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PubMed2000

Molecular systematics of the African electric fishes (Mormyroidea: teleostei) and a model for the evolution of their electric organs.

We present a new molecular phylogeny for 41 species of African mormyroid electric fishes derived from the 12S, 16S and cytochrome b genes and the nuclear RAG2 gene. From this, we reconstruct the evolution of the complex electric organs of these fishes. Phylogenetic results are generally concordant with earlier preliminary molecular studies of a smaller group of species and with the osteology-based classification of Taverne, which divides the group into the Gymnarchidae and the Mormyridae, with the latter including the subfamilies Petrocephalinae (Petrocephalus) and Mormyrinae (all remaining taxa). However, we find that several genera previously recognized by Taverne are non-monophyletic. Within the Mormyrinae, the genus Myomyrus is the sister group to all the remaining taxa. Other well-supported clades within this group are recovered. A reconstruction of electrocyte evolution on the basis of our best-supported topology suggests that electrocytes with penetrating stalks evolved once early in the history of the mormyrids followed by multiple paedomorphic reversals to electrocytes with non-penetrating stalks.

Animals↗
PubMed1995

The maximum information principle and the evolution of nucleotide sequences.

The probability distributions of bases in nucleotide sequences are deduced from the maximum information principle by maximizing the entropy (due to random mutation of bases) under certain constraints (Markovian entropy, G + C content, etc, due to selection). Two formulations are given with respect to different selective constraints. The deviations of theoretical distributions from experimental data are lower than 10% for most sequences. It is shown that the Lagrange multipliers change from species to species systematically--i.e. selective constraints correlate with evolution.

Animals↗
PubMed2000

The evolution of the atpbeta-rbcL intergenic spacer in the epacrids (Ericales) and its systematic and evolutionary implications.

Sequence data from the noncoding region separating the plastid genes atpbeta and rbcL were gathered for 27 epacrid taxa, representing all previously recognized infrafamilial groups, and four outgroup taxa (Ericaceae), to address several persistent phylogenetic questions in the group. Parsimony analyses were conducted on these data, as well as on a complementary rbcL sequence dataset assembled from the literature and the combined dataset. The atpbeta-rbcL spacer was notable for the high frequency of insertion-deletion mutations (indels); their distributions were coded as binary characters and included as a adjunct matrix in some of the analyses. The phylogenetic patterns derived from the spacer and rbcL data and the combined analyses, both including and excluding the indel data, concur in resolving seven major lineages corresponding to the tribes of Crayn et al. (1998, Aust. J. Bot. 46, 187-200), viz. Prionoteae, Archerieae, Oligarrheneae, Cosmelieae, Richeeae, Epacrideae, and Styphelieae. The relationships of the tribes and within Styphelieae, however, are not convincingly resolved. Minor conflicts in the positions of some taxa between the spacer and the rbcL trees are poorly supported. Among epacrids, the spacer region provided more cladistically informative characters than rbcL and resulted in trees with lower homoplasy. Further, the spacer data, when analyzed alone and when combined with rbcL, resolved several clades that could not be retrieved on rbcL data alone and provided increased support for many other relationships. The evolution of a putative three-base inversion associated with a hairpin secondary structure in the spacer region is discussed in the light of the inferred phylogeny.

Classification↗
PubMed1999

Evolution of thyroid hormone binding by transthyretins in birds and mammals.

Transthyretin, a protein synthesized and secreted by the choroid plexus and liver, binds thyroid hormones in extracellular compartments. This binding prevents accumulation of thyroid hormones in the lipids of membranes, establishing extracellular thyroid hormone pools for the distribution of the hormones throughout the body and brain. The N-termini of the transthyretin subunits are longer and more hydrophobic in chicken than in eutherian transthyretins. Here, we show that this is a general structural feature of avian transthyretins. Systematic changes of protein structure during evolution result from selection pressure leading to changes in function. The evolution of transthyretin function, namely, the binding of thyroid hormones, was studied in nine vertebrate species. The affinity of thyroxine binding to transthyretin is lowest in avians (mean Kd of about 30 nm), intermediate in metatherians (mean Kd of about 17 nm) and highest in eutherians (mean Kd of about 11 nm). The affinity for 3,5,3'-triiodothyronine shows an opposite trend, being four times higher for avian transthyretins than for mammalian transthyretins.

Amino Acid Sequence↗
PubMed1996

Mitochondrial gene sequences and the molecular systematics of the artiodactyl subfamily bovinae.

Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla. The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). Although the phylogenetic analyses grouped Bison as sister to Bos, the genus Bison was paraphyletic, with the American bison being most closely related to species of Bos rather than to the European bison. COII data also supported a close relationship between African (Syncerus) and Asian (bubalus) buffaloes, the monophyly of the tribe Bovini, and a sister-group relationship between the tribes Bovini and Boselaphini. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa.

Animals↗
PubMed2001

Evolution of the FAD2-1 fatty acid desaturase 5' UTR intron and the molecular systematics of Gossypium (Malvaceae).

The FAD2-1 microsomal omega-6 desaturase gene contains a large intron ( approximately 1133 bp [base pairs]) in the 5' untranslated region that may participate in gene regulation and, in GOSSYPIUM:, is evolving at an evolutionary rate useful for elucidating recently diverged lineages. FAD2-1 is single copy in diploid GOSSYPIUM: species, and two orthologs are present in the allotetraploid species. Among the diploid species, the D-genome FAD2-1 introns have accumulated substitutions 1.4-1.8 times faster than the A-genome introns. In the tetraploids, the difference between the D-subgenome introns and their A-subgenome orthologs is even greater. The substitution rate of the intron in the D-genome diploid G. gossypioides more closely approximates that of the A genome than other D genome species, highlighting its unique evolutionary history. However, phylogenetic analyses support G. raimondii as the closest living relative of the D-subgenome donor. The Australian K-genome species diverged 8-16 million years ago into two clades. One clade comprises the sporadically distributed, erect to suberect coastal species; a second clade comprises the more widely spread, prostrate, inland species. A comparison of published gene trees to the FAD2-1 intron topology suggests that G. bickii arose from an early divergence, but that it carries a G. australe-like rDNA captured via a previously undetected hybridization event.

Journal Article↗
PubMed2003

The geometry of the marmot (rodentia: sciuridae) mandible: phylogeny and patterns of morphological evolution.

Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Sciurid morphology can be used as model to test the congruence between morphological change and phylogeny because sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken. Geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared, and mean mandible shape were used to investigate morphological evolution in the genus Marmota. Three major trends were observed. First, the phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cytochrome b sequence, receive support from mandible morphology. When other sciurid genera were included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs, and ground squirrels) was strengthened by the morphological data. Second, the marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. Third, allopatric speciation in peripheral isolates may have acted as a powerful force for modeling shape. This hypothesis is strongly supported by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.

Adaptation, Biological↗
PubMed2000

Evolution of schistosomiasis-induced pathology after therapy and interruption of exposure to schistosomes: a review of ultrasonographic studies.

Ultrasonography (US) is suitable for diagnosing schistosomiasis-related organic pathology and is particularly useful to assess its evolution after therapy and/or interruption of exposure to the Schistosoma parasites. Evolution of pathology after treatment: Regression of hepatic abnormalities in Schistosma mansoni-infected children and adolescents has been observed already from 7 months post-therapy on. This does, however, not occur in all cases: individual differences are great ranging from spontaneous regression of pathology without treatment to persistence of pathology lasting for years after therapy even without re-infection. Intensity and duration of exposure, different parasite strains, patients' age and genetic background all influence the evolution of pathology. In communities at continuous exposure to S. mansoni infection, repeated re-treatment is required to control hepatosplenic morbidity. In Schistosoma japonicum infection, changes around the portal tree may regress, but characteristic diffuse abnormalities described as 'network pattern' abnormalities do not resolve. In Schistosoma haematobium infection bladder abnormalities and urinary tract obstruction frequently resolve after treatment. Clinically relevant pathology may resurge from 1 year after therapy on if exposure continues. Subjects with more advanced pathology before therapy, appear to be at higher risk of pathology re-appearance. Evolution of pathology after interruption of exposure to schistosomiasis: Knowledge on the evolution of pathology induced by S. mansoni is limited to some reports in emigrants and to the experience of ultrasonographists working in areas, where transmission has been partially interrupted. Due to the longevity of the parasite, infection may last for many years. Even after elimination of the parasites severe pathology may persist for long. In S. haematobium infection spontaneous healing after interruption of re-exposure may occur, but cases have been reported where urogenital lesions led to complications many years after exposure. Contrary to hepatosplenic and urinary pathology, knowlegde on the evolution of other organic abnormalities is very limited: studies on the evolution of biliary abnormalities or intestinal pathology have not been published. Genital pathology may be induced by all Schistosoma spp. Post-therapy evolution of genital schistosomiasis is largely ignored. In some European travellers partial regression of prostatic fibrosis has been described. Schistosomal adnexitis leading to infertility and/or ectopic pregnancy has been reported occurring many years after interruption of exposure. Ultrasonography (US) has never been used to study the influence of schistosomiasis on pregnancy. Concluding, current knowlegde on the evolution of pathology after treatment and/or interruption of exposure is still fragmentary. Frequently, fibrosis reverses after therapy, but advanced pathology may persist for long. Therefore, the possibility of severe clinical complications has to be taken into account, even if the infection is inactive since many years. In interventions aimed at controlling schistosomiasis-related morbidity, evolution of pathology must be monitored by US in representative patient cohorts. Further systematic US-studies are needed not only on the evolution of hepatosplenic and urinary pathology but also on that of intestinal, biliary and genital pathology induced by schistosomiasis, as well as on the influence of schistosomiasis on the outcome of pregnancy.

