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Wood JR, Zhou C, Cole TL, Coleman M, Anderson DP, Lyver PO, Tan S, Xiang X, Long X, Luo S, Lou M, Southon JR, Li Q, Zhang G. Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica. Nat Commun 2025; 16:1798. [PMID: 40044673 PMCID: PMC11883008 DOI: 10.1038/s41467-025-56925-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 02/05/2025] [Indexed: 03/09/2025] Open
Abstract
We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.
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Affiliation(s)
- Jamie R Wood
- Australian Centre for Ancient DNA, School of Biological Sciences, North Terrace Campus, University of Adelaide, Adelaide, South Australia, Australia.
- Environment Institute, University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia.
| | - Chengran Zhou
- BGI Research, Wuhan, China
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China
| | - Theresa L Cole
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Morgan Coleman
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Dean P Anderson
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Phil O'B Lyver
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Shangjin Tan
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Xiang
- BGI Research, Wuhan, China
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China
| | - Xinrui Long
- BGI Research, Wuhan, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Senyu Luo
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miao Lou
- College of Life Sciences, Wuhan University, Wuhan, China
| | - John R Southon
- Department of Earth System Science, University of California-Irvine, Irvine, California, USA
| | - Qiye Li
- BGI Research, Wuhan, China
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology and Women's Hospital at Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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2
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Koptekin D, Yapar E, Vural KB, Sağlıcan E, Altınışık NE, Malaspinas AS, Alkan C, Somel M. Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data. Genome Biol 2025; 26:6. [PMID: 39789608 PMCID: PMC11721506 DOI: 10.1186/s13059-024-03462-w] [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: 11/26/2023] [Accepted: 12/16/2024] [Indexed: 01/12/2025] Open
Abstract
We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine and zenodo.org/records/14234666), masking reads only at positions possibly affected by PMD. We propose graph alignment coupled with bamRefine as a simple strategy to minimize data loss and bias, and urge the community to publish FASTQ files.
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Affiliation(s)
- Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Etka Yapar
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biology, Lund University, Lund, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe, Ankara, Turkey
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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3
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Haarkötter C, Roca-Rada X, Saiz M, Vinueza-Espinosa DC, Gálvez X, Medina-Lozano MI, Díaz-Ruiz D, Álvarez JC, Llamas B, Lorente JA, Austin J. Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones. Genes (Basel) 2024; 16:23. [PMID: 39858570 PMCID: PMC11764906 DOI: 10.3390/genes16010023] [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: 11/18/2024] [Revised: 12/17/2024] [Accepted: 12/24/2024] [Indexed: 01/27/2025] Open
Abstract
In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains. BACKGROUND/OBJECTIVES This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis. METHODS Six highly degraded human bones from the Spanish Civil War (1936-1939) were quantified with Quantifiler™ Trio and amplified with GlobalFiler™. Independently, partially UDG-treated double-stranded DNA libraries were generated and shotgun sequenced to screen for endogenous human DNA content. Subsequently, libraries were enriched with the Twist Bioscience "Twist Ancient DNA" reagent enrichment kit, which had not been previously tested for forensic purposes. RESULTS The results show that the samples behave similarly with both approaches (well-preserved samples yield good results). However, capture enrichment provides some new relevant insights, suggesting that its implementation in current NGS forensic platforms could be beneficial. CONCLUSIONS Shotgun results show that the analyzed samples exhibit the same characteristics as ancient DNA samples in terms of DNA fragmentation and molecular damage, which may enhance the value of this approach when authenticating the endogenous DNA of forensic samples.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Xavier Roca-Rada
- Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; (X.R.-R.); (B.L.); (J.A.)
- Faculty of Arts and Humanities, University of Coimbra, 3000-214 Coimbra, Portugal
| | - María Saiz
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Diana C. Vinueza-Espinosa
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Xiomara Gálvez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Daniel Díaz-Ruiz
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Bastien Llamas
- Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; (X.R.-R.); (B.L.); (J.A.)
