1
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Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam P, Brooke MDL, Sweet P, Gopalakrishnan S, Gilbert MTP. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evol Appl 2024; 17:e13739. [PMID: 38948538 PMCID: PMC11212007 DOI: 10.1111/eva.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.
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Affiliation(s)
- Emily L. Cavill
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Xin Sun
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | - Anna Zora
- Fregate Island Sanctuary LtdVictoriaSeychelles
| | | | | | | | | | - Paul Sweet
- American Museum of Natural HistoryNew YorkUSA
| | | | - M. Thomas P. Gilbert
- The Globe Institute, University of CopenhagenCopenhagenDenmark
- University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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2
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Gignac PM, Valdez D, Morhardt AC, Lynch LM. Buffered Lugol's Iodine Preserves DNA Fragment Lengths. Integr Org Biol 2024; 6:obae017. [PMID: 38887427 PMCID: PMC11182668 DOI: 10.1093/iob/obae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/05/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (I2KI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (I2E); (2) 3.75% wt/vol. I2KI; and (3) 3.75% wt/vol. buffered I2KI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining-potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered I2KI and control samples, which were not, themselves, significantly different. Our results implicate buffered I2KI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.
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Affiliation(s)
- P M Gignac
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - D Valdez
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
| | - A C Morhardt
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - L M Lynch
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
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3
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Ouerghi F, Krane DE, Edge MD. On forensic likelihood ratios from low-coverage sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595821. [PMID: 38854110 PMCID: PMC11160658 DOI: 10.1101/2024.05.24.595821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
With advances in sequencing technology, forensic workers can access genetic information from increasingly challenging samples. A recently published computational approach, IBDGem , analyzes sequencing reads, including from low-coverage samples, in order to arrive at likelihood ratios for tests of identity. Here, we show that likelihood ratios produced by IBDGem test a null hypothesis different from the traditional one used in a forensic genetics context. In particular, rather than testing the hypothesis that the sample comes from a person unrelated to the person of interest, IBDGem tests the hypothesis that the sample comes from an individual who is included in the reference sample used to run the method. This null hypothesis is not generally of forensic interest, because the defense hypothesis is not that the evidence comes from an individual included in a reference panel. Further, it does not take into account genetic variation outside the reference panel, and as a result, the computed likelihood ratios can be much larger than likelihood ratios computed for the standard forensic null hypothesis, often by many orders of magnitude, thus potentially creating an impression of stronger evidence for identity than is warranted. We lay out this result and illustrate it with examples, giving suggestions for directions that might lead to likelihood ratios that have the traditional interpretation.
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4
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Meiri M, Bar-Oz G. Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. Trends Genet 2024; 40:398-409. [PMID: 38423916 PMCID: PMC11079635 DOI: 10.1016/j.tig.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.
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Affiliation(s)
- Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Haifa, 3498837 Mount Carmel, Israel
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5
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Bali GK, Cuenca D, Wallin J. Effects and considerations of multiplexing ForenSeq Kintelligence libraries with a negative control. Electrophoresis 2024; 45:852-866. [PMID: 38449358 DOI: 10.1002/elps.202300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024]
Abstract
The negative template control or negative amplification control has been an essential component of the forensic DNA analysis workflow that helps monitor contamination. As such, the inclusion of a negative control in forensic DNA analysis has been a requirement for all laboratories audited under the FBI's Quality Assurance Standards. As massively parallel sequencing (MPS) becomes more conventional in forensic laboratories, considerations for the inclusion of a negative control in every sequencing run can be evaluated. Although the inclusion of a negative control in library preparation and the first sequencing run has a practical function, there is less utility for its inclusion in all subsequent sequencing runs for that library preparation. Although this is universal to all MPS assays, it is most relevant for an assay that has a low sample multiplexing capacity, such as the ForenSeq Kintelligence Kit (Qiagen/Verogen, Inc.). The ForenSeq Kintelligence Kit is an investigative genetic genealogy (IGG) sequencing-based assay that targets 10,230 forensically relevant single-nucleotide polymorphisms. The manufacturer recommends multiplexing 3 libraries per sequencing run, which includes controls. The purpose of this study was to investigate the effect of the inclusion of a negative control in every Kintelligence sequencing run. We observed that the library generated from a negative amplification control will take 7%-14% of the run output. The loss of sequencing space taken by a negative control decreased the available output for DNA-containing samples, leading in some cases to allele or locus dropout and accompanying higher numbers of sixth to seventh order unknown associations in GEDmatch PRO.
