The mysterious evolutionary origin for the GNE gene and the root of bilateria.

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

authors： Roy SW,Penny D

更新日期：2006-12-01 00:00:00

abstract：:We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known g...

journal_title：Molecular biology and evolution

authors： Xu L,Bickhart DM,Cole JB,Schroeder SG,Song J,Tassell CP,Sonstegard TS,Liu GE

更新日期：2015-03-01 00:00:00

abstract：:Evidence is growing that homologous recombination is a powerful source of genetic variability among closely related free-living bacteria. Here we investigate the extent of recombination among housekeeping genes of the endosymbiotic bacteria Wolbachia. Four housekeeping genes, gltA, dnaA, ftsZ, and groEL, were sequence...

journal_title：Molecular biology and evolution

authors： Baldo L,Bordenstein S,Wernegreen JJ,Werren JH

更新日期：2006-02-01 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：:A central problem in evolutionary theory concerns the mechanisms by which adaptations requiring multiple mutations emerge in natural populations. We develop a series of expressions that clarify the scaling of the time to establishment of complex adaptations with population size, mutation rate, magnitude of the selecti...

journal_title：Molecular biology and evolution

authors： Lynch M,Abegg A

更新日期：2010-06-01 00:00:00

abstract：:Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 6...

journal_title：Molecular biology and evolution

authors： Yu N,Zhao Z,Fu YX,Sambuughin N,Ramsay M,Jenkins T,Leskinen E,Patthy L,Jorde LB,Kuromori T,Li WH

更新日期：2001-02-01 00:00:00

abstract：:The phylogenetic relationships of the biflagellate protist group Apusomonadidae have been unclear despite the availability of some molecular data. We analyzed sequences from 6 nuclear encoded genes-small-subunit rRNA, large-subunit rRNA, alpha-tubulin, beta-tubulin, actin, and heat shock protein 90-to infer the phylog...

journal_title：Molecular biology and evolution

authors： Kim E,Simpson AG,Graham LE

更新日期：2006-12-01 00:00:00

abstract：:Drosophila melanogaster, unlike mammals, has seven insulin-like peptides (DILPS). In Drosophila, all seven genes (dilp1-7) are single copy in the 12 species studied, except for D. grimshawi with two tandem copies of dilp2. Our comparative analysis revealed that genes dilp1-dilp7 exhibit differential functional constra...

journal_title：Molecular biology and evolution

authors： Guirao-Rico S,Aguadé M

更新日期：2011-05-01 00:00:00

abstract：:A phylogenetic analysis of sex-chromosomal zinc-finger genes (Zfx and Zfy) indicates that the genes have not evolved completely independently since their initial separation. The sequence similarities suggest gene conversion in the last exon between the duplicated Y-chromosomal genes Zfy-1 and Zfy-2 in the mouse. There...

journal_title：Molecular biology and evolution

authors： Pamilo P,Bianchi NO

更新日期：1993-03-01 00:00:00

abstract：:Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees...

journal_title：Molecular biology and evolution

authors： Zhang C,Scornavacca C,Molloy EK,Mirarab S

更新日期：2020-11-01 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：:Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations...

journal_title：Molecular biology and evolution

authors： Zhang J

更新日期：2004-07-01 00:00:00

abstract：:The comparative genomics of the transition of the opportunistic pathogen Pseudomonas aeruginosa from a free-living environmental strain to one that causes chronic infection in the airways of cystic fibrosis (CF) patients remain poorly studied. Chronic infections are thought to originate from colonization by a single s...

journal_title：Molecular biology and evolution

authors： Dettman JR,Kassen R

更新日期：2021-01-23 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

authors： Navidi WC,Beckett-Lemus L

更新日期：1992-11-01 00:00:00

abstract：:We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Usi...

journal_title：Molecular biology and evolution

authors： Zhang L,Li WH

更新日期：2005-12-01 00:00:00

abstract：:The major histocompatibility complex (MHC) class II molecule consists of noncovalently associated alpha and beta chains. In mammals studied so far, the class II MHC can be divided into a number of regions, each containing one or more alpha-chain genes (A genes) and beta-chain genes (B genes), and it has been known for...

journal_title：Molecular biology and evolution

authors： Hughes AL,Nei M

更新日期：1990-11-01 00:00:00

abstract：:The marine cyanobacterium Prochlorococcus MED4 has the smallest sequenced genome of any photosynthetic organism. Prochlorococcus MED4 shares many genomic characteristics with chloroplasts and bacterial endosymbionts, including a reduced coding capacity, missing DNA repair genes, a minimal transcriptional regulatory ne...

journal_title：Molecular biology and evolution

authors： Hu J,Blanchard JL

更新日期：2009-01-01 00:00:00

abstract：:Direct sequencing of polymerase chain reaction products is now an expanding area of plant systematics and evolution. Within angiosperms the rbcL gene has been widely sequenced and used for inferring plant phylogenies at higher taxonomic levels. Unfortunately rbcL does not usually contain enough information to resolve ...

journal_title：Molecular biology and evolution

authors： Gielly L,Taberlet P

更新日期：1994-09-01 00:00:00

abstract：:Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is r...

journal_title：Molecular biology and evolution

authors： Mendes FK,Hahn Y,Hahn MW

更新日期：2016-12-01 00:00:00

abstract：:Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps o...

journal_title：Molecular biology and evolution

authors： Scofield DG,Hong X,Lynch M

更新日期：2007-04-01 00:00:00

abstract：:The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 g...

journal_title：Molecular biology and evolution

authors： Yang Z,Wafula EK,Honaas LA,Zhang H,Das M,Fernandez-Aparicio M,Huang K,Bandaranayake PC,Wu B,Der JP,Clarke CR,Ralph PE,Landherr L,Altman NS,Timko MP,Yoder JI,Westwood JH,dePamphilis CW

更新日期：2015-03-01 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

authors： Wertheim JO,Smith MD,Smith DM,Scheffler K,Kosakovsky Pond SL

更新日期：2014-09-01 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：: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：:Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the...

journal_title：Molecular biology and evolution

authors： Ranz JM,Díaz-Castillo C,Petersen R

更新日期：2012-01-01 00:00:00

abstract：:Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constan...

journal_title：Molecular biology and evolution

authors： Gingerich PD

更新日期：1986-05-01 00:00:00

abstract：:To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon an...

journal_title：Molecular biology and evolution

authors： Kawakita A,Sota T,Ascher JS,Ito M,Tanaka H,Kato M

更新日期：2003-01-01 00:00:00

abstract：:Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecula...

journal_title：Molecular biology and evolution

authors： Pupko T,Huchon D,Cao Y,Okada N,Hasegawa M

更新日期：2002-12-01 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：:We report the results of a phylogenetic survey of the retrotransposon copia in the melanogaster subgroup of the Drosophila genus. The polymerase chain reaction was used to amplify the copia 5' long terminal repeat and the adjacent untranslated leader region from representative melanogaster subgroup species. Restrictio...

journal_title：Molecular biology and evolution

authors： Jordan IK,McDonald JF

更新日期：1998-09-01 00:00:00