Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “rate of evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,117 records · Page 62Linked to original sources
PubMed1987

Human 27-kDa calbindin complementary DNA sequence. Evolutionary and functional implications.

Human 27-kDa calbindin cDNA clones were selected by antibody screening from lambda gt11 brain libraries. The sequence revealed an open reading frame coding for a protein of 261 amino acids, containing four active calcium-binding domains, and two modified domains that had presumably lost their calcium-binding capability. Comparison with chick and bovine calbindins showed that the protein was highly conserved in evolution (evolutionary rate: 0.3 x 10(-9) amino acid-1 year-1) and that active and inactive domains were equally conserved. From the data we postulate that calbindin has an important physiological function involving protein--protein interactions. Comparison of calcium-binding domains from various proteins suggested that all members of the troponin C superfamily derive from a common two-domained ancestor, but that duplications leading to calbindin and to the four-domained calcium-binding proteins took place independently on different branches of the evolutionary tree. Preliminary data showed that another calcium-binding protein, homologous to calbindin, is present in the brain and encoded by a different gene.

Amino Acid Sequence↗
PubMed1996

How rapidly does the human mitochondrial genome evolve?

The results of an empirical nucleotide-sequencing approach indicate that the evolution of the human mitochondrial noncoding D-loop is both more rapid and more complex than is revealed by standard phylogenetic approaches. The nucleotide sequence of the D-loop region of the mitochondrial genome was determined for 45 members of a large matrilineal Leber hereditary optic neuropathy pedigree. Two germ-line mutations have arisen in members of one branch of the family, thereby leading to triplasmic descendants with three mitochondrial genotypes. Segregation toward the homoplasmic state can occur within a single generation in some of these descendants, a result that suggests rapid fixation of mitochondrial mutations as a result of developmental bottlenecking. However, slow segregation was observed in other offspring, and therefore no single or simple pattern of segregation can be generalized from the available data. Evidence for rare mtDNA recombination within the D-loop was obtained for one family member. In addition to these germ-line mutations, a somatic mutation was found in the D-loop of one family member. When this genealogical approach was applied to the nucleotide sequences of mitochondrial coding regions, the results again indicated a very rapid rate of evolution.

Child↗
PubMed2003

Selective instability: maternal effort and the evolution of gene activation and deactivation rates.

We previously used simulations of gene expression to demonstrate that rapid activation and deactivation rates stabilized outcomes in stochastic systems. We hypothesized that transient single allele inactivation of an autosomal gene during gametogenesis or very early embryogenesis could have a selective advantage if it permits the functional sampling of each allele and precludes committing maternal effort to an embryo with a deleterious mutation. To test this hypothesis, we simulated the evolution of gene expression activation and deactivation rates and imposed two different selective pressures on the populations: (a). late selection against individuals that cannot maintain a threshold level of gene product that occurs after the investment of maternal effort (i.e., after birth); or (b). early selection: in addition to late selection, maintenance of the gene product above a threshold level was necessary for early development prior to commitment of maternal effort. We found that the opportunity to save reproductive effort from early selection caused the evolution of higher deactivation rates and lower activation rates than in the late selection condition. Thus, we predict that in the special case where early selection can save maternal investment in non-viable offspring, gene expression activation rates and deactivation rates might be selected to permit sampling of the product from each allele.

Evolution, Molecular↗
PubMed1989

Structure and expression of dog apolipoprotein A-I, E, and C-I mRNAs: implications for the evolution and functional constraints of apolipoprotein structure.

