Evidence of positively selected sites in mammalian alpha-defensins.

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：:The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a phylogenetic marker for studying eukaryotic evolution. However, a disturbing problem, the artifactual polyphyly of ciliates, is always observed. It has been suggested that the addition of new sequences will help to circumvent this problem. Thus...

journal_title：Molecular biology and evolution

authors： Moreira D,Le Guyader H,Philippe H

更新日期：1999-02-01 00:00:00

abstract：:Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...

journal_title：Molecular biology and evolution

authors： Nicolaisen LE,Desai MM

更新日期：2012-11-01 00:00:00

abstract：:Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....

journal_title：Molecular biology and evolution

authors： Leino MW,Hagenblad J

更新日期：2010-04-01 00:00:00

abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

journal_title：Molecular biology and evolution

authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

更新日期：2003-11-01 00:00:00

abstract：:Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the n...

journal_title：Molecular biology and evolution

authors： Stern DB,Crandall KA

更新日期：2018-08-01 00:00:00

abstract：:From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoid...

journal_title：Molecular biology and evolution

authors： De Giorgi C,Lanave C,Musci MD,Saccone C

更新日期：1991-07-01 00:00:00

abstract：:For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load ...

journal_title：Molecular biology and evolution

authors： Renaut S,Rieseberg LH

更新日期：2015-09-01 00:00:00

abstract：:Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...

journal_title：Molecular biology and evolution

authors： Chen D,Cremona MA,Qi Z,Mitra RD,Chiaromonte F,Makova KD

更新日期：2020-12-16 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：:We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produc...

journal_title：Molecular biology and evolution

authors： Bryant D,Moulton V

更新日期：2004-02-01 00:00:00

abstract：:Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid spe...

journal_title：Molecular biology and evolution

authors： Wang J,Dong S,Yang L,Harris A,Schneider H,Kang M

更新日期：2020-09-01 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：:Sequence variation among 10 alleles of the alcohol dehydrogenase (Adh) gene of the Hawaiian drosophilid D. mimica was analyzed with reference to the evolutionary history of the Hawaiian subgroup as well as to levels and patterns of polymorphism of the Adh gene in continental drosophilid species. The Adh gene of D. mim...

journal_title：Molecular biology and evolution

authors： Ayala FJ,Campbell CD,Selander RK

更新日期：1996-12-01 00:00:00

abstract：:Full-length L1 elements have been shown to possess, at their 5' end, tandem repeats called "A" or "F" types. By sequencing the 5' region of two large L1 copies that did not hybridize to A or F probes, we have identified a new sequence that is found at the 5' end of many L1 elements and that we call "V." The element ch...

journal_title：Molecular biology and evolution

authors： Jubier-Maurin V,Cuny G,Laurent AM,Paquereau L,Roizes G

更新日期：1992-01-01 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：:The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the famil...

journal_title：Molecular biology and evolution

authors： Opazo JC,Hoffmann FG,Natarajan C,Witt CC,Berenbrink M,Storz JF

更新日期：2015-04-01 00:00:00

abstract：:We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...

journal_title：Molecular biology and evolution

authors： Katoh K,Standley DM

更新日期：2013-04-01 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：:We have investigated intron evolution in the compact genomes of 2 closely related species of pufferfishes, Fugu rubripes and Tetraodon nigroviridis, that diverged about 32 million years ago (MYA). Analysis of 148,028 aligned intron positions in 13,547 gene pairs using human as an outgroup identified 57 and 24 intron l...

journal_title：Molecular biology and evolution

authors： Loh YH,Brenner S,Venkatesh B

更新日期：2008-03-01 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：:Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental ad...

journal_title：Molecular biology and evolution

authors： Mychaleckyj JC,Havt A,Nayak U,Pinkerton R,Farber E,Concannon P,Lima AA,Guerrant RL

更新日期：2017-03-01 00:00:00

abstract：:Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these ch...

journal_title：Molecular biology and evolution

authors： Lawrence JG,Dykhuizen DE,DuBose RF,Hartl DL

更新日期：1989-01-01 00:00:00

abstract：:Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We pre...

journal_title：Molecular biology and evolution

authors： Murrell B,Moola S,Mabona A,Weighill T,Sheward D,Kosakovsky Pond SL,Scheffler K

更新日期：2013-05-01 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：:The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to select...

journal_title：Molecular biology and evolution

authors： Haasl RJ,Payseur BA

更新日期：2013-02-01 00:00:00

abstract：:Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...

journal_title：Molecular biology and evolution

authors： Hirsh AE,Fraser HB,Wall DP

更新日期：2005-01-01 00:00:00

abstract：:Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...

journal_title：Molecular biology and evolution

authors： Vieira C,Lepetit D,Dumont S,Biémont C

更新日期：1999-09-01 00:00:00

abstract：:The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information con...

journal_title：Molecular biology and evolution

authors： Misof B,Rickert AM,Buckley TR,Fleck G,Sauer KP

更新日期：2001-01-01 00:00:00

abstract：:Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...

journal_title：Molecular biology and evolution

authors： Rajan V

更新日期：2013-03-01 00:00:00