Abstract：
:The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the lenghtof any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Foulds LR,Hendy MD,Penny Ddoi
10.1007/BF01732868subject
Has Abstractpub_date
1979-07-18 00:00:00pages
127-49issue
2eissn
0022-2844issn
1432-1432journal_volume
13pub_type
杂志文章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 a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9172-7
更新日期：2008-11-01 00:00:00
abstract：:The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006366
更新日期：1998-07-01 00:00:00
abstract：:Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-012-9491-6
更新日期：2012-04-01 00:00:00
abstract：:Universal scale of the sequence conservation has been recently introduced based on omnipresence of the protein sequence motifs across species. A large spectrum of short sequences, up to eight residues has been found to reside in all or almost all prokaryotic organisms. By this discovery a principally novel quantitativ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0190-4
更新日期：2006-11-01 00:00:00
abstract：:Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we in...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0020-0
更新日期：2005-03-01 00:00:00
abstract：:Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0198-4
更新日期：2007-06-01 00:00:00
abstract：:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20-24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computatio...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-013-9563-2
更新日期：2013-06-01 00:00:00
abstract：:TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2352-y
更新日期：2002-11-01 00:00:00
abstract：:Synechococcus and Prochlorococcus have made great contributions to earth's photosynthetic biomass. ATP-binding cassette (ABC) protein systems have been characterized to play important roles in various physiological functions, including carbon fixation, phosphate assimilation, and vitamin B(12) metabolism. In this stud...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9259-9
更新日期：2009-10-01 00:00:00
abstract：:Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was "relocated" from the ancestral locus to the derived location. Gene...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9849-5
更新日期：2018-07-01 00:00:00
abstract：:Analysis of cDNAs from Macrovipera lebetina transmediterranea (Mlt) and Echis ocellatus (Eo) venom gland libraries encoding disintegrins argued strongly for a common ancestry of the messengers of short disintegrins and those for precursors of dimeric disintegrin chains. We now report the sequence analysis of disintegr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0161-4
更新日期：2007-02-01 00:00:00
abstract：:The symbiotic protists of the lower termite have been regarded as a model of early-branched eukaryotes because of their simple cellular systems and morphological features. However, cultivation of these symbiotic protists is very difficult. For this reason, these interesting protists have not been well characterized in...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010129
更新日期：2001-01-01 00:00:00
abstract：:Marine mussels of the genus Mytilus have two types of mitochondrial DNA with separate paternal and maternal inheritance. Females are homoplasmic for an F genome that is transmitted to all offspring, whereas males are heteroplasmic for this F genome and for a highly diverged (> 20%) M genome that is transmitted only to...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-0019-y
更新日期：2003-01-01 00:00:00
abstract：:The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist bet...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102651
更新日期：1991-06-01 00:00:00
abstract：:Long amino acid repeats are often observed in eukaryotic proteins. In humans, several neurological disorders are caused by proteins containing abnormally long polyglutamines. However, no systematic analysis has attempted to investigate the relationship between reiterations of particular amino acids and protein functio...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006601
更新日期：1999-12-01 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：: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 ev...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02198844
更新日期：1996-02-01 00:00:00
abstract：:The kinetics of synonymous codon change and species divergence is described in a matrix formalism that is equally applicable to all levels of codon degeneracy and all levels of codon or nucleotide bias. Based on the formalism it is possible to calculate the sum of all synonymous substitution rate constants from the ob...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00186546
更新日期：1995-09-01 00:00:00
abstract：:The simple codominant expression of the alleles at the self-incompatibility locus ( S) of Solanaceae and their extraordinary spectrum of sequence diversity present an ideal case for understanding the molecular forces that shape the sequence polymorphism of genes involved in recognition reactions. Here, with unpreceden...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0080-3
更新日期：2002-06-01 00:00:00
abstract：:Androgen effects mediated by the androgen receptor (AR) are essential for male reproductive development and virilization. Comparison of AR DNA coding sequence from five primate species, Homo sapiens (human), Pan troglodytes (chimpanzee), Papio hamadryas (baboon), Macaca fascicularis (macaque), and Eulemur fulvus colla...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006391
更新日期：1998-09-01 00:00:00
abstract：:The complete mitochondrial DNA (mtDNA) sequence of the brine shrimp Artemia franciscana has been determined. It extends the present knowledge of mitochondrial genomes to the crustacean class and supplies molecular markers for future comparative studies in this large branch of the arthropod phylum. Artemia mtDNA is 15,...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160272
更新日期：1994-10-01 00:00:00
abstract：:Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010148
更新日期：2001-02-01 00:00:00
abstract：:Previous observations have indicated that Drosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) of Drosophila simulans (Dsim) DNA that fails to hybridize t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099998
更新日期：1990-03-01 00:00:00
abstract：:Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiment...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0250-9
更新日期：2006-12-01 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：: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：:The mitochondrial genome of yeast (S. cerevisiae or S. carlsbergensis) appears to be formed by 60-70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01796120
更新日期：1976-12-31 00:00:00
abstract：:In this paper we present an iterative character weighting method for the construction of phyletic trees. An initial tree is used to calculate the character weights, which are the number of mutations normalized so that the possible range is corrected for. The weights obtained are used to adjust the tree; this process i...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101127
更新日期：1990-10-01 00:00:00
abstract：:Frugivorous and nectarivorous bats rely largely on hepatic glycogenesis and glycogenolysis for postprandial blood glucose disposal and maintenance of glucose homeostasis during short time starvation, respectively. The glycogen synthase 2 encoded by the Gys2 gene plays a critical role in liver glycogen synthesis. To te...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9600-1
更新日期：2014-01-01 00:00:00
abstract：:Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010087
更新日期：2000-09-01 00:00:00
