SEARCH · PubMed Health

Results for “Divergence dates”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 91 records · Page 5Linked to original sources

PubMed2001

The rates of molecular evolution in rodent and primate mitochondrial DNA.

A higher rate of molecular evolution in rodents than in primates at synonymous sites and, to a lesser extent, at amino acid replacement sites has been reported previously for most nuclear genes examined. Thus in these genes the average ratio of amino acid replacement to synonymous substitution rates in rodents is lower than in primates, an observation at odds with the neutral model of molecular evolution. Under Ohta's mildly deleterious model of molecular evolution, these observations are seen as the consequence of the combined effects of a shorter generation time (driving a higher mutation rate) and a larger effective population size (resulting in more effective selection against mildly deleterious mutations) in rodents. The present study reports the results of a maximum-likelihood analysis of the ratio of amino acid replacements to synonymous substitutions for genes encoded in mitochondrial DNA (mtDNA) in these two lineages. A similar pattern is observed: in rodents this ratio is significantly lower than in primates, again consistent only with the mildly deleterious model. Interestingly the lineage-specific difference is much more pronounced in mtDNA-encoded than in nuclear-encoded proteins, an observation which is shown to run counter to expectation under Ohta's model. Finally, accepting certain fossil divergence dates, the lineage-specific difference in amino acid replacement-to-synonymous substitution ratio in mtDNA can be partitioned and is found to be entirely the consequence of a higher mutation rate in rodents. This conclusion is consistent with a replication-dependent model of mutation in mtDNA.

Animals↗

PubMed2002

Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome.

Many copies of nuclear counterparts of mitochondrial DNA (mtDNA) were found in nuclear DNA from sperm heads of the domestic dog, Canis familiaris, by DNA-DNA hybridization and DNA sequencing. Nuclear counterparts homologous to the mtDNA D-loop region were cloned into lambda phage vectors (EMBL4 and lambda gt11), and nucleotide sequences of seven different mtDNA pseudogenes were then determined. The seven pseudogenes were E3 (474 bp; 82% homology with canine mtDNA), E13 (1867 bp; 67%), 8B (2375 bp; 78%), 12A (2650 bp; 79%), 33 (4131 bp; 86%), 47 (4251 bp; 86%), and E17 (5721 bp; 71%). These seven mtDNA pseudogenes corresponded to portions of cytoplasmic mtDNA containing the genes ile, ND1, leu, 16S rRNA, val, 12S rRNA, phe, D-loop, pro, thr, cytb, and glu. A neighbor-joining phylogenetic tree constructed from 12S rRNA sequences in mtDNA pseudogenes 8B, 33, 47, and E17 and in 10 mtDNA fragments from other species showed that these four pseudogenes form a monophyletic clade with canine mtDNA. A neighbor-joining phylogenetic tree based on the 318-bp cytb region showed that the canine pseudogenes existed before the divergence of 17 related canids, and their divergence dates were calculated at around 4.4 to 8.6 million years ago.

Animals↗

PubMed2002

Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses.

We report a genomic and morphologic study of the European Eyach (EYA) virus (genus Coltivirus, family Reoviridae) and a comparative analysis with the American Colorado tick fever (CTF) virus (the type species of the genus). The previously established, but distant, antigenic relationship between these viruses was strengthened by genetic findings (presence of cognate genes, amino acid identity between 55 and 88%, similar conserved terminal motifs, suspected read-through phenomenon in segment 9 of both viruses) and by indistinguishable ultramicroscopic morphologies. Moreover, putative constitutive modifying enzyme activities were suspected to be carried out by homologous viral proteins (RNA-dependent RNA polymerase, methyl/guanylyl transferase, NTPase). These findings, together with the comparative analysis to genomes of southeast Asian isolates, support the recent classification of arboviruses with 12 segments of dsRNA within two distinct genera (genus Coltivirus and genus Seadornavirus) and raise interesting questions about the evolutionary origins of coltiviruses. The previously proposed hypothesis that EYA virus was derived from an ancestral virus introduced in Europe with the migration of lagomorphs from North-America, would imply a divergence date between American and European isolates of over 50 million years ago (MYA). This analysis allows for the first time to propose an evolutionary rate for virus dsRNA genomes which was found to be in the order of 10(-8) to 10(-9) mutations/nt/year, a rate similar to that of dsDNA genomes.

