| 1. |
- Cockerill, Christopher Alan, 1994-, et al.
(författare)
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Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)
- 2022
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 13:11
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Tidskriftsartikel (refereegranskat)abstract
- Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.
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| 2. |
- Måsviken, Johannes, 1990-, et al.
(författare)
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Elevational variation of spider and insect communities in the Swedish mountains
- 2023
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Ingår i: Ecosphere. - 2150-8925. ; 14:6
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Tidskriftsartikel (refereegranskat)abstract
- Mountain topography gives rise to often dramatic climate-driven elevation gradients in primary productivity, which can generate substantial biodiversity variation. Therefore, mountain areas may be particularly useful for evaluating the ecological consequences of climate change. Arthropods are the most diverse animal phylum, which play important roles in most ecosystems. However, despite their ecological importance, we have limited information on how arthropods vary along elevation gradients. We investigated how taxonomic richness, taxonomic composition, and spatial structuring of spider and insect communities varied along elevation gradients and among three geographic locations in a mountain region of northern Sweden. The locations provided a latitude gradient spanning approximately 3° (from 62° N to 65° N), but were otherwise selected to contain similar environmental characteristics. Taxonomic richness of both spiders and insects declined monotonically with increasing elevation, and there were limited differences between the geographic locations in such declines. Taxonomic composition varied with elevation for both taxonomic groups, but also differed among the three sites. Linyphiid spiders were more widely distributed along the elevation gradients than other spider taxa, whereas a broad taxonomic range of insects occurred over almost all elevations. We observed nested as well as modular spatial distributions of both spider and insect communities along the elevation gradients. While the modular patterns suggest that species turnover has generated distinct communities at different elevations, some generalist species were still widespread throughout large parts of the gradients. Our results point to smaller differences among geographic locations than among taxonomic groups in how taxonomic richness and community structuring varied with elevation. We interpret these results as support for taxonomically specific adaptations to environmental conditions being important for structuring arthropod communities. We also suggest that climate-driven changes to arthropod communities in mountain environments may be regulated by two not mutually exclusive processes, one in which generalist species may become more dominant and shift their ranges upward and one in which high-elevation specialists may go extinct because of increasingly fragmented habitats.
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| 3. |
- Måsviken, Johannes, 1990-, et al.
(författare)
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The relative importance of abiotic and biotic environmental conditions for taxonomic, phylogenetic, and functional diversity of spiders across spatial scales
- 2023
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Ingår i: Oecologia. - 0029-8549 .- 1432-1939. ; 202:2, s. 261-273
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Tidskriftsartikel (refereegranskat)abstract
- Both abiotic and biotic conditions may be important for biodiversity. However, their relative importance may vary among different diversity dimensions as well as across spatial scales. Spiders (Araneae) offer an ecologically relevant system for evaluating variation in the relative strength abiotic and biotic biodiversity regulation. We quantified the relative importance of abiotic and biotic conditions for three diversity dimensions of spider communities quantified across two spatial scales. Spiders were surveyed along elevation gradients in northern Sweden. We focused our analysis on geomorphological and climatic conditions as well as vegetation characteristics, and quantified the relative importance of these conditions for the taxonomic, phylogenetic, and functional diversity of spider communities sampled across one intermediate (500 m) and one local (25 m) scale. There were stronger relationships among diversity dimensions at the local than the intermediate scale. There were also variation in the relative influence of abiotic and biotic conditions among diversity dimensions, but this variation was not consistent across spatial scales. Across both spatial scales, vegetation was related to all diversity dimensions whereas climate was important for phylogenetic and functional diversity. Our study does not fully support stronger abiotic regulation at coarser scales, and conversely stronger abiotic regulation at more local scales. Instead, our results indicate that community assembly is shaped by interactions between abiotic constrains in species distributions and biotic conditions, and that such interactions may be both scale and context dependent.
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| 4. |
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| 5. |
- von Seth, Johanna, et al.
