| 1. |
- 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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| 2. |
- 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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| 3. |
- Larsson, Petter, et al.
(författare)
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Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox
- 2019
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 374:1788
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Tidskriftsartikel (refereegranskat)abstract
- Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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| 4. |
- Lord, Edana, et al.
(författare)
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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
- 2020
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 30:19
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Tidskriftsartikel (refereegranskat)abstract
- Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a similar to 18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bolling-Allerod interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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| 5. |
- Broushaki, Farnaz, et al.
(författare)
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Early Neolithic genomes from the eastern Fertile Crescent.
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 353:6298
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Tidskriftsartikel (refereegranskat)abstract
- We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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| 6. |
- Dehasque, Marianne, et al.
(författare)
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Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia
- 2021
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 259
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Tidskriftsartikel (refereegranskat)abstract
- To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.
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| 7. |
- Dehasque, Marianne, et al.
(författare)
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Inference of natural selection from ancient DNA
- 2020
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Ingår i: Evolution Letters. - : JOHN WILEY & SONS LTD. - 2056-3744. ; 4:2, s. 94-108
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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| 8. |
- Dehasque, Marianne, 1993-
(författare)
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Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biodiversity is declining globally. Yet, the biological and genetic processes associated with these declines on a longer timescale are still poorly understood. Ancient DNA is a powerful tool to study evolution in real-time. Despite advances in the field, there is further need for refinement of laboratory and computational techniques. In this thesis, I used mitochondrial and nuclear genomes, as well as radiocarbon data, to study the evolutionary history and extinction dynamics of the woolly mammoth (Mammuthus primigenius). In Chapter I, I developed and optimized a silica column-based extraction protocol for ancient DNA. Based on systematic tests, I advise against routine use of pretreatment methods, like bleach wash and/or predigestion, for well-preserved permafrost samples. Furthermore, I suggest that USER enzyme, which removes uracil from damaged DNA molecules, is effective at half the concentration compared to an established control protocol. Finally, I did not find a significant difference between different silica columns for the clean-up steps, or concentrator columns with different DNA retention sizes. In Chapter II, I used five high coverage Siberian mammoth genomes to develop a method based on differences in read depth to identify indels, insertions and deletions, in the mammoth genome. The results show that indels are enriched in intergenic regions, suggesting strong selection against structural variants affecting gene function. Nevertheless, 87 genes were identified that were severely affected. These genes are related to various functions like body-fat distribution, fur growth and hair shape, body temperature, and body size, and most likely represent important adaptations to the cold steppe-tundra. In Chapter III, I studied the population and extinction dynamics of the woolly mammoths in Siberia by combining Bayesian age models from radiocarbon data with inferences from complete mitogenomes. The results show that the woolly mammoth’s extinction was a complex process with consecutive extirpations, but also partial recolonizations, occurring in different Siberian localities. I hypothesize that Wrangel Island, one of the last refugia of the woolly mammoth, was colonized by mammoths from, or closely related to, a population from central or western Siberia. Mammoths reappeared on the island around 10 ky ago, where they became isolated due to rising sea levels, and went extinct around 4 ky ago. To investigate the genetic consequences of the founder bottleneck event of Wrangel Island and long-term survival at small population size, I analyzed time-series data of 21 woolly mammoth genomes in Chapter IV. Changes in heterozygosity and inbreeding show that while the initial bottleneck was dramatic, the population recovered fast and remained remarkably stable. Analysis of mutation load shows that mammoths purged highly deleterious mutations over time, but also accumulated slightly deleterious mutations, indicating reduced efficacy of selection. Nevertheless, there were no clear signs of a mutational meltdown, and it remains a mystery why mammoths went extinct on the island. In conclusion, this thesis presents methodological advances for DNA extraction and detecting structural variants (i.e., deletions) in ancient genomes. Furthermore, I demonstrate that extinctions are a complex process. Finally, I show that ancient DNA is a powerful tool to study evolutionary processes over long timescales.
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| 9. |
- Dehasque, Marianne, et al.
(författare)
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Temporal dynamics of woolly mammoth genome erosion prior to extinction
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A large number of species have recently recovered from near-extinction events. Understanding the genetic consequences of severe population declines followed by demographic recoveries is key to predict the long-term viability of species in order to mitigate future extinction risks. Although these species have avoided the immediate extinction threat, their long-term viability remains questionable due to the genetic consequences of population declines, which are not understood on a time scale beyond a few generations. The woolly mammoth (Mammuthus primigenius) population on Wrangel Island is an excellent model system to investigate long-term genetic consequences of a population bottleneck. Mammoths became isolated on the island in the early Holocene due to rising sea levels, and persisted for over 200 generations (~6,000 years) before becoming extinct ~4,000 years ago. To study the evolutionary processes leading up to the extinction of the woolly mammoth on the island, we analysed 21 Siberian woolly mammoth genomes, including that of one of the last known mammoths. Our results show that the Wrangel Island mammoths recovered quickly from an initially severe bottleneck, and subsequently remained demographically stable during the ensuing 6 millennia. Further, we find that highly deleterious mutations were gradually purged from the population, whereas there was an accumulation of mildly deleterious mutations. The gradual purging of highly deleterious mutations suggests an ongoing inbreeding depression that lasted for hundreds of generations. This time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked present-day populations.
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| 10. |
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