Americas↗

PubMed1989

Nucleotide sequences of immunoglobulin-epsilon pseudogenes in man and apes and their phylogenetic relationships.

To understand the phylogenetic relationships between hominoids, the nucleotide sequences of immunoglobulin-epsilon processed pseudogenes from chimpanzee, gorilla and orangutan were determined. The basic structures of these processed pseudogenes agreed with their human counterpart. Although the degrees of nucleotide differences between man and the African apes had no statistical significance, all the analytical data examined supported the theory that chimpanzee is the closest relative of man. This result was consistent with that deduced by our recent qualitative study. Studies on the nucleotide sequences of globin genes have suggested that the molecular clock runs more slowly in hominoids than in non-hominoid primates. According to the present data, however, further retardation of the evolutionary rate was not observed in the human lineage. Assuming that orangutan diverged 14 million years ago and that the evolutionary rate between the orangutan lineage and the lineage leading to the other three species is constant, the divergence dates of chimpanzee and gorilla were estimated to be 4.9(+/- 0.9) and 5.9(+/- 0.9) million years ago, respectively.

Animals↗

PubMed1989

The Drosophila melanogaster RPS17 gene encoding ribosomal protein S17.

A human ribosomal protein S17 cDNA [Chen et al., Proc. Natl. Acad. Sci. USA 83 (1986) 6907-6911] was used as heterologous probe to isolate S17 clones from Drosophila genomic and cDNA recombinant libraries. Five S17 genomic clones were recognized; all contained overlapping regions of a single chromosomal site. Subsequently the Drosophila RPS17 gene was mapped by in situ hybridization to chromosome 3L, band 67B1-5. The locus spans approximately 1000 bp of DNA and includes four exons. It is preceded by conventional CAAT and TATA RNA polymerase II promoter motifs. The 131 amino acid protein encoded within Drosophila RPS17 is similar to ribosomal proteins from several other eukaryotes. Comparison of eukaryotic S17 proteins' primary structures as well as the number and location of their genes' intervening sequences suggest that S17 is a relatively recent addition to the ribosomal protein family, probably post-dating divergence of eukaryotes and prokaryotes.

Amino Acid Sequence↗

PubMed2004

[A new species of wild mice on the Island of Cyprus].

A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.

Animals↗

PubMed2005

A rhesus macaque radiation hybrid map and comparative analysis with the human genome.

The genomes of nonhuman primates are powerful references for better understanding the recent evolution of the human genome. Here we compare the order of 802 genomic markers mapped in a rhesus macaque (Macaca mulatta) radiation hybrid panel with the human genome, allowing for nearly complete cross-reference to the human genome at an average resolution of 3.5 Mb. At least 23 large-scale chromosomal rearrangements, mostly inversions, are needed to explain the changes in marker order between human and macaque. Analysis of the breakpoints flanking inverted chromosomal segments and estimation of their duplication divergence dates provide additional evidence implicating segmental duplications as a major mechanism of chromosomal rearrangement in recent primate evolution.

Animals↗

PubMed1979

The use of amino acid sequence analysis in assessing evolution.

The thirteen year history of assessing evolution by amino acid sequence analysis has made apparent the limitations imposed upon this system by the finite nature of the characters. This finiteness exists on several levels and ultimately expresses itself as parallelism, back mutation and the retention of primitive characters in the sequences of proteins from present day species and the putative ancestral protein chains. Sequence analysis shares these problems with other molecular approaches, but because it is concerned both with the nucleotide substitutions in the genome and with the functional roles of proteins, it has unique advantages. For example, the large fluctuation in the rate of fixation of mutations in a protein's evolution can be detected and used to point out the unreliability of any molecular clock for estimating divergence dates. Moreover, when consideration is given to studies which assign functional significance to specific amino acid sites in a protein, changes in function during the descent of a protein can be appreciated and their significance correlated with organismal evolution.

Amino Acid Sequence↗

PubMed2003

The influence of tick behavior, biotope and host specificity on concerted evolution of the platelet aggregation inhibitor savignygrin, from the soft tick Ornithodoros savignyi.

