The Genotype-Phenotype Relationships in the Light of Natural Selection.

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：: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：:The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, wi...

journal_title：Molecular biology and evolution

authors： Strasburg JL,Kane NC,Raduski AR,Bonin A,Michelmore R,Rieseberg LH

更新日期：2011-05-01 00:00:00

abstract：:Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...

journal_title：Molecular biology and evolution

authors： Lischer HE,Excoffier L,Heckel G

更新日期：2014-04-01 00:00:00

abstract：:Comparisons between human and rodent DNA sequences are widely used for the identification of regulatory regions (phylogenetic footprinting), and the importance of such intergenomic comparisons for promoter annotation is expanding. The efficacy of such comparisons for the identification of functional regulatory element...

journal_title：Molecular biology and evolution

authors： Dermitzakis ET,Clark AG

更新日期：2002-07-01 00:00:00

abstract：:Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...

journal_title：Molecular biology and evolution

authors： Librado P,Orlando L

更新日期：2018-06-01 00:00:00

abstract：:The acquisition of photosynthesis by eukaryotic cells through enslavement of a cyanobacterium represents one of the most remarkable turning points in the history of life on Earth. In addition to endosymbiotic gene transfer, the acquisition of a protein import apparatus and the coordination of gene expression between h...

journal_title：Molecular biology and evolution

authors： Colleoni C,Linka M,Deschamps P,Handford MG,Dupree P,Weber AP,Ball SG

更新日期：2010-12-01 00:00:00

abstract：:Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...

journal_title：Molecular biology and evolution

authors： Cardona T,Murray JW,Rutherford AW

更新日期：2015-05-01 00:00:00

abstract：:Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellula...

journal_title：Molecular biology and evolution

authors： DeBarry JD,Kissinger JC

更新日期：2011-10-01 00:00:00

abstract：:We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...

journal_title：Molecular biology and evolution

authors： Kivisild T,Tolk HV,Parik J,Wang Y,Papiha SS,Bandelt HJ,Villems R

更新日期：2002-10-01 00:00:00

abstract：:DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated non...

journal_title：Molecular biology and evolution

authors： Chan YW,Mohr R,Millard AD,Holmes AB,Larkum AW,Whitworth AL,Mann NH,Scanlan DJ,Hess WR,Clokie MR

更新日期：2011-08-01 00:00:00

abstract：:Assessing the influence of three-dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies ha...

journal_title：Molecular biology and evolution

authors： Kleinman CL,Rodrigue N,Lartillot N,Philippe H

更新日期：2010-07-01 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：:As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed,...

journal_title：Molecular biology and evolution

authors： Martin MD,Vieira FG,Ho SY,Wales N,Schubert M,Seguin-Orlando A,Ristaino JB,Gilbert MT

更新日期：2016-02-01 00:00:00

abstract：:This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibli...

journal_title：Molecular biology and evolution

authors： Daniels SB,Chovnick A,Boussy IA

更新日期：1990-11-01 00:00:00

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：:The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...

journal_title：Molecular biology and evolution

authors： Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

更新日期：2010-03-01 00:00:00

abstract：:Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishabl...

journal_title：Molecular biology and evolution

authors： Venkatesh B,Ravi V,Lee AP,Warren WC,Brenner S

更新日期：2013-01-01 00:00:00

abstract：:Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of exta...

journal_title：Molecular biology and evolution

authors： Mitchell KJ,Pratt RC,Watson LN,Gibb GC,Llamas B,Kasper M,Edson J,Hopwood B,Male D,Armstrong KN,Meyer M,Hofreiter M,Austin J,Donnellan SC,Lee MS,Phillips MJ,Cooper A

更新日期：2014-09-01 00:00:00

abstract：:The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such...

journal_title：Molecular biology and evolution

authors： Wróbel B,Torres-Puente M,Jiménez N,Bracho MA,García-Robles I,Moya A,González-Candelas F

更新日期：2006-06-01 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：:Protein interactions are central to most biological processes. We investigated the dynamics of emergence of the protein interaction network of Saccharomyces cerevisiae by mapping origins of proteins on an evolutionary tree. We demonstrate that evolutionary periods are characterized by distinct connectivity levels of t...

journal_title：Molecular biology and evolution

authors： Kunin V,Pereira-Leal JB,Ouzounis CA

更新日期：2004-07-01 00:00:00

abstract：:Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely base...

journal_title：Molecular biology and evolution

authors： Stalder T,Cornwell B,Lacroix J,Kohler B,Dixon S,Yano H,Kerr B,Forney LJ,Top EM

更新日期：2020-06-01 00:00:00

abstract：:The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. T...

journal_title：Molecular biology and evolution

authors： Wilbur WJ

更新日期：1985-09-01 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：:Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we c...

journal_title：Molecular biology and evolution

authors： Choi YJ,Fontenla S,Fischer PU,Le TH,Costábile A,Blair D,Brindley PJ,Tort JF,Cabada MM,Mitreva M

更新日期：2020-01-01 00:00:00

abstract：:Pax genes play key regulatory roles in embryonic and sensory organ development in metazoans but their evolution and ancestral functions remain widely unresolved. We have isolated a Pax gene from Placozoa, beside Porifera the only metazoan phylum that completely lacks nerve and sensory cells or organs. These simplest k...

journal_title：Molecular biology and evolution

authors： Hadrys T,DeSalle R,Sagasser S,Fischer N,Schierwater B

更新日期：2005-07-01 00:00:00

abstract：:Significance levels obtained from a chi 2 contingency test are suspect when sample sizes are small. Traditionally this has meant that data must be combined. However, such an approach may obscure heterogeneity and hence potentially reduce the power of the statistical test. In this paper, we present a Monte Carlo soluti...

journal_title：Molecular biology and evolution

authors： Roff DA,Bentzen P

更新日期：1989-09-01 00:00:00

abstract：:The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequen...

journal_title：Molecular biology and evolution

authors： Bolívar P,Mugal CF,Rossi M,Nater A,Wang M,Dutoit L,Ellegren H

更新日期：2018-10-01 00:00:00

abstract：:Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spe...

journal_title：Molecular biology and evolution

authors： Haasl RJ,Payseur BA

更新日期：2010-12-01 00:00:00