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PubMed1981

Sequence divergence of nucleus-confined polyadenylated ribonucleic acids in Friend erythroleukemic cells.

For determination of whether any potential protein-coding RNA sequences are confined to the nucleus in Friend cells, a comparison has been made of the sequence divergence of polyadenylated RNA molecules which are either nucleus confined or transported to the cytoplasm. Both unique DNA and cDNA probes enriched in such sequences were reacted with a large excess of mouse or rat DNA. The extent of hybridization and the thermal stability of hybrids formed under various stringency conditions were used as a measure of the amount of sequence divergence which had taken place. The results confirmed that messenger sequences are relatively conserved during evolution. Furthermore, experiments involving both unique DNA probes representative of the full length of nucleus-confined RNA molecules and cDNA probes complementary to their poly(A)-adjacent fragments indicated that the polyadenylated nucleus-confined sequences have, on average, diverged during evolution much more than mRNA sequences. The vast majority of these sequences therefore probably do not represent potential mRNAs which are confined to the nucleus and subject to posttranscriptional control in a manner similar to those which have been demonstrated in sea urchins [Wold, B., Klein, W. H., Hough-Evans, B. R., Britten, R. J., & Davidson, E. H. (1978) Cell (Cambridge, Mass.) 14, 941-950].

Animals↗
PubMed2001

Comparative FISH mapping of human cDNA clones to chromosomes of the musk shrew (Suncus murinus, Insectivora).

Forty-one cDNA clones of human functional genes were newly mapped to chromosomes of the musk shrew (Suncus murinus, Insectivora) by fluorescence in situ hybridization, and a comparative cytogenetic map of 51 genes, including 10 genes reported in our previous study, was constructed between human (HSA) and musk shrew (SMU) chromosomes. In this comparative map, the 51 genes localized to human autosomes, except HSA 8, 16, and 20, were mapped to 15 shrew autosomes, except SMU 4, 16, 17 and 18. Twelve conserved segments were identified between human and shrew chromosomes, and six segments among the musk shrew, human, and mouse. Our results defined the presence of at least one inversion and several interchromosomal rearrangements that occurred during evolution after the two species diverged from a common ancestor. Localization of three major histocompatibility complex (MHC) genes to shrew chromosome 3 suggested that the MHC genes of the musk shrew are located in a cluster on chromosome 3. The cytogenetic map constructed in this study is the first cytogenetic map with many functional genes in insectivore species. This approach provides clues for clarifying the chromosomal evolution in this order.

Animals↗
PubMed2004

The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily.

BACKGROUND: Structure conservation constrains evolutionary sequence divergence, resulting in observable sequence patterns. Most current models of protein evolution do not take structure into account explicitly, being unsuitable for investigating the effects of structure conservation on sequence divergence. To this end, we recently developed the Structurally Constrained Protein Evolution (SCPE) model. The model starts with the coding sequence of a protein with known three-dimensional structure. At each evolutionary time-step of an SCPE simulation, a trial sequence is generated by introducing a random point mutation in the current coding DNA sequence. Then, a "score" for the trial sequence is calculated and the mutation is accepted only if its score is under a given cutoff, lambda. The SCPE score measures the distance between the trial sequence and a given reference sequence, given the structure. In our first brief report we used a "global score", in which the same reference sequence, the ancestral one, was used at each evolutionary step. Here, we introduce a new scoring function, the "local score", in which the sequence accepted at the previous evolutionary time-step is used as the reference. We assess the model on the UDP-N-acetylglucosamine acyltransferase (LPXA) family, as in our previous report, and we extend this study to all other members of the left-handed parallel beta helix fold (LbetaH) superfamily whose structure has been determined. RESULTS: We studied site-dependent entropies, amino acid probability distributions, and substitution matrices predicted by SCPE and compared with experimental data for several members of the LbetaH superfamily. We also evaluated structure conservation during simulations. Overall, SCPE outperforms JTT in the description of sequence patterns observed in structurally constrained sites. Maximum Likelihood calculations show that the local-score and global-score SCPE substitution matrices obtained for LPXA outperform the JTT model for the LPXA family and for the structurally constrained sites of class i of other members within the LbetaH superfamily. CONCLUSION: We extended the SCPE model by introducing a new scoring function, the local score. We performed a thorough assessment of the SCPE model on the LPXA family and extended it to all other members of known structure of the LbetaH superfamily.

