| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- De Wit, Pierre, 1978, et al.
(författare)
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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the rst-ever transcriptome assembly for this species, and found 3,233 di erentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to di erentially expressed genes, the most notable being “alkaloid metabolic process”. Within this category, we found eight di erentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the di erentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxi cation. This is a rst step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.
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| 5. |
- Johannesson, Kerstin, 1955, et al.
(författare)
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Non-random paternity of offspring in a highly promiscuous marine snail suggests postcopulatory sexual selection
- 2016
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Ingår i: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 70:8, s. 1357-1366
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Tidskriftsartikel (refereegranskat)abstract
- In the marine snail Littorina saxatilis females are highly polyandrous, resulting in simultaneous broods of offspring sired by similar to 20 males. Such high polyandry, in combination with female sperm storage, is likely to promote postcopulatory sexual selection among males. In addition, females may gain direct reproductive benefits from multiple mating. Investigating sexual selection in males and female benefits in relation to the number of sires, we put single virgin females in aquaria with one, two, five or ten males for 80 days, during which each female mated a majority of available males. After removal of the males, females continued to produce offspring during > 1 year. Offspring genotypes of 27 families showed multiple paternity with 76 % of males contributing to juveniles, but paternity deviated from random with one or a few males siring the majority of the offspring. Larger males tended to be overrepresented among the sires. Female reproductive output (newborn or juvenile stage) did, however, not increase with number of sires, and females seemed not limited by the number of available males. Because previous studies have shown that females are seemingly indiscriminative in their mate choice, and given that they mate many hundreds of times in their lifespan, this suggests there is comparatively limited scope for premating sexual selection in this species. Hence, we interpret these results mainly in the light of postcopulatory sexual selection. Sexual selection is a main component of evolution. In that context, mating behaviour is central, although it sometimes appears puzzling, even maladaptive. For example, matings are costly; still, in some species, females mate multiple times and with numerous males. Why this behaviour has evolved is intriguing. Extensive numbers of matings suggest less efficient precopulatory mate choice, opening for postcopulatory sexual selection through cryptic female choice and sperm competition. Using a highly promiscuous snail species with internal fertilisation and long-term sperm storage, we identified the fathers of 549 offspring. We found that while females mated most males available, the offspring were non-randomly distributed among mated males and large males were overrepresented among the sires. This suggests that sexual selection predominantly occurs after mating and that males benefit from size-related effects. Yet, we could not find any female benefits from mating multiple males.
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| 6. |
- Marques, João P, et al.
(författare)
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Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L.obtusata and L. saxatilis.
- 2017
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 32, s. 41-47
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Tidskriftsartikel (refereegranskat)abstract
- The flat periwinkles, Littorina fabalis and L.obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L.saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L.saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L.fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on dN/dS ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.
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| 7. |
- Morales, Hernán E., 1985, et al.
(författare)
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Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast
- 2019
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:12
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Tidskriftsartikel (refereegranskat)abstract
- The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.
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| 8. |
- Panova, Marina, 1973, et al.
(författare)
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A molecular phylogeny of the north-east Atlantic species of the genus Idotea (Isopoda) with focus on the Baltic Sea
- 2017
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 46:2, s. 188-199
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Tidskriftsartikel (refereegranskat)abstract
- Today, the marine isopods of the genus Idotea Fabricius, 1798 consist of 26 accepted species. Most species can be found in the Northern Hemisphere. While some species have a cosmopolitan distribution, others are endemic to a few coastlines. In the Baltic Sea, Idotea species have a key role as important meso-grazers. Only three species can be found in this brackish environment, I. balthica, I. chelipes and I. granulosa, while nine species are described from the whole European coast. The goal of the present study was to reconstruct the phylogeny of the genus Idotea and to test whether the Baltic low-salinity tolerant species represent a single lineage within the genus. The phylogeny of north-east Atlantic Idotea species was investigated based on a fragment of the nuclear gene 28S and the mitochondrial gene COI for eight Idotea species. The phylogenetic reconstructions showed that the genus Idotea might not be monophyletic. Neither I. linearis nor I. urotoma did belong to the separated and well-supported Idotea clade of I. balthica, I. chelipes, I. emarginata, I. granulosa, I. metallica and I. pelagica. The three Idotea species found in the Baltic belonged to different lineages, with estimated COI-based divergence time older than 7 Myr. This suggests that the tolerance to low salinity has likely evolved in the genus Idotea more than once.
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| 9. |
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| 10. |
- Ravinet, Mark, 1986, et al.
(författare)
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Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:1, s. 287-305
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Tidskriftsartikel (refereegranskat)abstract
- Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small ‘wave’ ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, ‘crab’ ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel, and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However, the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this, we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities amongst ecotype pairs on three close islands (<10 km distance) connected by weak gene flow (Nm ~ 0.03) and with recent common ancestry (<10 000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8–28% of positive outliers were shared between two islands and ~2–9% were shared amongst all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
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