Abstract：
:Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of amino acid substitutions in the plant gene eIF4E to evaluate the performance of these methods in detecting site-specific positive selection. We documented for the first time a molecular signature of positive selection within a recessive resistance gene in plants. We then used two statistical platforms, Phylogenetic Analysis Using Maximum Likelihood and Hypothesis Testing Using Phylogenies (HyPhy), to look for site-specific positive selection. Their relative power and accuracy are assessed by comparing the sites they identify as being positively selected with those of resistance-determining amino acids. Our results indicate that although both methods are surprisingly accurate in their identification of resistance sites, HyPhy appears to more accurately identify biologically significant amino acids using our data set.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Cavatorta JR,Savage AE,Yeam I,Gray SM,Jahn MMdoi
10.1007/s00239-008-9172-7subject
Has Abstractpub_date
2008-11-01 00:00:00pages
551-9issue
5eissn
0022-2844issn
1432-1432journal_volume
67pub_type
杂志文章abstract：:Phylogenetic relationships among eight species of the Drosophila buzzatii species complex (D. mulleri subgroup; D. repleta species group) and D. hamatofila were determined by sequencing the mitochondrial cytochrome oxidase subunit I, II, and III genes. The species examined included members of the martensis cluster (D....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173155
更新日期：1995-12-01 00:00:00
abstract：:Studies so far have correlated the variation in the composition of snake venoms with the target prey population and snake's diet. Here we present the first example of an alternative evolutionary link between venom composition and dietary adaptation of snakes. We describe a dinucleotide deletion in the only three finge...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0138-0
更新日期：2005-01-01 00:00:00
abstract：:By a chromosome walking strategy the DNA region from Methanococcus vannielii flanking the genes for protein synthesis elongation factor (EF) 1 alpha and EF-2 was cloned and sequenced. A gene organization of 5' - beta' - open reading frame (ORF) 1 - ORF2 - S12 - S7 - EF-2 - EF-1 alpha - S10 - ORF3 - ORF4 - 3' was found...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02106178
更新日期：1989-07-01 00:00:00
abstract：:Amino acid substitution models represent substitution rates among amino acids during the evolution. The models play an important role in analyzing protein sequences, especially inferring phylogenies. The rapid evolution of flaviviruses is expanding the threat in public health. A number of models have been estimated fo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-020-09943-3
更新日期：2020-07-01 00:00:00
abstract：:We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estim...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0087-9
更新日期：2002-07-01 00:00:00
abstract：:Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2656-1
更新日期：2004-11-01 00:00:00
abstract：:The alpha-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show 37-66% identity with one an...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02338832
更新日期：1996-09-01 00:00:00
abstract：:Evaporation of a solution of thymidine plus either the exo or the endo diastereomer of uridine cyclic 2',3'-O, O-phosphorothioate (U greater than p(S) in 1,2-diaminoethane hydrochloride buffer gave the 2',5' and 3',5' isomers of (P-thio) uridylylthymidine (Up(S)dT) in a ratio of 1:2 with a combined yield of about 20%....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01731369
更新日期：1979-11-01 00:00:00
abstract：:The complete or partial sequences of 47 E. coli ribosomal proteins described in the literature have been examined by computerized search and matching programs. In contrast to results previously reported by other investigators, sequence homologies were uncovered among some of these ribosomal proteins that are well beyo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732666
更新日期：1980-05-01 00:00:00
abstract：:Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged g...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00178872
更新日期：1993-10-01 00:00:00
abstract：:Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during th...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0185-1
更新日期：2006-06-01 00:00:00
abstract：:Two families of high-cysteine chorion proteins in Bombyx mori are encoded in 15 tandemly arranged nonidentical gene pairs. It is assumed that this locus arose by duplication with subsequent sequence divergence. We have compared DNA sequences from two such neighboring pairs of genes in an attempt to understand the mann...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02104732
更新日期：1984-01-01 00:00:00
abstract：:A cDNA encoding a new member of the gene family of major royal jelly proteins (MRJPs) from the honeybee, Apis mellifera, was isolated and sequenced. Royal jelly (RJ) is a secretion of the cephalic glands of nurse bees. The origin and biological function of the protein component (12.5%, w/w) of RJ is unknown. We show t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006551