Dog apolipoprotein (apo) C-I, A-I, and E cDNA clones were identified in a dog liver cDNA library in lambda gt10 by hybridization to synthetic oligonucleotide probes with the corresponding human DNA sequences. The longest clone for each apolipoprotein was completely sequenced. The apoC-I cDNA sequence predicts a protein of 62 residue mature peptide preceded by a 26 amino acid signal peptide. The apoA-I cDNA sequence predicts a 242 residue mature peptide, a 6 residue pro-segment, and an 18 residue signal peptide. The apoE cDNA, which lacks the signal peptide region, predicts a mature peptide of 291 amino acid residues. Slot blot hybridization of total RNA isolated from various dog tissues to dog apoC-I, A-I, and E cDNA probes indicates that apoC-I mRNA is detectable in liver only, apoA-I mRNA is present in liver and small intestine, though the concentration in the latter tissue is only approximately 15% of that in the liver, and apoE mRNA is present in multiple tissues including liver, jejunum, urinary bladder, ileum, colon, brain, kidney, spleen, pancreas, and testis with relative concentrations (%) of 100, 17.5, 7.5, 6.9, 5.9, 5.5, 5.0, 3.3, 1.0, and 1.0, respectively. These tissue distributions indicate that nascent lipoprotein particles produced in the dog small intestine would contain apoA-I and apoE but not apoC-I. The widespread tissue distribution of apoE mRNA indicates that like other mammals, peripheral synthesis of apoE contributes significantly to the total apoE pool in dog. We next compared the cDNA sequences among different vertebrate species for apoC-I (human and dog), A-I (human, rat, dog, rabbit and chicken), and E (human, rat, dog and rabbit) and calculated the rate of nucleotide substitution for each gene. Our results indicate that apoC-I has evolved rather rapidly and that on the whole, apoA-I is more conservative than apoE, contradictory to an earlier suggestion. ApoA-I is also more conservative than a region (residues 4204-4536) at the carboxyl-terminal portion, but less conservative than a region (residues 595-979) at the amino-terminal portion of apoB-100. Some regions in each of the apolipoproteins studied are better conserved than others and the rate of evolution of individual regions seems to be related to the stringency of functional requirements. Finally, we estimate that the human apoC-I pseudogene arose more than 35 million years ago, becoming nonfunctional soon after its formation.

Amino Acid Sequence↗
PubMed2003

Evidence for co-evolution of gene order and recombination rate.

There is increasing evidence in eukaryotic genomes that gene order is not random, even allowing for tandem duplication. Notably, in numerous genomes, genes of similar expression tend to be clustered. Are there other reasons for clustering of functionally similar genes? If genes are linked to enable genetic, rather than physical clustering, then we also expect that clusters of certain genes might be associated with blocks of reduced recombination rates. Here we show that, in yeast, essential genes are highly clustered and this clustering is independent of clustering of co-expressed genes and of tandem duplications. Adjacent pairs of essential genes are preferentially conserved through evolution. Notably, we also find that clusters of essential genes are in regions of low recombination and that larger clusters have lower recombination rates. These results suggest that selection acts to modify both the fine-scale intragenomic variation in the recombination rate and the distribution of genes and provide evidence for co-evolution of gene order and recombination rate.

Biological Evolution↗
PubMed1987

Structure and expression of dog apolipoprotein C-II and C-III mRNAs. Implications for the evolution and functional constraints of apolipoprotein structure.

The complete cDNAs for canine apolipoprotein (apo) C-II and C-III have been cloned in the plasmid vector, pUC-18, and the phage vector, lambda gt11. With 32P-labeled nick-translated cDNAs as hybridization probes, apoC-II and apoC-III mRNAs were found to be expressed in canine liver, jejunum, ileum, colon, pancreas, spleen, ovary, and bladder at the following relative concentrations: 100, 35, 30, 10, 15, 5, 30, and 2% for apoC-II, and 100, 35, 15, 2, 20, 5, 30, and 5% for apoC-III. Neither mRNA was detected in canine brain, kidney, lung, muscle, oviduct, uterus, or testis. Both mRNAs are approximately 700 nucleotides in length. Complete sequence analysis revealed that apoC-II mRNA codes for a protein of 101 amino acid residues including 22 residues in the signal peptide and 79 residues in the mature peptide region. ApoC-III mRNA codes for a protein of 100 amino acid residues, including 20 in the signal peptide and 80 residues in the mature peptide region. It contains a single cysteine residue in position 54. Secondary structural analysis shows the presence of two regions each of amphipathic helix for apoC-II (residues 14-33 and 44-63) and apoC-III (residues 16-33 and 50-69). Computer analysis of the amphipathic helical regions demonstrates the importance of variation in the dihedral angles of the side chains in the charge microenvironment of the helices. Statistical analysis of sequence similarities between human apoC-II, apoC-III, apoA-II, apoA-I, apoE, and apoA-IV, and dog apoC-II and apoC-III, and rat apoC-III, apoA-II, apoA-I, apoE, and apoA-IV indicates that all these proteins have evolved rapidly, especially in the rat in which apoC-III has evolved at three times the rate in man and dog. Further, the shorter apolipoproteins, apoA-II, apoC-II, and a-poC-III, have evolved more rapidly than the longer ones, apoA-I, apoE, and apoA-IV. Some regions in the individual apolipoproteins are better conserved than others. The rate of evolution of individual regions seems to be related to the stringency of their functional requirements.

