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PubMed2003

The evolution of the music faculty: a comparative perspective.

We propose a theoretical framework for exploring the evolution of the music faculty from a comparative perspective. This framework addresses questions of phylogeny, adaptive function, innate biases and perceptual mechanisms. We argue that comparative studies can make two unique contributions to investigations of the origins of music. First, musical exposure can be controlled and manipulated to an extent not possible in humans. Second, any features of music perception found in nonhuman animals must not be part of an adaptation for music, and must rather be side effects of more general features of perception or cognition. We review studies that use animal research to target specific aspects of music perception (such as octave generalization), as well as studies that investigate more general and shared systems of the mind/brain that may be relevant to music (such as rhythm perception and emotional encoding). Finally, we suggest several directions for future work, following the lead of comparative studies on the language faculty.

Animals↗
PubMed2000

Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome.

Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

Arabidopsis↗
PubMed2001

The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies.

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.

Animals↗
PubMed2000

The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements.

The R and B genes of maize regulate the anthocyanin biosynthetic pathway and constitute a small gene family whose evolution has been shaped by polyploidization and transposable element activity. To compare the evolution of regulatory genes in the distinct but related genomes of rice and maize, we previously isolated two R homologues from rice (Oryza sativa). The Ra1 gene on chromosome 4 can activate the anthocyanin pathway, whereas the Rb gene, of undetermined function, maps to chromosome 1. In this study, rice R genes have been further characterized. First, we found that an Rb cDNA can induce pigmentation in maize suspension cells. Second, another rice R homologue (Ra2) was identified that is more closely related to Ra1 than to Rb. Domesticated rice and its wild relatives harbor multiple Ra-like and Rb-like genes despite the fact that rice is a true diploid with the smallest genome of all the grass species analyzed to date. Finally, several miniature inverted-repeat transposable elements (MITEs) were found in R family members. Their possible role in hastening the divergence of R genes is discussed.

Amino Acid Sequence↗
PubMed1981

Simulation of protein evolution by random fixation of allowed codons.

Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin alpha and beta chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 X 10(-10) to 10(-8) accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.

Amino Acids↗
PubMed1992

Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and compared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The molecular sequence chosen is demonstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point mutations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a moderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearman's rank correlation test, which requires only relative magnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the number of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approximate to a clocklike model within restricted echinoid clades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.

Animals↗
PubMed1991

Comparative methods for explaining adaptations.

The ways that taxonomic differences in morphology, behaviour or life history are related to each other and to differences in lifestyle have been used regularly to test ideas about the selective forces involved in their evolution. Such comparative tests have been transformed recently by using increased statistical rigour. The realization that the statistical model against which comparisons are made is a model of how evolution proceeds, forms the basis of a new generation of comparative tests that are grounded properly on phylogenetic reconstruction.

Adaptation, Physiological↗
PubMed2004

Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres.

The recent release of sequences of several unexplored yeast species that cover an evolutionary range comparable to the entire phylum of chordates offers us a unique opportunity to investigate how genes involved in adaptation have been shaped by evolution. We have examined how three different sets of genes, all related to adaptative processes at the genomic level, have evolved in hemiascomycetes: (1) the mating-type genes that govern sexuality, (2) the silencing genes that are connected to regulation of mating-type cassettes and to telomere position effect, and (3) the gene families found repeated in subtelomeric regions. We report new combinations of mating-type genes and cassettes in hemiascomycetous species; we show that silencing proteins diverge rapidly. We have also found that in all species studied, subtelomeric gene families exist and are specific to each species.

Amino Acid Sequence↗
PubMed2004

Can fat explain the human brain's big bang evolution?-Horrobin's leads for comparative and functional genomics.

When David Horrobin suggested that phospholipid and fatty acid metabolism played a major role in human evolution, his 'fat utilization hypothesis' unified intriguing work from paleoanthropology, evolutionary biology, genetic and nervous system research in a novel and coherent lipid-related context. Interestingly, unlike most other evolutionary concepts, the hypothesis allows specific predictions which can be empirically tested in the near future. This paper summarizes some of Horrobin's intriguing propositions and suggests as to how approaches of comparative genomics published in Cell, Nature, Science and elsewhere since 1997 may be used to examine his evolutionary hypothesis. Indeed, systematic investigations of the genomic clock in the species' mitochondrial DNA, the Y and autosomal chromosomes as evidence of evolutionary relationships and distinctions can help to scrutinize associated predictions for their validity, namely that key mutations which differentiate us from Neanderthals and from great apes are in the genes coding for proteins which regulate fat metabolism, and particularly the phospholipid metabolism of the synapses of the brain. It is concluded that beyond clues to humans' relationships with living primates and to the Neanderthals' cognitive performance and their disappearance, the suggested molecular clock analyses may provide crucial insights into the biochemical evolution-and means of possible manipulation-of our brain.

Animals↗
PubMed2005

Comparative interactomics.

