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- Backström, Niclas
(författare)
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Adaptive evolution in passerine birds
- 2014
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Ingår i: Encyclopedia of Life Sciences. - : Wiley. - 1476-9506. - 9780470015902
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Adaptive evolution is the process whereby mutations that provide the carrier with a selective advantage increase in frequency in a population via the process of natural selection. Passerines are widespread, common and long-term targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats, for example, beak size and wing shape, and they are, therefore, an important study system to understand adaptive evolution. Recent technological advancements have made it easier to investigate the mechanistic and evolutionary underpinnings of adaptive evolution by allowing genome sequence data to be generated in almost any species of interest. However, it is important to assess the contribution of neutral forces like demographic events and GC-biased gene conversion before concluding that selection has shaped the patterns observed in genomic data. Initial analyses in passerines have identified candidate genes that might be involved in, for example, song learning, beak morphology, disease resistance, high-altitude adaptation and exploratory behavior, but functional verifications are needed to establish a causative relationship between the identified genes and the traits. Key Concepts:Key Concepts: * Passerines are widespread, generally common and easy targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats and they have, therefore, played an important role in previous studies concerning behaviour, ecology and evolution. * A full understanding of passerine adaptations requires an integrative approach aiming at identifying and characterising both proximate (mechanistic) and ultimate (evolutionary) underpinnings to adaptive traits. * The recent advancements in molecular techniques allows for using both comparative genomics, expression profiling, candidate gene approaches and classical association and QTL mapping strategies to identify the genetic basis of adaptive traits in passerines. * Groundwork studies of ecological genetics and genomics using comparative approaches, expression profiling and candidate genes are now accumulating and in a handful of cases we have an idea about the genetic basis of adaptive traits related to, for example, dietary specialisation, learning, exploratory behaviour, immune response and high-altitude adaptations in passerines. * Demographic history and other neutral processes, for example, GC-biased gene conversion (gcBGC), may mimic signals of selection and it is important to verify findings of adaptive evolution using independent methods.
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- Backström, Niclas, 1969-
(författare)
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Gene Mapping in Ficedula Flycatchers
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.
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- Boman, Jesper, et al.
(författare)
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Evolution of hybrid inviability associated with chromosome fusions
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. However, less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we used crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We mapped candidate loci for hybrid inviability by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability factors were predominantly found in fast-evolving regions with reduced recombination rates, especially in regions where chromosome fusions have occurred. By analyzing sequencing coverage, we excluded aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reductions in recombination rate caused by fusions. These results highlight that the extensive variation in chromosome numbers observed across the tree of life does not only distinguish species but can also be involved in speciation by being hotspots for the early evolution of postzygotic reproductive isolation.
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- Boman, Jesper
(författare)
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Genetic architecture of speciation
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- New species are formed either by the splitting of a lineage in two or through hybridization of divergent lineages. Using genetics to understand the origin and persistence of species is a central theme in evolutionary biology. The genetic architecture of speciation refers to the number, types and effect sizes of different genetic loci underlying the process of speciation. Insightful models and painstaking laboratory and field work have provided the first sketches of the genetic architecture of speciation in a handful of model organisms. In this thesis, I explore different aspects of speciation genetics in several less studied model systems: from birds to butterflies. In Paper I, I investigate the genetic architecture of hybrid inviability between chromosomal races of the wood white butterfly (Leptidea sinapis) and find an association between chromosome fusions and the evolution of hybrid inviability. In Paper II, I study whether the many chromosomal differences separating the L. sinapis races show evidence of non-Mendelian inheritance. We observe the preferential inheritance of the ancestral state at chromosome fusions in line with the meiotic drive model. Thus, meiotic drive acts against karyotype change and thus potentially opposes the evolution of reproductive isolation. Recent work has highlighted that epigenetic mechanisms, such as DNA methylation, could be important for the dysfunction of hybrids. In Paper III, we test this prediction in naturally occurring hybrids between the collared flycatcher (F. albicollis) and the pied flycatcher (F. hypoleuca). I show that DNA methylation differences in promoter regions are often correlated with signatures of differential gene expression between species, but does not predict misexpression in hybrids. Hybridization between species is expected to reduce the genetic differentiation and erode species differences. However, hybridization can also be the trigger of speciation if the combination of alleles and traits allow the hybrid species to persist. In Paper IV, I discover a hybrid Aricia butterfly species on the island of Öland in the Baltic Sea. Using whole-genome resequencing data and species models I infer that the main hybridization event occurred approximately 54,000 years ago, long before Öland arose from the sea after the last ice age. To conclude, this thesis highlights different aspects of speciation genetics: from the genetic underpinnings of viability of hybrids (Paper I and III) to causes of speciation (Paper II and IV). Hopefully this work will provide a few more lines to the blueprint that is our understanding of the genetic architecture of speciation
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- Boman, Jesper, et al.
