1. |
- Atag, Gözde, et al.
(författare)
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Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:5
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Tidskriftsartikel (refereegranskat)abstract
- Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (N-e). Meanwhile, N-e and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term N-e, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
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2. |
- 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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3. |
- Dehasque, Marianne, et al.
(författare)
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA
- 2022
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 13:4
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Tidskriftsartikel (refereegranskat)abstract
- Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.
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4. |
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5. |
- 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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6. |
- 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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7. |
- 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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8. |
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9. |
- Díez-del-Molino, David, 1984-, et al.
(författare)
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Genomics of adaptive evolution in the woolly mammoth
- 2023
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Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 33:9, s. 1753-1764
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Tidskriftsartikel (refereegranskat)abstract
- Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of tradi-tional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
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10. |
- Dussex, Nicolas, et al.
(författare)
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Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics
- 2021
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 288:1957
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Forskningsöversikt (refereegranskat)abstract
- Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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12. |
- Feuerborn, Tatiana R., et al.
(författare)
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Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.Results: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.Conclusions: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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13. |
- 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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14. |
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15. |
- Rosengren, Erika, et al.
(författare)
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches
- 2021
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Ingår i: Diversity. - : MDPI AG. - 1424-2818. ; 13:8
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Forskningsöversikt (refereegranskat)abstract
- Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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16. |
- van der Valk, Tom, et al.
(författare)
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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome
- 2022
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Ingår i: iScience. - : Elsevier BV. - 2589-0042. ; 25:8
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Tidskriftsartikel (refereegranskat)abstract
- Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment.
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18. |
- van der Valk, Tom, et al.
(författare)
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Million-year-old DNA sheds light on the genomic history of mammoths
- 2021
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 591:7849, s. 265-269
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Tidskriftsartikel (refereegranskat)abstract
- Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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