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Publikasjoner (10 av 111) Visa alla publikasjoner
Gilardet, A., Lord, E., Oteo Garcia, G., Xenikoudakis, G., Douka, K., Wooller, M. J., . . . Dalén, L. (2025). A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening. Molecular Ecology Resources
Åpne denne publikasjonen i ny fane eller vindu >>A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening
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2025 (engelsk)Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Artikkel i tidsskrift (Fagfellevurdert) Epub ahead of print
Abstract [en]

Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.

Emneord
96-column plate, ancient DNA, DNA extraction, high-throughput
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-240154 (URN)10.1111/1755-0998.14077 (DOI)001415410200001 ()39912442 (PubMedID)2-s2.0-105001864724 (Scopus ID)
Tilgjengelig fra: 2025-03-04 Laget: 2025-03-04 Sist oppdatert: 2025-05-06
Chacón-Duque, J. C., Thomas Thorpe, J. A., Li, W., Dehasque, M., Pečnerová, P., Barlow, A., . . . Dalén, L. (2025). A Million Years of Mammoth Mitogenome Evolution. Molecular biology and evolution, 42(4), Article ID msaf065.
Åpne denne publikasjonen i ny fane eller vindu >>A Million Years of Mammoth Mitogenome Evolution
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2025 (engelsk)Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 42, nr 4, artikkel-id msaf065Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-Time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-Time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Emneord
deep-Time DNA, mammoths, mitogenomes, molecular clock dating, palaeogenomics, phylogenetics
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-242989 (URN)10.1093/molbev/msaf065 (DOI)001463164300001 ()40202893 (PubMedID)2-s2.0-105002791877 (Scopus ID)
Tilgjengelig fra: 2025-05-08 Laget: 2025-05-08 Sist oppdatert: 2025-05-08bibliografisk kontrollert
Lan, T., Li, H., Liu, B., Shi, M., Tian, Y., Sahu, S. K., . . . Xu, Y. (2025). Revealing extensive inbreeding and less-efficient purging of deleterious mutations in wild Amur tigers in China. Journal of Genetics and Genomics
Åpne denne publikasjonen i ny fane eller vindu >>Revealing extensive inbreeding and less-efficient purging of deleterious mutations in wild Amur tigers in China
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2025 (engelsk)Inngår i: Journal of Genetics and Genomics, ISSN 1673-8527Artikkel i tidsskrift (Fagfellevurdert) Epub ahead of print
Abstract [en]

Inbreeding increases genome homozygosity within populations, which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits. In small populations, genetic purging that occurs under pressure of natural selection acts as an opposing force, contributing to a reduction of deleterious alleles. Both inbreeding and genetic purging are paramount in the field of conservation genomics. The Amur tiger (Panthera tigris altaica) lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet. Using genome-wide assessment and comparison, we reveal substantially higher and more extensive inbreeding in wild Amur tigers (FROH = 0.50) than in captive individuals (FROH = 0.24). However, a relatively reduced number of loss-of-function mutations in wild Amur tigers is observed when compared with captive individuals, indicating a genetic purging of relatively large-effect inbreeding load. The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicate a less-efficient genetic purging, with purifying selection also contributing to this process. These findings provide valuable insights for future conservation of Amur tigers.

Emneord
Conservation genomics, Genetic purging, Inbreeding, Mutational load, Panthera tigris altaica
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-240414 (URN)10.1016/j.jgg.2024.12.004 (DOI)39674273 (PubMedID)2-s2.0-85213965570 (Scopus ID)
Tilgjengelig fra: 2025-03-07 Laget: 2025-03-07 Sist oppdatert: 2025-03-07
Stewart, J. R., Alsos, I. G., Brown, A. G., Dalén, L. & Heintzman, P. D. (2025). The progressive evolution of cold-adapted species. Trends in Ecology & Evolution
Åpne denne publikasjonen i ny fane eller vindu >>The progressive evolution of cold-adapted species
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2025 (engelsk)Inngår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383Artikkel, forskningsoversikt (Fagfellevurdert) Epub ahead of print
Abstract [en]

The evolution of cold-adapted terrestrial species underwent two main phases. First, the genera of cold-adapted taxa appeared during the Late Pliocene to Early Pleistocene. The modern day and Late Pleistocene cold-adapted species then arose during and after the Middle Pleistocene Transition. These species evolved through one or more of the following processes: out of the temperate zone, evolving in situ, or through montane preadaptation. Palaeogenetic studies are greatly contributing to our understanding of the timings and modes of evolution of cold-adapted species as well as when their specialised traits evolved. The evolution of polar plant and beetle species is claimed to show greater stasis than that of vertebrates, but could instead reflect morphological conservatism that can be tested with palaeogenetics.

Emneord
adaptation, birds, boreal, climate, mammals, Milankovitch cycles, Pleistocene, tundra
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-244166 (URN)10.1016/j.tree.2025.04.005 (DOI)2-s2.0-105005170846 (Scopus ID)
Tilgjengelig fra: 2025-06-16 Laget: 2025-06-16 Sist oppdatert: 2025-06-16
More, K. D., Dalén, L. & Orlando, L. (2025). Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals. Molecular Ecology Resources
Åpne denne publikasjonen i ny fane eller vindu >>Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals
2025 (engelsk)Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Artikkel i tidsskrift (Fagfellevurdert) Epub ahead of print
Abstract [en]

In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.

