| 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. |
- Ghenu, A. H., et al.
(författare)
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Conflict between heterozygote advantage and hybrid incompatibility in haplodiploids (and sex chromosomes)
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:19, s. 3935-3949
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Tidskriftsartikel (refereegranskat)abstract
- In many diploid species, the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Zchromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization. Here, hybrid females have increased survivorship but hybrid males are inviable. To understand how the unusual hybrid population may be maintained, we developed a mathematical model with hybrid incompatibility, female heterozygote advantage, recombination and assortative mating. The rugged fitness landscape resulting from the co-occurrence of heterozygote advantage and hybrid incompatibility results in a sexual conflict in haplodiploids, which is caused by the ploidy difference. Thus, whereas heterozygote advantage always promotes long-term polymorphism in diploids, we find various outcomes in haplodiploids in which the population stabilizes either in favour of males, females or via maximizing the number of introgressed individuals. We discuss these outcomes with respect to the potential long-term fate of the Finnish wood ant population and provide approximations for the extension of the model to multiple incompatibilities. Moreover, we highlight the general implications of our results for speciation and hybridization in haplodiploids versus diploids and how the described fitness relationships could contribute to the outstanding role of sex chromosomes as hotspots of sexual antagonism and genes involved in speciation.
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| 3. |
- Kulmuni, J., et al.
(författare)
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Instability of natural selection at candidate barrier loci underlying speciation in wood ants
- 2020
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29:20, s. 3988-3999
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Tidskriftsartikel (refereegranskat)abstract
- Speciation underlies the generation of novel biodiversity. Yet, there is much to learn about how natural selection shapes genomes during speciation. Selection is assumed to act against gene flow at barrier loci, promoting reproductive isolation. However, evidence for gene flow and selection is often indirect and we know very little about the temporal stability of barrier loci. Here we utilize haplodiploidy to identify candidate male barrier loci in hybrids between two wood ant species. As ant males are haploid, they are expected to reveal recessive barrier loci, which can be masked in diploid females if heterozygous. We then test for barrier stability in a sample collected 10 years later and use survival analysis to provide a direct measure of natural selection acting on candidate male barrier loci. We find multiple candidate male barrier loci scattered throughout the genome. Surprisingly, a proportion of them are not stable after 10 years, natural selection apparently switching from acting against to favouring introgression in the later sample. Instability of the barrier effect and natural selection for introgressed alleles could be due to environment-dependent selection, emphasizing the need to consider temporal variation in the strength of natural selection and the stability of the barrier effect at putative barrier loci in future speciation work.
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| 4. |
- 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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| 5. |
- Reeve, James, et al.
(författare)
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Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)
- 2023
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L.saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L.arcana, hinting at an ancient origin.
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| 6. |
- van Riemsdijk, I., et al.
(författare)
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Testing an hypothesis of hybrid zone movement for toads in France
- 2019
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:5, s. 1070-1083
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Tidskriftsartikel (refereegranskat)abstract
- Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
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| 7. |
- Westram, A. M., et al.
(författare)
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Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:13, s. 3169-3186
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Tidskriftsartikel (refereegranskat)abstract
- Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations - 'outlier loci' (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false-positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated F-ST when sequenced in new samples from the original locations and also not to follow predictable geographical patterns of elevated F-ST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of F-ST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased F-ST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared with more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated in geographically distant locations. We discuss possible explanations for this unexpected result.
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| 8. |
- Westram, Anja M., et al.
(författare)
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Using replicate hybrid zones to understand the genomic basis of adaptive divergence
- 2021
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Ingår i: MOLECULAR ECOLOGY. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:15, s. 3797-3814
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Tidskriftsartikel (refereegranskat)abstract
- Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder-rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
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| 9. |
- Beresford, J., et al.
(författare)
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Widespread hybridization within mound-building wood ants in Southern Finland results in cytonuclear mismatches and potential for sex-specific hybrid breakdown
- 2017
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083. ; 26:15, s. 4013-4026
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization and gene flow between diverging lineages are increasingly recognized as common evolutionary processes, and their consequences can vary from hybrid breakdown to adaptive introgression. We have previously found a population of wood ant hybrids between Formica aquilonia and F. polyctena that shows antagonistic effects of hybridization: females with introgressed alleles show hybrid vigour, whereas males with the same alleles show hybrid breakdown. Here, we investigate whether hybridization is a general phenomenon in this species pair and analyse 647 worker samples from 16 localities in Finland using microsatellite markers and a 1200-bp mitochondrial sequence. Our results show that 27 sampled nests contained parental-like gene pools (six putative F. polyctena and 21 putative F. aquilonia) and all remaining nests (69), from nine localities, contained hybrids of varying degrees. Patterns of genetic variation suggest these hybrids arise from everal hybridization events or, instead, have backcrossed to the parental gene pools to varying extents. In contrast to expectations, the mitochondrial haplotypes of the parental species were not randomly distributed among the hybrids. Instead, nests that were closer to parental-like F. aquilonia for nuclear markers preferentially had F. polyctena's mitochondria and vice versa. This systematic pattern suggests there may be underlying selection favouring cytonuclear mismatch and hybridization. We also found a new hybrid locality with strong genetic differences between the sexes similar to those predicted under antagonistic selection on male and female hybrids. Further studies are needed to determine the selective forces that act on male and female genomes in these newly discovered hybrids.
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| 10. |
- Faria, R., et al.
(författare)
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Advances in Ecological Speciation: an integrative approach
- 2014
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083. ; 23:3, s. 513-521
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Tidskriftsartikel (refereegranskat)abstract
- The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.
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