Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “parallel 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 1,423 records · Page 79Linked to original sources
PubMed2003

A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean.

A molecular phylogeny is presented for the subfamily Littorininae (including representatives of all subgeneric taxa and all members of a group of southern-temperate species formerly classified as 'Nodilittorina'), based on sequence data from two nuclear (18S rRNA, 28S rRNA) and two mitochondrial (12S rRNA, CO1) genes. The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data. In particular, 'Nodilittorina' is polyphyletic and is here divided into four genera (Echinolittorina, Austrolittorina, Afrolittorina new genus, and the monotypic Nodilittorina s.s.). The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily. The two living species of Mainwaringia are remarkable for a greatly elevated rate of evolution in all four genes examined; it is suggested that this may be connected with their protandrous hermaphroditism, which is unique in the family. The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters. The fossil record of littorinids is poor, but ages of clades are estimated using a calibration based on a Lower Eocene age of the genus Littoraria. Using these estimates, the antitropical distribution of Littorina and Afrolittorina is an ancient pattern of possibly Cretaceous age. The five members of Austrolittorina show a Gondwanan distribution in Australia, New Zealand, and South America. Based on the morphological uniformity within this clade, relatively recent (Plio-Pleistocene) trans-Pacific dispersal events seemed a likely explanation, as proposed for numerous other congeneric marine taxa. However, molecular estimation of ages of divergence suggest an initial vicariance between Australian and South American lineages at 40-73Ma, contemporary with the later stages of fragmentation of the Gondwanan supercontinent, followed by more recent (but still mid-Cenozoic) dispersal events across the Tasman Sea and the Pacific Ocean. Afrolittorina is another Cretaceous clade, now restricted to southern Africa and southern Australia, but divergence between these lineages (29-55Ma) post-dates Gondwanan fragmentation. Within both Austrolittorina and Afrolittorina all sister-species divergences are estimated to fall in the range 10-47Ma, so that there is no evidence for speciation events in the Plio-Pleistocene.

Adaptation, Biological↗
PubMed2007

Morphological changes in pedal phalanges through ornithopod dinosaur evolution: a biomechanical approach.

The evolution of ornithopod dinosaurs provides a well-documented example of the transition from digitigrady to subunguligrady. During this transition, the ornithopod pes was drastically altered from the plesiomorphic dinosaurian morphology (four digits, claw-shaped unguals, strongly concavo-convex joints, phalanges longer than wide, excavated collateral ligament fossae, presence of sagittal ridge, and prominent processes for the attachment of tendons) to a more derived condition (tridactyly, modification of the unguals into hooves, phalanges wider and thinner than long, lack of collateral ligament fossae, loss of sagittal ridge and tendon attachment processes, relatively flattened articular surfaces). These changes are particularly noteworthy given the overall conservatism in pedal morphology seen across Dinosauria. But what are the functional consequences of these specific morphological transitions? To study them, we examine a wide range of pedal morphologies in four non-avian dinosaurs and two birds. Our analyses of the external morphology, two-dimensional models (using Finite Element Analysis), and internal bone structure demonstrate that this evolutionary shift was accompanied by a loss of digit mobility and flexibility. In addition, pedal posture was modified to better align the pes with the main direction of the ground reaction force, thus becoming well suited to support high loads. These conclusions can be applied to other, parallel evolutionary changes (in both dinosaurs and mammals) that involved similar transitions to a subunguligrade posture.

Animals↗
PubMed2006

GARD: a genetic algorithm for recombination detection.

MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. AVAILABILITY: Freely available http://www.datamonkey.org/GARD/

Algorithms↗
PubMedDate not supplied

Normal renal function 8 to 13 years after cyclosporin A therapy in 285 diabetic patients.

