Abstract:
:MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-world DNA data. Recently, graphics processor unit (GPU) has shown its power as a coprocessor (or rather, an accelerator) in many fields. This article describes an efficient implementation a(MC)(3) (aMCMCMC) for MrBayes (MC)(3) on compute unified device architecture. By dynamically adjusting the task granularity to adapt to input data size and hardware configuration, it makes full use of GPU cores with different data sets. An adaptive method is also developed to split and combine DNA sequences to make full use of a large number of GPU cards. Furthermore, a new "node-by-node" task scheduling strategy is developed to improve concurrency, and several optimizing methods are used to reduce extra overhead. Experimental results show that a(MC)(3) achieves up to 63× speedup over serial MrBayes on a single machine with one GPU card, and up to 170× speedup with four GPU cards, and up to 478× speedup with a 32-node GPU cluster. a(MC)(3) is dramatically faster than all the previous (MC)(3) algorithms and scales well to large GPU clusters.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Bao J,Xia H,Zhou J,Liu X,Wang Gdoi
10.1093/molbev/mst043subject
Has Abstractpub_date
2013-06-01 00:00:00pages
1471-9issue
6eissn
0737-4038issn
1537-1719pii
mst043journal_volume
30pub_type
杂志文章abstract::Measuring natural selection on genomic elements involved in the cis-regulation of gene expression--such as transcriptional enhancers and promoters--is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these non...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst134
更新日期:2013-11-01 00:00:00
abstract::The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm012
更新日期:2007-04-01 00:00:00
abstract::The ability to counter periods of low humidity is an important determinant of distribution range in Drosophila. Climate specialists with low physiological tolerance to desiccation stress are restricted to the tropics and may lack the ability to further increase resistance through evolution. Although the physiological ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr294
更新日期:2012-05-01 00:00:00
abstract::Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Ex...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp037
更新日期:2009-06-01 00:00:00
abstract::Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic an...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst036
更新日期:2013-06-01 00:00:00
abstract::A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecie...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz305
更新日期:2020-05-01 00:00:00
abstract::Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy074
更新日期:2018-06-01 00:00:00
abstract::We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For exa...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003906
更新日期:2001-07-01 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 capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp278
更新日期:2010-03-01 00:00:00
abstract::Identification of recently gained spliceosomal introns would provide crucial evidence in the continuing debate concerning the age and evolutionary significance of introns. A previously published genomic analysis reported to have identified 122 introns that had been gained since the divergence of the nematodes Caenorha...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl098
更新日期:2006-12-01 00:00:00
abstract::Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh265
更新日期:2005-01-01 00:00:00
abstract::The plant genus Lycium (Solanaceae) originated in the Americas and includes approximately 85 species that are distributed worldwide. The vast majority of Old World species occur in southern Africa and eastern Asia. In this study, we examine biogeographic relationships among Old World species using a phylogenetic appro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq253
更新日期:2011-01-01 00:00:00
abstract::Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss223
更新日期:2013-02-01 00:00:00
abstract::Protein-protein interaction networks have evolved mainly through connectivity rewiring and gene duplication. However, how protein function influences these processes and how a network grows in time have not been well studied. Using protein-protein interaction data and genomic data from the budding yeast, we first exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi249
更新日期:2006-01-01 00:00:00
abstract::Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040244
更新日期:1995-07-01 00:00:00
abstract::This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the composition...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003916
更新日期:2001-07-01 00:00:00
abstract::Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn043
更新日期:2008-05-01 00:00:00
abstract::The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026156
更新日期:1999-06-01 00:00:00
abstract::One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg119
更新日期:2003-07-01 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::Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy248
更新日期:2019-03-01 00:00:00
abstract::Animal microRNAs (miRNAs) are short RNAs that function as posttranscriptional regulators of gene expression by binding to the target mRNAs. Noting that some miRNAs are highly conserved in evolution, we explored the possibility of evolutionary conservation of their targets. We identified human orthologues of experiment...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm195
更新日期:2007-11-01 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::Homologues of glucosephosphate isomerase (GPI, EC 5.3.1.9) were purified to homogeneity and kinetically characterized from Mytilus edulis and Isognomon alatus, two bivalve molluscs experiencing contrasting thermal environments. The enzyme isolated from I. alatus functions at warmer temperatures (25-35 C) than GPI from...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040346
更新日期:1985-05-01 00:00:00
abstract::In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the av...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg034
更新日期:2003-04-01 00:00:00
abstract::Ion channels have played a substantial role in the evolution of novel traits across all of the domains of life. A fascinating example of a novel adaptation is the convergent evolution of electric organs in the Mormyroid and Gymnotiform electric fishes. The regulated currents that flow through ion channels directly gen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu145
更新日期:2014-08-01 00:00:00
abstract::Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msi212
更新日期:2005-11-01 00:00:00
abstract::Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw235
更新日期:2017-02-01 00:00:00
abstract::Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organism...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr011
更新日期:2011-06-01 00:00:00