Observations of amino acid gain and loss during protein evolution are explained by statistical bias.

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：:Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and ante...

journal_title：Molecular biology and evolution

authors： Teeling EC,Hedges SB

更新日期：2013-09-01 00:00:00

abstract：:Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of over...

journal_title：Molecular biology and evolution

authors： Sabatini LM,Ota T,Azen EA

更新日期：1993-05-01 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：:To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems ...

journal_title：Molecular biology and evolution

authors： Aris-Brosou S

更新日期：2005-02-01 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 complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the gene...

journal_title：Molecular biology and evolution

authors： Schmitz J,Ohme M,Zischler H

更新日期：2000-09-01 00:00:00

abstract：:Serotonin is a neurotransmitter that plays an important role in regulating behavior and personality in humans and other mammals. Polymorphisms in genes coding for the serotonin receptor subtype 1A (HTR1A), the serotonin transporter (SLC6A4), and the serotonin degrading enzyme monoamine oxidase A (MAOA) are associated ...

journal_title：Molecular biology and evolution

authors： Staes N,Sherwood CC,Freeman H,Brosnan SF,Schapiro SJ,Hopkins WD,Bradley BJ

更新日期：2019-07-01 00:00:00

abstract：:Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be hi...

journal_title：Molecular biology and evolution

authors： Guisinger MM,Kuehl JV,Boore JL,Jansen RK

更新日期：2011-01-01 00:00:00

abstract：:In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also exp...

journal_title：Molecular biology and evolution

authors： Ho AT,Hurst LD

更新日期：2021-01-04 00:00:00

abstract：:Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny a...

journal_title：Molecular biology and evolution

authors： Mugridge NB,Morrison DA,Jäkel T,Heckeroth AR,Tenter AM,Johnson AM

更新日期：2000-12-01 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：: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：:In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1995-01-01 00:00:00

abstract：:Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...

journal_title：Molecular biology and evolution

authors： Smukowski Heil CS,DeSevo CG,Pai DA,Tucker CM,Hoang ML,Dunham MJ

更新日期：2017-07-01 00:00:00

abstract：:A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogen...

journal_title：Molecular biology and evolution

authors： Lipson M,Reich D

更新日期：2017-04-01 00:00:00

abstract：:The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, e...

journal_title：Molecular biology and evolution

authors： Zhan Z,Ding Y,Zhao R,Zhang Y,Yu H,Zhou Q,Yang S,Xiang H,Wang W

更新日期：2012-05-01 00:00:00

abstract：:There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult p...

journal_title：Molecular biology and evolution

authors： Shavit L,Penny D,Hendy MD,Holland BR

更新日期：2007-11-01 00:00:00

abstract：:We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative...

journal_title：Molecular biology and evolution

authors： Plotkin JB,Dushoff J,Desai MM,Fraser HB

更新日期：2006-08-01 00:00:00

abstract：:Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Caenorhabditis nematodes-...

journal_title：Molecular biology and evolution

authors： Irimia M,Rukov JL,Penny D,Garcia-Fernandez J,Vinther J,Roy SW

更新日期：2008-02-01 00:00:00

abstract：:Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the result...

journal_title：Molecular biology and evolution

authors： Wayne RK,Van Valkenburgh B,O'Brien SJ

更新日期：1991-05-01 00:00:00

abstract：:Signaling peptides enable communication between cells, both within and between individuals, and are therefore key to the control of complex physiological and behavioral responses. Since their small sizes prevent direct transmission to secretory pathways, these peptides are often produced as part of a larger polyprotei...

journal_title：Molecular biology and evolution

authors： Rogers DW,McConnell E,Miller EL,Greig D

更新日期：2017-12-01 00:00:00

abstract：:The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and...

journal_title：Molecular biology and evolution

authors： Langdon QK,Peris D,Kyle B,Hittinger CT

更新日期：2018-11-01 00:00:00

abstract：:Malaria is a deadly disease that causes nearly one million deaths each year. To develop methods to control and eradicate malaria, it is important to understand the genetic basis of Plasmodium falciparum adaptations to antimalarial treatments and the human immune system while taking into account its demographic history...

journal_title：Molecular biology and evolution

authors： Chang HH,Park DJ,Galinsky KJ,Schaffner SF,Ndiaye D,Ndir O,Mboup S,Wiegand RC,Volkman SK,Sabeti PC,Wirth DF,Neafsey DE,Hartl DL

更新日期：2012-11-01 00:00:00

abstract：:The minimum-evolution (ME) method of phylogenetic inference is based on the assumption that the tree with the smallest sum of branch length estimates is most likely to be the true one. In the past this assumption has been used without mathematical proof. Here we present the theoretical basis of this method by showing ...

journal_title：Molecular biology and evolution

authors： Rzhetsky A,Nei M

更新日期：1993-09-01 00:00:00

abstract：:zeta-Crystallin is a novel nicotinamide adenine dinucleotide phosphate:quinone reductase, present at enzymatic levels in various tissues of different species, which is highly expressed in the lens of some hystricomorph rodents and camelids. We report here the complementary DNA (cDNA) cloning of zeta-crystallin from li...

journal_title：Molecular biology and evolution

authors： Gonzalez P,Hernández-Calzadilla C,Rao PV,Rodriguez IR,Zigler JS Jr,Borrás T

更新日期：1994-03-01 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：:Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...

journal_title：Molecular biology and evolution

authors： Itoh T,Takemoto K,Mori H,Gojobori T

更新日期：1999-03-01 00:00:00

abstract：:This paper concludes that the statistical properties of protein evolution are compatible with a particular model of evolution by natural selection. The argument begins with a statistical description of the molecular clock based on a Poisson process with a randomly varying tick rate. If the time scale of the change of ...

journal_title：Molecular biology and evolution

authors： Gillespie JH

更新日期：1986-03-01 00:00:00

abstract：:Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...

journal_title：Molecular biology and evolution

authors： diCenzo GC,Mengoni A,Perrin E

更新日期：2019-03-01 00:00:00