| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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| 11. |
- 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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| 12. |
- 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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| 13. |
- 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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| 14. |
- 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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| 15. |
- 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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