(författare)
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Genomic trajectories of a near-extinction event in the Chatham Island black robin
- 2022
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 23
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Understanding the micro-evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.Results: We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.Conclusion: Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
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| 6. |
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| 7. |
- von Seth, Johanna, 1989-
(författare)
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The use of museum specimens in conservation genomics
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the face of an increasing number of species being threatened by extinction, museum collections can constitute a powerful resource for acquiring genomic data of endangered taxa. By utilising datasets that combine genomes from present-day populations with those from historical timepoints, several questions relevant for conservation can be investigated. In this thesis, I made use of museum specimens by combining historical and modern genomes to shed light on the genomic status of four species of conservation concern. The thesis focuses on change in genome diversity, inbreeding, and mutational load, but also divergence and structure of extinct populations and present-day populations from which sampling is difficult. Since the 1920’s, the now extinct Sumatran rhinoceros (Dicerorhinus sumatrensis) population on the Malay Peninsula likely experienced genomic erosion (chapter I). Inbreeding increased almost four-fold, and was possibly accompanied by inbreeding depression causing premature deaths and/or lowered reproductive success. Mutational load was higher in the only two remaining populations on Borneo and Sumatra, but as genomic diversity was also relatively high, a large portion of the species’ evolutionary potential might be retained if population sizes can recover quickly. The extinct New Zealand mainland kākāpō (Strigops habroptilus) population comprised higher genomic diversity and lower inbreeding, but higher mutational load, compared to the only extant population on Stewart Island (chapter II). Demographic reconstruction revealed a continuous population decline on Stewart Island since the population split between the mainland and Stewart Island populations around 10,000 years ago, and simulations demonstrated that this could have facilitated a higher efficacy of purifying selection on Stewart Island. While the arctic fox (Vulpes lagopus) is of least concern worldwide, the peripheral Scandinavian population has been threatened by extinction since the early 1900’s. A substantial increase in inbreeding was found in all Scandinavian subpopulations, but was most pronounced in southern Scandinavia (chapter III). In spite of ongoing inbreeding in the past century, genomic diversity remained stable in central and northern Scandinavia, possibly owing to post-bottleneck gene flow from Russia. The population bottleneck of a single breeding pair in the Chatham Island black robin (Petroica traversi) caused a four-fold increase in inbreeding and halved genomic diversity, but caused only minor changes in mutational load (chapter IV). In the light of population history, this suggests that prolonged periods of small population size have facilitated possibilities for purging of genetic load already prior to the historical decline. Overall, this thesis highlights not only the extensive genomic impact that anthropogenic-driven declines have had on genomic diversity of endangered animals, but also that the effect on mutational load varies between taxa.
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| 8. |
- Burnett, Hamish A., et al.
(författare)
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Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer
- 2023
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Ingår i: Evolutionary Applications. - 1752-4571. ; 16:9, s. 1531-1548
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.
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| 9. |
- Dalén, Love, 1980-, et al.
(författare)
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Deep-time paleogenomics and the limits of DNA survival
- 2023
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Ingår i: Science. - 0036-8075 .- 1095-9203. ; 382:6666, s. 48-53
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Tidskriftsartikel (refereegranskat)abstract
- Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
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| 10. |
- Dalén, Lové, 1980-, et al.
(författare)
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Recovery of DNA from Footprints in the snow
- 2008
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Ingår i: Canadian field-naturalist. - OTTAWA, Canada : OTTAWA FIELD-NATURALISTS CLUB. - 0008-3550. ; 121:3, s. 321-324
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Tidskriftsartikel (refereegranskat)abstract
- The recovery of trace amounts of DNA has been demonstrated to be a reliable tool in conservation genetics and has become a key component of modern forensic casework. To date, genetic data have been successfully recovered from a variety of sources, including biological fluids, faeces, clothing, and even directly from fingerprints. However, to our knowledge and despite their widespread occurrence and clear potential as a source of DNA, genetic information has not previously been recovered directly from footprints. Here, we extract and amplify mitochondrial DNA from a snow footprint, <48-hours old, made by a Swedish Arctic Fox (Alopex lagopus). Our results demonstrate that it is possible to recover Sufficient DNA from recent footprints to accurately type the source of the print, with implications for conservation biology and forensic science.
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| 11. |
- 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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| 12. |
- 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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| 13. |
- Dussex, Nicolas, et al.
(författare)
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Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer
- 2023
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Ingår i: iScience. - 2589-0042. ; 26:10
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Tidskriftsartikel (refereegranskat)abstract
- Typically much smaller in number than their mainland counterparts, island populations are ideal systems to investigate genetic threats to small populations. The Svalbard reindeer (Rangifer tarandus platyrhynchus) is an endemic subspecies that colonized the Svalbard archipelago ca. 6,000–8,000 years ago and now shows numerous physiological and morphological adaptations to its arctic habitat. Here, we report a de-novo chromosome-level assembly for Svalbard reindeer and analyze 133 reindeer genomes spanning Svalbard and most of the species’ Holarctic range, to examine the genomic consequences of long-term isolation and small population size in this insular subspecies. Empirical data, demographic reconstructions, and forward simulations show that long-term isolation and high inbreeding levels may have facilitated the reduction of highly deleterious—and to a lesser extent, moderately deleterious—variation. Our study indicates that long-term reduced genetic diversity did not preclude local adaptation to the High Arctic, suggesting that even severely bottlenecked populations can retain evolutionary potential.
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| 14. |
- Dussex, Nicolas, et al.
(författare)
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Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
- 2023
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Ingår i: Communications Biology. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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| 15. |
- Hempel, Elisabeth, et al.
(författare)
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Blue Turns to Gray : Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus)
- 2022
-
Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:12
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Tidskriftsartikel (refereegranskat)abstract
- The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
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| 16. |
- Hold, Katharina, et al.
(författare)
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Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos
- 2024
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.
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| 17. |
- 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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| 18. |
- Laikre, Linda, 1960-, et al.
