Abstract:
:The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assumption of a global molecular clock. Recently, two studies have instead reported time estimates apparently consistent with the fossil record. Here, we demonstrate that methodological problems in these studies cast doubt on the accuracy and interpretations of the results obtained. In the study by Peterson et al., young time estimates were obtained because fossil calibrations were used as maximum limits rather than as minimum limits, and not because invertebrate calibrations were used. In the study by Aris-Brosou and Yang, young time estimates were obtained because of problems with rate models and other methods specific to the study, and not because Bayesian methods were used. This also led to many anomalous findings in their study, including a primate-rodent divergence at 320 MYA. With these results aside, molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Blair JE,Hedges SBdoi
10.1093/molbev/msi039subject
Has Abstractpub_date
2005-03-01 00:00:00pages
387-90issue
3eissn
0737-4038issn
1537-1719pii
msi039journal_volume
22pub_type
信件abstract::Restriction site variations in nuclear ribosomal DNA (rDNA) spacers and mitochondrial DNA (mtDNA) were examined in several populations of mole rats with variable numbers of chromosomes, which represented the two superspecies Spalax leucodon (2n = 38, 54, or 62) and Spalax ehrenbergi (2n = 52, 54, 58, or 60). Sequence ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025574
更新日期:1996-01-01 00:00:00
abstract::This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolut...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040173
更新日期:1994-11-01 00:00:00
abstract::Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst271
更新日期:2014-04-01 00:00:00
abstract::The acrosomal protein bindin attaches sperm to eggs during sea urchin fertilization. Complementary to ongoing functional biochemical studies, I take a comparative approach to explore the molecular evolution of bindin in a group of closely related free-spawning echinoid species. Two alleles of the mature bindin gene we...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025902
更新日期:1998-12-01 00:00:00
abstract::Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv091
更新日期:2015-08-01 00:00:00
abstract::Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp149
更新日期:2009-10-01 00:00:00
abstract::A major limitation on ability to reconstruct bacterial evolution is the lack of dated ancestors that might be used to evaluate and calibrate molecular clocks. Vertically transmitted symbionts that have cospeciated with animal hosts offer a firm basis for calibrating sequence evolution in bacteria, since fossils of the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026071
更新日期:1999-11-01 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::It has recently been claimed that older genes tend to evolve more slowly than newer ones (Alba and Castresana 2005). By simulation of genes of equal age, we show that the inverse correlation between age and rate is an artifact caused by our inability to detect homology when evolutionary distances are large. Since evol...
journal_title:Molecular biology and evolution
pub_type: 评论,信件
doi:10.1093/molbev/msj006
更新日期:2006-01-01 00:00:00
abstract::Chaperone-mediated autophagy (CMA) is a major pathway of lysosomal proteolysis recognized as a key player of the control of numerous cellular functions, and whose defects have been associated with several human pathologies. To date, this cellular function is presumed to be restricted to mammals and birds, due to the a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa127
更新日期:2020-10-01 00:00:00
abstract::Here we report the peculiarities of molecular evolution and divergence of paralogous heterochromatic clusters of the testis- expressed X-linked Stellate and Y-linked Su(Ste) tandem repeats. It was suggested that Stellate and Su(Ste) clusters affecting male fertility are the amplified derivatives of the unique euchroma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026348
更新日期:2000-05-01 00:00:00
abstract::The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes cover...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst272
更新日期:2014-04-01 00:00:00
abstract::Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx226
更新日期:2017-11-01 00:00:00
abstract::Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this met...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm207
更新日期:2007-11-01 00:00:00
abstract::Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search st...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu300
更新日期:2015-01-01 00:00:00
abstract::Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepanc...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss236
更新日期:2013-02-01 00:00:00
abstract::The genetic basis of organisms' adaptation to different environments is a central issue of molecular evolution. The budding yeast Saccharomyces cerevisiae and its relatives predominantly ferment glucose into ethanol even in the presence of oxygen. This was suggested to be an adaptation to glucose-rich habitats, but th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq184
更新日期:2011-01-01 00:00:00
abstract::The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy166
更新日期:2018-11-01 00:00:00
abstract::The human major histocompatibility complex (Mhc) is a chromosomal segment approximately 4 million bp long that contains > or = 84 genes. Some of these genes code for the class I and class II molecules, while the remaining genes code for complement components, cytochrome P450, tumor necrosis factor, and many other, unr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a039999
更新日期:1993-01-01 00:00:00
abstract::The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040310
更新日期:1984-02-01 00:00:00
abstract::Pseudogenes are defined as nonfunctional DNA sequences with homology to functional protein-coding genes, and they typically contain nonfunctional mutations within the presumptive coding region. In theory, pseudogenes can also be caused by mutations in upstream regulatory regions, appearing as open reading frames with ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq298
更新日期:2011-03-01 00:00:00
abstract::DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated non...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr041
更新日期:2011-08-01 00:00:00
abstract::Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current b...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu063
更新日期:2014-05-01 00:00:00
abstract::Hybrid males resulting from crosses between closely related species of Drosophila are sterile. The F1 hybrid sterility phenotype is mainly due to defects occurring during late stages of development that relate to sperm individualization, and so genes controlling sperm development may have been subjected to selective d...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj074
更新日期:2006-03-01 00:00:00
abstract::The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with tho...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx100
更新日期:2017-06-01 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::During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj036
更新日期:2006-02-01 00:00:00
abstract::As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw144
更新日期:2016-11-01 00:00:00
abstract::Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mut...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx051
更新日期:2017-06-01 00:00:00
abstract::The malaria parasite's chloroquine resistance transporter (CRT) is an integral membrane protein localized to the parasite's acidic digestive vacuole. The function of CRT is not known and the protein was originally described as a transporter simply because it possesses 10 transmembrane domains. In wild-type (chloroquin...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh205
更新日期:2004-10-01 00:00:00