Acyltransferases↗
PubMed2004

Phylogenetic identification of Pneumocystis murina sp. nov., a new species in laboratory mice.

Pneumocystis is a fungal genus that contains multiple species. One member of the genus that has not been formally analysed for its phylogenetic relationships and possible species status is the Pneumocystis found in laboratory mice, Pneumocystis murina sp. nov. (type strain ATCC PRA-111(T)=CBS 114898(T)), formerly known as Pneumocystis carinii f. sp. muris. To advance research in this area, approximately 3000 bp of additional DNA sequence were obtained from the locus encoding rRNAs. This sequence and others were used to determine genetic distances between P. murina and other members of the genus. These distances indicated that P. murina DNA is most similar to that of the species of Pneumocystis found in laboratory rats. Nevertheless, P. murina is at least as diverged from these other Pneumocystis species as species in other fungal genera are from each other. The 18S rRNA gene sequence divergence exhibited by P. murina could not be ascribed to accelerated evolution of this gene as similar levels of divergence were observed at seven other loci. When five genes were used to construct phylogenetic trees for five Pneumocystis taxa, including P. murina, all the trees had the same topology, indicating that genes do not flow among these taxa. The gene trees were all strongly supported by statistical tests. When sequences from the rRNA-encoding locus were used to estimate the time of divergence of P. murina, the results indicated that P. murina is as old as the mouse. Taken together, these data support previous recognition of multiple species in the genus and indicate that P. murina is a phylogenetic species as well.

Animals↗
PubMed2001

Recent trends in the initial surgical treatment of primary hyperparathyroidism: a review.

INTRODUCTION: The standard treatment of primary hyperparathyroidism has long been, and for many surgeons still is, a cervicotomy with presentation of all parathyroid glands. The last two decades have been marked by a progress in localization and identification techniques, together with a general trend towards less invasive surgery. This evolution resulted in numerous and diverging new surgical strategies, all claiming to be as effective as the conventional neck exploration, but resulting in fewer complications and better cosmesis. We want to give an overview and a realistic positioning of these new techniques. METHODOLOGY: A literature search using PubMed from January 1980 to December 2000, combined with reference checking, identified the most important articles describing the new strategies. We present the evolution in the thinking, the data supplied, and our critical remarks. RESULTS AND CONCLUSION: The initial random unilateral exploration was followed by trials to achieve a more guided unilateral exploration. Different adjuncts developed can be classified as preoperative (isotope scanning, ultrasonography, computer tomographic scanning) and intraoperative (intraoperative intact parathyroid hormone measurement, intraoperative 99mTc sestamibi scanning). The surgical techniques using these adjuncts range from a classic collar type incision followed by a unilateral exploration, over external exploration (unilateral or bilateral) through a very small incision, to endoscopic neck exploration. Reported outcomes of these techniques are presented, and all aspects mentioned are labeled as T-1 (preoperative), T0 (intraoperative), or T + 1 (results and complications) features. The reported results seem to indicate there is a place for a less invasive approach, but should be interpreted with caution seeing the ever present selection bias in the described population.

Humans↗
PubMed2006

Experimental evidence that predation promotes divergence in adaptive radiation.

Adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Recent studies have identified general patterns in adaptive radiation and inferred that resource competition is a primary factor driving phenotypic divergence. The role and importance of other processes, such as predation, remains controversial. Here we use Timema stick insects to show that adaptive radiation can be driven by divergent selection from visual predators. Ecotypes using different host-plant species satisfy criteria for the early stages of adaptive radiation and differ in quantitative aspects of color, color pattern, body size, and body shape. A manipulative field experiment demonstrates that the direction and strength of divergent selection on these traits is strongly positively correlated with the direction and magnitude of their population divergence in nature but only when selection is estimated in the presence of predation. Our results indicate that both competition and predation may commonly serve as mechanisms of adaptive radiation.

Adaptation, Biological↗
PubMed2002

The evolution of wing color in Colias butterflies: heritability, sex linkage, and population divergence.

We investigated the genetic background of intraspecific variation in wing color across an elevational gradient in the butterfly Colias philodice eriphyle. The degree of wing melanization was an accelerating function of elevation, and differences in wing melanization persisted in a common environment. Full-sibling analysis and parent-offspring regression yielded consistent, moderate to high heritabilities for the degree of wing melanization. The breeding experiments also demonstrated that wing melanization is strongly sex linked. Because traits that differentiate sister species also tend to be sex linked, our results suggest that the genetic mechanisms underlying intraspecific differences in wing melanization are not fundamentally different from those that have been shown to differentiate sister species.

Analysis of Variance↗
PubMed2006

Evidence for an immune function of lepidopteran silk proteins.

Hemolymph coagulation stops bleeding and protects against infection. Clotting factors include both proteins that are conserved during evolution as well as more divergent proteins in different species. Here we show that several silk proteins also appear in the clot of the greater wax moth Galleria mellonella. RT-PCR analysis reveals that silk proteins are expressed in immune tissues and induced upon wounding in both Galleria and Ephestia kuehniella, a second pyralid moth. Our results support the idea that silk proteins were co-opted for immunity and coagulation during evolution.

Animals↗
PubMed2003

Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats.

Molecular and morphological hypotheses disagree on the phylogenetic position of New Zealand's short-tailed bat Mystacina tuberculata. Most morphological analyses place Mystacina in the superfamily Vespertilionoidea, whereas molecular studies unite Mystacina with the Neotropical noctilionoids and imply a shared Gondwanan history. To date, competing hypotheses for the placement of Mystacina have not been addressed with a large concatenation of nuclear protein sequences. We investigated this problem using 7.1kb of nuclear sequence data that included segments from five nuclear protein-coding genes for representatives of 14 bat families and six laurasiatherian outgroups. We employed the Thorne/Kishino method of molecular dating, allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution on different branches on the phylogenetic tree, to estimate basal divergence times within key chiropteran clades. Maximum likelihood, minimum evolution, maximum parsimony, and Bayesian posterior probabilities all provide robust support for the association of Mystacina with the South American noctilionoids. The basal divergence within Chiroptera was estimated at 67mya and the mystacinid/noctilionoid split was calculated at 47mya. Although the mystacinid lineage is too young to have originated in New Zealand before it split from the other Gondwanan landmasses (80mya), the exact geographic origin of these lineages is still uncertain and will not be answered until more fossils are found. It is most probable that Mystacina dispersed from Australia to New Zealand while other noctilionoid bats either remained in or dispersed to South America.

Animals↗
PubMed2005

Loss of dispensable genes is not adaptive in yeast.

A substantial share of genes identified in yeast can be deleted without visible phenotypic effects. Current debate concentrates on the possible roles of seemingly dispensable genes. The costs of maintaining unnecessary functions has attracted little attention. The hypothesis of antagonistic pleiotropy postulates that adaptations to different constituents of the environment are likely to interfere with each other, and therefore loss of unnecessary functions is potentially advantageous. We tested an entire collection of nonessential yeast gene deletions in a benign and nutritionally rich environment in which the number of dispensable genes was particularly high. We applied a series of competition experiments that could detect differences in relative fitness of approximately 0.005. No beneficial deletions were found, except perhaps for the deletion of about a dozen genes that slightly improved competitive ability; however, a functional explanation of the fitness advantage is lacking. The paucity of beneficial gene deletions is striking because genetic adaptations to laboratory conditions are regularly observed in yeast. However, it accords with the finding that the gene contents of four species of Saccharomyces are nearly identical, despite up to 20 million years of independent evolution and extensive DNA sequence divergence. Such extreme conservation of functions would be improbable if there were periods of selection promoting the loss of temporarily dispensable genes. The evident cohesion of the yeast genomes may be their evolved feature or an intrinsic property of complex genetic systems.

