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Arsuaga JL, Martínez I, Gracia-Téllez A, Carretero JM, Esquivel A, García N, Lorenzo C, Quam R, Aramburu A, Sala N, Trueba J. How the Sima de los Huesos was won. Anat Rec (Hoboken) 2024; 307:2225-2245. [PMID: 38813936 DOI: 10.1002/ar.25509] [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: 03/29/2024] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024]
Abstract
Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.
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Affiliation(s)
- Juan-Luis Arsuaga
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
| | - Ignacio Martínez
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Universidad de Alcalá, Alcalá de Henares, Spain
| | - Ana Gracia-Téllez
- Departamento de Geología, Geografía y Medio Ambiente, Área de Paleontología, Facultad de Ciencias, Universidad de Alcalá, Madrid, Spain
| | - José-Miguel Carretero
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
- Laboratorio de Evolución Humana, Universidad de Burgos, Burgos, Spain
- Unidad Asociada de I+D+i al CSIC Vidrio y Materiales del Patrimonio Cultural (VIMPAC), Burgos, Spain
| | - Alfonso Esquivel
- Fundación Ciudad de la Energía - CIUDEN, F.S.P. Cl. de la Energía, Ponferrada, Spain
| | - Nuria García
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
- Grupo UCM Ecosistemas Cuaternarios Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Carlos Lorenzo
- Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Àrea de Prehistòria, Tarragona, Spain
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
| | - Rolf Quam
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Universidad de Alcalá, Alcalá de Henares, Spain
- Department of Anthropology, Binghamton University (SUNY), New York, New York, USA
- Division of Anthropology, American Museum of Natural History, New York, New York, USA
| | - Arantza Aramburu
- Departamento de Geología, Área de Mineralogía y Petrología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Nohemi Sala
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
- Centro Nacional de Investigación sobre Evolución Humana-CENIEH, Burgos, Spain
| | - Javier Trueba
- Madrid Scientific Films, Villanueva de la Cañada, Spain
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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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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Orlando L. A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered. Bioessays 2014; 36:598-605. [PMID: 24706482 DOI: 10.1002/bies.201400018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By combining state-of-the-art approaches in ancient genomics, Meyer and co-workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at Sierra de Atapuerca, Spain about 400,000 years ago. This achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as Neanderthals and Denisovans. Molecular phylogenetic reconstructions placed the Atapuercan as a sister group to Denisovans, although its morphology suggested closer affinities with Neanderthals. In addition to possibly challenging our interpretation of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene to genomics, thereby extending the scope of ancient DNA to the last million years.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martínez I, Gracia A, de Castro JMB, Carbonell E, Pääbo S. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 2013; 505:403-6. [PMID: 24305051 DOI: 10.1038/nature12788] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/17/2013] [Indexed: 12/22/2022]
Abstract
Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
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Affiliation(s)
- Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany [2] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Juan-Luis Arsuaga
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ignacio Martínez
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Área de Paleontología, Depto. de Geografía y Geología, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - Ana Gracia
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Área de Paleontología, Depto. de Geografía y Geología, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | | | - Eudald Carbonell
- 1] Institut Català de Paleoecologia Humana i Evolució Social, C/Marcel·lí Domingo s/n (Edifici W3), Campus Sescelades, 43007 Tarragona, Spain [2] Àrea de Prehistòria, Dept. d'Història i Història de l'Art, Univ. Rovira i Virgili, Fac. de Lletres, Av. Catalunya, 35, 43002 Tarragona, Spain
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A 2013; 110:15758-63. [PMID: 24019490 DOI: 10.1073/pnas.1314445110] [Citation(s) in RCA: 744] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.
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Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JF, Al-Rasheid KAS, Gilbert TMP, Willerslev E, Orlando L. Improving the performance of true single molecule sequencing for ancient DNA. BMC Genomics 2012; 13:177. [PMID: 22574620 PMCID: PMC3430569 DOI: 10.1186/1471-2164-13-177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.
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Affiliation(s)
- Aurelien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 Øster Voldgade, København, 1350, Denmark
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Depaulis F, Orlando L, Hänni C. Using classical population genetics tools with heterochroneous data: time matters! PLoS One 2009; 4:e5541. [PMID: 19440242 PMCID: PMC2678253 DOI: 10.1371/journal.pone.0005541] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 04/15/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. METHODOLOGY/PRINCIPAL FINDINGS We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). CONCLUSIONS/SIGNIFICANCE Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.
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Affiliation(s)
- Frantz Depaulis
- Laboratoire d'Ecologie et Evolution, CNRS UMR 7625, UPMC Paris Universitas, Ecole Normale Supérieure, Paris, France
| | - Ludovic Orlando
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Catherine Hänni
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
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Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc Natl Acad Sci U S A 2008; 105:5123-8. [PMID: 18347332 DOI: 10.1073/pnas.0712223105] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endangered brown bear populations (Ursus arctos) in Iberia have been suggested to be the last fragments of the brown bear population that served as recolonization stock for large parts of Europe during the Pleistocene. Conservation efforts are intense, and results are closely monitored. However, the efforts are based on the assumption that the Iberian bears are a unique unit that has evolved locally for an extended period. We have sequenced mitochondrial DNA (mtDNA) from ancient Iberian bear remains and analyzed them as a serial dataset, monitoring changes in diversity and occurrence of European haplogroups over time. Using these data, we show that the Iberian bear population has experienced a dynamic, recent evolutionary history. Not only has the population undergone mitochondrial gene flow from other European brown bears, but the effective population size also has fluctuated substantially. We conclude that the Iberian bear population has been a fluid evolutionary unit, developed by gene flow from other populations and population bottlenecks, far from being in genetic equilibrium or isolated from other brown bear populations. Thus, the current situation is highly unusual and the population may in fact be isolated for the first time in its history.
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Orlando L, Pagés M, Calvignac S, Hughes S, Hänni C. Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths? Biol Lett 2007; 3:57-9; discussion 60-3. [PMID: 17443966 PMCID: PMC2373798 DOI: 10.1098/rsbl.2006.0536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.
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Affiliation(s)
- Ludovic Orlando
- Paleogenetics and Molecular Evolution; IFR128, Lyon, F-69007, France; Universiti Lyon 1, Lyon, F-69007, France.
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