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Affiliation(s)
- Gunmeet Kaur Bali
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
| | - Daniela Cuenca
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
| | - Jeanette Wallin
- California Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California, USA
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6
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Sundararaman B, Shapiro K, Packham A, Camp LE, Meyer RS, Shapiro B, Green RE. Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii. Food Microbiol 2024; 118:104403. [PMID: 38049278 DOI: 10.1016/j.fm.2023.104403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/15/2023] [Indexed: 12/06/2023]
Abstract
Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases. Surveillance methods must therefore screen for these pathogens at various stages of water distribution and of food from production to consumption. Detection using nucleic acid amplification methods offer rapid identification, but such methods have limited utility for characterizing populations, variant types or virulence traits of pathogens. Whole genome sequencing (WGS) can be used to determine this information. However, pathogens must be isolated and cultured to yield sufficient DNA for WGS, which is laborious or not feasible for certain stages of parasites like oocysts of Toxoplasma gondii. We previously developed the Circular Nucleic acid Enrichment Reagent (CNER) method to make whole genome enrichment (WGE) baits for difficult-to-grow bacterial pathogens. WGE using CNERs facilitates direct sequencing of pathogens from samples without the need to isolate and grow them. Here, we made WGE-CNERs for T. gondii to demonstrate the use of the CNER method to make baits to enrich the large genomes of water and foodborne protozoan pathogens. By sequencing, we detected as few as 50 parasites spiked in an oyster hemolymph matrix. We discuss the use of WGE-CNERs for genomic surveillance of food and waterborne pathogens.
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Affiliation(s)
| | - Karen Shapiro
- One Health Institute, UC Davis, USA; Department of Pathology, Microbiology, and Immunology, UC Davis, USA.
| | | | - Lauren E Camp
- Department of Pathology, Microbiology, and Immunology, UC Davis, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA; Howard Hughes Medical Institute, UC Santa Cruz, USA
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7
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Laine J, Mak SST, Martins NFG, Chen X, Gilbert MTP, Jones FC, Pedersen MW, Romundset A, Foote AD. Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Curr Biol 2024; 34:1142-1147.e6. [PMID: 38350445 DOI: 10.1016/j.cub.2024.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.
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Affiliation(s)
- Jan Laine
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Nuno F G Martins
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Xihan Chen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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8
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Cheng JC, Swarup N, Wong DTW, Chia D. A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection. Front Oncol 2024; 14:1332004. [PMID: 38511142 PMCID: PMC10951391 DOI: 10.3389/fonc.2024.1332004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024] Open
Abstract
In clinical oncology, cell-free DNA (cfDNA) has shown immense potential in its ability to noninvasively detect cancer at various stages and monitor the progression of therapy. Despite the rapid improvements in cfDNA liquid biopsy approaches, achieving the required sensitivity to detect rare tumor-derived cfDNA still remains a challenge. For next-generation sequencing, the perceived presentation of cfDNA is strongly linked to the extraction and library preparation protocols. Conventional double-stranded DNA library preparation (dsDNA-LP) focuses on assessing ~167bp double-stranded mononucleosomal (mncfDNA) and its other oligonucleosomal cell-free DNA counterparts in plasma. However, dsDNA-LP methods fail to include short, single-stranded, or nicked DNA in the final library preparation, biasing the representation of the actual cfDNA populations in plasma. The emergence of single-stranded library preparation (ssDNA-LP) strategies over the past decade has now allowed these other populations of cfDNA to be studied from plasma. With the use of ssDNA-LP, single-stranded, nicked, and ultrashort cfDNA can be comprehensively assessed for its molecular characteristics and clinical potential. In this review, we overview the current literature on applications of ssDNA-LP on plasma cfDNA from a potential cancer liquid biopsy perspective. To this end, we discuss the molecular principles of single-stranded DNA adapter ligation, how library preparation contributes to the understanding of native cfDNA characteristics, and the potential for ssDNA-LP to improve the sensitivity of circulating tumor DNA detection. Additionally, we review the current literature on the newly reported species of plasma ultrashort single-stranded cell-free DNA plasma, which appear biologically distinct from mncfDNA. We conclude with a discussion of future perspectives of ssDNA-LP for liquid biopsy endeavors.
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Affiliation(s)
- Jordan C. Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
- Stanford Cancer Institute, Stanford University, Stanford, CA, United States
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David T. W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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9
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Emery MV, Bolhofner K, Spake L, Ghafoor S, Versoza CJ, Rawls EM, Winingear S, Buikstra JE, Loreille O, Fulginiti LC, Stone AC. Targeted enrichment of whole-genome SNPs from highly burned skeletal remains. J Forensic Sci 2024. [PMID: 38415845 DOI: 10.1111/1556-4029.15482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.