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia
| | - Jose Antonio Lorente
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, PTS Granada, Av. Investigación 11, 18016 Granada, Spain; (C.H.); (M.S.); (D.C.V.-E.); (X.G.); (M.I.M.-L.); (D.D.-R.); (J.C.Á.)
| | - Jeremy Austin
- Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; (X.R.-R.); (B.L.); (J.A.)
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4
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Ravishankar S, Perez V, Davidson R, Roca-Rada X, Lan D, Souilmi Y, Llamas B. Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. Brief Bioinform 2024; 26:bbae646. [PMID: 39674265 DOI: 10.1093/bib/bbae646] [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: 07/18/2024] [Revised: 11/03/2024] [Accepted: 11/28/2024] [Indexed: 12/16/2024] Open
Abstract
Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.
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Affiliation(s)
- Shyamsundar Ravishankar
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Vilma Perez
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
| | - Roberta Davidson
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Xavier Roca-Rada
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Faculty of Arts and Humanities, University of Coimbra, Coimbra, Portugal
| | - Divon Lan
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Genozip Limited, Hong Kong
| | - Yassine Souilmi
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA (ACAD) and The Environment Institute, The School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
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5
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Souilmi Y, Wasef S, Williams MP, Conroy G, Bar I, Bover P, Dann J, Heiniger H, Llamas B, Ogbourne S, Archer M, Ballard JWO, Reed E, Tobler R, Koungoulos L, Walshe K, Wright JL, Balme J, O’Connor S, Cooper A, Mitchell KJ. Ancient genomes reveal over two thousand years of dingo population structure. Proc Natl Acad Sci U S A 2024; 121:e2407584121. [PMID: 38976766 PMCID: PMC11287250 DOI: 10.1073/pnas.2407584121] [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: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Sally Wasef
- Ancient DNA Facility, Defence Genomics, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD4059, Australia
- Innovation Division, Forensic Science Queensland, Queensland Health, Coopers Plains, QLD4108, Australia
| | - Matthew P. Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Department of Biology, The Pennsylvania State University, State College, PA16802
| | - Gabriel Conroy
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD4111, Australia
| | - Pere Bover
- Fundación Agencia Aragonesa para la Investigacióny el Desarrollo (ARAID), Zaragoza50018, Spain
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA)-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza50009, Spain
| | - Jackson Dann
- Grützner Laboratory of Comparative Genomics, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Holly Heiniger
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, ActonACT2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA5000, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Michael Archer
- Earth and Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales Sydney, SydneyNSW2052, Australia
| | - J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC3052, Australia
| | - Elizabeth Reed
- Ecology and Evolutionary Biology, School of Biological Sciences, The University of Adelaide, AdelaideSA5005, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Acton, ACT2601, Australia
| | - Loukas Koungoulos
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW2010, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Keryn Walshe
- School of Anthropology and Archaeology, University of Auckland, Auckland1010, New Zealand
| | - Joanne L. Wright
- Queensland Department of Education, Kelvin Grove State College, Kelvin Grove, QLD4059, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, WA6009, Australia
| | - Sue O’Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Alan Cooper
- Gulbali Institute, Charles Sturt University, Albury, NSW2640, Australia
| | - Kieren J. Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- Manaaki Whenua—Landcare Research, Lincoln, Canterbury7608, New Zealand
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Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N. Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes. Forensic Sci Int Genet 2024; 71:103060. [PMID: 38796876 DOI: 10.1016/j.fsigen.2024.103060] [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: 11/07/2023] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024]
Abstract
In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.
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Affiliation(s)
- Nikolaos Psonis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece.
| | - Despoina Vassou
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Argyro Nafplioti
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Eugenia Tabakaki
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
| | - Alexandros Stamatakis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Nikos Poulakakis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
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7
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Dolenz S, van der Valk T, Jin C, Oppenheimer J, Sharif MB, Orlando L, Shapiro B, Dalén L, Heintzman PD. Unravelling reference bias in ancient DNA datasets. Bioinformatics 2024; 40:btae436. [PMID: 38960861 PMCID: PMC11254355 DOI: 10.1093/bioinformatics/btae436] [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: 07/24/2023] [Revised: 03/22/2024] [Accepted: 07/02/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. RESULTS For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. AVAILABILITY AND IMPLEMENTATION AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).
