Abstract:
:The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Axelsson E,Willerslev E,Gilbert MT,Nielsen Rdoi
10.1093/molbev/msn163subject
Has Abstractpub_date
2008-10-01 00:00:00pages
2181-7issue
10eissn
0737-4038issn
1537-1719pii
msn163journal_volume
25pub_type
杂志文章abstract::In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In the lake whitefis...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn235
更新日期:2009-01-01 00:00:00
abstract::Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS)....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss266
更新日期:2013-03-01 00:00:00
abstract::We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymou...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004231
更新日期:2003-01-01 00:00:00
abstract::Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx098
更新日期:2017-07-01 00:00:00
abstract::We have sequenced the mitochondrial DNA (mtDNA) of Hyaloraphidium curvatum, an organism previously classified as a colorless green alga but now recognized as a lower fungus based on molecular data. The 29.97-kbp mitochondrial chromosome is maintained as a monomeric, linear molecule with identical, inverted repeats (1....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004084
更新日期:2002-03-01 00:00:00
abstract::Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh188
更新日期:2004-09-01 00:00:00
abstract::Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNA(Lys) needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr005
更新日期:2011-06-01 00:00:00
abstract::The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003935
更新日期:2001-08-01 00:00:00
abstract::Evolutionary parsimony is an easy-to-use method of phylogenetic inference that is based on nucleic acid sequences and that does not require the assumption that evolutionary processes in the various sites on the molecule are identical. It does, however, require a parameter constraint, known as the "balanced transversio...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040784
更新日期:1992-11-01 00:00:00
abstract::The diatom Phaeodactylum tricornutum harbors a plastid that is surrounded by four membranes and evolved by way of secondary endosymbiosis. Like land plants, most of its plastid proteins are encoded as preproteins on the nuclear genome of the host cell and are resultantly redirected into the organelle. Because two more...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp079
更新日期:2009-08-01 00:00:00
abstract::The quantitative immunological technique of micro-complement fixation (MC'F) has been routinely used during the past decade to assess evolutionary relationships among living vertebrate species. The large data base that has been generated, along with the excellent correlations between immunologically measured genetic d...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040405
更新日期:1986-09-01 00:00:00
abstract::Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene fam...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msw140
更新日期:2016-10-01 00:00:00
abstract::Although there is substantial evidence that, in animals, male-inherited neutral DNA evolves at a higher rate than female-inherited DNA, the relative evolutionary rate of male- versus female-inherited DNA has not been investigated in plants. We compared the substitution rates at neutral sites of maternally and paternal...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004151
更新日期:2002-06-01 00:00:00
abstract::Sponges (Porifera) are among the simplest living and the earliest branching metazoans. They hold a pivotal role for studying genome evolution of the entire metazoan branch, both as an outgroup to Eumetazoa and as the closest branching phylum to the common ancestor of all multicellular animals (Urmetazoa). In order to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq174
更新日期:2010-12-01 00:00:00
abstract::R2 non-long terminal repeat retrotransposable elements insert specifically into the 28S rRNA genes of a wide range of animals. These elements maintain long-term stable relationships with the host genome. By scoring the variation present at the 5' ends of individual R2 copies, lines of Drosophila simulans have been ide...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm250
更新日期:2008-01-01 00:00:00
abstract::Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss265
更新日期:2013-03-01 00:00:00
abstract::The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collecte...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm209
更新日期:2007-12-01 00:00:00
abstract::Protein interactions are central to most biological processes. We investigated the dynamics of emergence of the protein interaction network of Saccharomyces cerevisiae by mapping origins of proteins on an evolutionary tree. We demonstrate that evolutionary periods are characterized by distinct connectivity levels of t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh085
更新日期:2004-07-01 00:00:00
abstract::One challenge of analyzing samples of DNA sequences is to account for the nonnegligible polymorphisms produced by error when the sequencing error rate is high or the sample size is large. Specifically, those artificial sequence variations will bias the observed single nucleotide polymorphism (SNP) frequency spectrum, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp059
更新日期:2009-07-01 00:00:00
abstract::Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four contine...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh089
更新日期:2004-08-01 00:00:00
abstract::The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa147
更新日期:2020-10-01 00:00:00
abstract::The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy149
更新日期:2018-10-01 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::Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm005
更新日期:2007-03-01 00:00:00
abstract::Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv206
更新日期:2016-01-01 00:00:00
abstract::Complex metazoan bodies require cell-to-cell communication for development, a process often mediated by signaling molecules binding to specific receptors. Relatively few signaling pathways have been recruited during evolution to build multicellular animals from unicellular zygotes. Of these few signaling pathways, one...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst222
更新日期:2014-02-01 00:00:00
abstract::Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, howev...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx109
更新日期:2017-07-01 00:00:00
abstract::The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, and single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated in a large palindrome in the European rabbit (Oryctolagus cuniculus). Furthermo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq139
更新日期:2010-11-01 00:00:00
abstract::Some of the assumptions underlying estimates of DNA and protein sequence divergence are examined. A solution for the variance of these estimates that allows for different mutation rates and different population sizes in each species and for an arbitrary structure in the initial population is obtained. It is shown that...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040303
更新日期:1983-12-01 00:00:00