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Affiliation(s)
- Matthew V Emery
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Katelyn Bolhofner
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
- School of Interdisciplinary Forensics, Arizona State University, Glendale, Arizona, USA
| | - Laure Spake
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Suhail Ghafoor
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Cyril J Versoza
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Erin M Rawls
- School of Life Sciences, Arizona State University, Life Sciences C, Tempe, Arizona, USA
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jane E Buikstra
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
| | - Odile Loreille
- FBI Laboratory, DNA Support Unit, Quantico, Virginia, USA
| | - Laura C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Maricopa County Office of the Medical Examiner, Phoenix, Arizona, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Arizona State University, Life Sciences C, Tempe, Arizona, USA
- Center for Bioarchaeology, Arizona State University, Tempe, Arizona, USA
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10
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Lin AT, Hammond-Kaarremaa L, Liu HL, Stantis C, McKechnie I, Pavel M, Pavel SSM, Wyss SSÁ, Sparrow DQ, Carr K, Aninta SG, Perri A, Hartt J, Bergström A, Carmagnini A, Charlton S, Dalén L, Feuerborn TR, France CAM, Gopalakrishnan S, Grimes V, Harris A, Kavich G, Sacks BN, Sinding MHS, Skoglund P, Stanton DWG, Ostrander EA, Larson G, Armstrong CG, Frantz LAF, Hawkins MTR, Kistler L. The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge. Science 2023; 382:1303-1308. [PMID: 38096292 PMCID: PMC7615573 DOI: 10.1126/science.adi6549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
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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Affiliation(s)
- Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
| | - Liz Hammond-Kaarremaa
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Vancouver Island University, Nanaimo, BC, Canada
| | - Hsiao-Lei Liu
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Chris Stantis
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
| | - Michael Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
| | - Susan sa'hLa mitSa Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
- Coast Salish Wool Weaving Center, Skokomish Nation, WA, USA
- The Evergreen State College, Olympia, WA, USA
| | | | | | | | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Angela Perri
- Department of Anthropology, Texas A&M University, College Station, TX, USA
- Chronicle Heritage, Phoenix, AZ, USA
| | - Jonathan Hartt
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sophy Charlton
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, NL, Canada
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gwénaëlle Kavich
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - David W G Stanton
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Greger Larson
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
| | - Chelsey G Armstrong
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Melissa T R Hawkins
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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11
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Jäger HY, Atz Zanotelli D, Maixner F, Nicklisch N, Alt KW, Meller H, Pap I, Szikossy I, Pálfi G, Zink AR. Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. Tuberculosis (Edinb) 2023; 143S:102392. [PMID: 38012935 DOI: 10.1016/j.tube.2023.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 11/29/2023]
Abstract
Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.
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Affiliation(s)
- Heidi Y Jäger
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Daniel Atz Zanotelli
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary.
| | - Albert R Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
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12
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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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13
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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14
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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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15
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Dalén L, Heintzman PD, Kapp JD, Shapiro B. Deep-time paleogenomics and the limits of DNA survival. Science 2023; 382:48-53. [PMID: 37797036 PMCID: PMC10586222 DOI: 10.1126/science.adh7943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
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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Affiliation(s)
- Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE- 10405 Stockholm, Sweden
| | - Peter D. Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Joshua D. Kapp
- Department of Biomolecular Engineering, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz; Santa Cruz, California, 95064, USA
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16
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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17
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Rasmussen L, Fontsere C, Soto-Calderón ID, Guillen R, Savage A, Hansen AJ, Hvilsom C, Gilbert MTP. Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact. Mol Ecol 2023; 32:5514-5527. [PMID: 37702122 DOI: 10.1111/mec.17130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.
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Affiliation(s)
- Linett Rasmussen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iván D Soto-Calderón
- Laboratorio de Genética Animal. Grupo Agrociencias, Biodiversidad y Territorio, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Medellín, Colombia
| | | | | | - Anders Johannes Hansen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
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18
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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19
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Nguyen R, Kapp JD, Sacco S, Myers SP, Green RE. A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data. J Hered 2023; 114:504-512. [PMID: 37381815 PMCID: PMC10445519 DOI: 10.1093/jhered/esad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023] Open
Abstract
Several methods exist for detecting genetic relatedness or identity by comparing DNA information. These methods generally require genotype calls, either single-nucleotide polymorphisms or short tandem repeats, at the sites used for comparison. For some DNA samples, like those obtained from bone fragments or single rootless hairs, there is often not enough DNA present to generate genotype calls that are accurate and complete enough for these comparisons. Here, we describe IBDGem, a fast and robust computational procedure for detecting genomic regions of identity-by-descent by comparing low-coverage shotgun sequence data against genotype calls from a known query individual. At less than 1× genome coverage, IBDGem reliably detects segments of relatedness and can make high-confidence identity detections with as little as 0.01× genome coverage.
