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1.
A polymorphic noncoding region of chloroplast DNA (cpDNA) was successfully amplified by the polymerase chain reaction (PCR) from various oak wood samples, including recent and more ancient (about 600-years-old) samples from different oak species. Adaptation of DNA isolation and amplification protocols was necessary to obtain this result. Polymorphisms useful to distinguish species or geographical origin of these samples could be scored through sequencing. These polymorphisms include one substitution and two microsatellite-type polymorphisms, due to a variable number of A/T repeats. Identical results were obtained independently in two separate laboratories. 相似文献
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Stefanie Wagner Frédéric Lagane Andaine Seguin‐Orlando Mikkel Schubert Thibault Leroy Erwan Guichoux Emilie Chancerel Inger Bech‐Hebelstrup Vincent Bernard Cyrille Billard Yves Billaud Matthias Bolliger Christophe Croutsch Katarina Čufar Frédérique Eynaud Karl Uwe Heussner Joachim Köninger Fabien Langenegger Frédéric Leroy Christine Lima Nicoletta Martinelli Garry Momber André Billamboz Oliver Nelle Antoni Palomo Raquel Piqué Marianne Ramstein Roswitha Schweichel Harald Stäuble Willy Tegel Xavier Terradas Florence Verdin Christophe Plomion Antoine Kremer Ludovic Orlando 《Molecular ecology》2018,27(5):1138-1154
Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management. 相似文献
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P. Francalacci 《Human Evolution》1995,10(1):81-91
The recovery, amplification and sequencing of nucleic acids from ancient smaples opens new possibilities in many different
fields, such as anthropology, archeaology, population genetics, animal and plant evolutionary studies, and forensic medicine.
The sample processing for DNA extraction and PCR amplification represents the most delicate phase of ancient DNA analysis,
with a major impact on the reproducibility and reliability of the results. In this paper some extraction protocols are reviewed
and discussed, with particular reference to the removal of the inhibitory substances usually present in extract from ancient
tissues. The effect of contamination from extraneous DNA, a possible source of misleading results, is discussed and guidelines
to detect and circumvent the problem are given. 相似文献
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Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits 下载免费PDF全文
David A. Gold Jacqueline Robinson Aisling B. Farrell John M. Harris Olaf Thalmann David K. Jacobs 《Ecology and evolution》2014,4(4):329-336
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. 相似文献
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Yanti Rachmayanti Ludger Leinemann Oliver Gailing Reiner Finkeldey 《Plant Molecular Biology Reporter》2006,24(1):45-55
A successful DNA extraction from wood yielding appropriate DNA quality for PCR amplification allows molecular genetic investigations
of wood tissue. Genotypes, the origin of sampled material, and species can be identified based on an investigation of wood
if suitable information on genetic variation patterns within and among species is available. Potential applications are in
forensics and in the control of the timber and wood trade. We extracted DNA from wood of Dipterocarpaceae, a family that dominates
rainforests and comprises many important timber species in Southeast Asia. Several different DNA isolation techniques were
compared and optimized for wood samples from natural populations and from wood processing enterprises. The quality of the
DNA was tested by spectrophotometry, PCR amplification, and PCR inhibitor tests. An average DNA yield of 2.2 μg was obtained
per 50–100 mg of dried wood sample. Chloroplast DNA (cpDNA) regions of different length were amenable to PCR amplification
from the extracted DNA. Modification of DNA isolation techniques by the addition of polyvinylpyrrolidone (PVP) addition up
to 3.1% into lysis buffer reduced PCR inhibition effectively. In order to evaluate the extraction method, we analyzed leaves
and wood from the same tree by PCR amplification, genotyping and sequencing of chloroplast microsatellites. 相似文献
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The ability to retrieve DNA from ancient specimens has been one of the greatest achievements of the past decade, and has opened
a totally new field of research with applications in seemingly distant domains such as archeobotany, the molecular phylogeny
of extinct genomes, human paleopathology and the genetic of ancient human populations. However, extraction of ancient DNA
has often a very low rate of success, prompting researchers to develop screening methods for the selection of promising specimens.
With this goal in mind, we studied the amino acid content of nine human bones of ancient origin. We demonstrate that a single
HPLC chromatogram is indicative of the integrity of ancient bone proteins. Among five specimens containing amplifiable DNA,
four exhibited a protein content similar to that of contemporary bone protein content. Three of the four specimens, from which
we were unable to extract any amplifiable DNA, had an amino acid content strikingly different from that of contem-porary bone.
A non-parametric statistical test, Kendall's tau, was used to show that protein content and PCR products, are probably correlated
(at a 95% confidence level). In addition, the D/L Asp and D/L Glu racemization ratios obtained are indicative of the presence
of ancient organic compounds. We propose that protein analysis should be systematically performed in studies where there are
many samples in order to select the specimens that are most likely to contain retrievable ancient DNA. 相似文献
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Iñiguez AM Reinhard K Carvalho Gonçalves ML Ferreira LF Araújo A Paulo Vicente AC 《International journal for parasitology》2006,36(13):1419-1425
Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further pinworm paleoepidemiological studies. 相似文献
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Jorge Victor Wilfredo Cachay Wester Vanny Judith Soplapuco Vilchez Carlos Eduardo Wester La Torre Luis Alberto Rodriguez-Delfin 《Genetics and molecular biology》2020,43(4)
Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies. 相似文献
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The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th–17th century burial population from the Canary Islands,Spain 下载免费PDF全文
Jonathan Santana Rosa Fregel Emma Lightfoot Jacob Morales Martha Alamón José Guillén Marco Moreno Amelia Rodríguez 《American journal of physical anthropology》2016,159(2):300-312
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The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future. 相似文献
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Junichi M. Imoto Kenji Saitoh Takeshi Sasaki Takahiro Yonezawa Jun Adachi Yuri P. Kartavtsev Masaki Miya Mutsumi Nishida Naoto Hanzawa 《Gene》2013
The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily. 相似文献