| 1. |
- Ronquist, Fredrik, et al.
(författare)
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Phylogeny, evolution and classification of gall wasps : the plot thickens.
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.
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| 2. |
- Caputo, Andrea, et al.
(författare)
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The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration
- 2019
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 366:2
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Tidskriftsartikel (refereegranskat)abstract
- Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen (N2)-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes, 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99–100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin and copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100–50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.
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| 3. |
- Dalen, Love, et al.
(författare)
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Identifying Bird Remains Using Ancient DNA Barcoding
- 2017
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Ingår i: Genes. - : MDPI AG. - 2073-4425 .- 2073-4425. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
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| 4. |
- Díez, Beatriz, et al.
(författare)
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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community : Structure, Potential Function and Evolution.
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.
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| 5. |
- Lilja, Tobias, et al.
(författare)
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Species identification of Swedish mosquitoes through DNA metabarcoding
- 2017
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Ingår i: Journal of the European Mosquito Control Association. ; 35, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- DNA-barcoding utilises a fragment of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify most animal species. Using next generation sequencing (NGS), this method can be further developed into metabarcoding processes that allow the simultaneous identification of several species from a mixed sample. We created a database of COI sequences of 27 mosquito species collected in Sweden, and combined our data with 27 additional sequences from GenBank to cover the taxa recently documented in Sweden and to include possible invasive taxa. Comparisons show that COI metabarcoding reliably identifies 41 of 54 species and the remainder to species group. Using three independent primer pairs along the COI gene, we further developed this barcoding approach to simultaneously identify Swedish mosquitoes in communities using NGS and quantify relative abundance of each mosquito species in the sample, using bioinformatics methods. We tested the accuracy of the metabarcoding method using communities assembled from morphologically identified mosquitoes, revealing 80% positive identification rate and the estimates of population structure which reflects the input sample. We conclude that metabarcoding is useful as a high throughput identification technique and for the quantification of species.
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| 6. |
- Swenson, Ulf, 1959-, et al.
(författare)
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Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus
- 2018
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Ingår i: Australian Systematic Botany. - 1030-1887 .- 1446-5701. ; 31, s. 120-165
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Tidskriftsartikel (refereegranskat)abstract
- Pleioluma (Baill.) Baehni (Sapotaceae) circumscribes some 40 medium-sized trees and shrubs, many gynodioecious, in Australia, Malesia and New Caledonia. Systematics of the group is unclear and delimitations of species are notoriously difficult. We explore species boundaries in New Caledonia by multiple accessions of ‘species’, molecules and morphology in a Bayesian framework. The molecular phylogenetic signal is weak, but morphology provides enough information to support groups, species and recognition of one cryptic species. Pleioluma is then revised for New Caledonia, a genus distinguished by areolate higher leaf venation, sepals being pubescent on both surfaces, stamens inserted in or below the middle of the corolla tube, presence of staminodes, foliaceous cotyledons and endosperm. Seventeen endemic species are recognised with descriptions, recognition notes, distributions, etymologies and conservation assessments. Six species are described as new, of which four are assigned IUCN preliminary status as Critically Endangered and in urgent need of protection (Pleioluma acutifolia Swenson & Munzinger, P. belepensis Swenson & Munzinger, P. butinii Swenson & Munzinger and P. tchingouensis Swenson & Munzinger). The new species, P. dioica Swenson & Munzinger and P. tenuipedicellata Swenson & Munzinger are respectively assessed as Data Deficient and Vulnerable. The micro-endemic species P. vieillardii (Baill.) Swenson & Munzinger, confined to the Koniambo massif, is also critically endangered and needs urgent conservation management.
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| 7. |
- Vigil-Stenman, Theoden, et al.
(författare)
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Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis
- 2015
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: Insertion sequences (ISs) are approximately 1 kbp long jumping genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I (cut-and-paste) Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium 'Nostoc azollae' 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of 'Nostoc azollae' 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria. Results: Insertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location (local hopping) and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500 bp were identified in the 67 genomes investigated. In the genome of 'Nostoc azollae' 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style. Conclusions: The apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium 'Nostoc azollae' 0708 and in other obligate prokaryotic symbionts.
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| 8. |
- Zepeda Mendoza, Marie Lisandra, et al.
(författare)
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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:3, s. 1-23
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Tidskriftsartikel (refereegranskat)abstract
- Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.
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| 9. |
- Nylander, Andreas, 1988, et al.
(författare)
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Reliability investigation of a carbon nanotube array thermal interface material
- 2019
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Ingår i: Energies. - : MDPI AG. - 1996-1073 .- 1996-1073. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- As feature density increases within microelectronics, so does the dissipated power density, which puts an increased demand on thermal management. Thermal interface materials (TIMs) are used at the interface between contacting surfaces to reduce the thermal resistance, and is a critical component within many electronics systems. Arrays of carbon nanotubes (CNTs) have gained significant interest for application as TIMs, due to the high thermal conductivity, no internal thermal contact resistances and an excellent conformability. While studies show excellent thermal performance, there has to date been no investigation into the reliability of CNT array TIMs. In this study, CNT array TIMs bonded with polymer to close a Si-Cu interface were subjected to thermal cycling. Thermal interface resistance measurements showed a large degradation of the thermal performance of the interface within the first 100 cycles. More detailed thermal investigation of the interface components showed that the connection between CNTs and catalyst substrate degrades during thermal cycling even in the absence of thermal expansion mismatch, and the nature of this degradation was further analyzed using X-ray photoelectron spectroscopy. This study indicates that the reliability will be an important consideration for further development and commercialization of CNT array TIMs.
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