BACKGROUND: Cyclosporin A (CyA) may induce acute nephrotoxicity. The question has been raised of the possible long-term unfavorable course of CyA-induced lesions. Advantage was taken of a large cohort of diabetic patients treated for several months using moderate CyA dosage to evaluate the long-term evolution of renal function in such patients. METHODS: Two hundred and eighty five recently diagnosed type 1 diabetic patients having received CyA for a mean of 19.9 months were monitored for 13 years, in parallel with 100 similar patients treated with insulin alone. RESULTS: In the CyA-treated group, a transient increase in creatininemia levels occurred during the first 18 months of treatment associated with a transient increase in renal vascular resistance. Both effects disappeared later on: creatininemia levels then remained normal. Inulin and p-aminohippurate (PAH) clearances remained normal throughout follow-up. Neither permanent renal failure nor progressive deterioration of renal function occurred in either group or in individual patients. A 10 to 12% increase in inulin and PAH clearance was elicited by IV amino acid infusion at 7 to 10 years, a finding consistent with a normal renal functional reserve. Patients with moderate kidney lesions on biopsy at 1 year had normal and stable clearance values at 7 to 13 years. The prevalence of arterial hypertension and retinopathy was lower in the CyA-treated group than in the control group, possibly because of the tighter metabolic control obtained in the CyA group. CONCLUSION: These results suggest that low-dose CyA treatment combined with thorough monitoring does not result in long-term renal dysfunction.

Adult↗
PubMed2000

Sexual selection and the evolution of exclusive paternal care in arthropods.

Internal fertilization and anisogamy are thought to impede the evolution of exclusive paternal care by reducing paternity assurance and increasing male promiscuity. The potential role of sexual selection in easing these constraints is currently being examined in vertebrates but has not been seriously studied in most arthropods. To distinguish the effects of sexual from natural selection on the evolution of arthropod paternal care, I tested predictions of the state of several life history and behavioural traits under both forms of selection across all known taxa with exclusive paternal care. The results suggest parallels between prezygotic nuptial gifts and exclusive postzygotic paternal care and support the hypothesis that, in arthropods, male behaviours that enhance female reproductive success either directly by releasing females from the fecundity constraints of maternal care (enhanced fecundity hypothesis) or indirectly by identifying mates with superior genes (handicap principle) are traits on which sexual selection has acted. Under such conditions males willing to guard young become preferred mates for gravid females and enjoy greater promiscuity than males unable or unwilling to guard. Females use nest construction or the act of guarding another female's eggs as honest signals of paternal intent and quality. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1999

Randomized acquisition for the suppression of systematic F1 artifacts in two-dimensional NMR spectroscopy.

2D spectra, particularly for homonuclear correlation, can show a variety of artifactual signals in the F1 domain. Common sources include carry-over of signal modulation from one transient to the next ("rapid pulsing artifacts") and systematic variations in room temperature ("parallel diagonals"). In both cases there is one very simple expedient which can greatly reduce the impact of these sources of error. Multidimensional data sets are almost invariably recorded by simply incrementing or decrementing evolution periods, largely for reasons of convenience and historical precedent. If instead the sampling of the evolution periods is carried out in random order, the perturbations responsible for the sharp F1 signals in the conventional experiment manifest themselves as t1 noise. Since the randomized acquisition redistributes coherent artifactual signals randomly in F1, the maximum artifactual signal is substantially reduced in the randomized experiment and no longer appears in the form of misleading distinct peaks.

Magnetic Resonance Spectroscopy↗
PubMed1985

Diagnostic fetal blood sampling for the haemoglobinopathies--10-year experience.

The development of methods for fetal blood sampling in the second trimester of pregnancy offers the possibility of fetal diagnosis for couples at risk for having children with a haemoglobinopathy. We review the evolution of 10 years' experience of fetal blood sampling for 681 patients. The obstetric risk associated with the procedure has fallen from an initial 15% (in the first 87 pregnancies) to about 3%, in parallel with increased experience, improved ultrasound control, identification of the causes of complications and implementation of simple steps to avert them.

Diseases in Twins↗
PubMed2004

Validation of the FAMACHA eye color chart for detecting clinical anemia in sheep and goats on farms in the southern United States.

