapitel (refereegranskat)
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| 22. |
- Parducci, Laura, 1965-, et al.
(författare)
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Ancient plant DNA in lake sediments
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 214:3, s. 924-942
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Forskningsöversikt (refereegranskat)abstract
- Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant a DNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that a DNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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| 23. |
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| 24. |
- Parducci, Laura, et al.
(författare)
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Glacial Survival of Boreal Trees in Northern Scandinavia
- 2012
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 335:6072, s. 1083-1086
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Tidskriftsartikel (refereegranskat)abstract
- It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trondelag in central Norway dating back similar to 10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andoya refugium in northwestern Norway as early as similar to 22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.
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| 25. |
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| 26. |
- Parducci, Laura, et al.
(författare)
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Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia
- 2013
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 22:13, s. 3511-3524
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Tidskriftsartikel (refereegranskat)abstract
- Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
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| 27. |
- Parducci, Laura, 1965-, et al.
(författare)
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Proxy comparison in ancient peat sediments : pollen, macrofossil and plant DNA
- 2015
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 370:1660, s. 20130382-
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Tidskriftsartikel (refereegranskat)abstract
- We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
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| 28. |
- Parducci, Laura, 1965-
(författare)
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Quaternary DNA : A Multidisciplinary Research Field
- 2019
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Ingår i: Quaternary. - : MDPI AG. - 2571-550X. ; 2:4
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Forskningsöversikt (refereegranskat)abstract
- The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.
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| 29. |
- Parducci, Laura, 1965-, et al.
(författare)
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Reconstructing past vegetation communities using ancient DNA from lake sediments
- 2018
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Ingår i: Paleogenomics. - Cham : Springer. - 9783030047528 ; , s. 163-187
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Bokkapitel (refereegranskat)abstract
- The field of ancient DNA has received much attention since the mid-1980s, when the first sequences of extinct species were obtained from museum and archaeological specimens. Early analyses focused on organellar DNA (mitochondrial in animals and chloroplast in plants) as these are present in multiple copies in the cells making isolation and analyses easier. Within the last decade, however, with considerable advances in high-throughput DNA sequencing technology and bioinformatics, it has become possible to analyse the more informative nuclear genome of a larger number of ancient samples and from a larger variety of substrates and environments. Here, we present recent progress made to reconstruct ancient vegetation communities from lake sediments and review recent key findings in the field. We synthesize and discuss the sources of plant DNA in sediment, the issues relating to DNA preservation after deposition, the criteria required for authentication and the technical advances recently made in the field for the analyses and the taxonomic identification of plant ancient DNA sequences obtained from these complex substrates. Together, these advances mean that we are on the way to an explosion of new information for the investigation of ancient plant environments.
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| 30. |
- Parducci, Laura, et al.
(författare)
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Response to Comment on "Glacial Survival of Boreal Trees in Northern Scandinavia"
- 2012
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 338:6108, s. 742-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Birks et al. question our proposition that trees survived the Last Glacial Maximum (LGM) in Northern Scandinavia. We dispute their interpretation of our modern genetic data but agree that more work is required. Our field and laboratory procedures were robust; contamination is an unlikely explanation of our results. Their description of Endletvatn as ice-covered and inundated during the LGM is inconsistent with recent geological literature.
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| 31. |
- Parducci, Laura, 1965-, et al.
(författare)
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Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
- 2019
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
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| 32. |
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| 33. |
- Parducci, Laura, 1965-, et al.
(författare)
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The real significance of ancient DNA
- 2017
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 104:6, s. 800-802
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 34. |
- Ribeiro, Maria Margarida, et al.
(författare)
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Genetic diversity and divergence at the Arbutus unedo L. (Ericaceae) westernmost distribution limit
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:4
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Tidskriftsartikel (refereegranskat)abstract
- Mediterranean forests are fragile ecosystems vulnerable to recent global warming and reduction of precipitation, and a long-term negative effect is expected on vegetation with increasing drought and in areas burnt by fires. We investigated the spatial distribution of genetic variation of Arbutus unedo in the western Iberia Peninsula, using plastid markers with conservation and provenance regions design purposes. This species is currently undergoing an intense domestication process in the region, and, like other species, is increasingly under the threat from climate change, habitat fragmentation and wildfires. We sampled 451 trees from 15 natural populations from different ecological conditions spanning the whole species' distribution range in the region. We applied Bayesian analysis and identified four clusters ( north, centre, south, and a single-population cluster). Hierarchical AMOVA showed higher differentiation among clusters than among populations within clusters. The relatively low within-clusters differentiation can be explained by a common postglacial history of nearby populations. The genetic structure found, supported by the few available palaeobotanical records, cannot exclude the hypothesis of two independent A. unedo refugia in western Iberia Peninsula during the Last Glacial Maximum. Based on the results we recommend a conservation strategy by selecting populations for conservation based on their allelic richness and diversity and careful seed transfer consistent with current species' genetic structure.
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| 35. |
- Shamsabad, Masoumeh Mahmoudi, et al.
(författare)
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Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region
- 2019
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Ingår i: Systematics and Biodiversity. - : Taylor & Francis. - 1477-2000 .- 1478-0933. ; 17:4, s. 412-421
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Tidskriftsartikel (refereegranskat)abstract
- Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA-trnH and rpl32-trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.
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| 36. |
- Suyama, Yoshihisa, et al.
(författare)
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Analysis of short DNA fragments from Holocene peatmoss samples
- 2008
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 18:6, s. 1003-1006
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes our recent attempt to isolate and analyse DNA from old plant remains of the common peatmoss Sphagnum fuscum retrieved from a peat core collected in the mire Fuglmyra, in central Norway. DNA was recoverable and usable from sub-fossilized (10–450 years old) plant remains of the peatmoss. A chloroplast (trnL) and two nuclear (ITS2 and RAPDf) regions were co-amplified from 80 samples of different ages. The RAPDf region was the only variable one with three different haplotypes found among five samples. Comparison of the ancient sequences with modern sequences found in the extant population occurring at the same site ascertained a genetic link between modern and fossil samples of this species. This retrieval of ancient DNA from sub-fossilized moss remains isolated from peat cores has important implications for the palaeoecology of peatmosses by allowing direct estimates of plant population dynamics in space and time.
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| 37. |
- Tsuda, Yoshiaki, et al.
(författare)
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The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies) : cryptic refugia as stepping stones to the west?
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:12, s. 2773-2789
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Tidskriftsartikel (refereegranskat)abstract
- Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive STRUCTURE plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
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