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Affiliation(s)
- Stephanie Dolenz
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden
- Science for Life Laboratory, Stockholm, SE-171 65, Sweden
| | - Chenyu Jin
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden
- Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, United States
| | - Muhammad Bilal Sharif
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT, CNRS UMR5288), University Paul Sabatier, Faculté de Santé, Toulouse, 31000, France
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, United States
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, SE-114 18, Sweden
- Department of Zoology, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Peter D Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-106 91, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, SE-106 91, Sweden
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8
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Almeida da Paz M, Warger S, Taher L. Disregarding multimappers leads to biases in the functional assessment of NGS data. BMC Genomics 2024; 25:455. [PMID: 38720252 PMCID: PMC11078754 DOI: 10.1186/s12864-024-10344-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous ("multimappers"). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar members are left unexplored. RESULTS In particular, disregarding multimappers leads to the underrepresentation in epigenetic studies of recently active transposable elements, such as AluYa5, L1HS and SVAs. Furthermore, this common strategy also has implications for transcriptomic analysis: members of repetitive gene families, such the ones including major histocompatibility complex (MHC) class I and II genes, are under-quantified. CONCLUSION Revealing inherent biases that permeate routine tasks such as functional enrichment analysis, our results underscore the urgency of broadly adopting multimapper-aware bioinformatic pipelines -currently restricted to specific contexts or communities- to ensure the reliability of genomic and transcriptomic studies.
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Affiliation(s)
| | - Sarah Warger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
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9
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Hempel E, Faith JT, Preick M, de Jager D, Barish S, Hartmann S, Grau JH, Moodley Y, Gedman G, Pirovich KM, Bibi F, Kalthoff DC, Bocklandt S, Lamm B, Dalén L, Westbury MV, Hofreiter M. Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Curr Biol 2024; 34:2020-2029.e6. [PMID: 38614080 DOI: 10.1016/j.cub.2024.03.051] [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: 12/20/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.
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Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany.
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA; Department of Anthropology, University of Utah, 260 South Central Campus Drive, Salt Lake City, UT 84112, USA; Origins Centre, University of the Witwatersrand, 2000 Johannesburg, Republic of South Africa
| | - Michaela Preick
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Deon de Jager
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - José H Grau
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA; Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | | | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniela C Kalthoff
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 10405 Stockholm, Sweden
| | | | - Ben Lamm
- Colossal Biosciences, Dallas, TX 75247, USA
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, Box 50007, 10405 Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20c, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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10
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Yin PK, Xiao H, Yang ZB, Yang DS, Yang YH. Shotgun metagenomics reveals the gut microbial diversity and functions in Vespa mandarinia (Hymenoptera: Vespidae) at multiple life stages. Front Microbiol 2024; 15:1288051. [PMID: 38529182 PMCID: PMC10961340 DOI: 10.3389/fmicb.2024.1288051] [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: 09/03/2023] [Accepted: 02/12/2024] [Indexed: 03/27/2024] Open
Abstract
Wasps play important roles as predators and pollinators in the ecosystem. The Jingpo minority residing in Yunnan Province, China, has a traditional practice of using wine infused with mature wasps as a customary remedy for managing rheumatoid arthritis. The larva of the wasp is also a tasteful folk dish that has created a tremendous market. There is a paucity of survival knowledge, which has greatly restricted their potential applications in food and healthcare. Recent research has highlighted the importance of gut microbiota in insect growth. Nevertheless, there is still a lack of understanding regarding the composition, changes, and functions of the gut microbiota in Vespa mandarinia during development. In this research, the gut microbiota were investigated across three growth stages of Vespa mandarinia using a metagenomic technology. The result revealed that there are significant variations in the proportion of main gut microbes during the metamorphosis of Vespa mandarinia. Tenericutes were found to dominate during the larval stage, while Proteobacteria emerged as the dominant group post-pupation. Through a comprehensive analysis of the gut microbiota metagenome, this study revealed functional differences in the wasp gut microbiota at various growth stages. During the larval stage, the gut microbiota plays a central role in promoting metabolism. Following pupation, the gut microbiota exhibited diversified functions, likely due to the complex environments and diverse food sources encountered after metamorphosis. These functions included amino acid metabolism, compound degradation, and defense mechanisms. This research provides an extensive dataset on the gut microbiota during the metamorphosis of Vespa mandarinia, contributing to a deeper understanding of the influence of gut microbiota on wasp growth. Furthermore, this study uncovers a unique microbial treasure within insect guts, which is important for advancing the application of wasps in the fields of food and medicine.