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Affiliation(s)
- Remy Nguyen
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Steven P Myers
- California Department of Justice Jan Bashinski DNA Laboratory, Richmond, CA, United States
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
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20
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Utzeri VJ, Cilli E, Fontani F, Zoboli D, Orsini M, Ribani A, Latorre A, Lissovsky AA, Pillola GL, Bovo S, Gruppioni G, Luiselli D, Fontanesi L. Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph. Sci Rep 2023; 13:13635. [PMID: 37604894 PMCID: PMC10442435 DOI: 10.1038/s41598-023-40746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.
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Affiliation(s)
- Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy.
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Daniel Zoboli
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Massimiliano Orsini
- Laboratory of Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'università 10, 35120, Legnaro, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Adriana Latorre
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Andrey A Lissovsky
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Gian Luigi Pillola
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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21
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Hernández‐Alonso G, Ramos‐Madrigal J, Sun X, Scharff‐Olsen CH, Sinding MS, Martins NF, Ciucani MM, Mak SST, Lanigan LT, Clausen CG, Bhak J, Jeon S, Kim C, Eo KY, Cho S, Boldgiv B, Gantulga G, Unudbayasgalan Z, Kosintsev PA, Stenøien HK, Gilbert MTP, Gopalakrishnan S. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecol Evol 2023; 13:e10404. [PMID: 37546572 PMCID: PMC10401669 DOI: 10.1002/ece3.10404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.
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Affiliation(s)
- Germán Hernández‐Alonso
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jazmín Ramos‐Madrigal
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Xin Sun
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Nuno F. Martins
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Sarah S. T. Mak
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Liam Thomas Lanigan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Cecilie G. Clausen
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jong Bhak
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
- Department of Biomedical Engineering, College of Information‐Bio Convergence EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
- Personal Genomics InstituteGenome Research FoundationOsongKorea
| | - Sungwon Jeon
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
| | | | - Kyung Yeon Eo
- Department of Animal Health & WelfareSemyung UniversityJecheonKorea
| | - Seong‐Ho Cho
- Natural History MuseumKyungpook National UniversityGunwiKorea
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary SynthesisNational University of MongoliaUlaanbaatarMongolia
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of SciencesYekaterinburgRussia
- Ural Federal UniversityEkaterinburgRussia
| | - Hans K. Stenøien
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - M. Thomas P. Gilbert
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Bioinformatics, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
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22
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Settlecowski AE, Marks BD, Manthey JD. Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens. Ecol Evol 2023; 13:e10407. [PMID: 37565027 PMCID: PMC10410627 DOI: 10.1002/ece3.10407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/28/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high-throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: (1) double-stranded DNA (dsDNA), single tube (KAPA); (2) single-stranded DNA (ssDNA), multi-tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi-tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best-performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.
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Affiliation(s)
- Amie E. Settlecowski
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Ben D. Marks
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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23
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Salazar L, Burger R, Forst J, Barquera R, Nesbitt J, Calero J, Washburn E, Verano J, Zhu K, Sop K, Kassadjikova K, Ibarra Asencios B, Davidson R, Bradley B, Krause J, Fehren-Schmitz L. Insights into the genetic histories and lifeways of Machu Picchu's occupants. SCIENCE ADVANCES 2023; 9:eadg3377. [PMID: 37494435 DOI: 10.1126/sciadv.adg3377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.
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Affiliation(s)
- Lucy Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Richard Burger
- Department of Anthropology, Yale University, New Haven, CT 06511-3707, USA
| | - Janine Forst
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Jason Nesbitt
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Jorge Calero
- Department of Archaeology, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru
| | - Eden Washburn
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John Verano
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
| | - Kimberly Zhu
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Korey Sop
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kalina Kassadjikova
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bebel Ibarra Asencios
- Department of Anthropology, Tulane University, New Orleans, LA 70118, USA
- Department of Archaeology, Universidad Nacional Santiago Antúnez de Mayolo, Huaraz 02002, Peru
| | - Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brenda Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
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24
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Fontani F, Boano R, Cinti A, Demarchi B, Sandron S, Rampelli S, Candela M, Traversari M, Latorre A, Iacovera R, Abondio P, Sarno S, Mackie M, Collins M, Radini A, Milani C, Petrella E, Giampalma E, Minelli A, Larocca F, Cilli E, Luiselli D. Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant'Angelo (Calabria, Italy). Sci Rep 2023; 13:11978. [PMID: 37488251 PMCID: PMC10366206 DOI: 10.1038/s41598-023-39250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023] Open
Abstract
The Neolithic burial of Grotta di Pietra Sant'Angelo (CS) represents a unique archaeological finding for the prehistory of Southern Italy. The unusual placement of the inhumation at a rather high altitude and far from inhabited areas, the lack of funerary equipment and the prone deposition of the body find limited similarities in coeval Italian sites. These elements have prompted wider questions on mortuary customs during the prehistory of Southern Italy. This atypical case requires an interdisciplinary approach aimed to build an integrated bioarchaeological profile of the individual. The paleopathological investigation of the skeletal remains revealed the presence of numerous markers that could be associated with craft activities, suggesting possible interpretations of the individual's lifestyle. CT analyses, carried out on the maxillary bones, showed the presence of a peculiar type of dental wear, but also a good density of the bone matrix. Biomolecular and micromorphological analyses of dental calculus highlight the presence of a rich Neolithic-like oral microbiome, the composition of which is consistent with the presence pathologies. Finally, paleogenomic data obtained from the individual were compared with ancient and modern Mediterranean populations, including unpublished high-resolution genome-wide data for 20 modern inhabitants of the nearby village of San Lorenzo Bellizzi, which provided interesting insights into the biodemographic landscape of the Neolithic in Southern Italy.
