| 1. |
- Kutschera, Verena E., et al.
(författare)
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Purifying Selection in Corvids Is Less Efficient on Islands
- 2020
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:2, s. 469-474
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Tidskriftsartikel (refereegranskat)abstract
- Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size N-e. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.
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| 2. |
- Dussex, Nicolas, et al.
(författare)
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A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:4, s. 973-986
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Tidskriftsartikel (refereegranskat)abstract
- Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
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| 3. |
- Dussex, Nicolas, et al.
(författare)
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Population genomics of the critically endangered kākāpō
- 2021
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:1
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Tidskriftsartikel (refereegranskat)abstract
- Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
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| 4. |
- Bergmann, O., et al.
(författare)
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The Age of Olfactory Bulb Neurons in Humans
- 2012
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Ingår i: Neuron. - : Elsevier BV. - 0896-6273 .- 1097-4199. ; 74:4, s. 634-639
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Tidskriftsartikel (refereegranskat)abstract
- Continuous turnover of neurons in the olfactory bulb is implicated in several key aspects of olfaction. There is a dramatic decline postnatally in the number of migratory neuroblasts en route to the olfactory bulb in humans, and it has been unclear to what extent the small number of neuroblasts at later stages contributes new neurons to the olfactory bulb. We have assessed the age of olfactory bulb neurons in humans by measuring the levels of nuclear bomb test-derived C-14 in genomic DNA. We report that C-14 concentrations correspond to the atmospheric levels at the time of birth of the individuals, establishing that there is very limited, if any, postnatal neurogenesis in the human olfactory bulb. This identifies a fundamental difference in the plasticity of the human brain compared to other mammals.
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| 5. |
- Forstner, O., et al.
(författare)
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Isobar suppression in AMS using laser photodetachment
- 2008
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms. ; 266:19-20, s. 4565-4568
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Tidskriftsartikel (refereegranskat)abstract
- We are investigating the possibility of using laser photodetachment of negative atomic and molecular ions as an additional isobaric selection filter in accelerator mass spectrometry. The aim of this study is to find a possibility to further improve the detection limit for long-lived heavy radionuclides at AMS facilities. We will focus on the astrophysical relevant radionuclide 182Hf, which is one of the isotopes measured with the 3 MV tandem AMS facility VERA (Vienna Environmental Research Accelerator) at the University of Vienna. Laser-induced isobar suppression is also of importance for radioactive-beam facilities. The present detection limit for measuring the isotope ratio 182Hf/Hf at VERA is 1×10-11. The limiting factor is the strong background of the stable isobar 182W. Currently this background is suppressed using suitable molecular ions in the injection stage. Selective laser photodetachment of the negative ions at the injector can lead to an additional suppression of the interfering isobar. Test experiments have been carried out at the negative ion laser spectroscopy setup at Göteborg University. In a small ion beam apparatus pulsed tunable laser radiation is used to measure the photodetachment cross-section of different atomic and molecular negative ions. We will present studies of the photodetachment process for various tungsten and hafnium molecules with the aim to find a selective isobaric suppression scheme using laser photodetachment spectroscopy in combination with AMS.
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| 6. |
- Kurland, Sara, et al.
(författare)
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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 11448-11463
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Tidskriftsartikel (refereegranskat)abstract
- Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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| 7. |
- Kutschera, Verena E., et al.
(författare)
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GenErode : a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
- 2022
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Ingår i: BMC Bioinformatics. - : Springer Nature. - 1471-2105. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. Results: Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). Conclusions: GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
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| 8. |
- Martschini, M., et al.
(författare)
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AMS of Cl-36 with the VERA 3 MV tandem accelerator
- 2013
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Ingår i: Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 294, s. 115-120
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Tidskriftsartikel (refereegranskat)abstract
- Recent progress with compact ionization chambers has opened new possibilities for isobar Refraining from the additional use of degrader foils has the benefit of high transmission to the detector Precision and accuracy have been thoroughly assessed over the last two years. Since drifts in the Recently we also explored novel techniques for additional sulfur suppression already in the ion source.
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| 9. |
- Mugal, Carina, et al.
(författare)
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Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio omega for Closely Related Species
- 2020
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:1, s. 260-279
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Tidskriftsartikel (refereegranskat)abstract
- The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio omega, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of omega in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution alpha. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of omega and alpha for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of omega and alpha at different time-scales and for several choices of sample sizes.
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| 10. |
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