Abstract:
:Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a non-parametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo, this coalescent model is often estimated in conjunction with a molecular clock model to produce time-stamped phylogenetic trees. We here provide a practical guide to using BEAST and its accompanying applications for the purpose of drawing inference under these models. We focus on best practices, potential pitfalls and recommendations that can be generalized to other software packages for Bayesian inference. This protocol shows how to use TempEst, BEAUti and BEAST 1.10 (http://beast.community/), LogCombiner as well as Tracer in a complete workflow.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Hill V,Baele Gdoi
10.1093/molbev/msz172subject
Has Abstractpub_date
2019-07-31 00:00:00eissn
0737-4038issn
1537-1719pii
5541799pub_type
杂志文章abstract::Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv025
更新日期:2015-05-01 00:00:00
abstract::A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera ap...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj107
更新日期:2006-05-01 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::Homeobox genes encode transcription factors involved in many aspects of developmental processes. The homeodomain-leucine zipper (HD-Zip) genes, which are characterized by the presence of both a homeodomain and a leucine zipper motif, form a clade within the homeobox superfamily and were previously reported only from v...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003828
更新日期:2001-04-01 00:00:00
abstract::Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesize...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa281
更新日期:2020-11-04 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::Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn112
更新日期:2008-08-01 00:00:00
abstract::The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outs...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw221
更新日期:2017-01-01 00:00:00
abstract::Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental ad...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw249
更新日期:2017-03-01 00:00:00
abstract::Statistical analyses of DNA sequences of the preproglucagon genes from bovine, human, hamster, and anglerfish suggest that a gene duplication creating two anglerfish genes (AF I and II) occurred about 160 Myr ago, long after the separation of fish and mammals. The analyses further suggest that the internal duplication...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040322
更新日期:1984-07-01 00:00:00
abstract::tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba caste...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa270
更新日期:2020-10-23 00:00:00
abstract::Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr124
更新日期:2011-10-01 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::Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale re...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu326
更新日期:2015-03-01 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::Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonize new environments. However, few studies have characterized the functions of HGT genes experimentally or examined postacquisi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy082
更新日期:2018-08-01 00:00:00
abstract::Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellula...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr103
更新日期:2011-10-01 00:00:00
abstract::The mitochondrial inner and outer membranes are composed of a variety of integral membrane proteins, assembled into the membranes posttranslationally. The small translocase of the inner mitochondrial membranes (TIMs) are a group of approximately 10 kDa proteins that function as chaperones to ferry the imported protein...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm031
更新日期:2007-05-01 00:00:00
abstract::It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic pr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq204
更新日期:2011-01-01 00:00:00
abstract::With whole-genome sequences being completed at an increasing rate, it is important to develop and assess tools to analyze them. Following annotation of the protein content of a genome, one can compare sequences with previously characterized homologous genes to detect novel functions within specific proteins in the evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003745
更新日期:2001-11-01 00:00:00
abstract::Immunoglobulin diversity is generated primarily by the heavy- and light-chain variable-region gene families. To understand the pattern of long-term evolution of the heavy-chain variable-region (VH) gene family, which is composed of a large number of member genes, the evolutionary relationships of representative VH gen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040127
更新日期:1994-05-01 00:00:00
abstract::The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the envir...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu251
更新日期:2014-12-01 00:00:00
abstract::Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to faci...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst213
更新日期:2014-02-01 00:00:00
abstract::Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu185
更新日期:2014-09-01 00:00:00
abstract::Molecular evolutionary rates within two protistan and three metazoan taxa were estimated using divergence times derived from fossil records. The results indicate that the small-subunit rRNA sequences within Dasycladales (Chlorophyta) and Bacillariophyceae evolved at a rate approximately two to three times faster than ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025653
更新日期:1996-09-01 00:00:00
abstract::That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm196
更新日期:2007-12-01 00:00:00
abstract::The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extre...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy134
更新日期:2018-10-01 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::Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary histo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy221
更新日期:2019-02-01 00:00:00
abstract::ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate and introduces several new featur...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz189
更新日期:2020-01-01 00:00:00