(författare)
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On the origin of an insular hybrid butterfly species
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Most species arise from the divergence of two populations within a species, but this is not only way speciation can occur. A new species can also evolve when diverging lineages hybridize and give rise to a persistent and ecologically differentiated species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process have been difficult to gain. Recent access to large-scale, whole-genome sequencing data and development of novel analytical methods have made it more feasible to statistically test for hybrid origin of lineages. Here we report the discovery of a hybrid butterfly lineage. This lineage is mainly inhabiting an island in the Baltic Sea in Northern Europe and was previously described as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analyzing whole-genome resequencing data, we conclude that horkei originated as a consequence of hybridization between A. artaxerxes and A. agestis. We show that this hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range. Horkei must therefore have persisted long enough to be able to colonize its current distribution range, despite that this range lies between the current ranges of the parental species. The hybrid origin, the maintenance of genomic integrity through time periods with dramatic climatic changes and the expression of a combination of parental traits - such as voltinism and host plant use - suggest that horkei can be considered a distinct species (Aricia horkei stat. nov.). Thus, we add to a growing list of hybrid speciation cases in animals.
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| 8. |
- Culicchi, Alessandro, 1989-
(författare)
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Ecological and evolutionary effects of anthropogenic change in freshwater fish communities
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Environmental change is ongoing, driven by human activities that have profoundly modified the modern world. Natural ecosystems are directly affected by these anthropogenic activities. This thesis explores the effects of anthropogenic change on natural ecosystems. Being this an extremely broad topic, we narrow down our research to some key areas of investigation, without aiming to be exhaustive. We also explore related themes. In Paper I, we review the effects of anthropogenic change on the process of speciation. We show that human intervention can alter geography or selective regimes. In both cases, this can either lead to an increase or decrease in reproductive isolation between species. In the following papers, we focus on the study case of two sister species with similar morphology and ecological niches, the common bream (Abramis brama) and the white bream (Blicca bjoerkna). In Paper II, we demonstrate that changes in abiotic and biotic conditions in lakes can disrupt the delicate co-occurrence and abundance patterns between the two species. In particular, increases in turbidity, predation and competition pose a threat to the local survival of white bream. In Paper III, we examine the effects of abiotic and biotic conditions on the phenotype of our species of interest. For this purpose, we focus on the average individual size and its relative difference between the species as a phenotypic proxy. We show that the relative difference in size is quite insensitive to external perturbations. However, we find that the presence of pike in the lake increases the similarity in the size between the study species. This can potentially threaten niche specialisation and species cohesion. Throughout Paper II and Paper III, we investigate the temporal trends of environmental and biotic factors over the last few decades, finding an increase in temperature, turbidity and the proportion of perch, along with a decrease in the proportions of pike and roach. In Paper IV, we conduct a genomic study based on whole-genome resequencing, which reveals that the morphological approach is inadequate for the taxonomical identification of our study species. Genomic data also show that hybridisation occurs, but it does not pose an immediate threat to species cohesion in the study area. Intra-specific genetic variation is low, and it suggests a pattern of isolation-by-distance. Overall, this thesis highlights that an analysis of anthropogenic influences on natural systems should be approached from different angles, to provide a comprehensive overview of such a complex phenomenon.