Emneord
ancient DNA, domestication, environmental DNA, palaeogenomics, target enrichment
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-243093 (URN)10.1111/1755-0998.14112 (DOI)001462101600001 ()2-s2.0-105002247368 (Scopus ID)
Tilgjengelig fra: 2025-05-08 Laget: 2025-05-08 Sist oppdatert: 2025-05-08
Hold, K., Lord, E., Brealey, J. C., Le Moullec, M., Bieker, V. C., Ellegaard, M. R., . . . Dussex, N. (2024). Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos. Scientific Reports, 14(1), Article ID 4143.
Åpne denne publikasjonen i ny fane eller vindu >>Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos
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2024 (engelsk)Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 14, nr 1, artikkel-id 4143Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

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.

HSV kategori
Identifikatorer
urn:nbn:se:su:diva-227457 (URN)10.1038/s41598-024-54296-2 (DOI)001167132500005 ()38374421 (PubMedID)2-s2.0-85185446057 (Scopus ID)
Tilgjengelig fra: 2024-03-14 Laget: 2024-03-14 Sist oppdatert: 2025-02-01bibliografisk kontrollert
Poquérusse, J., Brown, C. L., Gaillard, C., Doughty, C., Dalén, L., Gallagher, A. J., . . . Hysolli, E. (2024). Assessing contemporary Arctic habitat availability for a woolly mammoth proxy. Scientific Reports, 14, Article ID 9804.
Åpne denne publikasjonen i ny fane eller vindu >>Assessing contemporary Arctic habitat availability for a woolly mammoth proxy
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2024 (engelsk)Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 14, artikkel-id 9804Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12–15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska’s North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska’s North Slope could support densities of 0.0–0.38 woolly mammoth km−2 (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.

Emneord
Biomass, Carrying capacity, Ecological engineering, Remote sensing, Woolly mammoth proxy
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-235481 (URN)10.1038/s41598-024-60442-7 (DOI)001211293200094 ()38684726 (PubMedID)2-s2.0-85191792742 (Scopus ID)
Tilgjengelig fra: 2024-11-21 Laget: 2024-11-21 Sist oppdatert: 2024-11-21bibliografisk kontrollert
Hempel, E., Faith, J. T., Preick, M., de Jager, D., Barish, S., Hartmann, S., . . . Hofreiter, M. (2024). Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Current Biology, 34(9), 2020-2029, e1-e6
Åpne denne publikasjonen i ny fane eller vindu >>Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size
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2024 (engelsk)Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 34, nr 9, s. 2020-2029, e1-e6Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability. Moreover, small population size may promote gene flow with congeners and outbreeding depression. Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa, populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat. However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species’ unique traits.

HSV kategori
Identifikatorer
urn:nbn:se:su:diva-232532 (URN)10.1016/j.cub.2024.03.051 (DOI)001239686300001 ()38614080 (PubMedID)2-s2.0-85191484860 (Scopus ID)
Tilgjengelig fra: 2024-08-19 Laget: 2024-08-19 Sist oppdatert: 2024-08-19bibliografisk kontrollert
Münger, X., Robin, M., Dalén, L. & Grossen, C. (2024). Facilitated introgression from domestic goat into Alpine ibex at immune loci. Molecular Ecology, 33(14), Article ID e17429.
Åpne denne publikasjonen i ny fane eller vindu >>Facilitated introgression from domestic goat into Alpine ibex at immune loci
2024 (engelsk)Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 33, nr 14, artikkel-id e17429Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1–2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.

Emneord
Alpine ibex (Capra ibex), ancient genomics, anthropogenic hybridization, introgression, population genetics
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-232242 (URN)10.1111/mec.17429 (DOI)001240701900001 ()38847234 (PubMedID)2-s2.0-85195562727 (Scopus ID)
Tilgjengelig fra: 2024-08-12 Laget: 2024-08-12 Sist oppdatert: 2025-02-07bibliografisk kontrollert
van der Valk, T. & Dalén, L. (2024). From genomic threat assessment to conservation action [Letter to the editor]. Cell, 187(5), 1038-1041
Åpne denne publikasjonen i ny fane eller vindu >>From genomic threat assessment to conservation action
2024 (engelsk)Inngår i: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 187, nr 5, s. 1038-1041Artikkel i tidsskrift, Letter (Fagfellevurdert) Published
Abstract [en]

Genomic approaches have the potential to play a pivotal role in conservation, both to detect threats to species and populations and to restore biodiversity through actions. We here separate these approaches into two subdisciplines, vulnerability and restoration genomics, and discuss current applications, outstanding questions, and future potential.

 

HSV kategori
Identifikatorer
urn:nbn:se:su:diva-235986 (URN)10.1016/j.cell.2024.01.038 (DOI)001209004700001 ()38428386 (PubMedID)2-s2.0-85185702830 (Scopus ID)
Tilgjengelig fra: 2024-11-26 Laget: 2024-11-26 Sist oppdatert: 2025-02-01bibliografisk kontrollert
Organisasjoner
Identifikatorer
ORCID-id: ORCID iD iconorcid.org/0000-0001-6307-8188