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Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A 2021; 118:2024176118. [PMID: 34099548 PMCID: PMC8214697 DOI: 10.1073/pnas.2024176118] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
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2
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X-Reality Museums: Unifying the Virtual and Real World Towards Realistic Virtual Museums. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app11010338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Culture is a field that is currently entering a revolutionary phase, no longer being a privilege for the few, but expanding to new audiences who are urged to not only passively consume cultural heritage content, but actually participate and assimilate it on their own. In this context, museums have already embraced new technologies as part of their exhibitions, many of them featuring augmented or virtual reality artifacts. The presented work proposes the synthesis of augmented, virtual and mixed reality technologies to provide unified X-Reality experiences in realistic virtual museums, engaging visitors in an interactive and seamless fusion of physical and virtual worlds that will feature virtual agents exhibiting naturalistic behavior. Visitors will be able to interact with the virtual agents, as they would with real world counterparts. The envisioned approach is expected to not only provide refined experiences for museum visitors, but also achieve high quality entertainment combined with more effective knowledge acquisition.
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Benoit J, Legendre LJ, Tabuce R, Obada T, Mararescul V, Manger P. Brain evolution in Proboscidea (Mammalia, Afrotheria) across the Cenozoic. Sci Rep 2019; 9:9323. [PMID: 31249366 PMCID: PMC6597534 DOI: 10.1038/s41598-019-45888-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
As the largest and among the most behaviourally complex extant terrestrial mammals, proboscideans (elephants and their extinct relatives) are iconic representatives of the modern megafauna. The timing of the evolution of large brain size and above average encephalization quotient remains poorly understood due to the paucity of described endocranial casts. Here we created the most complete dataset on proboscidean endocranial capacity and analysed it using phylogenetic comparative methods and ancestral character states reconstruction using maximum likelihood. Our analyses support that, in general, brain size and body mass co-evolved in proboscideans across the Cenozoic; however, this pattern appears disrupted by two instances of specific increases in relative brain size in the late Oligocene and early Miocene. These increases in encephalization quotients seem to correspond to intervals of important climatic, environmental and faunal changes in Africa that may have positively selected for larger brain size or body mass.
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Affiliation(s)
- Julien Benoit
- Evolutionary Studies Institute (ESI), University of the Witwatersrand, Braamfontein, 2050, Johannesburg, South Africa.
| | - Lucas J Legendre
- Jackson School of Geosciences, The University of Texas at Austin, 2275 Speedway Stop C9000, Austin, TX, United States
| | - Rodolphe Tabuce
- Institut des Sciences de L'Evolution de Montpellier, Université Montpellier 2, Place Eugène Batillon, F-34095 Montpellier, cedex 05, Montpellier, France
| | - Theodor Obada
- Academy of Sciences of Moldova, Institute of Zoology, Chişinău, Moldova
| | | | - Paul Manger
- School of Anatomical Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, South Africa
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4
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Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara. PLoS One 2018; 13:e0202394. [PMID: 30183732 PMCID: PMC6124704 DOI: 10.1371/journal.pone.0202394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/02/2018] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.
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Bokma F, Godinot M, Maridet O, Ladevèze S, Costeur L, Solé F, Gheerbrant E, Peigné S, Jacques F, Laurin M. Testing for Depéret's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data. Syst Biol 2015; 65:98-108. [PMID: 26508768 PMCID: PMC4678255 DOI: 10.1093/sysbio/syv075] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/23/2015] [Indexed: 11/25/2022] Open
Abstract
Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed “Cope's rule” but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.
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Affiliation(s)
- Folmer Bokma
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden;
| | - Marc Godinot
- UMR 7207, CNRS/MNHN/UPMC, Ecole Pratique des Hautes Etudes, Paris, France
| | - Olivier Maridet
- Jurassica Museum, route de Fontenais 21, 2900 Porrentruy, Switzerland
| | - Sandrine Ladevèze
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Loïc Costeur
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001 Basel, Switzerland; and
| | - Floréal Solé
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, 29, rue Vautier, 1000 Brussels, Belgium
| | - Emmanuel Gheerbrant
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Stéphane Peigné
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Florian Jacques
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Michel Laurin
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
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6
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Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
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7
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Sen S, Barrier E, Crété X. Late Pleistocene Dwarf Elephants from the Aegean Islands of Kassos and Dilos, Greece. ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Gold DA, Robinson J, Farrell AB, Harris JM, Thalmann O, Jacobs DK. Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits. Ecol Evol 2014; 4:329-36. [PMID: 24634719 PMCID: PMC3936381 DOI: 10.1002/ece3.928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/30/2022] Open
Abstract
Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.
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Affiliation(s)
- David A Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Aisling B Farrell
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - John M Harris
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - Olaf Thalmann
- Department of Biology, Division of Genetics and Physiology, University of Turku Itäinen Pitkäkatu 4, Turku 20014, Finland
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
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9
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Druzhkova AS, Thalmann O, Trifonov VA, Leonard JA, Vorobieva NV, Ovodov ND, Graphodatsky AS, Wayne RK. Ancient DNA analysis affirms the canid from Altai as a primitive dog. PLoS One 2013; 8:e57754. [PMID: 23483925 PMCID: PMC3590291 DOI: 10.1371/journal.pone.0057754] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.