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| 9. |
- Höök, Lars, et al.
(författare)
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Dualistic dosage compensation and rapid evolution of expression balance in response to W chromosome degeneration in Leptidea butterflies
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The evolution of dimorphic sex chromosomes from initially homologous autosomes is generally explained by sex-specific selection to maintain linkage between a sex determining locus and genes that are beneficial to the same sex. While initially beneficial, the strong linkage and reduced recombination causes differentiation and degeneration of many initially shared genes. Reduced copy numbers can have severe consequences for the balance of gene expression levels between sex-linked genes and the rest of the genome. Consequently, dosage compensation has evolved independently in different lineages to mitigate the detrimental effects of unbalanced expression of sex-linked genes in the heterogametic sex. However, the variation in sex chromosome regulation in different lineages, puts the need to restore expression to ancestral levels into question. In particular, a general difference has been observed between male- (XY) and female-heterogametic (ZW) systems. In contrast to the X chromosome upregulation in heterogametic males in the XY-systems, the Z chromosomes are rarely upregulated in the heterogametic females in organisms with ZW-systems. Instead, the Z chromosomes are often downregulated in the homogametic males to achieve inter-sexual balance. Although progress has been made to understand what causes this discrepancy, comparative approaches are limited by long divergence times and ancient sex chromosome systems. An attractive approach is therefore to study the evolution of gene regulation on recently derived neo-sex chromosomes, formed through fusions between ancestral sex chromosomes and autosomes. Here, we investigated dosage compensation of neo-sex chromosomes in three closely related butterflies in the cryptic wood white clade (Leptidea). Importantly, the species have acquired multiple sex chromosomes, and dosage compensation could therefore have evolved repeatedly in the clade. Our analyses reveal a mixture of gene expression patterns which suggests that distinct modes of dosage compensation have evolved on the different Z chromosomes. In addition, we detect evidence that dosage balancing mechanisms have been rapidly recruited to the youngest neo-Z chromosome, to counteract an ongoing degeneration of neo-W gametologs. The results add to a growing list of examples where diverse dosage compensation mechanisms can evolve within a single species, and suggests that various regulatory mechanisms are not restricted to specific sex chromosome systems.
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| 10. |
- Höök, Lars, 1980-, et al.
(författare)
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Temporal dynamics of faster neo-Z evolution in butterflies
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The faster-Z/X hypothesis predicts that sex-linked genes should diverge faster than autosomal genes and may therefore play important roles in speciation. However, studies across different lineages have shown mixed support for this effect, a variation that has been explained by various evolutionary mechanisms. So far, most analyses have focused on systems with old and well differentiated sex chromosomes, but less is known about divergence of more recently acquired neo-sex chromosomes. In the female heterogametic order Lepidoptera (moths and butterflies), fusions between the ancestral Z chromosome and autosomes are relatively frequent, but the evolutionary dynamics of neo Z-linked genes have not been explored in detail. Here, we analysed the faster-Z effect in Leptidea sinapis, a butterfly with an exceptionally reorganized genome and three Z chromosomes. We show that the neo-Z chromosomes have been acquired in a stepwise fashion, resulting in distinct strata of differentiation and masculinization. While Z-linked divergence generally seems to have been driven by adaptive processes, the relative effects of selection and drift showed a temporal trend where selection has been more prevalent for genes located on older Z linked regions, causing increased divergence of Z-linked genes with female-biased expression. In contrast, the intensity of selection on genes located on the most recently acquired neo-Z chromosome (Z3) appears to have been hampered by the presence of gametologs on the largely intact, homologous neo-W chromosome. However, the intermediately aged neo-Z chromosome (Z2), which is completely differentiated from W gametologs, showed less evolutionary constraint than the ancestral Z, resulting in particularly fast evolution. Our results therefore support that neo-sex chromosomes can constitute temporary hot-spots of adaptation and divergence. The underlying dynamics are likely causally linked to shifts in selective constraints, evolution of gene expression and the degeneration of W-linked gametologs which gradually expose Z-linked genes to selection.
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