| 1. |
- Abalde, Samuel, et al.
(författare)
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A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae)
- 2021
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Ingår i: Toxins. - : MDPI AG. - 2072-6651 .- 2072-6651. ; 13:9, s. 642-642
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Tidskriftsartikel (refereegranskat)abstract
- Venoms are complex mixtures of proteins that have evolved repeatedly in the animal kingdom. Cone snail venoms represent one of the best studied venom systems. In nature, this venom can be dynamically adjusted depending on its final purpose, whether to deter predators or hunt prey. Here, the transcriptome of the venom gland and the proteomes of the predation-evoked and defensive venoms of the molluscivorous cone snail Cylinder ammiralis were catalogued. A total of 242 venom-related transcripts were annotated. The conotoxin superfamilies presenting more different peptides were O1, O2, T, and M, which also showed high expression levels (except T). The three precursors of the J superfamily were also highly expressed. The predation-evoked and defensive venoms showed a markedly distinct profile. A total of 217 different peptides were identified, with half of them being unique to one venom. A total of 59 peptides ascribed to 23 different protein families were found to be exclusive to the predatory venom, including the cono-insulin, which was, for the first time, identified in an injected venom. A total of 43 peptides from 20 protein families were exclusive to the defensive venom. Finally, comparisons of the relative abundance (in terms of number of peptides) of the different conotoxin precursor superfamilies showed that most of them present similar abundance regardless of the diet.
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| 2. |
- Abalde, Samuel, et al.
(författare)
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Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 186, s. 107838-107838
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Tidskriftsartikel (refereegranskat)abstract
- The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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| 3. |
- Abalde, Samuel, et al.
(författare)
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The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes
- 2023
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Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group’s main clades and whose origin has been dated more than 400 million years ago.Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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| 4. |
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| 5. |
- Abu El-Enen, M.M., et al.
(författare)
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P–T path and timing of crustal thickening during amalgamation of East and West Gondwana: A case study from the Hafafit Metamorphic Complex, Eastern Desert of Egypt.
- 2016
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Ingår i: Lithos. - : Elsevier BV. - 0024-4937 .- 1872-6143. ; 263, s. 213-238
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Tidskriftsartikel (refereegranskat)abstract
- The southeastern sector of the Hafafit Metamorphic Complex, southern Eastern Desert of Egypt comprises infrastructural orthogneisses of tonalite and syenogranite parentage, amphibolites, and a volcano-sedimentary association. These are overthrust by an obducted suprastructural ophiolite nappes via the Nugrus thrust. The protolith of the biotite–hornblende-gneisses was formed during island-arc accretion, while that of the garnet–biotite gneisses were formed in a within-plate regime, consistent with a transition to a post-collisional setting. The volcano-sedimentary association comprises interbedded and intercalated highly foliated metapelitic schists, metabasites, and leucocratic gneisses, deposited in a back-arc basin. The metapelites and the leucocratic gneisses originated from immature Fe-shales and arkoses derived from intermediate-mafic and acidic igneous rocks, respectively, via weak chemical weathering in a tectonically active island arc terrane. The intercalated amphibolites were derived from tholeiitic basalts generated in a back-arc setting.The volcano-sedimentary association was metamorphosed under upper-amphibolite facies conditions with pressures of 9–13 kbar and temperatures of 570–675 °C, as derived from conventional geothermobarometry and pseudosection calculation. A steep, tight clockwise P–T path is constrained and a geothermal gradient around 20 °C/km is estimated for the peak metamorphism. We assume that deformation and metamorphism are due to crustal thickening during the collision of East and West Gondwana, where peak metamorphism took place in the middle to lower crust at 33 km average crustal depth. This was followed by a subsequent quasi-isothermal decompression due to rapid exhumation during wrench tectonics. Sinistral transcurrent shearing with extensional denudation resulted in vertical ductile thinning that was accompanied by heat input from magmatism, as indicated by a higher geothermal gradient during retrograde metamorphism and exhumation of the complex.U–Pb data from magmatic zircons yields protolith ages of 731 ± 3 Ma for the biotite–hornblende gneisses and 646 ± 12 Ma for the garnet–biotite gneisses. Conforming to field evidence, our geochronology data point to a depositional age of the volcano-sedimentary cover at around 650 Ma. The age of metamorphism is constrained by a low Th/U ratio of a zircon grain crystallized at an age of 597 ± 6 Ma.
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| 6. |
- ACOSTA HOSPITALECHE, Carolina, et al.