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Affiliation(s)
- Anna S. Druzhkova
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olaf Thalmann
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Vladimir A. Trifonov
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (Consejo Superior de Investigaciones Científicas), Seville, Spain
| | - Nadezhda V. Vorobieva
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai D. Ovodov
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander S. Graphodatsky
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
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10
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Abstract
The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan 'Palaeoloxodon' creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of 'P'. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.
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Affiliation(s)
- Victoria L Herridge
- Palaeontology Department, Natural History Museum, , Cromwell Road, London SW7 5BD, UK.
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11
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Abstract
Multiple displacement amplification (MDA) is an isothermal, sequence-independent method for the amplification of high molecular weight DNA that is driven by φ29 DNA polymerase (DNAP). Here we report digital MDA (dMDA), an ultrasensitive method for quantifying nucleic acid fragments of unknown sequence. We use the new assay to show that our custom φ29 DNAP preparation is free of contamination at the limit of detection of the dMDA assay (1 contaminating molecule per assay microliter). Contamination in commercially available preparations is also investigated. The results of the dMDA assay provide strong evidence that the so-called 'template-independent' MDA background can be attributed to high-molecular weight contaminants and is not primer-derived in the commercial kits tested. dMDA is orders of magnitude more sensitive than PCR-based techniques for detection of microbial genomic DNA fragments and opens up new possibilities for the ultrasensitive quantification of DNA fragments in a wide variety of application areas using MDA chemistry and off-the-shelf hardware developed for digital PCR.
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Affiliation(s)
- Paul C Blainey
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, 318 Campus Drive, Stanford, CA 94305, USA
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12
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Avelar DM, Linardi PM. Use of Multiple Displacement Amplification as Pre-polymerase Chain Reaction (Pre-PCR) to amplify genomic DNA of siphonapterids preserved for long periods in scientific collections. Parasit Vectors 2010; 3:86. [PMID: 20840790 PMCID: PMC2945329 DOI: 10.1186/1756-3305-3-86] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 09/15/2010] [Indexed: 11/10/2022] Open
Abstract
The recently developed Multiple Displacement Amplification technique (MDA) allows for the production of a large quantity of high quality genomic DNA from low amounts of the original DNA. The goal of this study was to evaluate the performance of the MDA technique to amplify genomic DNA of siphonapterids that have been stored for long periods in 70% ethanol at room temperature. We subjected each DNA sample to two different methodologies: (1) amplification of mitochondrial 16S sequences without MDA; (2) amplification of 16S after MDA. All the samples obtained from these procedures were then sequenced. Only 4 samples (15.4%) subjected to method 1 showed amplification. In contrast, the application of MDA (method 2) improved the performance substantially, with 24 samples (92.3%) showing amplification, with significant difference. Interestingly, one of the samples successfully amplified with this method was originally collected in 1909. All of the sequenced samples displayed satisfactory results in quality evaluations (Phred ≥ 20) and good similarities, as identified with the BLASTn tool. Our results demonstrate that the use of MDA may be an effective tool in molecular studies involving specimens of fleas that have traditionally been considered inadequately preserved for such purposes.
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Affiliation(s)
- Daniel M Avelar
- Departamento de Parasitologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Caixa Postal 486, Avenida Antônio Carlos, 6627, Campus UFMG, Minas Gerais, 31270-901, Brazil.
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13
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PALOMBO MR. Body size structure of Pleistocene mammalian communities: what support is there for the âisland ruleâ? Integr Zool 2009; 4:341-56. [DOI: 10.1111/j.1749-4877.2009.00175.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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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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15
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Binladen J, Gilbert MTP, Willerslev E. 800,000 year old mammoth DNA, modern elephant DNA or PCR artefact? Biol Lett 2007; 3:55-6; discussion 60-3. [PMID: 17443965 PMCID: PMC2373799 DOI: 10.1098/rsbl.2006.0537] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely in samples, which are recovered from warm environments and are relatively old (e.g. more than 100,000 years), these findings come as a great surprise. Here, we show that problems exist with the methodological approaches used in the study. First, the nested PCR technique as reported is nonsensical--one of the second round 'nested' primers falls outside the amplicon of the first round PCR. More worryingly, the binding region of one of the first round primers (Elcytb320R) falls within the short 43 base pair reported mammoth sequence, specifically covering two of the three reportedly diagnostic Elephas polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants.
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16
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Poulakakis N, Parmakelis A, Lymberakis P, Mylonas M, Zouros E, Reese DS, Glaberman S, Caccone A. It remains a mammoth DNA fragment. A reply to and. Biol Lett 2006. [DOI: 10.1098/rsbl.2006.0555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Aris Parmakelis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Moysis Mylonas
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Eleftherios Zouros
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - David S Reese
- Peabody Museum of Natural History, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
| | - Scott Glaberman
- Department of Ecology and Evolutionary Biology and Yale Institute of Biospheric Studies, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology and Yale Institute of Biospheric Studies, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
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