Frequent Retroviral Gene Co-option during the Evolution of Vertebrates.

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

authors： Konrad A,Thompson O,Waterston RH,Moerman DG,Keightley PD,Bergthorsson U,Katju V

更新日期：2017-06-01 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：:Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...

journal_title：Molecular biology and evolution

authors： Wu J,Susko E

更新日期：2011-05-01 00:00:00

abstract：:The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...

journal_title：Molecular biology and evolution

authors： Tofanelli S,Bertoncini S,Castrì L,Luiselli D,Calafell F,Donati G,Paoli G

更新日期：2009-09-01 00:00:00

abstract：:Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex ch...

journal_title：Molecular biology and evolution

authors： Conte MA,Clark FE,Roberts RB,Xu L,Tao W,Zhou Q,Wang D,Kocher TD

更新日期：2020-12-10 00:00:00

abstract：:DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, p...

journal_title：Molecular biology and evolution

authors： Crozat E,Winkworth C,Gaffé J,Hallin PF,Riley MA,Lenski RE,Schneider D

更新日期：2010-09-01 00:00:00

abstract：:The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the ex...

journal_title：Molecular biology and evolution

authors： John U,Fensome RA,Medlin LK

更新日期：2003-07-01 00:00:00

abstract：:We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...

journal_title：Molecular biology and evolution

authors： Ford MJ,Yoon CK,Aquadro CF

更新日期：1994-03-01 00:00:00

abstract：:Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and cha...

journal_title：Molecular biology and evolution

authors： Gluck-Thaler E,Haridas S,Binder M,Grigoriev IV,Crous PW,Spatafora JW,Bushley K,Slot JC

更新日期：2020-10-01 00:00:00

abstract：:The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer s...

journal_title：Molecular biology and evolution

authors： Sourdis J,Nei M

更新日期：1988-05-01 00:00:00

abstract：:Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

journal_title：Molecular biology and evolution

authors： Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

更新日期：2008-10-01 00:00:00

abstract：:The RIIIS/J inbred mouse strain is a model for type 1 von Willebrand disease (VWD), a common human bleeding disorder. Low von Willebrand factor (VWF) levels in RIIIS/J are due to a regulatory mutation, Mvwf1, which directs a tissue-specific switch in expression of a glycosyltransferase, B4GALNT2, from intestine to blo...

journal_title：Molecular biology and evolution

authors： Johnsen JM,Teschke M,Pavlidis P,McGee BM,Tautz D,Ginsburg D,Baines JF

更新日期：2009-03-01 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

authors： Terekhanova NV,Bazykin GA,Neverov A,Kondrashov AS,Seplyarskiy VB

更新日期：2013-06-01 00:00:00

abstract：:Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as ...

journal_title：Molecular biology and evolution

authors： Hamashima K,Tomita M,Kanai A

更新日期：2016-02-01 00:00:00

abstract：:Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental...

journal_title：Molecular biology and evolution

authors： Shan X,Liu Z,Dong Z,Wang Y,Chen Y,Lin X,Long L,Han F,Dong Y,Liu B

更新日期：2005-04-01 00:00:00

abstract：:IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficien...

journal_title：Molecular biology and evolution

authors： Minh BQ,Schmidt HA,Chernomor O,Schrempf D,Woodhams MD,von Haeseler A,Lanfear R

更新日期：2020-05-01 00:00:00

abstract：:Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERN...

journal_title：Molecular biology and evolution

authors： Adrion JR,Galloway JG,Kern AD

更新日期：2020-06-01 00:00:00

abstract：:Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolate...

journal_title：Molecular biology and evolution

authors： Li M,Xu J,Algarra Alarcon A,Carlin S,Barbaro E,Cappellin L,Velikova V,Vrhovsek U,Loreto F,Varotto C

更新日期：2017-10-01 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：:Unlike mammals, fish are able to regenerate axons in their central nervous system. This difference has been partly attributed to the loss/acquisition of inhibitory proteins during evolution. Nogo-A--the longest isoform of the reticulon4 (rtn4) gene product--is commonly found in mammalian myelin where it acts as a pote...

journal_title：Molecular biology and evolution

authors： Shypitsyna A,Málaga-Trillo E,Reuter A,Stuermer CA

更新日期：2011-04-01 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：:Much of evolutionary change is mediated at the level of gene expression, yet our understanding of regulatory evolution remains unsatisfying. In light of recent data indicating that transcription factor binding sites undergo substantial turnover between species, we attempt to quantify the process of binding site turnov...

journal_title：Molecular biology and evolution

authors： Dermitzakis ET,Bergman CM,Clark AG

更新日期：2003-05-01 00:00:00

abstract：:The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. In larval muscle and tubular and abdominal muscles of adults, all of the six exons are included in the spliced mRNA, whereas, in the fibrillar indirect flight muscle of adult, exon 5 is exclu...

journal_title：Molecular biology and evolution

authors： Leicht BG,Lyckegaard EM,Benedict CM,Clark AG

更新日期：1993-07-01 00:00:00

abstract：:Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, w...

journal_title：Molecular biology and evolution

authors： He F,Arce AL,Schmitz G,Koornneef M,Novikova P,Beyer A,de Meaux J

更新日期：2016-08-01 00:00:00

abstract：:We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates-four fro...

journal_title：Molecular biology and evolution

authors： Silberman JD,Simpson AG,Kulda J,Cepicka I,Hampl V,Johnson PJ,Roger AJ

更新日期：2002-05-01 00:00:00

abstract：:Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...

journal_title：Molecular biology and evolution

authors： Turbeville JM,Field KG,Raff RA

更新日期：1992-03-01 00:00:00

abstract：:We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which...

journal_title：Molecular biology and evolution

authors： Grünewald S,Forslund K,Dress A,Moulton V

更新日期：2007-02-01 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

authors： Darriba D,Posada D,Kozlov AM,Stamatakis A,Morel B,Flouri T

更新日期：2020-01-01 00:00:00

abstract：:Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model t...

journal_title：Molecular biology and evolution

authors： Forsberg R,Christiansen FB

更新日期：2003-08-01 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

authors： Hsieh P,Hallmark B,Watkins J,Karafet TM,Osipova LP,Gutenkunst RN,Hammer MF

更新日期：2017-11-01 00:00:00