Adolescent↗
PubMed1991

Taxonomy, evolution and life cycles.

Three lectures were given, the first on haplodiploidy in the Oxyurida (Nematoda), the second on rodent Oxyurida and the third on the life cycle of Leishmania (Kinetoplastida, Trypanosomatidae). The oral communications and posters were divided into five subsections, covering systematics at supraspecific, specific and subspecific levels, evolution, and life cycles of parasites with hosts in both aquatic and terrestrial environments. A wide range of topics was discussed, including recent developments in the fields of genetics and cellular and molecular biology, and computer-assisted numerical taxonomy.

Animals↗
PubMed2002

Models of intracellular transport and evolution of the Golgi complex.

We have performed a systematic analysis of models explaining the mechanisms of the intracellular biosecretory transport. The models assessed include not only those based on one mechanism (the dissociation model (and its individual case, the vesicular model), the progression model (and its individual cases, the cisterna maturation/progression and the carrier maturation models), and the lateral diffusion model (and its individual case, the bolus model), but also combined models of transport (the percolating-vesicles model and the synthetic model), including several transport mechanisms. Most of these models are not able to explain recent data on the evolution of genes involved in intracellular transport and Golgi evolution. The carrier maturation model proposing that fusion of the large cargo domain with the distal (closer to the plasmalemma) compartment precedes fission of the domain from the proximal compartment exhibits the best performance in correlation with the available information on evolution of the biosecretory pathway.

Biological Evolution↗
PubMed1990

The Syphaciinae (Oxyuridae, Nematoda) parasitic in rodents and lagomorpha. Numerical taxonomy. Cladistic analysis of evolution.

Two different methods are successively used for the systematic study of the Syphaciinae, a parasitic group of pin-worms specific for the Rodents and Lagomorpha. The statistical method permits to build a "phenetic classification"; the cladistic method permits to build a "phylogenetic classification". The classification finally proposed is principally found on the results of the morphological study of the parasites, but has also in view the integration of all available data concerning the biology, the biogeography and the phylogeny of the hosts.

Animals↗
PubMed2002

Microevolutionary genomics of bacteria.

The availability of multiple complete genome sequences from the same species can facilitate attempts to systematically address basic questions in genome evolution. We refer to such efforts as "microevolutionary genomics". We report the results of comparative analyses of complete intraspecific genome (and proteome) sequences from four bacterial species--Chlamydophila pneumoniae, Escherichia coli, Helicobacter pylori and Neisseria meningitidis. Comparisons of average synonymous (K(s)) and nonsynonymous (K(a)) substitution rates were used to assess the influence of various biological factors on the rate of protein evolution. For example, E. coli experiences the most intense purifying selection of the species analyzed, and this may be due to the relatively larger population size of this species. In addition, essential genes were shown to be more evolutionarily conserved than nonessential genes in E. coli and duplicated genes have higher rates of evolution than unique genes for all species studied except C. pneumoniae. Different functional categories of genes were shown to evolve at significantly different rates emphasizing the role of category-specific functional constraints in determining evolutionary rates. Finally, functionally characterized genes tend to be conserved between strains, while uncharacterized genes are over-represented among the unique, strain-specific genes. This suggests the possibility that nonessential genes are responsible for driving the evolutionary diversification between strains.

Bacteria↗
PubMed2001

Estimating the need for radiotherapy for lung cancer: an evidence-based, epidemiologic approach.