Adaptation, Physiological↗
PubMed2002

Gene duplications in the prototypical cephalochordate amphioxus.

The new discipline of Evolutionary Developmental Biology (Evo-Devo) is facing the fascinating paradox of explaining morphological evolution using conserved pieces or genes to build divergent animals. The cephalochordate amphioxus is the closest living relative to the vertebrates, with a simple, chordate body plan, and a genome directly descended from the ancestor prior to the genome-wide duplications that occurred close to the origin of vertebrates. Amphioxus morphology may have remained relatively invariant since the divergence from the vertebrate lineage, but the amphioxus genome has not escaped evolution. We report the isolation of a second Emx gene (AmphiEmxB) arising from an independent duplication in the amphioxus genome. We also argue that a tandem duplication probably occurred in the Posterior part of the Hox cluster in amphioxus, giving rise to AmphiHox14, and discuss the structure of the chordate and vertebrate ancestral clusters. Also, a tandem duplication of Evx in the amphioxus lineage produced a prototypical Evx gene (AmphiEvxA) and a divergent gene (AmphiEvxB), no longer involved in typical Evx functions. These examples of specific gene duplications in amphioxus, and other previously reported duplications summarized here, emphasize the fact that amphioxus is not the ancestor of the vertebrates but 'only' the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.

Amino Acid Sequence↗
PubMed2006

Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96.

Nup96 is involved in a lethal hybrid incompatibility between 2 fruit fly species, Drosophila melanogaster and Drosophila simulans. Recurrent adaptive evolution drove the rapid functional divergence of Nup96 in both the D. melanogaster and the D. simulans lineages. Functional divergence of Nup96 between these 2 species is unexpected as Nup96 encodes part of the Nup107 subcomplex, an architectural component of nuclear pore complexes, the macromolecular channels in nuclear envelopes that mediate nucleocytoplasmic traffic in all eukaryotes. Here we study the evolutionary histories of 5 of Nup96's protein interactors--3 stable Nup107 subcomplex proteins (Nup75, Nup107, and Nup133) and 2 mobile nucleoporins (Nup98 and Nup153)--and show that all 5 have experienced recurrent adaptive evolution. These results are consistent with selection-driven coevolution among molecular interactors within species causing the incidental evolution of incompatible interactions seen in hybrids between species. We suggest that genetic conflict-driven processes may have contributed to the rapid molecular evolution of Nup107 subcomplex genes.

Animals↗
PubMed2004

Comparative genomics of major histocompatibility complexes.

The major histocompatibility complex (MHC) is a gene dense region found in all jawed vertebrates examined to date. The MHC contains a high percentage of immune genes, in particular genes involved in antigen presentation, which are generally highly polymorphic. The region plays an important role in disease resistance. The clustering of MHC genes could be advantageous for co-evolution or regulation, and its study in many species is desirable. Even though some linkage of MHC genes is apparent in all gnathostomes, the genomic organization can differ greatly by species, suggesting rapid evolution of MHC genes after divergence from a common ancestor. Previous reviews of comparative MHC organization have been written when relatively fragmentary sequence and mapping data were available on many species. This review compares maps of MHC gene orders in commonly studied species, where extensive sequencing has been performed.

Animals↗
PubMed2000

Distal-less-related homeobox genes of vertebrates: evolution, function, and regulation.