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Affiliation(s)
- Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy.
| | - Rosa Boano
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Alessandra Cinti
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Sarah Sandron
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Mirko Traversari
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Adriana Latorre
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Rocco Iacovera
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Paolo Abondio
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Meaghan Mackie
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
- Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Faculty of Health and Medical Sciences, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, København, Denmark
- School of Archeology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew Collins
- Faculty of Health and Medical Sciences, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, København, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
| | - Anita Radini
- School of Archeology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Chantal Milani
- SIOF - Italian Society of Forensic Odontology, Strada Degli Schiocchi 12, 41124, Modena, Italy
| | - Enrico Petrella
- Radiology Unit, Morgagni-Pierantoni Hospital, AUSL Romagna, Via Carlo Forlanini 34, 47121, Forlì, Italy
| | - Emanuela Giampalma
- Radiology Unit, Morgagni-Pierantoni Hospital, AUSL Romagna, Via Carlo Forlanini 34, 47121, Forlì, Italy
| | - Antonella Minelli
- Department of Humanities, Education and Social Sciences, University of Molise, Via Francesco De Sanctis, 86100, Campobasso, Italy
| | - Felice Larocca
- Speleo-Archaeological Research Group, University of Bari, Piazza Umberto I 1, 70121, Bari, Italy
- Speleo-Archaeological Research Centre "Enzo dei Medici", Via Lucania 3, 87070, Roseto Capo Spulico (CS), Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy.
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25
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Creydt M, Fischer M. Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts. Molecules 2023; 28:4872. [PMID: 37375427 DOI: 10.3390/molecules28124872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.
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Affiliation(s)
- Marina Creydt
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
| | - Markus Fischer
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
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26
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Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science 2023; 380:eabn5887. [PMID: 37104591 PMCID: PMC10184777 DOI: 10.1126/science.abn5887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 11/23/2022] [Indexed: 04/29/2023]
Abstract
We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.
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Affiliation(s)
- Katherine L. Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Heather J. Huson
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - Kathleen Morrill
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ming-Shan Wang
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Xue Li
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Krishnamoorthy Srikanth
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | | | - Elinor K. Karlsson
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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27
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Thomas JT, Cavagnino C, Kjelland K, Anderson E, Sturk-Andreaggi K, Daniels-Higginbotham J, Amory C, Spatola B, Moran K, Parson W, Marshall C. Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples. Genes (Basel) 2023; 14:genes14050994. [PMID: 37239354 DOI: 10.3390/genes14050994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.
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Affiliation(s)
- Jacqueline Tyler Thomas
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA
| | - Courtney Cavagnino
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA
| | - Katelyn Kjelland
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- Amentum Services Inc. (Contractor Supporting the AFMES-AFDIL), Germantown, MD 20876, USA
| | - Elise Anderson
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- Amentum Services Inc. (Contractor Supporting the AFMES-AFDIL), Germantown, MD 20876, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA
| | - Jennifer Daniels-Higginbotham
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Brian Spatola
- National Museum of Health and Medicine, Anatomical Division, Defense Health Agency, Silver Spring, MD 20910, USA
| | - Kimberlee Moran
- Forensic Science Program, Department of Chemistry, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA
- SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
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28
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Fernandes DM, Sirak KA, Cheronet O, Novak M, Brück F, Zelger E, Llanos-Lizcano A, Wagner A, Zettl A, Mandl K, Duffet Carlson KS, Oberreiter V, Özdoğan KT, Sawyer S, La Pastina F, Borgia E, Coppa A, Dobeš M, Velemínský P, Reich D, Bell LS, Pinhasi R. Density separation of petrous bone powders for optimized ancient DNA yields. Genome Res 2023; 33:622-631. [PMID: 37072186 PMCID: PMC10234301 DOI: 10.1101/gr.277714.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/11/2023] [Indexed: 04/20/2023]
Abstract
Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30 to 2.35 g/cm3 and 2.35 to 2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm3 intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.