(författare)
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Historical perspective of Otto Nordenskjöld´s Antarctic fossil penguin collection and Carl Wiman’s contribution
- 2017
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Ingår i: Polar Record. - Cambridge. - 0032-2474 .- 1475-3057. ; 53:4, s. 364-375
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Tidskriftsartikel (refereegranskat)abstract
- The early explorer and scientist Otto Nordenskjöld, leader of the Swedish South Polar Expedition of 1901–1903, was the first to collect Antarctic penguin fossils. The site is situated in the northeastern region of Seymour Island and constitutes one of the most important localities in the study of fossilised penguins. The task of describing these specimens together with fossilised whale remains was given to Professor Carl Wiman (1867–1944) at Uppsala University, Sweden. Although the paradigm for the systematic study of penguins has changed considerably over recent years, Wiman's contributions are still remarkable. His establishment of grouping by size as a basis for classification was a novel approach that allowed them to deal with an unexpectedly high morphological diversity and limited knowledge of penguin skeletal anatomy. In the past, it was useful to provide a basic framework for the group that today could be used as ‘taxon free’ categories. First, it was important to define new species, and then to establish a classification based on size and robustness. This laid the foundation for the first attempts to use morphometric parameters for the classification of isolated penguin bones. The Nordenskjöld materials constitute an invaluable collection for comparative purposes, and every year researchers from different countries visit this collection.
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| 7. |
- Adam, Birgit, et al.
(författare)
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N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community
- 2016
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 10:2, s. 450-459
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the role of N2-fixation by the colony-forming cyanobacterium, Aphanizomenon spp., for the plankton community and N-budget of the N-limited Baltic Sea during summer by using stable isotope tracers combined with novel secondary ion mass spectrometry, conventional mass spectrometry and nutrient analysis. When incubated with 15N2, Aphanizomenon spp. showed a strong 15N-enrichment implying substantial 15N2-fixation. Intriguingly, Aphanizomenon did not assimilate tracers of 15NH4+ from the surrounding water. These findings are in line with model calculations that confirmed a negligible N-source by diffusion-limited NH4+ fluxes to Aphanizomenon colonies at low bulk concentrations (<250 nm) as compared with N2-fixation within colonies. No N2-fixation was detected in autotrophic microorganisms <5 mum, which relied on NH4+ uptake from the surrounding water. Aphanizomenon released about 50% of its newly fixed N2 as NH4+. However, NH4+ did not accumulate in the water but was transferred to heterotrophic and autotrophic microorganisms as well as to diatoms (Chaetoceros sp.) and copepods with a turnover time of ~5 h. We provide direct quantitative evidence that colony-forming Aphanizomenon releases about half of its recently fixed N2 as NH4+, which is transferred to the prokaryotic and eukaryotic plankton forming the basis of the food web in the plankton community. Transfer of newly fixed nitrogen to diatoms and copepods furthermore implies a fast export to shallow sediments via fast-sinking fecal pellets and aggregates. Hence, N2-fixing colony-forming cyanobacteria can have profound impact on ecosystem productivity and biogeochemical processes at shorter time scales (hours to days) than previously thought.
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| 8. |
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| 9. |
- Adrian, Brent, et al.
(författare)
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New Miocene Carnivora (Mammalia) from Moruorot and Kalodirr, Kenya
- 2018
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Ingår i: Palaeontologia Electronica. - : Coquina Press. - 1935-3952 .- 1094-8074. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- We describe new carnivoran fossils from Kalodirr and Moruorot, two late EarlyMiocene sites in the Lothidok Formation of West Turkana, Kenya. The fossils include anew species of viverrid, Kichechia savagei sp. nov., a new genus and species of felid,Katifelis nightingalei gen. et sp. nov., and an unidentified musteloid. We also reportnew records of the amphicyonid Cynelos macrodon. These new fossils increase theknown diversity of African Early Miocene carnivorans and highlight regional differencesin Africa.
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| 10. |
- Adroit, Benjamin, et al.
(författare)
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Are morphological characteristics of Parrotia (Hamamelidaceae) pollen species diagnostic?
- 2022
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Ingår i: Review of Palaeobotany and Palynology. - Amsterdam : Elsevier BV. - 0034-6667 .- 1879-0615. ; 307, s. 104776-104776
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Tidskriftsartikel (refereegranskat)abstract
- Parrotia persica is one of the most notable endemic relict tree species growing in the Hyrcanian forest at the southern Caspian Sea. The recent discovery of sibling species Parrotia subaequalis, occurring in the temperate forests of south-eastern China, offers the opportunity to compare their morphology and ecological preferences and to dig deeper into the paleophytogeographic history of the genus from a perspective. Since pollen morphology of these species would be essential to unravel the origin and evolution of these Arcto-Tertiary species, the present study aimed to investigate whether it is possible to segregate pollen from these two species. Therefore, a detailed combined light- and scanning electron microscopy-based pollen-analysis of each taxon was conducted, the pollen was described, measured, and compared using statistical approaches and principal component analyses to establish unbiased results. The correlation-based principal component analysis achieved for each species shows an overall good superposition of pollen grains measured in equatorial and polar views in the first principal plane, revealing that the P. persica pollen is morphometrically as homogeneous as that of P. subaequalis. Then, the significant difference, mainly driven by lumen density, has been highlighted between the two species. Ultimately, the cross-validation of the resulting two-species linear discriminants classifier shows that based upon this reference dataset, (sub)fossil pollen grain can now be confidently assigned to either of the two species with an 85.8% correct-assignment rate. This opens new doors in the affiliation of fossil Parrotia pollen and suggests that previous pollen records need to be revised.
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