BACKGROUND AND OBJECTIVES: Current estimates of the proportion of cancer patients who will require radiotherapy (RT) are based almost entirely on expert opinion. The objective of this study was to use an evidence-based approach to estimate the proportion of incident cases of lung cancer that will require RT at any point in the evolution of the illness. METHODS: A systematic review of the literature was undertaken to identify indications for RT for lung cancer, and to ascertain the level of evidence that supported each indication. An epidemiologic approach was then used to estimate the incidence of each indication for RT in a typical North American population of lung cancer patients. The effect of sampling error on the estimated appropriate rate of RT was calculated mathematically, and the effect of systematic error, was estimated by sensitivity analysis. RESULTS: It was shown that 53.6% +/- 3.3% of small-cell lung cancer (SCLC) cases develop one or more indications for RT at some point in the course of the illness, 45.4% +/- 4.3% in their initial treatment, and 8.2% +/- 1.5% later for recurrence of progression. Overall, 64.3% +/- 4.7% of non-small-cell lung cancer (NSCLC) cases require RT, 45.9% +/- 4.3% in their initial treatment, and 18.3% +/- 1.8% later in the course of the illness. The proportion of NSCLC cases that ever require RT is stage dependent; 41.0% +/- 5.5% in Stage I; 54.5% +/- 6.5% in Stage II; 83.5% +/- 10.6% in Stage III; and 65.7% +/- 7.6% in Stage IV. In total, 61.0% +/- 3.9% of all patients with lung cancer will develop one or more indications for RT at some point in the illness, 44.6% +/- 3.6% in their initial treatment, and 16.5% +/- 1.5% later for recurrence or progression. CONCLUSION: This method provides a rational starting point for the long-term planning of radiation services, and for the audit of access to RT at the population level. We now plan to extend this study to the other major cancer sites to enable us to estimate the appropriate RT treatment rate for the cancer population as a whole.

Algorithms↗
PubMed1996

Somatic microsatellite mutations as molecular tumor clocks.

Microsatellite (MS) mutations can potentially unravel the past of mutator phenotype tumors, with greater genetic diversity expected in older regions. Rapid clonal expansions of xenografts were characterized by relatively homogenous MS alleles, whereas greater diversity was observed in a colorectal cancer with the greatest variation in its adjacent adenoma. A subcutaneous lung cancer metastasis demonstrated diversity consistent with its one-month clinical duration and evidence of active mitosis during dormancy. The genetic legacy inherent to multistep tumorigenesis provides direct estimates of tumor ages, with up to thousands of cell divisions and high death rates necessary to yield the observed diversities. MS molecular tumor clocks have the unique potential to systematically reconstruct the early and occult evolution of individual human mutator phenotype tumors.

Adenocarcinoma↗
PubMed1999

Self-assembly of helical ribbons.

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54 +/- 2 degrees, and low pitch, with a pitch angle of 11 +/- 2 degrees. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range 30-47 degrees, is occasionally found. These experimental findings suggest that the helical ribbons are crystalline rather than liquid crystal in nature and also suggest that molecular chirality may not be the determining factor in helix formation. The large yields of helices produced will permit a systematic investigation of their individual kinetic evolution and their elastic moduli.

Bile Acids and Salts↗
PubMed1998

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

Adenosine Triphosphatases↗
PubMed1999

Systematic biology of gymnotiform and mormyriform electric fishes: phylogenetic relationships, molecular clocks and rates of evolution in the mitochondrial rRNA genes

The phylogenetic relationships of both African and South American electric fish orders are reviewed at their intra-ordinal level taking into consideration recent studies in which cladistic principles have been employed. Several concordant topologies emerge from the different data sets, but some unsettled issues still remain. From the studies available, a consensus topology has been suggested for the Mormyriformes and for the Gymnotiformes. Subsequently, the evolutionary relationships of these two electric fish clades are considered within each respective superorder, i.e. in relation to the other osteoglossomorph and ostariophysan orders. The inter-ordinal phylogenies are used as a framework to test the molecular clock hypothesis with two gene fragments of the mitochondrial genome. Gymnotiformes, Siluriformes and Characiformes are accumulating mutations at the same pace in relation to their respective outgroups, but for all the other combinations of sister clades tested the molecular clock can be statistically rejected. Fossil records are then surveyed and used to calibrate absolute rates of genetic differentiation for each main lineage (orders) of both osteoglossomorphs and ostariophysans. The most conserved regions (stems) of the 12S and 16S gene fragments used are evolving at an average rate of 0.123 % 10(6 )years-1 for the osteoglossomorphs and 0.137 % 10(6 )years-1 for the ostariophysans, with no significant difference between these two values. The rate of mutation in the loops, the faster-evolving segments, estimated for closely related electric fish taxa is 0.82 % 10(6 )years-1 for four Brienomyrus species and 1.01 % 10(6 )years-1 for the four eigenmanniid genera. When the entire molecule (loops + stems) is considered, the rate of mutation in both mormyriforms and gymnotiforms converges to a rounded value of 0.23 % 10(6 )years-1.

Journal Article↗