(författare)
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Planned cull endangers Swedish wolf population
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 377:6602
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Tidskriftsartikel (refereegranskat)abstract
- In May, the Swedish Parliament announced a goal to reduce the Swedish wolf population from about 400 to about 200 individuals (1). This action further threatens this highly endangered population, which is genetically isolated and inbred. Scientific advice for improvements has not been implemented (2, 3).The Swedish Parliament proposed this drastic cull at a time when biodiversity is a global focus. The 50-year anniversary of the first UN conference on the environment was celebrated in June, and the UN Convention on Biological Diversity (CBD) will soon finalize its global biodiversity framework for 2020 to 2050. Sweden’s actions are inconsistent with the country’s obligations under the CBD and European Union law.Few wild populations are as well studied as the Scandinavian wolf. Genetic monitoring has provided a full pedigree since the population was reestablished in the 1980s after extinction, and the data confirm persisting genetic isolation (4–6). Hunting, conducted both legally and illegally, has prevented population expansion and the influx of genetic variation.Three founders comprised the population’s genetic origin until 2007, and only three more wolves have subsequently contributed genetically to the present population (6). The genetic base is thus extremely narrow, and genomic erosion has been confirmed (7, 8). The average level of inbreeding is similar to the level found in the offspring of two full siblings (6). Inbreeding in this population has been shown to reduce litter size (4). Also, high frequencies of anatomical defects (9) and male reproductive disorders (10) have been observed.To make this population viable, population size and immigration must increase. So far, the population has been too small, and limited immigration followed by inbreeding could lead to extinction, similar to the Isle Royale wolf population (11). The goal should be to recreate a well-connected metapopulation spanning Scandinavia and Finland with a genetically effective population size of over 500, in line with the proposed CBD indicator (12). Considerably more genetic exchange than the current one-migrant-per-generation aim is needed (3).
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| 19. |
- Le Duc, D., et al.
(författare)
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. We also found that Steller's sea cows' abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction.
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| 20. |
- Lin, Audrey T., et al.
(författare)
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The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge
- 2023
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Ingår i: Science. - 0036-8075 .- 1095-9203. ; 382:6676, s. 1303-1308
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Tidskriftsartikel (refereegranskat)abstract
- Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton", collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
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| 21. |
- Lord, Edana, et al.
(författare)
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Population dynamics and demographic history of Eurasian collared lemmings
- 2022
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Ingår i: BMC Ecology and Evolution. - : Springer Science and Business Media LLC. - 2730-7182. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.Results: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.Conclusions: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.
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| 22. |
- Mármol-Sánchez, Emilio, et al.
(författare)
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Historical RNA expression profiles from the extinct Tasmanian tiger
- 2023
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Ingår i: Genome Research. - 1088-9051 .- 1549-5469. ; 33:8, s. 1299-1316
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Tidskriftsartikel (refereegranskat)abstract
- Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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| 23. |
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| 24. |
- Pečnerová, Patrícia, et al.
(författare)
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Population genomics of the muskox' resilience in the near absence of genetic variation
- 2024
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 33:2
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Tidskriftsartikel (refereegranskat)abstract
- Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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| 25. |
- Pochon, Zoé, et al.
(författare)
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aMeta : an accurate and memory-efficient ancient metagenomic profiling workflow
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
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| 26. |
- Rabiniak, Emilia, et al.
(författare)
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Late Pleistocene and Holocene pikas (Mammalia, Lagomorpha) from Europe and the validity of Ochotona spelaea : New insights based on mtDNA analysis
- 2023
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Ingår i: Palaeontologia Electronica. - : Coquina Press. - 1935-3952 .- 1094-8074. ; 26:1
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Tidskriftsartikel (refereegranskat)abstract
- Pikas were among small mammals that inhabited mammoth steppes during the last glacial. The evolutionary history of ochotonids in Europe is relatively well studied, although the taxonomic status of many described forms remains ambiguous, and the majority of extant species of the genus Ochotona are poorly represented in the fossil record. The present study aims to analyse the taxonomic relationships of a sample of Late Pleistocene-Holocene pikas based on mtDNA data and to clarify the status of the species described from Europe. A phylogenetic analysis has revealed that pikas form two large clades: one includes O. pusilla and the other includes the extant Asian and North American species. The study of haplotypes has shown similar results. The analysis supports the view that in the Late Pleistocene and Holocene O. pusilla was distributed throughout Europe, and its geographic range has contracted to the east until reaching its modern limits. The analysis of samples provided evidence that O. pusilla had survived in Eastern Europe until relatively recently and disappeared only about 150 years ago. The molecular data inferred from mtDNA do not support the species status of O. spelaea, despite morphological differences possibly related to the particular ecology of the Late Pleistocene.
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| 27. |
- Sánchez-Barreiro, Fátima, et al.
(författare)
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Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
- 2023
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Ingår i: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 40:9
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Tidskriftsartikel (refereegranskat)abstract
- The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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| 28. |
- 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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