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| 2. |
- Ament-Velásquez, Sandra Lorena, Ph.D. 1988-, et al.
(författare)
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The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:11
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Tidskriftsartikel (refereegranskat)abstract
- Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation.
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| 3. |
- Bendixsen, Devin P., et al.
(författare)
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Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries
- 2021
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Ingår i: Frontiers in Fungal Biology. - : Frontiers Media SA. - 2673-6128. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
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| 4. |
- Boynton, Primrose, et al.
(författare)
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Yeast ecology and communities
- 2022
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Ingår i: Yeast. - : Wiley. - 0749-503X .- 1097-0061. ; 39:1-2, s. 3-3
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Delmore, Kira, et al.
(författare)
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Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation
- 2024
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Ingår i: Cold Spring Harbor Perspectives in Biology. - 1943-0264. ; 16:2
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Forskningsöversikt (refereegranskat)abstract
- Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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| 8. |
- Rêgo, Alexandre, 1994-
(författare)
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Quo vadis? Insights into the determinants of evolutionary dynamics
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Predicting future evolutionary outcomes and explaining past and current patterns of biodiversity are fundamental goals in evolutionary biology. Trajectories of evolving populations are determined by evolutionary mechanisms (natural selection, mutation, genetic drift, and gene flow) and the environment in which the populations are found. Our ability to predict and explain evolution are thus dependent on understanding how, and when, these mechanisms and the environment affect evolutionary outcomes. However, many nuances exist in the interactions of these mechanisms with each other. Furthermore, environments can be incredibly complex– too complex to capture fully when designing controlled experiments to test evolutionary hypotheses. It is clear that several challenges exist in composing a comprehensive synthesis of the determinants of evolution.In this thesis, I have contributed to our understanding of evolutionary dynamics and outcomes by exploring how the above-stated factors affect inferences and predictions of evolution. I leveraged both computational and biological systems to answer several evolutionary questions. I first used simulations to estimate the effects fluctuating population size had on deterministic trajectories of adaptive alleles (Paper I). I found that declines in population size can alter the rate at which adaptive sweeps occur. As a consequence of altered rates of sweeps, our ability to infer accurate strengths of selection is decreased, even when selection is very strong. In a second experiment (Paper II), I used the seed beetle Callosobruchus maculatus to investigate (1) whether environments which imposed stronger selection would result in higher phenotypic and genomic parallelism, and (2) whether the degree of parallelism was dependent on the evolutionary history of populations. Despite expectations that adaptation to the environment which imposed stronger selection would result in higher parallelism, the opposite results were observed. However, the degree of parallelism within treatments varied considerably among populations of different evolutionary histories. In a final experiment (Paper III), I explored how environmental complexity alters the dynamics and outcomes of evolution using populations of the yeast Saccharomyces cerevisiae evolved in a full-factorial combination of several environments. I found that trade-off evolution was prevalent in complex environments, and the dynamics of evolution were dependent on the level of environmental complexity and the inclusion of specific stressors. Finally, I used the same evolved populations of yeast to ask whether the outcomes of evolution in highly complex environments could be predicted based on outcomes in populations evolved to the individual components of the complex environment (Paper IV). Across all biological levels, there existed very little predictability from evolution to the individual environmental components.The conclusions of this thesis align with the outcomes of numerous prior investigations into the predictability of evolution– it depends on context. However, this thesis highlights the importance of often-overlooked elements such as: (1) the capacity of demography to alter predictable trajectories of selected alleles, (2) the impact of evolutionary histories on the identification of parallelism in replicated populations, and (3) the potential omission of key ecological factors essential for adequately describing evolution in nature.
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| 9. |
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| 10. |
- Stelkens, Rike, 1978-, et al.
(författare)
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The evolutionary and ecological potential of yeast hybrids
- 2022
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Ingår i: Current Opinion in Genetics and Development. - : Elsevier BV. - 0959-437X .- 1879-0380. ; 76
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Tidskriftsartikel (refereegranskat)abstract
- Recent findings in yeast genetics and genomics have advanced our understanding of the evolutionary potential unlocked by hybridization, especially in the genus Saccharomyces. We now have a clearer picture of the prevalence of yeast hybrids in the environment, their ecological and evolutionary history, and the genetic mechanisms driving (and constraining) their adaptation. Here, we describe how the instability of hybrid genomes determines fitness across large evolutionary scales, highlight new hybrid strain engineering techniques, and review tools for comparative hybrid genome analysis. The recent push to take yeast research back ‘into the wild’ has resulted in new genomic and ecological resources. These provide an arena for quantitative genetics and allow us to investigate the architecture of complex traits and mechanisms of adaptation to rapidly changing environments. The vast genetic diversity of hybrid populations can yield insights beyond those possible with isogenic lines. Hybrids offer a limitless supply of genetic variation that can be tapped for industrial strain improvement but also, combined with experimental evolution, can be used to predict population responses to future climate change — a fundamental task for biologists.
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| 11. |
- Tavakolian, Nik, et al.
(författare)
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Shepherd : accurate clustering for correcting DNA barcode errors
- 2022
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 38:15, s. 3710-3716
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: DNA barcodes are short, random nucleotide sequences introduced into cell populations to track the relative counts of hundreds of thousands of individual lineages over time. Lineage tracking is widely applied, e.g. to understand evolutionary dynamics in microbial populations and the progression of breast cancer in humans. Barcode sequences are unknown upon insertion and must be identified using next-generation sequencing technology, which is error prone. In this study, we frame the barcode error correction task as a clustering problem with the aim to identify true barcode sequences from noisy sequencing data. We present Shepherd, a novel clustering method that is based on an indexing system of barcode sequences using k-mers, and a Bayesian statistical test incorporating a substitution error rate to distinguish true from error sequences.Results: When benchmarking with synthetic data, Shepherd provides barcode count estimates that are significantly more accurate than state-of-the-art methods, producing 10–150 times fewer spurious lineages. For empirical data, Shepherd produces results that are consistent with the improvements seen on synthetic data. These improvements enable higher resolution lineage tracking and more accurate estimates of biologically relevant quantities, e.g. the detection of small effect mutations.Availability and implementation: A Python implementation of Shepherd is freely available at: https://www.github.com/Nik-Tavakolian/Shepherd.
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| 12. |
- Zhang, Zebin, et al.
(författare)
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Recombining Your Way Out of Trouble : The Genetic Architecture of Hybrid Fitness under Environmental Stress
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:1, s. 167-182
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.
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