| 1. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 2. |
- Faria, R., et al.
(författare)
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Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
- 2019
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:6, s. 1375-1393
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Tidskriftsartikel (refereegranskat)abstract
- Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
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| 3. |
- Maltseva, Arina L., et al.
(författare)
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Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species
- 2021
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:12
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Tidskriftsartikel (refereegranskat)abstract
- Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207-603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species- specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome ("scaffolding enterotype") is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.
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| 4. |
- Maltseva, Arina L., et al.
(författare)
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Phylogeography of the closely related Littorina (Neritrema) species in the North-East Atlantic
- 2022
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Ingår i: Invertebrate Zoology. - : KMK Scientific Press. - 1812-9250 .- 1814-0815. ; 19:4, s. 404-424
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Tidskriftsartikel (refereegranskat)abstract
- Phylogeographic studies of evolutionary young species co-existing over a vast geographic area can provide insights in the process of evolutionary divergence and its cohesiveness in different parts of the species ranges. The Littorina snails of the ‘saxatilis’ cryptic group diverged in near-glacial time, and tend to live in sympatry. L. saxatilis is widely distributed on both sides of the North Atlantic, while L. arcana and L. compressa are patchy distributed on the shores of Europe and Atlantic islands. The biogeographic history of the Littorina ‘saxatilis’ cryptic group is still obscure, with L. saxatilis studied much better than the other two species. We evaluated the population structure of the three ‘saxatilis’ species on the coasts of Wales, the Norwegian and the Barents seas using several genetic markers: the mitochondrial cytochrome b gene (cytb, partial, 26 haplotypes for 268 sequences), nuclear (5 microsatellite loci in 458 individuals) and whole-genome (2bRAD, 63 417 loci in 114 individuals) markers. Analyses based on the cytb and microsatellite markers showed a deep divergence between the British and the North European populations of all three species with a high genetic similarity between their sympatric populations from Wales. L. compressa had the highest differentiation from both L. arcana and L. saxatilis and demonstrated the clear population structure due to allele frequency. The degree of the genetic differentiation between sympatric L. arcana and L. saxatilis in some regions was lower than between the regions within a species. Moreover, analyses of all three types of used markers indicate that the continental populations of L. arcana include individuals with contrasting genomic profiles. Our results suggest that L. arcana and L. compressa separated from their common ancestor L. islandica after L. saxatilis. The three sibling species survived glaciation in a refugium (or refugia) on the British coasts, separated from the mainland refugium (or refugia). After the glaciation, L. compressa colonised the mainland, most likely from a single European refugium. Post-glacial continental repopulation by L. arcana could have occurred from at least two sources, with two differentiated lineages still recognisable. Further inclusion of Littorina populations from South Norway and France is needed to complete the reconstruction of biogeographic history in these three evolutionary young species of Littorina snails.
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| 5. |
- Maltseva, Arina L, et al.
(författare)
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Premating barriers in young sympatric snail species.
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Sympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.
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| 6. |
- Maltseva, Arina L, et al.
(författare)
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Proteomic similarity of the Littorinid snails in the evolutionary context.
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation.Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.
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| 7. |
- Panova, Marina, 1973, et al.
(författare)
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First insights into the gut microbiomes and the diet of the Littorina snail ecotypes, a recently emerged marine evolutionary model
- 2022
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Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 365-78
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Tidskriftsartikel (refereegranskat)abstract
- Microbes can play a prominent role in the evolution of their hosts, facilitating adaptation to various environments and promoting ecological divergence. The Wave and Crab ecotypes of the intertidal snail Littorina saxatilis is an evolutionary model of rapid and repeated adaptation to environmental gradients. While patterns of genomic divergence of the Littorina ecotypes along the shore gradients have been extensively studied, their microbiomes have been so far overlooked. The aim of the present study is to start filling this gap by comparing gut microbiome composition of the Wave and Crab ecotypes using metabarcoding approach. Since Littorina snails are micro-grazers feeding on the intertidal biofilm, we also compare biofilm composition (i.e. typical snail diet) in the crab and wave habitats. In the results, we found that bacterial and eukaryotic biofilm composition varies between the typical habitats of the ecotypes. Further, the snail gut bacteriome was different from outer environments, being dominated by Gammaproteobacteria, Fusobacteria, Bacteroidia and Alphaproteobacteria. There were clear differences in the gut bacterial communities between the Crab and the Wave ecotypes as well as between the Wave ecotype snails from the low and high shores. These differences were both observed in the abundances and in the presence of different bacteria, as well as at different taxonomic level, from bacterial OTU's to families. Altogether, our first insights show that Littorina snails and their associated bacteria are a promising marine system to study co-evolution of the microbes and their hosts, which can help us to predict the future for wild species in the face of rapidly changing marine environments.
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| 8. |
- Polovodova Asteman, Irina, 1980, et al.
(författare)
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Spreading of an alien benthic foraminifer in the North Sea: a reason to be worried?
- 2023
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Ingår i: International Congress FORAMS2023, Perugia, Italy, 25-30th June. - Perugia, Italy : Micropress Europe & The Grzybowski Foundation.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In the Skagerrak-Kattegat (eastern North Sea), the alien benthic foraminifer Nonionella sp. T1 (previously referred to as “Nonionella stella”) was reported for the first time in 2011 and 2012 in the Swedish and southern Norwegian fjords, respectively. Based on dated sediment cores its first occurrence can be traced back to the 1980s in the Gullmar Fjord, to the 2000s in the Öresund and to 2010 in the Oslofjord. Since then, Nonionella sp T1 has spread all over the Kattegat and coastal Skagerrak, according to sampling campaigns performed between 2016 and 2022. The species is now highly abundant in the entire Kattegat, including the Öresund, as well as in fjord mouths of the seasonally hypoxic Gullmar Fjord, the oxic Hakefjord and the long-term polluted Idefjord as demonstrated by molecular and morphospecies data. At the same time, Nonionella sp T1 is rare to absent in the Baltic Sea, Skagerrak deep basin and in deep fjords of western and northern Norway. This study shows some preliminary results on the species’ present distribution in the study area and raises questions about the driving factors and potential effects on the local biodiversity.
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| 9. |
- Rafajlović, Marina, 1983, et al.
(författare)
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The Effect of Multiple Paternity on Genetic Diversity of Small Populations during and after Colonisation
- 2013
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 8:10
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration) has been reached. During colonisation, multiple mating by 2 10 males increased the heterozygosity by 10 300% in comparison with single paternity, while in the steady state the increase was 10-50% compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity.
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| 10. |
- Westram, A. M., et al.
(författare)
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Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow
- 2018
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Ingår i: Evolution Letters. - : Oxford University Press (OUP). - 2056-3744. ; 2:4, s. 297-309
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Tidskriftsartikel (refereegranskat)abstract
- Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.
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