Amino Acid Sequence↗
PubMed2001

A phylogenetic framework for the aquaporin family in eukaryotes.

A comprehensive evolutionary analysis of aquaporins, a family of intrinsic membrane proteins that function as water channels, was conducted to establish groups of homology (i.e., to identify orthologues and paralogues) within the family and to gain insights into the functional constraints acting on the structure of the aquaporin molecule structure. Aquaporins are present in all living organisms, and therefore, they provide an excellent opportunity to further our understanding of the broader biological significance of molecular evolution by gene duplication followed by functional and structural specialization. Based on the resulting phylogeny, the 153 channel proteins analyzed were classified into six major paralogous groups: (1) GLPs, or glycerol-transporting channel proteins, which include mammalian AQP3, AQP7, and AQP9, several nematode paralogues, a yeast paralogue, and Escherichia coli GLP; (2) AQPs, or aquaporins, which include metazoan AQP0, AQP1, AQP2, AQP4, AQP5, and AQP6; (3) PIPs, or plasma membrane intrinsic proteins of plants, which include PIP1 and PIP2; (4) TIPs, or tonoplast intrinsic proteins of plants, which include alphaTIP, gammaTIP, and deltaTIP; (5) NODs, or nodulins of plants; and (6) AQP8s, or metazoan aquaporin 8 proteins. Of these groups, AQPs, PIPs, and TIPs cluster together. According to the results, the capacity to transport glycerol shown by several members of the family was acquired only early in the history of the family. The new phylogeny reveals that several water channel proteins are misclassified and require reassignment, whereas several previously undetermined ones can now be classified with confidence. The deduced phylogenetic framework was used to characterize the molecular features of water channel proteins. Three motifs are common to all family members: AEF (Ala-Glu-Phe), which is located in the N-terminal domain; and two NPA (Asp-Pro-Ala) boxes, which are located in the center and C-terminal domains, respectively. Other residues are found to be conserved within the major groups but not among them. Overall, the PIP subfamily showed the least variation. In general, no radical amino acid replacements affecting tertiary structure were identified, with the exception of Ala-->Ser in the TIP subfamily. Constancy of rates of evolution was demonstrated within the different paralogues but rejected among several of them (GLP and NOD).

Amino Acid Motifs↗
PubMed1976

Water deficit and ethylene evolution by young cotton bolls.

Ethylene evolution and abscission of young cotton (Gossypium hirsutum L.) bolls were shown, in earlier papers, to increase when plants were subjected to conditions that decreased photosynthesis and sugar content of bolls (dim light, long warm nights). Moisture stress also increased ethylene evolution by young bolls, but it did not decrease their concentrations of fructose, glucose, or sucrose. When detached bolls were incubated for 16 or 24 hours at high or low humidity, their rate of ethylene evolution increased markedly at low humidity and slightly at high humidity. These results suggest that water deficit stimulates ethylene evolution by young bolls directly through partial desiccation, but do not exclude the possibility of a stimulus from moisture-stressed plants. Although attached and detached bolls both lost only a small percentage of their water content, detached bolls lost more for a given rate of ethylene evolution than bolls on moisture-stressed plants. The increased rate of ethylene evolution by young cotton bolls on plants subjected to a water deficit is probably adequate, in many cases, to cause their abscission.

Journal Article↗
PubMed2000

Evolutionary genomics: reading the bands.

The human genome is not a uniform structure but, instead, is a mosaic of bands. Some of these bands can be seen by the eye. Stained with Giemsa and viewed under the microscope each human chromosome has a prototypical pattern of light and dark bands (G and R bands respectively). Other bands are not so easily viewed. The human genome is, for example, a mosaic of isochores, blocks of DNA within which the proportion of the bases G and C at silent sites (introns, third positions in codons, intergene spacer) is fairly uniform. Recent work by Matassi and colleagues(1) has revealed what might be a new and unexpected banding pattern. They have found that the genes which are close together on the chromosome have similar rates of evolution. BioEssays 22:105-107, 2000.

