Browsing by Subject "parallel evolution"

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  • Galindo, Juan; Carvalho, Joao; Sotelo, Graciela; Duvetorp, Marten; Costa, Diana; Kemppainen, Petri; Panova, Marina; Kaliontzopoulou, Antigoni; Johannesson, Kerstin; Faria, Rui (2021)
    Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.
  • Shikano, Takahito; Laine, Veronika N.; Herczeg, Gabor; Vilkki, Johanna; Merilä, Juha (2013)
  • Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjørn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Wringe, Brendan; Fairweather, Robert; Bradbury, Ian R. (2020)
    Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
  • Coll Costa, Carla Jr (Helsingin yliopisto, 2021)
    The three-spined stickleback (Gasterosteus aculeatus) is a model organism for studies of parallel evolution in the wild; marine stickleback populations have repeatedly colonized and successfully adapted to different brackish and freshwater habitats. During Pleistocene glaciations, three-spined stickleback populations inhabiting high-latitude areas of Europe were eradicated, whereas populations residing in (or moving to) the south persisted in refugia. After the retreat of the ice sheets covering northern Europe, the high-latitude areas became recolonized by migration from south, and hence, today’s northern European populations are relatively young. Population genetic studies of European three-spined sticklebacks have usually been conducted at high-latitude areas where freshwater populations are typically less than 10.000 years old. Few studies have focused on southern populations, where more of the ancestral diversity is likely to reside. These studies have utilized a limited number of microsatellite markers and mtDNA sequence fragments, whereas studies of southern populations focusing on genome-wide diversity, in particular from the edge of the southern distribution limit in the Iberian Peninsula, are still missing. Here, I wanted to cover this gap in knowledge by carrying out an empirical and statistical study with RAD-seq data from southern and northern European populations of three-spined stickleback. The main aims of this study were two-fold. First, to investigate whether the southern European freshwater populations of the three-spined stickleback – which currently lack or have limited connection to ancestral marine populations carrying most of the standing genetic variation (SGV) – have lost genetic diversity due to population bottlenecks and inbreeding as compared to their northern European counterparts. Second, to compare the degree of genetic parallelism in southern vs. northern European populations in genomic regions which have been shown to be consistently associated with freshwater colonization in earlier studies. Under the assumption that the lack of continued access to SGV in the ancestral marine population reduces the likelihood of parallel evolution, I hypothesized that the degree of genetic parallelism in genomic regions subject to positive selection in freshwater environments is lower in the southern than in northern European populations. However, if a reduction in genetic diversity and/or cessation of gene flow between southern European freshwater and marine populations occurred following freshwater adaptation, the opposite pattern could be expected. I paid particular attention to chromosomal inversions associated with marine-freshwater adaptations identified in previous studies. The results confirmed my expectation of reduced genetic diversity in southern as compared to northern European stickleback populations. On the other hand, and contrary to what I expected, analysis of clusters of global parallelism involved in freshwater adaptation revealed that southern European populations exhibit a higher degree of genetic parallelism in response to freshwater colonisation than those from northern Europe. This suggests that the loss of genetic diversity in southern populations has occurred after they had adapted to freshwater environments, explaining the high degree of genetic parallelism in spite of the current low levels of genetic diversity. In addition, it could be that selection pressures in south are more homogenous than in north, which would also explain the higher degree of genetic parallelism observed in southern Europe. The findings presented here, challenge the current paradigm that parallel evolution is unlikely in populations with low genetic diversity and that have experienced recent bottlenecks.
  • Sowersby, Will; Cerca, José; Wong, Bob B.M.; Lehtonen, Topi K.; Chapple, David G.; Leal-Cardín, Mariana; Barluenga, Marta; Ravinet, Mark (2021)
    Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy lips, is associated with rocky lake substrates, and occurs patchily within Lakes Nicaragua and Managua. By contrast, the similar, but thin-lipped, congener, A. citrinellus, is more common and widespread. We investigated the evolutionary history of the large-lipped form, specifically regarding whether the trait has evolved independently in both lakes from ancestral thin-lipped populations, or via dispersal and/or admixture events. We collected samples from distinct locations in both lakes, and assessed differences in morphology and ecology. Using RAD-seq, we genotyped thousands of SNPs to measure population structure and divergence, demographic history, and admixture. We found significant between-species differences in ecology and morphology, local intraspecific differences in body shape and trophic traits, but only limited intraspecific variation in lip shape. Despite clear ecological differences, our genomic approach uncovered pervasive admixture between the species and low genomic differentiation, with species within lakes being genetically more similar than species between lakes. Taken together, our results suggest a single origin of large-lips, followed by pervasive admixture and adaptive introgression, with morphology being driven by local ecological opportunities, despite ongoing gene-flow.
  • Fang, Bohao; Kemppainen, Petri; Momigliano, Paolo; Merila, Juha (2021)
    Population genetic theory predicts that small effective population sizes (N-e) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.