SPIn: model selection for phylogenetic mixtures via linear invariants.

abstract：:A detailed assessment of the evolution and phylogenetic utility of two genes, ftsZ and wsp, was used to investigate the origin of male-killing Wolbachia, previously isolated from the ladybird Adalia bipunctata and the butterfly Acraea encedon. The analysis included almost all available sequences of B-group Wolbachia a...

journal_title：Molecular biology and evolution

authors： Schulenburg JH,Hurst GD,Huigens TM,van Meer MM,Jiggins FM,Majerus ME

更新日期：2000-04-01 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

authors： Liu X,Maxwell TJ,Boerwinkle E,Fu YX

更新日期：2009-07-01 00:00:00

abstract：:The organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rea...

journal_title：Molecular biology and evolution

authors： Bensch S,Härlid A

更新日期：2000-01-01 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

authors： Forget L,Ustinova J,Wang Z,Huss VA,Lang BF

更新日期：2002-03-01 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

authors： Rochette NC,Brochier-Armanet C,Gouy M

更新日期：2014-04-01 00:00:00

abstract：:The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wol...

journal_title：Molecular biology and evolution

authors： Zhang M,Sun G,Ren L,Yuan H,Dong G,Zhang L,Liu F,Cao P,Ko AM,Yang MA,Hu S,Wang GD,Fu Q

更新日期：2020-05-01 00:00:00

abstract：:Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA, and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection ...

journal_title：Molecular biology and evolution

authors： Laurin-Lemay S,Philippe H,Rodrigue N

更新日期：2018-06-01 00:00:00

abstract：:There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chr...

journal_title：Molecular biology and evolution

authors： Lercher MJ,Urrutia AO,Hurst LD

更新日期：2003-07-01 00:00:00

abstract：:The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It w...

journal_title：Molecular biology and evolution

authors： Carter R,Drouin G

更新日期：2010-05-01 00:00:00

abstract：:Proteomic analyses of the nucleolus have revealed almost 700 functionally diverse proteins implicated in ribosome biogenesis, nucleolar assembly, and regulation of vital cellular processes. However, this nucleolar inventory has not unveiled a specific consensus motif necessary for nucleolar binding. The ribosomal prot...

journal_title：Molecular biology and evolution

authors： Kundu-Michalik S,Bisotti MA,Lipsius E,Bauche A,Kruppa A,Klokow T,Kammler G,Kruppa J

更新日期：2008-03-01 00:00:00

abstract：:The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and the...

journal_title：Molecular biology and evolution

authors： Lucas-Lledó JI,Maddamsetti R,Lynch M

更新日期：2011-03-01 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

authors： Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MA

更新日期：2013-03-01 00:00:00

abstract：:The most frequent measure of phylogenetic uncertainty for splits is bootstrap support. Although large bootstrap support intuitively suggests that a split in a tree is well supported, it has not been clear how large bootstrap support needs to be to conclude that there is significant evidence that a hypothesized split i...

journal_title：Molecular biology and evolution

authors： Susko E

更新日期：2010-07-01 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

authors： Lake JA,Herbold CW,Rivera MC,Servin JA,Skophammer RG

更新日期：2007-01-01 00:00:00

abstract：:Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Op...

journal_title：Molecular biology and evolution

authors： Shutt TE,Gray MW

更新日期：2006-06-01 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

authors： Kogan GL,Epstein VN,Aravin AA,Gvozdev VA

更新日期：2000-05-01 00:00:00

abstract：:MicroRNA (miRNA) sponges are vital components of posttranscriptional gene regulation. Yet, only a limited number of miRNA sponges have been identified. Here, we show that the recently evolved noncoding tumor suppressor transcript, antisense RNA to TP73 gene (TP73-AS1), functions as a natural sponge of human-specific m...

journal_title：Molecular biology and evolution

authors： Hu H,Liu JM,Hu Z,Jiang X,Yang X,Li J,Zhang Y,Yu H,Khaitovich P

更新日期：2018-05-01 00:00:00

abstract：:Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutation...

journal_title：Molecular biology and evolution

authors： Novoa EM,Jungreis I,Jaillon O,Kellis M

更新日期：2019-10-01 00:00:00

abstract：:Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

journal_title：Molecular biology and evolution

authors： Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

更新日期：2015-07-01 00:00:00

abstract：:Full-length L1 elements have been shown to possess, at their 5' end, tandem repeats called "A" or "F" types. By sequencing the 5' region of two large L1 copies that did not hybridize to A or F probes, we have identified a new sequence that is found at the 5' end of many L1 elements and that we call "V." The element ch...

journal_title：Molecular biology and evolution

authors： Jubier-Maurin V,Cuny G,Laurent AM,Paquereau L,Roizes G

更新日期：1992-01-01 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

authors： Sorhannus U

更新日期：1996-09-01 00:00:00

abstract：:The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) con...

journal_title：Molecular biology and evolution

authors： Osborne PW,Ferrier DE

更新日期：2010-02-01 00:00:00

abstract：:Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

journal_title：Molecular biology and evolution

authors： Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

更新日期：2016-04-01 00:00:00

abstract：:The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of...

journal_title：Molecular biology and evolution

authors： Huelsenbeck JP

更新日期：1995-09-01 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

authors： van Oppen MJ,McDonald BJ,Willis B,Miller DJ

更新日期：2001-07-01 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

authors： Schott RK,Refvik SP,Hauser FE,López-Fernández H,Chang BS

更新日期：2014-05-01 00:00:00

abstract：:Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...

journal_title：Molecular biology and evolution

authors： Parkin EJ,Butlin RK

更新日期：2004-08-01 00:00:00

abstract：:Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have fou...

journal_title：Molecular biology and evolution

authors： Schrider DR,Hahn MW

更新日期：2010-01-01 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

authors： Helliwell KE,Wheeler GL,Leptos KC,Goldstein RE,Smith AG

更新日期：2011-10-01 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

authors： Geraldes A,Rambo T,Wing RA,Ferrand N,Nachman MW

更新日期：2010-11-01 00:00:00