Chromosome Banding↗
PubMed1983

Proliferative activity of bone marrow cells in primary dysmyelopoietic (preleukemic) syndromes.

The proliferative activity of bone marrow cells was studied in 24 patients with primary dysmyelopoiesis by means of flow cytometry and 3H-TdR autoradiography. Abnormal DNA content was found in two cases with aneuploid karyotypes. DNA content typical of a diploid population was observed in all patients with normal karyotype and in three patients with chromosomal aberrations. The fraction of bone marrow cells in S- and G2-phase was higher in primary acquired sideroblastic anemia and refractory anemia (without excess of blasts) than in refractory anemia with excess of blasts and chronic myelomonocytic leukemia. Regardless to the diagnosis, the patients with low fraction of cells in S- and G2-phase had short survival time and showed high rate of evolution into acute nonlymphoblastic leukemia. The labeling (LI) and mitotic (MI) indexes of both erythroblasts and granulocytic cells were decreased in nearly all patients. The lowest values of LI and MI of the granulocytic compartment were found in the patients who subsequently developed acute leukemia. These data suggest that cytokinetic analysis allows investigators to achieve useful information on the stage of disease in the dysmyelopoietic syndromes.

Adult↗
PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗
PubMed1987

Conserved sequence elements in the 5' region of the Ultrabithorax transcription unit.

Clones homologous to the 5' region of the Ultrabithorax gene of Drosophila melanogaster have been isolated from D. pseudoobscura, D. funebris and Musca domestica. Regions that encode most of the Ubx protein have been sequenced in all three of these species, and the 5' upstream region has been sequenced in D. funebris to a point 1000 bases upstream of the probable mRNA start site. Here we compare these sequences with those described elsewhere for D. melanogaster. Deduced amino acid sequences of the Ubx protein show 8% (D. pseudoobscura), 15% (D. funebris) and 22% (M. domestica) divergence from D. melanogaster. However, these figures mask very different rates of evolution in different regions of the protein. A glycine-rich (;hinge') region is conserved in each of these species, although its length is variable. Comparison of D. funebris and D. melanogaster sequences in the long 5' untranslated leader region of the mRNA, and in the region immediately upstream of the start point of transcription, reveals tightly conserved elements embedded in an otherwise non-homologous sequence. These conserved elements include a 118-bp region that spans the mRNA start site, an internally repetitive (TAA)(n) region in the untranslated leader and a short repeated motif immediately upstream of the ATG codon that initiates the major open reading frame of the Ubx protein. Two other conserved elements were identified upstream of the transcription start site; both elements have structural features consistent with a role as recognition sites for regulatory proteins.

Journal Article↗
PubMed2006

Codep: maximizing co-evolutionary interdependencies to discover interacting proteins.

Approaches for the determination of interacting partners from different protein families (such as ligands and their receptors) have made use of the property that interacting proteins follow similar patterns and relative rates of evolution. Interacting protein partners can then be predicted from the similarity of their phylogenetic trees or evolutionary distances matrices. We present a novel method called Codep, for the determination of interacting protein partners by maximizing co-evolutionary signals. The order of sequences in the multiple sequence alignments from two protein families is determined in such a manner as to maximize the similarity of substitution patterns at amino acid sites in the two alignments and, thus, phylogenetic congruency. This is achieved by maximizing the total number of interdependencies of amino acids sites between the alignments. Once ordered, the corresponding sequences in the two alignments indicate the predicted interacting partners. We demonstrate the efficacy of this approach with computer simulations and in analyses of several protein families. A program implementing our method, Codep, is freely available to academic users from our website: http://www.uhnresearch.ca/labs/tillier/.

Computer Simulation↗
PubMed1999

Specialized conservation of surface loops of myosin: evidence that loops are involved in determining functional characteristics.