Recent studies on sheep and goat farms in the southern United States indicate that multiple-anthelmintic resistance in Haemonchus contortus is becoming a severe problem. Though many factors are involved in the evolution of resistance, the proportion of the parasite population under drug selection is believed to be the single most important factor influencing how rapidly resistance develops. Therefore, where prevention of resistance is an important parallel goal of worm control, it is recommended to leave a portion of the animals untreated. Recently, a novel system called FAMACHA was developed in South Africa, which enables clinical identification of anemic sheep and goats. When H. contortus is the primary parasitic pathogen, this system can be applied on the farm level to reduce the number of treatments administered, thereby increasing the proportion of the worm population in refugia. Since most studies validating the FAMACHA method have been performed in South Africa, it is important that the method be tested in other regions before its use is broadly recommended. We performed a validation study of FAMACHA by testing the system in sheep (n = 847) and goats (n = 537) of various breeds and ages from 39 farms located in Arkansas, Georgia, Louisiana, Florida, and the US Virgin Islands. The color of the ocular conjunctiva of all animals were scored on a 1-5 scale using the FAMACHA card, and blood samples were collected from each animal for determination of packed cell volume (PCV). Fecal samples were also collected from a majority of the animals tested for performance of fecal egg counts (FEC). Correlations between PCV and eye scores, PCV and FEC, and FEC and eye scores were all highly significant for both sheep and goats (P < 0.001). Data for both FAMACHA scores and PCV were evaluated using two separate criteria for anemia: eye score values of 3, 4 and 5 or 4 and 5, and PCV values of < or =19 or < or =15 were considered anemic. Specificity was maximized when eye score values of 4 and 5 were considered anemic and PCV cut off for anemia was < or =19, but sensitivity was low. In contrast, sensitivity was 100% for both sheep and goats when eye score values of 3, 4 and 5 were considered anemic and PCV cut off was < or =15, but specificity was low. In both sheep and goats, predictive value of a negative was greater than 92% for all anemia and eye score categories, and was greater than 99% for both eye score categories when an anemia cutoff of < or =15 was used. Predictive value of a positive test was low under all criteria indicating that many non-anemic animals would be treated using this system. However, compared to conventional dosing practices where all animals are treated, a large proportion of animals would still be left untreated. These data indicate that the FAMACHA method is an extremely useful tool for identifying anemic sheep and goats in the southern US and US Virgin Islands. However, further studies are required to determine optimal strategies for incorporating FAMACHA-based selective treatment protocols into integrated nematode control programs.

Anemia↗
PubMed2000

High diversity of structurally heterozygous karyotypes and rDNA arrays in parthenogenetic aphids of the genus Trama (Aphididae: Lachninae).

Karyotypes of permanently parthenogenetic aphids of three species of the genus Trama show great diversity, particularly in the number and distribution of chromosomal elements containing highly repetitive sequences. Sampling at only a few sites in southern England, chromosome number varied from 14 to 23 in T. troglodytes, 9-12 in T. caudata and 10-14 in T. maritima, with some colonies having individuals of more than one karyotype. This variation was paralleled by differences in the number and distribution of rDNA arrays revealed by in situ hybridization. This high intraspecific karyotype diversity contrasts with very low genetic diversity in the same populations, suggesting rapid karyotype evolution. Although T. troglodytes feeds on many species of composite plants there was no evidence of any karyotype-associated host race formation.

Animals↗
PubMed1997

The "Dreadful Visitation": public health and public awareness in seventeenth-century London.

The decision was made in Britain three centuries ago that an educated populace was best able to deal with a public health crisis of staggering proportions--outbreaks of bubonic and pneumonic plague. As early as 1603, the printing press was enlisted to educate the public about urgent health issues. This education took several forms. The City of London, with the tacit permission of the Crown, printed bills of mortality that reported who was dying of what in London, detailed by parish, for the years in the seventeenth century when plague deaths were reported. New books about plague prevention and cures were published; older works were reprinted. The resulting wealth of data gave impetus to the evolution of the new field of epidemiological demographics, founded by John Graunt and Sir William Petty. Publishing in the plague years also established a model for informing the general populace that is not without parallel in today's "information society."

Disease Outbreaks↗
PubMed1998

Progressive brain failure after diffuse hypoxic ischemic brain injury: a serial MR and proton MR spectroscopic study.

The findings at sequential MR imaging and proton MR spectroscopy of a patient with profound hypoxic-ischemic brain injury are reported. The pattern of structural and biochemical changes observed closely reflected the known evolution of postasphyxic brain degeneration. Particularly noteworthy were the sharp decrease of cortical N-acetylaspartate in the acute phase, suggesting the severity of the neuronal insult, and the subsequent progressive increase of choline, paralleling the delayed degeneration of white matter.

Adult↗
PubMed2005

The agr radiation: an early event in the evolution of staphylococci.