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Affiliation(s)
- Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria;
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Florian Brück
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Evelyn Zelger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kellie Sara Duffet Carlson
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Department of History and Art History, Utrecht University, 3512 BS Utrecht, The Netherlands
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Francesco La Pastina
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, United Kingdom
| | - Emanuela Borgia
- Dipartimento di Scienze dell'Antichità, Sapienza Università di Roma, Rome 00185, Italy
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague 118 00, Czech Republic
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lynne S Bell
- Centre for Forensic Research, School of Criminology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria;
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, 1030 Vienna, Austria
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29
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Bardan F, Higgins D, Austin JJ. A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage. Forensic Sci Int Genet 2023; 63:102822. [PMID: 36525814 DOI: 10.1016/j.fsigen.2022.102822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
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Affiliation(s)
- Felicia Bardan
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia.
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30
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Museomics Provides Insights into Conservation and Education: The Instance of an African Lion Specimen from the Museum of Zoology “Pietro Doderlein”. DIVERSITY 2023. [DOI: 10.3390/d15010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative technological approaches are crucial to enhance naturalistic museum collections and develop information repositories of relevant interest to science, such as threatened animal taxa. In this context, museomics is an emerging discipline that provides a novel approach to the enhancement and exploitation of these collections. In the present study, the discovery of a neglected lion skeleton in the Museum of Zoology “Pietro Doderlein” of the University of Palermo (Italy) offered the opportunity to undertake a multidisciplinary project. The aims of the study consisted of the following: (i) adding useful information for museographic strategies, (ii) obtaining a new genetic data repository from a vulnerable species, (iii) strengthening public awareness of wildlife conservation, and (iv) sharing new learning material. The remains of the lion were examined with a preliminary osteological survey, then they were restored by means of 3D printing of missing skeletal fragments. Phylogenetic analyses based on cytochrome b sequence clearly indicate that the specimen belongs to the Central Africa mitochondrial clade. At the end of the study, the complete and restored skeleton was exhibited, along with all of the information and data available from this project. This study shows a useful approach for the restoration and enhancement of a museum specimen, with important opportunities for preserving biodiversity and driving specific conservation policies, but also for providing Life Science learning material.
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31
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Nichols RV, O’Connell BL, Mulqueen RM, Thomas J, Woodfin AR, Acharya S, Mandel G, Pokholok D, Steemers FJ, Adey AC. High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nat Commun 2022; 13:7627. [PMID: 36494343 PMCID: PMC9734657 DOI: 10.1038/s41467-022-35374-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a key epigenetic property that drives gene regulatory programs in development and disease. Current single-cell methods that produce high quality methylomes are expensive and low throughput without the aid of extensive automation. We previously described a proof-of-principle technique that enabled high cell throughput; however, it produced only low-coverage profiles and was a difficult protocol that required custom sequencing primers and recipes and frequently produced libraries with excessive adapter contamination. Here, we describe a greatly improved version that generates high-coverage profiles (~15-fold increase) using a robust protocol that does not require custom sequencing capabilities, includes multiple stopping points, and exhibits minimal adapter contamination. We demonstrate two versions of sciMETv2 on primary human cortex, a high coverage and rapid version, identifying distinct cell types using CH methylation patterns. These datasets are able to be directly integrated with one another as well as with existing snmC-seq2 datasets with little discernible bias. Finally, we demonstrate the ability to determine cell types using CG methylation alone, which is the dominant context for DNA methylation in most cell types other than neurons and the most applicable analysis outside of brain tissue.
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Affiliation(s)
- Ruth V. Nichols
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Brendan L. O’Connell
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA
| | - Ryan M. Mulqueen
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA
| | | | | | - Sonia Acharya
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Gail Mandel
- grid.5288.70000 0000 9758 5690Vollum Institute for Neuroscience, Oregon Health & Science University, Portland, OR USA
| | | | | | - Andrew C. Adey
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR USA
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32
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Martínez-García L, Ferrari G, Cuevas A, Atmore LM, López-Arias B, Culling M, Llorente-Rodríguez L, Morales-Muñiz A, Roselló-Izquierdo E, Quirós JA, Marlasca-Martín R, Hänfling B, Hutchinson WF, Jakobsen KS, Jentoft S, Orton D, Star B, Barrett JH. Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe. Proc Biol Sci 2022; 289:20221107. [PMID: 36259206 DOI: 10.1098/rspb.2022.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.
