| 1. |
- Alavioon, Ghazal, et al.
(författare)
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Haploid selection within a single ejaculate increases offspring fitness
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; :30, s. 8053-8058
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Tidskriftsartikel (refereegranskat)abstract
- An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.
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| 2. |
- Arnqvist, Göran, Professor, 1961-, et al.
(författare)
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
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Ingår i: G3. - : Oxford University Press. - 2160-1836. ; 14:2
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Tidskriftsartikel (refereegranskat)abstract
- Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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| 3. |
- Bernhardsson, Carolina, et al.
(författare)
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An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
- 2019
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Ingår i: G3. - : Genetics Society of America. - 2160-1836. ; 9:5, s. 1623-1632
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.
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| 4. |
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| 5. |
- Chase, Madeline, et al.
(författare)
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The combination of HiFi and HiC sequencing technologies enables the investigation of structural variants in speciation of Ficedula flycatchers
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Structural variants, typically defined as mutations affecting more than 50bp, have been shown to encompass a significant portion of the genome and can have large phenotypic effects. Additionally, increasing empirical evidence demonstrates that structural variants may play a substantial role in speciation, which could previously have been overlooked because of difficulties in identifying them with short-read data. However, with the increased availability of long-read sequencing technology we are now equipped better than ever to address this limitation and study the contribution of different types of structural variants to genetic variation within and genetic differentiation between closely related species. Here, we follow this approach and combine PacBio HiFi and HiC sequencing for two closely related passerine birds, the collared flycatcher and the pied flycatcher. This enables us to generate a chromosome-level genome assembly for both species, and identify structural variants between the two species. Based on population-level HiFi sequencing for both species, we then investigate patterns of single nucleotide diversity and differentiation within and between species and their association with different types of structural variation. We find widespread structural variation between the two species, where both the sex chromosomes show a disproportionate number of structural variants, which may help explain the suspected role of the Z-chromosome in contributing to genetic incompatibilities. We also find that genomic differentiation peaks are enriched in both translocations and inversions, which supports a mechanistic role of structural variation in population differentiation and speciation.
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| 6. |
- Chen, Hwei-yen, 1983-, et al.
(författare)
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Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
- 2023
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Ingår i: Evolution Letters. - : Oxford University Press. - 2056-3744. ; 7:6, s. 478-489
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Tidskriftsartikel (refereegranskat)abstract
- The effect of parental age on germline mutation rate across generations is not fully understood. While some studies report a positive linear relationship of mutation rate with increasing age, others suggest that mutation rate varies with age but not in a linear fashion. We investigated the effect of parental age on germline mutations by generating replicated mutation accumulation lines in Caenorhabditis remanei at three parental ages ("Young T1" [Day 1], "Peak T2" [Day 2], and "Old T5" [Day 5] parents). We conducted whole-genome resequencing and variant calling to compare differences in mutation rates after three generations of mutation accumulation. We found that Peak T2 lines had an overall reduced mutation rate compared to Young T1 and Old T5 lines, but this pattern of the effect varied depending on the variant impact. Specifically, we found no high-impact variants in Peak T2 lines, and modifiers and up- and downstream gene variants were less frequent in these lines. These results suggest that animals at the peak of reproduction have better DNA maintenance and repair compared to young and old animals. We propose that C. remanei start to reproduce before they optimize their DNA maintenance and repair, trading the benefits of earlier onset of reproduction against offspring mutation load. The increase in offspring mutation load with age likely represents germline senescence. Germline mutations play a key role in evolution through the generation of novel genotypes. Estimating the mutation rate in species, populations, and individuals is one way to understand the relative timeframe of evolutionary processes, for the timing of historical events and for estimating heritability of traits and diseases. Individual age at reproduction is known to affect the number of mutations being transferred into the next generation and generally mutation rate is thought to increase with increasing parental age. However, preventing mutations in germ cells is potentially costly and it may pay off to optimize germline genome repair and maintenance during peak reproductive periods, and relax it during nonpeak periods. This idea has been put forward to explain for example the reduction of gonad size in seasonally reproducing animals during nonreproductive periods and supported by the finding that the mutation rate seems to be higher in teenage men compared to men during their peak reproductive ages. We further tested this idea of a nonlinear relationship between age and mutation rate by performing a mutation accumulation experiment in a short-lived nematode. We kept experimental lines and allowed adults to reproduce at different ages in different lines, with some lines reproducing before, some during, and some after their reproductive peak. We found that mutation rates are higher in nematode lines reproducing before or after the reproductive peak compared to those reproducing during the peak. Our results therefore support the idea that germline genome maintenance and repair is potentially costly and that the mutation rate does not just increase with age but is optimized during the peak reproductive age of an organism.
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| 7. |
- David, Gabriel, et al.
(författare)
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Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.
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| 8. |
- Gil-Munoz, Francisco, et al.
(författare)
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QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)
- 2023
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Ingår i: Tree Genetics & Genomes. - : Springer Nature. - 1614-2942 .- 1614-2950. ; 19:3
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Tidskriftsartikel (refereegranskat)abstract
- Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned x normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.
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| 9. |
- Gudmunds, Erik, et al.
(författare)
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Contribution of ecdysone signaling to photoperiodic wing polyphenism in the water strider Gerris buenoi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Hormones play a decisive role in insect development and are central for regulating alternative life histories and phenotypic plasticity. A prominent form of plasticity is manifested in polyphenisms where discrete phenotypes, such as winged or wingless morphs, develop from the same genotype under different environmental cues. Here, hormones can induce the development of alternative morphs through interaction with specific environmental cues, e.g. nutrition, population density or photoperiod. 20-hydroxyecdysone (20E) and juvenile hormone (JH) are the two hormones which received most attention and have been shown to regulate numerous polyphenisms, for example seasonal morphs of butterflies or various castes in Hymenopterans. In this chapter we have investigated the possible role of these two hormones in the induction of alternative wing morphs in the water strider Gerris buenoi by combining RNAi, hormone injections or applications and RNA sequencing. RNAi targeting the ecdysone receptor (EcR), while highly lethal, had a significant effect on wing morph frequencies among the surviving individuals. Furthermore, analysis of RNAseq data of wing gene expression showed that many 20E-responsive genes were differentially regulated between long- and short-winged individuals. Taken together, the data presented here highlight 20E as a candidate hormone to modulate wing morph determination in G. buenoi.
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| 10. |
- Horvath, Robert, et al.
(författare)
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Selection on Accessible Chromatin Regions in Capsella grandiflora
- 2021
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:12, s. 5563-5575
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Tidskriftsartikel (refereegranskat)abstract
- Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (alpha) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.
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