Agr is a global regulatory system in the staphylococci, operating by a classical two-component signaling module and controlling the expression of most of the genes encoding extracellular virulence factors. As it is autoinduced by a peptide, encoded within the locus, that is the ligand for the signal receptor, it is a sensor of population density or a quorum sensor and is the only known quorum-sensing system in the genus. agr is conserved throughout the staphylococci but has diverged along lines that appear to parallel speciation and subspeciation within the genus. This divergence has given rise to a novel type of interstrain and interspecies cross-inhibition that represents a fundamental aspect of the organism's biology and may be a predominant feature of the evolutionary forces that have driven it. We present evidence, using a newly developed, luciferase-based agr typing scheme, that the evolutionary divergence of the agr system was an early event in the evolution of the staphylococci and long preceded the development of the nucleotide polymorphisms presently used for genotyping. These polymorphisms developed, for the most part, within different agr groups; mobile genetic elements appear also to have diffused recently and, with a few notable exceptions, have come to reside largely indiscriminately within the several agr groups.

Bacterial Proteins↗
PubMedDate not supplied

Evolution of the red nucleus and rubrospinal tract.

A red nucleus, defined by its relative position in the tegmentum mesencephali, its contralateral rubrospinal or rubrobulbar projections and by crossed cerebellar afferents, is found in terrestrial vertebrates and certain rays. A crossed rubrospinal tract occurs in anurans, limbed urodeles and reptiles, birds and mammals, but is apparently absent in boid snakes, caecilians and sharks. A distinct rubrospinal tract is found in certain rays which use their enlarged pectoral fins for locomotion. A crossed tegmentospinal tract, possibly a rubrospinal tract, is found in lungfishes. Although evidence was presented for a rubrospinal tract in more advanced snakes, the available experimental data in lower vertebrates suggest that the presence of a rubrospinal tract is related to the presence of limbs or limb-like structures. In the connectivity of the red nucleus in terrestrial vertebrates, 'levels' of complexity can be distinguished, paralleled by the development of the cerebellum. These 'grades of organization' are probably related to the type of motor performance the particular terrestrial vertebrates are capable of.

Afferent Pathways↗
PubMed2001

Migratory costs and the evolution of egg size and number in introduced and indigenous salmon populations.

The trade-off between reproductive investment and migration should be an important factor shaping the evolution of life-history traits among populations following their radiation into habitats with different migratory costs and benefits. An experimentally induced difference in migratory rigor for families of chinook salmon (Oncorhynchus tshawytscha), of approximately 86 km and 413 m elevation, exacted a cost to somatic energy reserves (approximately 17% reduction in metabolizable mass) and ovarian investment (13.7% reduction in ovarian mass). This cost was associated with a reduction in egg size and paralleled the phenotypic pattern of divergence between two introduced New Zealand populations of common origin, presently breeding at sites with different migration distances. The genetic pattern of divergence of these same populations, detected under common rearing, was consistent with compensation for migratory costs (the population that migrates farther invested more in ovarian mass), but egg number more than egg size was associated with this evolution. These evolutionary patterns are consistent with what is known of the inheritance of these traits and with trade-offs and constraints favoring initial evolution in offspring number over offspring size. Analysis of egg number-size patterns of other Pacific salmon populations in their native range supported the hypothesis that migration strongly influences patterns of reproductive allocation, favoring a higher ratio of egg number to egg size with greater migration distance.

Animal Migration↗
PubMed1998

The C-terminal SET domains of ALL-1 and TRITHORAX interact with the INI1 and SNR1 proteins, components of the SWI/SNF complex.

The ALL-1 gene was discovered by virtue of its involvement in human acute leukemia. Its Drosophila homolog trithorax (trx) is a member of the trx-Polycomb gene family, which maintains correct spatial expression of the Antennapedia and bithorax complexes during embryogenesis. The C-terminal SET domain of ALL-1 and TRITHORAX (TRX) is a 150-aa motif, highly conserved during evolution. We performed yeast two hybrid screening of Drosophila cDNA library and detected interaction between a TRX polypeptide spanning SET and the SNR1 protein. SNR1 is a product of snr1, which is classified as a trx group gene. We found parallel interaction in yeast between the SET domain of ALL-1 and the human homolog of SNR1, INI1 (hSNF5). These results were confirmed by in vitro binding studies and by demonstrating coimmunoprecipitation of the proteins from cultured cells and/or transgenic flies. Epitope-tagged SNR1 was detected at discrete sites on larval salivary gland polytene chromosomes, and these sites colocalized with around one-half of TRX binding sites. Because SNR1 and INI1 are constituents of the SWI/SNF complex, which acts to remodel chromatin and consequently to activate transcription, the interactions we observed suggest a mechanism by which the SWI/SNF complex is recruited to ALL-1/trx targets through physical interactions between the C-terminal domains of ALL-1 and TRX and INI1/SNR1.