更新日期：1999-08-01 00:00:00
abstract：:Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006416
更新日期：1998-11-01 00:00:00
abstract：:In Trypanoplasma borelli, a representative of the Bodonina within the Kinetoplastida, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was detected in both the cytosol and glycosomes. This situation is similar to that previously found in Trypanosomatidae, belonging to a different Kinetoplastida suborder. In T...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00164030
更新日期：1995-04-01 00:00:00
abstract：:We recently sequenced the genome of the first subterrestrial metazoan, the nematode Halicephalobus mephisto. A central finding was a dramatic expansion of genes encoding avrRpt2 induced gene (AIG1), and 70 kDa heat shock (Hsp70) domains. While the role of Hsp70 in thermotolerance is well established, the contribution ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09900-9
更新日期：2019-12-01 00:00:00
abstract：:DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9441-8
更新日期：2011-04-01 00:00:00
abstract：:The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2624-9
更新日期：2004-08-01 00:00:00
abstract：:Two protein-coding regions (cytochrome b, ATPase 8, and part of ATPase 6) from mitochondrial DNA of Cottus kessleri, Cottocomephorus grewingki, and Cottocomephorus inermis--Baikalian endemic sculpins--were amplified via polymerase chain reaction, and sequenced. Two novel primers--L8352 (5'-TAAAGATTGGTGAC TCCCAACCACC) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163855
更新日期：1992-01-01 00:00:00
abstract：:Insertions and deletions of entire codons have recently been discovered as a mechanism by which B cells, in addition to conventional base substitution, evolve the antibodies produced by their immunoglobulin genes. These events frequently seem to involve repetitive sequence motifs in the antibody-encoding genes, and it...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0049-2
更新日期：2002-03-01 00:00:00
abstract：:We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Compar...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175814
更新日期：1995-11-01 00:00:00
abstract：:Two catalytic functions were required, minimally, for the appearance of DNA in evolution: a ribonucleotide reductase (RNR) and a reverse transcriptase (RT). If one accepts the explanatory strength of the RNA world model, it is clear that DNA molecules arose in the RNA world at some stage during the early evolution of ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006368
更新日期：1998-08-01 00:00:00
abstract：:Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subd...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2472-z
更新日期：2003-10-01 00:00:00
abstract：:Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of seq...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006427
更新日期：1998-12-01 00:00:00
abstract：:It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochrome c and cytochrome b5 chains (Argos and Rossmann 1979), it can be inf...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01731583
更新日期：1980-12-01 00:00:00
abstract：:Evidence from a number of studies indicates that protein folding is dictated not only by factors stabilizing the native state, but also by potentially independent factors that create folding pathways. How natural selection might cope simultaneously with two independent factors was addressed in this study within the fr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9465-0
更新日期：2011-10-01 00:00:00
abstract：:Antibody binding site are formed by six hypervariable regions or complementarity determining regions (CDRs). The CDRs, three from the heavy chain and three from the light chain, are known as hypervariable segments and provide a surface complementary to that of the epitope. In recent work it was found that the amino ac...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175497
更新日期：1994-01-01 00:00:00
abstract：:A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9829-9
更新日期：2018-02-01 00:00:00
abstract：:Multiple phospholipase A2 (PLA2) isoenzymes found in a single snake venom induce a variety of pharmacological effects. These multiple forms are formed by gene duplication and accelerated evolution of exons. We examined the amino acid sequences of 127 snake venom PLA2 enzymes and their homologues to study in which loca...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006450
更新日期：1999-02-01 00:00:00
abstract：:An emergent problem in the study of pathogen evolution is our ability to determine the extent to which their rapidly evolving genomes recombine. Such information is necessary and essential for locating pathogenicity loci using association studies, and it also directs future screening, therapeutic and vaccination strat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2543-1
更新日期：2004-03-01 00:00:00