The molecular motor myosin has been the focus of considerable structure-function analysis. Of key interest are the portions of the protein that control the rate of ATP hydrolysis, the affinity for actin, and the velocity at which myosin moves actin. Two regions that have been implicated in determining these parameters are the "loop" regions at the junctions of the 25 kDa and 50 kDa domains and the 50 kDa and 20 kDa domains of the protein. However, the sequences of these regions are poorly conserved between different myosin families, suggesting that they are not constrained evolutionarily, and thus are relatively unimportant for myosin function. In order to address this apparent incongruity, we have performed an analysis of relative rates of observed evolutionary change. We found that the sequences of these loop regions appear to be actually more constrained than the sequences of the rest of the myosin molecule, when myosins are compared that are known to be kinetically or developmentally similar. This suggests that these loop regions could play an important role in myosin function and supports the idea that they are involved in modulating the specific kinetic characteristics that functionally differentiate one myosin isoform from another. Apparently "unconserved" loops may generally play a role in determining kinetic properties of enzymes, and similar analyses of relative rates of evolution may prove useful for the study of structure-function relationships in other protein families.

Amino Acid Sequence↗
PubMed1994

Phylogenetic analysis of green plant rbcL sequences.

DNA and derived amino acid sequences of the rbcL gene from selected photosynthetic bacteria, green algae, bryophytes, "fern allies," ferns, and seed plants were used to construct phylogenetic trees using parsimony algorithms. Internal support of clades was determined by the bootstrap and decay indices. External support was judged by comparison of trees with previous morphological and molecular cladograms. Some clades on all the trees are supported both internally and externally, but all of the trees are characterized by unsupported relationships of the bryophytes and fern allies. Trees produced by analyses of all three DNA positions have the highest levels of internal support, but many clades are still not supported externally or internally. Analyses using only the first and second positions of the DNA sequences and derived amino acid sequences produced trees with odd groupings and low levels of internal support for most of the clades. These results indicate that rbcL sequences may be too divergent to test phylogenetic relationships among major groups of green plants. Additional problems with constructing phylogenetic trees from rbcL sequences may be caused by RNA editing, pseudogenes, unequal rates of evolution, and inadequate taxon sampling. Whether RNA editing is a problem can be determined by sequencing amplified RNAs from selected taxa. If pseudogenes are suspected, purified chloroplast DNA should be used for amplification. It may be beneficial to include more taxa in subsequent analyses, but there are indications that historical extinctions will prevent adequate sampling of some groups, such as the bryophytes and fern allies.

Amino Acid Sequence↗
PubMed1998

Searching for substitution rate heterogeneity.

A permutation method for detecting regional substitution rate heterogeneity in DNA sequences is described. An estimated phylogeny for the sequences is required. The method is likelihood based and searches through all regions of a DNA sequence to find any regions that have an unusually large (or small) number of substitutions in comparison to an optimal substitution rate for the entire sequence. Likelihood ratio tests do not achieve proper statistical significance levels due to the large number of tests performed. Empirical corrections based on permutations are suggested and shown to give correct statistical accuracy. The ability of the method to detect rate heterogeneity is good even when the region is small and with less than twice the rate of evolution in the remainder of the sequence.

Algorithms↗
PubMed1998

Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau.

Phylogenetic relationships within the Laudakia caucasia species group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation of Laudakia populations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north-south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5-10 MYBP (million years before present)]. The shortest tree suggest the later hypothesis, and statistical tests reject the other two hypothesis. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north-south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61-0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.

Animals↗
PubMed2000

Phylogeography and speciation of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA.

The widespread, lowland toad Bufo valliceps has an unusual distribution in North and Middle America that straddles two major biogeographic areas; previous morphological studies of this species suggested the existence of two species. We used mitochondrial DNA sequences to examine the phylogeography of this species and discovered the existence of two distinct clades. We recognize these as two species: B. valliceps and B. nebulifer. These molecular data support morphological data from previous studies. Our results show low levels of molecular variation in a morphologically uniform temperate species (B. nebulifer) and high levels of molecular variation in a morphologically variable tropical species (B. valliceps), providing an example of molecules matching morphology. Two biogeographic hypotheses are tested to explain the current distribution of these species, based on a calibrated rate of evolution and the percent sequence divergence between the two species. A more recent Pleistocene dispersal event, followed by vicariance associated with rising sea level, is rejected in favor of an earlier Miocene-Pliocene vicariant hypothesis associated with the formation of the Trans-Mexican Neovolcanic Belt.

Animals↗