Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations.

abstract：:We review all instances in which the nuclear 5S rRNA genes of fungi, protist, nematode, and arthropod species have been reported to be linked to the tandemly repeated units of the rDNA, trans-spliced leader, and histone multigene families. The evolution of these gene arrangements is analyzed by mapping them to indepen...

journal_title：Molecular biology and evolution

authors： Drouin G,de Sá MM

更新日期：1995-05-01 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：:TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthri...

journal_title：Molecular biology and evolution

authors： Evans AL,Blackburn JWD,Taruc K,Kipp A,Dirk BS,Hunt NR,Barr SD,Dikeakos JD,Heit B

更新日期：2017-07-01 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：:Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of...

journal_title：Molecular biology and evolution

authors： Zou Z,Zhang J

更新日期：2015-08-01 00:00:00

abstract：:We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...

journal_title：Molecular biology and evolution

authors： Gaut BS,Clark LG,Wendel JF,Muse SV

更新日期：1997-07-01 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：:Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints...

journal_title：Molecular biology and evolution

authors： Gout JF,Lynch M

更新日期：2015-08-01 00:00:00

abstract：:Frequent positive selection is a hallmark of genes involved in the adaptive immune system of vertebrates, but the incidence of positive selection for genes underlying innate immunity in vertebrates has not been well studied. The toll-like receptors (TLRs) of the innate immune system represent the first line of defense...

journal_title：Molecular biology and evolution

authors： Wlasiuk G,Nachman MW

更新日期：2010-09-01 00:00:00

abstract：:Alu is a predominant short interspersed element (SINE) family in the human genome and consists of two monomer units connected by an A-rich linker. At present, dimeric Alu elements are active in humans, but Alu monomers are present as fossilized sequences. A comparative genome analysis of human and chimpanzee genomes r...

journal_title：Molecular biology and evolution

authors： Kojima KK

更新日期：2011-01-01 00:00:00

abstract：:The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collecte...

journal_title：Molecular biology and evolution

authors： Zhou R,Zeng K,Wu W,Chen X,Yang Z,Shi S,Wu CI

更新日期：2007-12-01 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

authors： Seo TK

更新日期：2008-05-01 00:00:00

abstract：:While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...

journal_title：Molecular biology and evolution

authors： Davison A,Blaxter M

更新日期：2005-05-01 00:00:00

abstract：:Light-dependent and dark-operative protochlorophyllide oxidoreductases (LPORs and DPORs) are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis ...

journal_title：Molecular biology and evolution

authors： Chernomor O,Peters L,Schneidewind J,Loeschcke A,Knieps-Grünhagen E,Schmitz F,von Lieres E,Kutta RJ,Svensson V,Jaeger KE,Drepper T,von Haeseler A,Krauss U

更新日期：2020-09-15 00:00:00

abstract：:The noncoding-DNA content of organelle and nuclear genomes can vary immensely. Both adaptive and nonadaptive explanations for this variation have been proposed. This study addresses a nonadaptive explanation called the mutational-hazard hypothesis and applies it to the mitochondrial, plastid, and nuclear genomes of th...

journal_title：Molecular biology and evolution

authors： Smith DR,Lee RW

更新日期：2010-10-01 00:00:00

abstract：:Detecting positive selection in species with heterogeneous habitats and complex demography is notoriously difficult and prone to statistical biases. The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found. Moreove...

journal_title：Molecular biology and evolution

authors： Huber CD,Nordborg M,Hermisson J,Hellmann I

更新日期：2014-11-01 00:00:00

abstract：:Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...

journal_title：Molecular biology and evolution

authors： Eng KH,Bravo HC,Keleş S

更新日期：2009-10-01 00:00:00

abstract：:Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to a...

journal_title：Molecular biology and evolution

authors： Pandya S,Struck TJ,Mannakee BK,Paniscus M,Gutenkunst RN

更新日期：2015-01-01 00:00:00

abstract：:Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...

journal_title：Molecular biology and evolution

authors： Foflonker F,Blaby-Haas CE

更新日期：2021-01-23 00:00:00

abstract：:The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial for nitrogen fixation. Previous phylogenetic analysis of the amino acid sequence of nifH suggested that this gene had been horizontally transferred from a proteobacterium to the gram-positive/cyanobacterial clade, although the confounding effects ...

journal_title：Molecular biology and evolution

authors： Hirsch AM,McKhann HI,Reddy A,Liao J,Fang Y,Marshall CR

更新日期：1995-01-01 00:00:00

abstract：:There are three common alleles (A, B, and O) at the human ABO blood group locus. We compared nucleotide sequences of these alleles, and relatively large numbers of nucleotide differences were found among them. These differences correspond to the divergence time of at least a few million years, which is unusually large...

journal_title：Molecular biology and evolution

authors： Saitou N,Yamamoto F

更新日期：1997-04-01 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

authors： Leblois R,Estoup A,Rousset F

更新日期：2003-04-01 00:00:00

abstract：:Genes encoding DNA replication proteins have been frequently exchanged between cells and mobile elements, such as viruses or plasmids. This raises potential problems to reconstruct their history. Here, we combine phylogenetic and genomic context analyses to study the evolution of the replicative minichromosome mainten...

journal_title：Molecular biology and evolution

authors： Krupovic M,Gribaldo S,Bamford DH,Forterre P

更新日期：2010-12-01 00:00:00

abstract：:Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional...

journal_title：Molecular biology and evolution

authors： Vernon D,Gutell RR,Cannone JJ,Rumpf RW,Birky CW Jr

更新日期：2001-09-01 00:00:00

abstract：:Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome o...

journal_title：Molecular biology and evolution

authors： Wang MS,Li Y,Peng MS,Zhong L,Wang ZJ,Li QY,Tu XL,Dong Y,Zhu CL,Wang L,Yang MM,Wu SF,Miao YW,Liu JP,Irwin DM,Wang W,Wu DD,Zhang YP

更新日期：2015-07-01 00:00:00

abstract：:With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...

journal_title：Molecular biology and evolution

authors： Kitazoe Y,Kishino H,Okabayashi T,Watabe T,Nakajima N,Okuhara Y,Kurihara Y

更新日期：2005-03-01 00:00:00

abstract：:Proteins present in the seminal fluid of Drosophila melanogaster (accessory gland proteins Acps) contribute to female postmating behavioral changes, sperm storage, sperm competition, and immunity. Consequently, male-female coevolution and host-pathogen interactions are thought to underlie the rapid, adaptive evolution...

journal_title：Molecular biology and evolution

authors： Wong A,Turchin MC,Wolfner MF,Aquadro CF

更新日期：2008-03-01 00:00:00

abstract：:Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific ...

journal_title：Molecular biology and evolution

authors： Mank JE,Nam K,Brunström B,Ellegren H

更新日期：2010-07-01 00:00:00

abstract：:Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retro...

journal_title：Molecular biology and evolution

authors： Wang J,Han GZ

更新日期：2020-11-01 00:00:00

abstract：:Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or trans...

journal_title：Molecular biology and evolution

authors： Rodriguez Barreto D,Garcia de Leaniz C,Verspoor E,Sobolewska H,Coulson M,Consuegra S

更新日期：2019-10-01 00:00:00