Homeobox genes of the Distal-less family have been identified in virtually all metazoan groups where they play roles in the ontogeny of these animals. The vertebrate Distal-less related genes (Dlx genes) are thought to have arisen as a result of a tandem gene duplication event followed by a number of larger genomic scale duplications and thus represent an interesting model with which to study the evolution of clustered gene families. Dlx genes are involved in the development of the forebrain, branchial arches, sensory organs, and limbs. Here we describe the current state of knowledge of the Dlx genes in terms of their developmental expression, how this expression is regulated and how the products of these genes function, once expressed. We highlight a number of recent studies that have shed light on the transcriptional regulation of this gene family. These findings have not only contributed to our understanding of the selective pressures involved in the maintenance of familial gene clustering in genomes, but also to our understanding of how genes may diverge in function during the course of evolution as a result of divergence of regulatory mechanisms.

Animals↗
PubMed1993

Structure, expression, and evolution of guinea pig serum amyloid P component and C-reactive protein.

The structure and expression of the pentraxins, serum amyloid P component (SAP), and C-reactive protein (CRP), have been investigated in the guinea pig. Northern blot analysis of hepatic RNA from animals in which acute inflammation had been induced by intraperitoneal injection of thioglycollate established that neither SAP or CRP is a major acute phase reactant in the guinea pig. Genomic clones of SAP and CRP were isolated and sequenced, and the gene and the derived protein sequences were compared with other mammalian homologues. Both genes have organizations typical of the pentraxin genes of other species, but some differences were defined in the regions that potentially determine the capacity of the pentraxin gene to be induced during acute inflammation. Nucleotide substitutions in coding regions have occurred at similar rates in the two pentraxin genes. Nonsynonymous substitution rates indicate that SAP and CRP are subject to similar, relatively low levels of constraint; at the amino acid sequence level the rate of evolution is approximately two replacements per site per 10(9) years. An estimate of the phylogenetic relationship among the pentraxin genes suggests that SAP and CRP arose as the result of a gene duplication event that occurred very early in mammalian evolution, but subsequent to the divergence of the reptilian ancestors of the mammalian and avian lineages. This raises doubts about the identity of proteins from fish, which have been previously characterized as CRP and SAP.

Acute-Phase Reaction↗
PubMed1983

Isolation and characterization of human myosin heavy chain genes.

We have isolated four unique human sarcomeric myosin heavy chain (MHC) genomic clones using rat MHC cDNA clones as probes. Three of these clones contain adult skeletal muscle-specific DNA sequences, whereas one clone contains embryonic skeletal muscle-specific sequences. This developmental and tissue specificity was determined by hybridization of each of the human clones to MHC mRNA from different muscle tissues. Cross-hybridization studies indicate that certain sequences of the human MHC genes have been conserved through evolution while other portions have diverged considerably. Preliminary evidence demonstrates that the MHC gene family is polymorphic in human populations. Each of the human MHC genes was shown to have repetitive sequences in multiple positions, both within the gene and in adjacent flanking DNA sequences. We have shown that, in contrast, four rat MHC genes have far fewer repetitive sequences even though two of the four genes contain the same muscle specificity as the human genes. Therefore, these genes may be useful to study gene evolution and repetitive sequence transposition.

Animals↗
PubMed1987

[Comparative anatomy of the velopharyngeal complex in mammals--excluding primates (1)].

From the anatomic element known with the man by the name of soft palatal-pharyngeal sphincter and which takes a major part in the phonation, the swallowing, the breathing, we have studied the evolutive morphology of the soft palatal-pharyngeal unity in several mammals. This unity which includes the levator palati and palatopharyngeus muscles is confirmed by the phylogenic and embryologic investigations. The comparative anatomy of the rat, rabbit, sheep and lion, allows to make obvious a evolutive line characterized by the gradual divergence of the axis of the two muscles common to the soft palatal and pharyngeal musculature, which could correspond with a phylogenic evolution.

Anatomy, Comparative↗
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↗