Abstract:
:Proof of authenticity is the greatest challenge in palaeogenetic research, and many safeguards have become standard routine in laboratories specialized on ancient DNA research. Here we describe an as-yet unknown source of artifacts that will require special attention in the future. We show that ancient DNA extracts on their own can have an inhibitory and mutagenic effect under PCR. We have spiked PCR reactions including known human test DNA with 14 selected ancient DNA extracts from human and nonhuman sources. We find that the ancient DNA extracts inhibit the amplification of large fragments to different degrees, suggesting that the usual control against contaminations, i.e., the absence of long amplifiable fragments, is not sufficient. But even more important, we find that the extracts induce mutations in a nonrandom fashion. We have amplified a 148-bp stretch of the mitochondrial HVRI from contemporary human template DNA in spiked PCR reactions. Subsequent analysis of 547 sequences from cloned amplicons revealed that the vast majority (76.97%) differed from the correct sequence by single nucleotide substitutions and/or indels. In total, 34 positions of a 103-bp alignment are affected, and most mutations occur repeatedly in independent PCR amplifications. Several of the induced mutations occur at positions that have previously been detected in studies of ancient hominid sequences, including the Neandertal sequences. Our data imply that PCR-induced mutations are likely to be an intrinsic and general problem of PCR amplifications of ancient templates. Therefore, ancient DNA sequences should be considered with caution, at least as long as the molecular basis for the extract-induced mutations is not understood.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Pusch CM,Bachmann Ldoi
10.1093/molbev/msh107subject
Has Abstractpub_date
2004-05-01 00:00:00pages
957-64issue
5eissn
0737-4038issn
1537-1719pii
msh107journal_volume
21pub_type
杂志文章abstract::The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as evolutionarily aware conservation scores, relative rates reveal key functional or strongly selected residues. Estimating rates in a phylogenetic context requires specifying a protein su...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy127
更新日期:2018-09-01 00:00:00
abstract::The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, wi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq270
更新日期:2011-05-01 00:00:00
abstract::Inactivation of the X chromosome in the male germ line has been suggested to contribute to the excess of gene movement off the X chromosome and the paucity of X-linked male-biased genes that have been observed in Drosophila species. Recent experimental work has demonstrated the transcriptional inactivation of the X ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq355
更新日期:2011-05-01 00:00:00
abstract::Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu068
更新日期:2014-05-01 00:00:00
abstract::About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi071
更新日期:2005-04-01 00:00:00
abstract::Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msr178
更新日期:2012-01-01 00:00:00
abstract::Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly differ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu064
更新日期:2014-05-01 00:00:00
abstract::With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi051
更新日期:2005-03-01 00:00:00
abstract::Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn148
更新日期:2008-09-01 00:00:00
abstract::Single-stranded DNA(ssDNA) viral life cycles must balance double-stranded DNA (dsDNA) and ssDNA biosynthesis. Previously published in vitro results suggest that microvirus C and host cell SSB proteins play antagonistic roles to achieve this balance. To investigate this in vivo, microvirus DNA replication was character...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu089
更新日期:2014-06-01 00:00:00
abstract::Members of the grass family (Poaceae) exhibit a broad range of inflorescence structures and other morphologies, making the grasses an interesting model system for studying the evolution of development. Here we present an analysis of the molecular evolution of FLORICAULA/LEAFY-like genes, which are important developmen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi095
更新日期:2005-04-01 00:00:00
abstract::Silks are strong protein fibers produced by a broad array of spiders and insects. The vast majority of known silks are large, repetitive proteins assembled into extended beta-sheet structures. Honeybees, however, have found a radically different evolutionary solution to the need for a building material. The 4 fibrous ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm171
更新日期:2007-11-01 00:00:00
abstract::In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh014
更新日期:2004-01-01 00:00:00
abstract::Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh117
更新日期:2004-07-01 00:00:00
abstract::Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their co...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy070
更新日期:2018-07-01 00:00:00
abstract::A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analys...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003958
更新日期:2001-09-01 00:00:00
abstract::The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos)...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn136
更新日期:2008-09-01 00:00:00
abstract::The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information con...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003717
更新日期:2001-01-01 00:00:00
abstract::With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy228
更新日期:2019-03-01 00:00:00
abstract::Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation with...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr318
更新日期:2012-06-01 00:00:00
abstract::How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa288
更新日期:2020-11-10 00:00:00
abstract::Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constan...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040391
更新日期:1986-05-01 00:00:00
abstract::In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss136
更新日期:2012-10-01 00:00:00
abstract::An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifyi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss187
更新日期:2012-12-01 00:00:00
abstract::Insertion and deletion (indel)-based analyses have great potential for rooting the tree of life, but their use has been limited because they require ubiquitous sequences that have not been horizontally/laterally transferred. Very few such sequences exist. Here we describe and demonstrate a new algorithm that can use n...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl140
更新日期:2007-01-01 00:00:00
abstract::As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv241
更新日期:2016-02-01 00:00:00
abstract::Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is tra...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg071
更新日期:2003-05-01 00:00:00
abstract::The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025768
更新日期:1997-03-01 00:00:00
abstract::Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to exper...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw094
更新日期:2016-08-01 00:00:00
abstract::The minimum-evolution (ME) method of phylogenetic inference is based on the assumption that the tree with the smallest sum of branch length estimates is most likely to be the true one. In the past this assumption has been used without mathematical proof. Here we present the theoretical basis of this method by showing ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040056
更新日期:1993-09-01 00:00:00