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Affiliation(s)
- Lourdes Martínez-García
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway.,Royal Botanic Garden Edinburgh, Edinburgh EH3 5NZ, UK
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Begoña López-Arias
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mark Culling
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Laura Llorente-Rodríguez
- Laboratory for Archaezoological Studies, Faculty of Archaeology, University of Leiden, Leiden 2311 EZ, The Netherlands
| | - Arturo Morales-Muñiz
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Juan Antonio Quirós
- Department of Geography, Prehistory and Archaeology, University of the Basque Country, Vitoria-Gasteiz 48940, Spain
| | | | - Bernd Hänfling
- Institute for Biodiversity and Freshwater Conservation, UHI-Inverness, Inverness, UK
| | - William F Hutchinson
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim 7012, Norway
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33
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Bieker VC, Battlay P, Petersen B, Sun X, Wilson J, Brealey JC, Bretagnolle F, Nurkowski K, Lee C, Barreiro FS, Owens GL, Lee JY, Kellner FL, van Boheeman L, Gopalakrishnan S, Gaudeul M, Mueller-Schaerer H, Lommen S, Karrer G, Chauvel B, Sun Y, Kostantinovic B, Dalén L, Poczai P, Rieseberg LH, Gilbert MTP, Hodgins KA, Martin MD. Uncovering the genomic basis of an extraordinary plant invasion. SCIENCE ADVANCES 2022; 8:eabo5115. [PMID: 36001672 PMCID: PMC9401624 DOI: 10.1126/sciadv.abo5115] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 05/31/2023]
Abstract
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.
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Affiliation(s)
- Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100 Kedah, Malaysia
| | - Xin Sun
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - François Bretagnolle
- UMR CNRS/uB 6282 Biogéosciences, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chris Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fátima Sánchez Barreiro
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jacqueline Y. Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fabian L. Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Myriam Gaudeul
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, National Herbarium (P), 57 rue Cuvier, CP39, 75005 Paris, France
| | | | - Suzanne Lommen
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
- Koppert Biological Systems, Department R&D Macrobiology, Veilingweg 14, 2651 BE Berkel en Rodenrijs, Netherlands
| | - Gerhard Karrer
- Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bruno Chauvel
- UMR Agroécologie, Institut Agro, INRAE, Univ. Bourgogne, Univ. Bourgogne-Franche-Comté, F-21000 Dijon, France
| | - Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Bojan Kostantinovic
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), Kőszeg, Hungary
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - M. Thomas P. Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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34
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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35
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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36
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Wang MS, Murray GGR, Mann D, Groves P, Vershinina AO, Supple MA, Kapp JD, Corbett-Detig R, Crump SE, Stirling I, Laidre KL, Kunz M, Dalén L, Green RE, Shapiro B. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nat Ecol Evol 2022; 6:936-944. [PMID: 35711062 DOI: 10.1038/s41559-022-01753-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/30/2022] [Indexed: 11/09/2022]
Abstract
Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are sister species possessing distinct physiological and behavioural adaptations that evolved over the last 500,000 years. However, comparative and population genomics analyses have revealed that several extant and extinct brown bear populations have relatively recent polar bear ancestry, probably as the result of geographically localized instances of gene flow from polar bears into brown bears. Here, we generate and analyse an approximate 20X paleogenome from an approximately 100,000-year-old polar bear that reveals a massive prehistoric admixture event, which is evident in the genomes of all living brown bears. This ancient admixture event was not visible from genomic data derived from living polar bears. Like more recent events, this massive admixture event mainly involved unidirectional gene flow from polar bears into brown bears and occurred as climate changes caused overlap in the ranges of the two species. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.
