Abstract：
:The evolutionary relationships of four eukaryotic kingdoms--Animalia, Plantae, Fungi, and Protista--remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants is lacking, and a preferred branching order of these and other eukaryotic lineages is still controversial even though molecular sequences from diverse eukaryotic taxa have been analyzed. We report a statistical analysis of 214 sequences of nuclear small-subunit ribosomal RNA (srRNA) gene undertaken to clarify these evolutionary relationships. We have considered the variability of substitution rates and the nonindependence of nucleotide substitution across sites in the srRNA gene in testing alternative hypotheses regarding the branching patterns of eukaryote phylogeny. We find that the rates of evolution among sites in the srRNA sequences vary substantially and are approximately gamma distributed with size and shape parameter equal to 0.76. Our results suggest that (1) the animals and true fungi are indeed closer to each other than to any other "crown" group in the eukaryote tree, (2) red algae are the closest relatives of animals, true fungi, and green plants, and (3) the heterokonts and alveolates probably evolved prior to the divergence of red algae and animal-fungus-green-plant lineages. Furthermore, our analyses indicate that the branching order of the eukaryotic lineages that diverged prior to the evolution of alveolates may be generally difficult to resolve with the srRNA sequence data.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Kumar S,Rzhetsky Adoi
10.1007/BF02198844subject
Has Abstractpub_date
1996-02-01 00:00:00pages
183-93issue
2eissn
0022-2844issn
1432-1432journal_volume
42pub_type
杂志文章abstract：:Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting that the different actins may have a functional significance. We ask her...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006125
更新日期：1997-01-01 00:00:00
abstract：:To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006277
更新日期：1998-01-01 00:00:00
abstract：:This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160324
更新日期：1995-10-01 00:00:00
abstract：:Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyano-bacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are "primitive" plast...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00170674
更新日期：1995-08-01 00:00:00
abstract：:Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should provide insights into the origin of genetic complexity in eukaryotes. W...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010074
更新日期：2000-08-01 00:00:00
abstract：:The genome of Glycine max (L.) Merr. cv. "Dare" contains a chlorophyll a/b binding (Cab) protein gene family consisting of 10 genes. The primary structures of two linked Cab genes (Cab 4 and Cab 5) were determined. A comparison of the nucleic acid and predicted amino acid sequences of Cab 4 and Cab 5 revealed a high d...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100210
更新日期：1989-09-01 00:00:00
abstract：:We present sequences of five novel RNase A superfamily ribonuclease genes of the bullfrog, Rana catesbeiana. All five genes encode ribonucleases that are similar to Onconase, a cytotoxic ribonuclease isolated from oocytes of R. pipiens. With amino acid sequence data from 14 ribonucleases from three Rana species (R. ca...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010188
更新日期：2001-07-01 00:00:00
abstract：:Molecular characteristics, especially 18S rDNA sequences, may be of great value for the study of bivalve evolution and its numerous morphological convergencies once the reliability of these data can be evaluated. The analysis of 11 published complete molluscan sequences and two new ones, Arca noae and Atrina pectinata...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02352300
更新日期：1996-07-01 00:00:00
abstract：:Pax genes encode transcription factors critical for metazoan development. Large-scale gene duplication with subsequent gene losses during vertebrate evolution has resulted in two human genes for each of the Pax1/9, Pax3/7, and Pax4/6 subfamilies and three for the Pax2/5/8 subfamily, compared to one each in the cephalo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9113-5
更新日期：2008-06-01 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：: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：:Three measures of sequence dissimilarity have been compared on a computer-generated model system in which substitutions in random sequences were made at randomly selected sites and the replacement character was chosen at random from the set of characters different from the original occupant of the site. The three meas...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02602925
更新日期：1989-12-01 00:00:00
abstract：:The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9456-1
更新日期：2011-08-01 00:00:00
abstract：:Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) l...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-016-9740-1
更新日期：2016-05-01 00:00:00
abstract：:We have investigated the evolvability of an insoluble random polypeptide, RP3-34, to a soluble form through iterative mutation and selection with the aid of the green fluorescent protein (GFP) folding reporter. To assess the solubility of the polypeptides in the selected clones of each generation, the polypeptide gene...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2542-2
更新日期：2004-02-01 00:00:00
abstract：:One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authenticat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0259-8
更新日期：2007-07-01 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：: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
abstract：:While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9149-6
更新日期：2008-12-01 00:00:00
abstract：:Exon-shuffling is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, its role in the creation of proteins in the ancestor of prokaryotes and eukaryotes is still debatable. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exon...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0318-y
更新日期：2005-09-01 00:00:00
abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9139-8
更新日期：2008-09-01 00:00:00
abstract：:All modern mammals contain a distinctive, highly repeated (> or = 50,000 members) family of long interspersed repeated DNA called the L1 (LINE 1) family. While the modern L1 families were derived from a common ancestor that predated the mammalian radiation approximately 80 million years ago, most of the members of the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02407302
更新日期：1993-01-01 00:00:00
abstract：:Nucleotide sequences for the kappa-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine kappa-...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173165
更新日期：1995-12-01 00:00:00
abstract：:The sequences of the adenylate kinase gene (adk) and the RecA gene (recA) were determined from the same isolates of Neisseria gonorrhoeae, N. meningitidis, N. lactamica, N. polysaccharea, N. cinerea, N. mucosa, N. pharyngis var. flava, N. flavescens, and N. animalis. The patterns of sequence divergence observed at adk...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02202111
更新日期：1996-12-01 00:00:00
abstract：:The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102804
更新日期：1991-12-01 00:00:00
abstract：:From the cloned mitochondrial DNAs (mtDNAs) isolated from two bisexual species, one Mediterranean, Artemia salina, and one American, Artemia franciscana, and two parthenogenetic (diploid and tetraploid) strains of Artemia parthenogenetica collected in Spain, physical maps have been constructed and compared. They are e...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00166162
更新日期：1994-02-01 00:00:00
abstract：:Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream pos...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006541
更新日期：1999-08-01 00:00:00
abstract：:Oxygen-free aqueous solutions of NH4CN (0.1 M, pH9) were exposed to gamma rays from a 60Co source, the mixture of nonvolatile products was fractionated, and the fractions were analyzed. The procedures were chosen to make effective investigations of radiolytic products, and to minimize the contributions of chemical cha...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732951
更新日期：1980-07-01 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：:The nucleotide sequences of 5S rRNAs from three protozoa, Bresslaua vorax, Euplotes woodruffi and Chlamydomonas sp. have been determined and aligned together with the sequences of 12 protozoa species including unicellular green algae already reported by the authors and others. Using this alignment, a phylogenic tree o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102316
更新日期：1983-01-01 00:00:00