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Affiliation(s)
- Peng-Kai Yin
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Huai Xiao
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Zhi-Bin Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Da-Song Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
| | - Yin-He Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
- College of Pharmacy, Dali University, Dali, China
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11
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Eisenhofer R, Wright S, Weyrich L. Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ 2024; 12:e16770. [PMID: 38440408 PMCID: PMC10911074 DOI: 10.7717/peerj.16770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/06/2024] Open
Abstract
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.
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Affiliation(s)
| | - Sterling Wright
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Laura Weyrich
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
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12
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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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13
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Ma H, Lao Y, Liu S, Ai J, Sun X, Zhang W, Kang M, Li J, Sun Y. The diurnal salivary glands transcriptome of Dermacentor nuttalli from the first four days of blood feeding. Ticks Tick Borne Dis 2023; 14:102178. [PMID: 37001418 DOI: 10.1016/j.ttbdis.2023.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
The ixodid tick Dermacentor nuttalli is distributed from southern Siberia to North China and is a vector of many pathogens. This species can have severe impacts on animal husbandry and human health. To date, the control of D. nuttalli is limited to the use of acaricides such as organophosphorus, synthetic pyrethroids and amidine pesticides. There are no environmentally friendly or reliable prevention and control measures, and little is known regarding key antigens involved in blood feeding. Salivary glands are major tissues involved in the blood feeding and pathogen transmission of ticks. Therefore, this study focused on salivary glands tissue to identify the dominant antigens of D. nuttalli involved in tick feeding. For this, high-throughput RNA sequencing (RNA-seq) was used for analysis. The transcriptome of female D. nuttalli ticks was assembled and characterized, and differentially expressed genes (DEGs) were identified in the salivary glands of ticks that had not fed (0 h) and of ticks after 24, 48, 72 and 96 h of feeding. There were 22,802,784, 22,275,013, 26,629,453, 24,982,389, and 22,596,230 high-quality clean reads obtained from salivary glands tissues at the five different blood feeding time points. The total number of annotated unigenes was 100,347. The differences in gene expression between different time points were compared, and functional enrichment was performed. Quantitative reverse transcription PCR (RT‒qPCR) was used to validate the RNA-seq results, the results of which showed that the differences in expressed transcripts presented similar trends. Among the identified DEGs, the most numerous were those with catalytic and binding activities and those involved in diverse metabolic pathways and cellular processes. The expression patterns of homologous and family-member proteins throughout the blood feeding period exhibited significant differences, strongly suggesting that the transcriptome composition is highly dynamic and likely subjected to important variation throughout the life cycle. Studies of gene sequences in D. nuttalli will greatly increase the information on tick protective antigens, which could potentially function as effective vaccine candidates or drug targets for the development of environmentally friendly acaricides.
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14
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Westbury MV, Lorenzen ED. Iteratively mapping ancient
DNA
to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Oliva A, Tobler R, Llamas B, Souilmi Y. Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment. Ecol Evol 2022; 11:18743-18748. [PMID: 35003706 PMCID: PMC8717315 DOI: 10.1002/ece3.8297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022] Open
Abstract
Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA-mem parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA-aln is still the gold-standard for ancient DNA read alignment .
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Affiliation(s)
- Adrien Oliva
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Raymond Tobler
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Bastien Llamas
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- National Centre for Indigenous GenomicsAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Yassine Souilmi
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- National Centre for Indigenous GenomicsAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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16
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Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol Evol 2021; 36:1049-1060. [PMID: 34456066 DOI: 10.1016/j.tree.2021.07.009] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023]
Abstract
Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
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