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Affiliation(s)
- Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Daniel Mann
- Department of Geosciences, University of Alaska, Fairbanks, AK, USA.,Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Alisa O Vershinina
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Megan A Supple
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarah E Crump
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ian Stirling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Wildlife Research Division, Environment and Climate Change Canada Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
| | - Michael Kunz
- University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA. .,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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37
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Irestedt M, Thörn F, Müller IA, Jønsson KA, Ericson PGP, Blom MPK. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins. Mol Ecol Resour 2022; 22:2672-2684. [PMID: 35661418 PMCID: PMC9542604 DOI: 10.1111/1755-0998.13660] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
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Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Filip Thörn
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Ingo A Müller
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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38
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Machine Learning-Based Models for Detection of Biomarkers of Autoimmune Diseases by Fragmentation and Analysis of miRNA Sequences. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Thanks to high-throughput data technology, microRNA analysis studies have evolved in early disease detection. This work introduces two complete models to detect the biomarkers of two autoimmune diseases, multiple sclerosis and rheumatoid arthritis, via miRNA analysis. Based on work the authors published previously, both introduced models involve complete pipelines of text mining methods, integrated with traditional machine learning methods, and LSTM deep learning. This work also studies the fragmentation of miRNA sequences to reduce the needed processing time and computational power. Moreover, this work studies the impact of obtaining two different library preparation kits (NEBNEXT and NEXTFLEX) on the detection accuracy for rheumatoid arthritis. Additional experiments are applied to the proposed models based on three different transcriptomic datasets. The results denote that the transcriptomic fragmentation model reported a biomarker detection accuracy of 96.45% on a sequence fragment size of 0.2, indicating a significant reduction in execution power while retaining biomarker detection accuracy. On the other hand, the LSTM model obtained a promising detection accuracy of 72%, implying savings in feature engineering processing. Additionally, the fragmentation model and the LSTM model reported 22.4% and 87.5% less execution time than work in the literature, respectively, denoting a considerable execution power reduction.
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39
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Ruiz-Gartzia I, Lizano E, Marques-Bonet T, Kelley JL. Recovering the genomes hidden in museum wet collections. Mol Ecol Resour 2022; 22:2127-2129. [PMID: 35578376 DOI: 10.1111/1755-0998.13631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Natural history museums hold vast collections of biomaterials. The collections in museums, often painstakingly sampled, are largely unexplored treasures that may help us better understand biodiversity on the planet. Museum collections are a unique window into the past of species long gone or currently declining due to human activity. From a molecular perspective, though, many museum samples are stored under conditions that hasten the damage of DNA, RNA, and proteins. For example, samples in wet collections are those stored in liquid preservatives, typically ethanol. These ethanol-preserved tissues are often, although not always, formalin-fixed prior to storage, which may damage DNA. In this and recent issues of Molecular Ecology Resources, Straube et al. (2021), O'Connell et al. (2022), and (Hahn et al.) explore different types of specimens from museum wet collections as new sources of DNA for scientific studies. All three articles found that for wet museum collections, overall specimen condition mattered most for recovering high quality genomic DNA.
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Affiliation(s)
- Irune Ruiz-Gartzia
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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40
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Suchan T, Chauvey L, Poullet M, Tonasso‐Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin‐Orlando A, Orlando L. Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour 2022; 22:2262-2274. [DOI: 10.1111/1755-0998.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Tomasz Suchan
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
- W. Szafer Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Marine Poullet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Laure Tonasso‐Calvière
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Benoit Clavel
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Andaine Seguin‐Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
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41
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Le Duc D, Velluva A, Cassatt-Johnstone M, Olsen RA, Baleka S, Lin CC, Lemke JR, Southon JR, Burdin A, Wang MS, Grunewald S, Rosendahl W, Joger U, Rutschmann S, Hildebrandt TB, Fritsch G, Estes JA, Kelso J, Dalén L, Hofreiter M, Shapiro B, Schöneberg T. Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow. SCIENCE ADVANCES 2022; 8:eabl6496. [PMID: 35119923 PMCID: PMC8816345 DOI: 10.1126/sciadv.abl6496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
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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Affiliation(s)
- Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Akhil Velluva
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Remi-Andre Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031 , SE-17121 Solna, Sweden
| | - Sina Baleka
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Faculty of Life and Environmental Sciences, University of Iceland, 102 Reykjavik, Iceland
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, 11221 Taipei, Taiwan
| | - Johannes R. Lemke
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - John R. Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, Irvine, CA 92697, USA
| | - Alexander Burdin
- Kamchatka Branch of Pacific Geographical Institute, Russian Academy of Science, 683000 Petropavlovsk-Kamchatsky, Russia
| | - Ming-Shan Wang
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sonja Grunewald
- Department of Dermatology, Venerology and Allergology, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museum and Curt-Engelhorn-Centre of Archaeometry, 68159 Mannheim, Germany
| | - Ulrich Joger
- State Museum of Natural History, 38106 Braunschweig, Germany
| | - Sereina Rutschmann
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Faculty of Veterinary Medicine, Free University Berlin, 14195 Berlin, Germany
| | - Guido Fritsch
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
| | - James A. Estes
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
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42
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Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
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43
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Cavill EL, Liu S, Zhou X, Gilbert MTP. To bee, or not to bee? One leg is the question. Mol Ecol Resour 2021; 22:1868-1874. [PMID: 34957693 DOI: 10.1111/1755-0998.13578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Abstract
Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry-preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a 'minimally destructive' method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry-preserved insects for future genomic studies.
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Affiliation(s)
- Emily Louisa Cavill
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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44
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Abstract
Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.
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45
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Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
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