Abstract:
:The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Nei M,Tajima F,Tateno Ydoi
10.1007/BF02300753subject
Has Abstractpub_date
1983-01-01 00:00:00pages
153-70issue
2eissn
0022-2844issn
1432-1432journal_volume
19pub_type
杂志文章abstract::Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endospe...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9013-0
更新日期:2007-09-01 00:00:00
abstract::The 5S ribosomal RNA sequences have been determined for the rhodoplast of the red alga Porphyra umbilicalis and the chloroplast of the conifer Juniperus media. The 5S RNA sequence of the Vicia faba chloroplast is corrected with respect to a previous report. A survey of the known sequences and secondary structures of 5...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02138372
更新日期:1988-01-01 00:00:00
abstract::The frequencies of ATG triplets in the genomes of various species were systematically analyzed, and the frequency of ATG triplets was significantly low around start codons in both prokaryotic and eukaryotic genomes. In eukaryotes, however, the frequency decrease before the start codon is much more evident than that af...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006460
更新日期:1999-02-01 00:00:00
abstract::A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006448
更新日期:1999-01-01 00:00:00
abstract::Proteins are commonly used as molecular targets against pathogens such as viruses and bacteria. However, pathogens can evolve rapidly permitting their populations to increase in protein diversity over time and thus escape to the activity of a molecular therapy. Subsequently, in order to design more durable and robust ...
journal_title:Journal of molecular evolution
pub_type: 信件
doi:10.1007/s00239-020-09953-1
更新日期:2020-08-01 00:00:00
abstract::In mammals, chicken-type (c-type) lysozymes are part of the innate immune system, killing bacteria by degrading peptidoglycan in their cell walls. Many of the studies on the evolution of c-type lysozymes have focused on its new digestive function, including the duplicated stomach lysozymes in ruminants. Similarly, in ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-019-09910-7
更新日期:2019-12-01 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::The major histocompatibility complex (MHC) consists of polymorphic frozen blocks (PFBs) that are linked to form megabase haplotypes. These blocks consist of polymorphic sequences and define regions where recombination appears to be inhibited. We have been able to show, using a highly polymorphic sequence centromeric o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006194
更新日期:1997-07-01 00:00:00
abstract::Phospholipid vesicles (liposomes) were subjected to dehydration-hydration cycles in the presence of 6-carboxyfluorescein or salmon sperm DNA. We found that the vesicles fused into multilamellar structures during dehydration with solutes trapped between the lamellae. Upon rehydration the lamellae swelled and formed lar...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01733047
更新日期:1982-01-01 00:00:00
abstract::In the present study we focus on the nucleotide and the inferred amino acid variation occurring in humans and other primate species for mitochondrial NAD(+)-dependent succinic semialdehyde dehydrogenase, a gene recently supposed to contribute to cognitive performance in humans. We determined 2527 bp of coding, introni...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0154-8
更新日期:2006-07-01 00:00:00
abstract::The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligo...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-017-9796-6
更新日期:2017-06-01 00:00:00
abstract::Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010240
更新日期:2001-10-01 00:00:00
abstract::The organization of histone gene clusters of the duck Cairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. The...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02102477
更新日期:1989-03-01 00:00:00
abstract::Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of th...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160152
更新日期:1994-09-01 00:00:00
abstract::We constructed a cDNA library for the beetle, Tribolium castaneum. This library was screened using a cloned amylase gene from Drosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02099856
更新日期:1987-01-01 00:00:00
abstract::The study of genetic evolution within the context of adaptive radiations offers insights to genes and selection pressures that result in rapid morphological change. Cichlid fishes are very species-rich and variable in coloration, behavior, and morphology, and so provide a classical model system for studying the geneti...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-011-9452-5
更新日期:2011-08-01 00:00:00
abstract::Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have re...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100041
更新日期:1987-01-01 00:00:00
abstract::Previous reports indicate that in laboratory strains of mice, males are distinct from females in possession of repetitive DNA, notably devoid of Eco RI and Hae III sites and rich in the simple tetranucleotides GATA/GACA. We report here that such sequences originated in an ancestor common to laboratory mice, Mus hortul...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100013
更新日期:1987-01-01 00:00:00
abstract::Simple sequence repeats (SSRs) in DNA sequences are tandem iterations of a single nucleotide or a short oligonucleotide. SSRs are subject to slipped-strand mutations and a common source of phase variation in bacteria and antigenic variation in pathogens. Significantly long SSRs are generally rare in prokaryotic genome...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9166-5
更新日期:2008-11-01 00:00:00
abstract::The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9146-9
更新日期:2008-10-01 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::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::Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color d...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:10.1007/s00239-019-09902-7
更新日期:2020-01-01 00:00:00
abstract::Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e., most of the codons in the genome) and presumed small selection coefficients, codon usage is an exce...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-2459-9
更新日期:2003-07-01 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::The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9068-6
更新日期:2008-03-01 00:00:00
abstract::In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed a significant correlation between duplication and conservation. Sys...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006580
更新日期:1999-11-01 00:00:00
abstract::A reaction which oligomerizes nucleotides under possible prebiotic conditions has been characterized. Nucleoside monophosphate in the presence of cyanamide at acid pH condenses to form dithymideine pyrophosphate and phosphodiester bonded compounds. Imidazole compounds and activated precursors such as nucleoside tripho...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732356
更新日期:1975-11-04 00:00:00
abstract::DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173183
更新日期:1995-12-01 00:00:00
abstract::Variation in structure among primate hemoglobins is associated with variation in function. This supports the hypothesis that most substitutions observed among homologous proteins in different species have been fixed by natural selection because they contribute to the fitness of the genotype. It does not support the co...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01653958
更新日期:1972-12-01 00:00:00