Ticks are obligate blood-feeding parasites that secrete anti-hemostatic components during feeding to enable control of the hemostatic system of the host. Complex interactions at the tick-host interface are an indication of the important role that the host played during tick evolution. The question is to what extent interaction with the host and the environment influences tick evolution. Previously, two isoforms (97% sequence identity) of savignygrin, an alphaIIbbeta3 antagonist, have been described. The presence of both isoforms within 20 random individuals confirmed that these isoforms must be recent gene duplicates. Analysis of the sequence differences between the isoforms shows a Kn/Ks ratio of 1, which indicates neutral selection for the isoforms. However, the biased localization of differences within the 3' end of the genes suggests that concerted evolution acts on the isoforms. Calculation of the divergence date between the isoforms (1.6-5.2 MYA) also indicates purifying selection, as ample time had passed after duplication, for inactivation of one gene copy. We conclude that concerted evolution has functioned to maintain a high copy number of the savignygrins in order for Ornithodoros savignyi to parasitize a wide host range. This contrasts with O. moubata that expresses the savignygrin homolog, disagregin, as a single copy at lower concentration levels and correlates with the confined habitat and consequently narrow host range of O. moubata. Recent "domestication" of O. savignyi due to animal husbandry practices could however, have reduced the selection constraints acting to maintain the gene copies as evidenced by the structural instability of one of the isoforms. Our results suggest that environmental factors and host associations do play an important role in the evolution of anti-hemostatic components in ticks.

Alleles↗

PubMedDate not supplied

Evidence on human origins from haemoglobins of African apes.

Molecular data have influenced views concerning human origins, first, by supporting the genealogical classification of Pan (chimpanzee) and Gorilla with Homo rather than with Pongo (orangutan) and, second, by suggesting that only a few million years separate humans and chimpanzees from their last common ancestor. Indeed, the cladistic distances in phylogenetic trees constructed from amino acid sequence data, on detecting many superimposed mutations, yielded a 'molecular-clock' divergence date between Homo and Pan of only 1-1.5 Myr BP. This date, which is even more recent than (4.2-5.3 Myr BP) calculated using phenetic distances from immunological and DNA-hybridization comparisons (Table 1), is too near the present considering the existence of 3-4 Myr-old fossils of bipedal human ancestors (and a 5.5 Myr-old jaw fragment assigned to Australopithecus). Perhaps decelerated sequence evolution occurred; alternatively, hominoid distances could have been underestimated, because chimpanzee and gorilla were represented mostly by sequences inferred from peptide amino acid compositions, as was the case for their haemoglobins. To help rectify this situation we report here the rigorously determined alpha- and beta-haemoglobin amino acid sequences not only of chimpanzee (Pan troglodytes) and Gorilla gorilla but also pygmy chimpanzee (Pan paniscus). Our findings favour the explanation of decelerated evolution and point to selection preserving perfected haemoglobin molecules.

Amino Acid Sequence↗

PubMed2002

Late Quaternary distributional stasis in the submediterranean mountain plant Anthyllis montana L. (Fabaceae) inferred from ITS sequences and amplified fragment length polymorphism markers.

Anthyllis montana is a submediterranean, herbaceous plant of the southern and central European mountains. The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from multiple accessions of the species and several closely related taxa. In addition, amplified fragment length polymorphism (AFLP) was analysed from 71 individuals of A. montana collected in 20 localities, mainly in the Pyrenees, Alps, Italian Peninsula and Balkans. Our ITS phylogeny showed a sequential branching pattern in A. montana, implying a western Mediterranean origin followed by an eastward migration. ITS clock calibrations suggest that speciation of A. montana took place at the Pliocene-Pleistocene boundary, while intraspecific divergence dates to Late Quaternary times (i.e. 0.7 million years ago). The AFLP analyses revealed a major genetic (west/east) subdivision within A. montana, probably caused by the massive glaciation of the Alps during this latter time period. The present-day absence of A. montana from vast parts of the Alps, which appear ecologically suitable for the species, together with the finding of evenly distributed AFLP variability within each of the two western and eastern lineages identified, is taken as evidence for a largely static Late Quaternary history without large-scale migration. High levels of AFLP variation observed among populations, together with weak or absent patterns of isolation by distance, seem to be in accord with long-term population insularization and distributional stasis. However, recent small-scale migration and a narrow hybrid zone between western and eastern lineages need to be postulated to explain the intermediate genetic composition of individuals from the Maritime Alps, a well-known suture-zone for other plant and animal species.

DNA, Ribosomal Spacer↗

PubMed1998

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.

Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

Animals↗

PubMed2005

A gamma mixture model better accounts for among site rate heterogeneity.

MOTIVATION: Variation of substitution rates across nucleotide and amino acid sites has long been recognized as a characteristic of molecular sequence evolution. Evolutionary models that account for this rate heterogeneity usually use a gamma density function to model the rate distribution across sites. This density function, however, may not fit real datasets, especially when there is a multimodal distribution of rates. Here, we present a novel evolutionary model based on a mixture of gamma density functions. This model better describes the among-site rate variation characteristic of molecular sequence evolution. The use of this model may improve the accuracy of various phylogenetic methods, such as reconstructing phylogenetic trees, dating divergence events, inferring ancestral sequences and detecting conserved sites in proteins. RESULTS: Using diverse sets of protein sequences we show that the gamma mixture model better describes the stochastic process underlying protein evolution. We show that the proposed gamma mixture model fits protein datasets significantly better than the single-gamma model in 9 out of 10 datasets tested. We further show that using the gamma mixture model improves the accuracy of model-based prediction of conserved residues in proteins. AVAILABILITY: C++ source codes are available from the authors upon request.

Chromosome Mapping↗

PubMed2003

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be approximately 20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

Algorithms↗

PubMed2003

High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas.

A total of 63 binary polymorphisms and 10 short tandem repeats (STRs) were genotyped on a sample of 2,344 Y chromosomes from 18 Native American, 28 Asian, and 5 European populations to investigate the origin(s) of Native American paternal lineages. All three of Greenberg's major linguistic divisions (including 342 Amerind speakers, 186 Na-Dene speakers, and 60 Aleut-Eskimo speakers) were represented in our sample of 588 Native Americans. Single-nucleotide polymorphism (SNP) analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.

Analysis of Variance↗

PubMed2005

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.

Chloroplasts↗

PubMed2004

Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K.

ORF57 protein of Kaposi's sarcoma-associated herpesvirus has a counterpart in all herpesvirus of mammals and birds and regulates gene expression at transcriptional and post-transcriptional levels. ORF57 was capable of self-interaction and bound a rapidly migrating form of heterogeneous nuclear ribonucleoprotein K (hnRNP K), a multifunctional cellular protein involved in gene expression. In virus infected cell extracts, ORF57 was present in a complex with hnRNP K that had protein kinase CK2 activity, and was phosphorylated by CK2. Different regions of ORF57 bound both catalytic alpha/alpha' and regulatory beta subunits of CK2. CK2 modification enhanced the ORF57-hnRNP K interaction, and may regulate the presence and activities of components in the complex. We suggest that ORF57 and hnRNP K interaction may modulate ORF57-mediated regulation of viral gene expression. Herpesviral ORF57 (Rhadinovirus) and ICP27 (Simplexvirus) proteins both interact with hnRNP K and CK2 implying that adaptation of the ancestral hnRNP K and CK2 to associate with viral regulatory ancestor protein likely pre-dates divergence of these Herpesviridae genera that occurred 200 million years ago.

Amino Acid Sequence↗

PubMed1991

Clustering of residence of multiple sclerosis patients at age 13 to 20 years in Hordaland, Norway.

Geographic and temporal variation and migration studies point to an exogenous agent in the etiology of multiple sclerosis. If infectious etiology is involved, space-time clustering would also be expected. The authors analyzed 381 patients with a clinical onset of multiple sclerosis between 1953 and 1987 in the county of Hordaland, Norway. Patients within the same birth cohort had lived significantly closer to each other than would be expected during ages 13-20 years, with peak clustering at age 18 years (p = 0.002). Clustering was also shown between patients in pairs comprised of one individual with initial remittent disease and the other with chronic progressive course of disease, suggesting a similar etiology for both clinical patterns. Clustering between cases with widely divergent dates of clinical onset provides evidence of marked variation in latency. No similar clustering was observed in age-, sex-, and area-matched hospital controls without multiple sclerosis, and no clustering was found among the cases when using fixed number of years before onset. These results are compatible with a common infectious agent, such as the Epstein-Barr virus, acquired in adolescence in genetically vulnerable persons who are also not protected by an infection acquired before this age of susceptibility. Susceptibility could be related to the route of transmission or to other age-related covariates or it may be hormonally mediated.

Adolescent↗