Amino Acid Sequence↗
PubMed1990

Evolution of nuclear DNA and the occurrence of sequences related to new small chromosomal DNAs in the trypanosomatid genus Endotrypanum.

Comparisons of nuclear DNA restriction fragment patterns were used to examine the evolutionary relatedness among 17 strains previously identified as Endotrypanum, a trypanosomatid parasite of sloths. Fragments were obtained with 6 restriction enzymes and analyzed by Southern blotting with hybridization probes from three loci. An estimate of the percent nucleotide sequence divergence among strains, delta, was calculated and used to construct molecular evolutionary trees. The 17 isolates fell into four distinct groups, one of which (group D) showed no more relationship to groups A-C than it did to other genera (Leishmania, Crithidia, Leptomonas, Trypanosoma), being too distant to be resolved with this method. These and other data suggest that group D may not actually be Endotrypanum. Molecular karyotype analysis revealed considerable variation among the chromosomes of these strains. One strain (LV88, group B) contained a linear 70-kb chromosome not evident in other isolates. Hybridization probes specific for this chromosome (LV88-70) were developed and revealed that related sequences were present at high levels in group B isolates and low levels in group A isolates, although a complex hybridization pattern was evident. Sequences related to LV88-70 were not present in groups C and D, nor in Leishmania major, showing that this DNA has a disjunct distribution which curiously parallels that of virus-like particles present in these isolates.

Animals↗
PubMed2025

NGATHA carpel development genes evolved in the common ancestor of seed plants.

The evolution of the carpel, the defining feature of angiosperms, remains a fundamental question in plant biology. Understanding how this organ originated is crucial because it underpins the reproductive success and diversity of flowering plants. Here, we investigated the functional conservation between gymnosperms and angiosperms of key transcription factors involved in carpel development. We found that Ginkgo biloba homologs can functionally substitute for their angiosperm counterparts in stigma development. We discovered that GbRAV5 is related to angiosperm NGA genes, challenging previous notions that these are exclusive to angiosperms, and we found a parallel loss of the AP2 domain in gymnosperms providing a rare snapshot of how protein families evolve. Conserved protein interactions and overlapping expression patterns of GbRAV5 and GbHEC in Ginkgo ovules suggest that the molecular toolkit for carpel development was largely present in the last common ancestor of seed plants, offering new insights into the evolution of reproductive structures.

Plant Proteins↗
PubMed2005

Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus.

In order to understand the impact of overlapping reading frames on natural selection by host CD8+ T lymphocytes (CD8(+)-TL), we analyzed the pattern of nucleotide substitution in simian immunodeficiency virus (SIV) genomes sampled from populations at time of death in 35 rhesus monkeys. Both the mean number of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and the mean number of synonymous nucleotide substitutions per synonymous site (d(S)) were elevated in overlap regions in comparison to non-overlap regions. Mean d(N) exceeded mean d(S) in CD8(+)-TL epitopes restricted by the host's class I major histocompatibility complex molecules. This pattern, which is indicative of positive Darwinian selection favoring amino acid changes in these epitopes, was seen in both overlap and non-overlap regions; but mean d(N) was particularly elevated in restricted CD8(+)-TL epitopes encoded in overlap regions. Amino acid changes from the inoculum were defined as parallel if the same amino acid change occurred at the same site independently in two or more monkeys, and a surprisingly high proportion (71.9%) of observed amino acid changes throughout the SIV genome occurred in parallel in different monkeys. The proportion of parallel changes in restricted epitopes encoded by overlapping reading frames was still higher (80%), supporting the hypothesis that the interaction of positive selection and overlapping reading frames enhances the probability of convergent or parallel amino acid change.

Animals↗