The behavior, morphology and response to stimuli in biological systems are dictated by the interactions between their components. These interactions, as we observe them now, are therefore shaped by genetic variations and selective pressure. Similar to what has been achieved by comparing genome structures and protein sequences, we hope to obtain valuable information about systems' evolution by comparing the organization of interaction networks and by analyzing their variation and conservation. Equally, significantly we can learn whether and how to extend the network information obtained experimentally in well-characterized model systems to different organisms. We conclude from our analysis that, despite the recent completion of several high throughput experiments aimed at the description of complete interactomes, the available interaction information is not yet of sufficient coverage and quality to draw any biologically meaningful conclusion from the comparison of different interactomes. Thus, the transfer of network information obtained from simple organism to evolutionary distant species should be carried out and considered with caution. By using smaller higher-confidence datasets, a larger fraction of interactions is shown to be conserved; this suggests that with the development of more accurate experimental and informatic approaches, we will soon be in the position to study the network evolution.

Animals↗
PubMed2005

Correlative radiological, self-assessment and clinical analysis of evolution in instrumented dorsal and lateral fusion for degenerative lumbar spine disease. Autograft versus coralline hydroxyapatite.

This prospective longitudinal randomized clinical and radiological study compared the evolution of instrumented posterolateral lumbar and lumbosacral fusion using either coralline hydroxyapatite (CH), or iliac bone graft (IBG) or both in three comparable groups, A, B and C, which included 19, 18 and 20 patients, respectively, who suffered from symptomatic degenerative lumbar spinal stenosis and underwent decompression and fusion. The patients were divided randomly according to the graft used and the side that it was applied. The spines of group A received autologous IBG bilaterally; group B, IBG on the left side and hydroxyapatite mixed with local bone and bone marrow on the right side; group C, hydroxyapatite mixed with local bone and bone marrow bilaterally. The age of the patients in the groups A, B and C was 61+/-11 years, 64+/-8 years and 58+/-8 years, respectively. The SF-36, Oswestry Disability Index (ODI), and Roland-Morris (R-M) surveys were used for subjective evaluation of the result of the surgery and the Visual Analogue Scale (VAS) for pain severity. Plain roentgenograms including anteroposterior, lateral and oblique views, and lateral plus frontal bending views of the instrumented spine and CT scan were used to evaluate the evolution of the posterolateral fusion in all groups and sides. Two independent senior orthopaedic radiologists were asked to evaluate first the evolution of the dorsolateral bony fusion 3-48 months postoperatively with the Christiansen's radiologic method, and secondly the hydroxyapatite resorption course in the spines of groups B and C. The diagnosis of solid spinal fusion was definitively confirmed with the addition of the bending views, CT scans and self-assessment scores. The intraobserver and interobserver agreement (r) for radiological fusion was 0.71 and 0.69, respectively, and 0.83 and 0.76 for evaluation of CH resorption. T(12)-S(1) lordosis and segmental angulation did not change postoperatively. There was no radiological evidence for non-union on the plain roentgenograms and CT scans. Radiological fusion was achieved 1 year postoperatively and was observed in all groups and vertebral segments. Six months postoperatively there was an obvious resorption of hydroxyapatite granules at the intertransverse intersegmental spaces in the right side of the spines of group B and both sides of group C. The resorption of hydroxyapatite was completed 1 year postoperatively. Bone bridging started in the third month postoperatively in all instrumented spines and all levels posteriorly as well as between the transverse processes in the spines of the group A and on the left side of the spines of group B where IBG was applied. SF-36, ODI, and R-M score improved postoperatively in a similar way in all groups. There was one pedicle screw breakage at the lowermost instrumented level in group A and two in group C without radiologically visible pseudarthrosis, which were considered as having non-union. Operative time and blood loss were less in the patients of group C, while donor site complaints were observed in the patients of the groups A and B only. This study showed that autologous IBG remains the "gold standard" for achieving solid posterior instrumented lumbar fusion, to which each new graft should be compared. The incorporation of coralline hydroxyapatite mixed with local bone and bone marrow needs adequate bleeding bone surface. Subsequently, hydroxyapatite was proven in this series to not be appropriate for intertransverse posterolateral fusion, because the host bone in this area is little. However, the use of hydroxyapatite over the decorticated laminae that represents a wide host area was followed by solid dorsal fusion within the expected time.

Aged↗
PubMed1994

[Long-term evolution of immunologic and thyroid function in Graves disease according different therapeutic options].

BACKGROUND: A prospective study was carried out to compare the evolution of thyroid hormones, thyroglobulin (Tg) and immunoglobulins inhibiting the binding of thyrotropin to its receptor (TBII) in patients with Graves disease treated with antithyroid drugs, radioactive iodine and subtotal thyroidectomy. METHODS: Ninety-five patients with Graves disease were studied, being distributed according to clinical criteria: Group I (n = 35) patients treated with antithyroid drugs; Group II (n = 30) patients who received 131I; and Group III (n = 30) patients treated with subtotal thyroidectomy. The thyroid hormones, Tg, antithyroglobulin antibodies and TBII were determined by radioimmunoassay (RIA), prior to treatment, and at 1, 3, 6, 12, 24, and 36 months of follow up, except in those patients from Group III who were followed up to 24 months. RESULTS: The rate of reactivation at 12 months did not significantly differ among the three groups. At 24 months a higher percentage of reactivations was observed in Group I (42%), versus Group II (16%, p < 0.001) and Group III (13%, p < 0.005). At 36 months reactivation was 30% in Group I, versus 5% in Group II (p < 0.01). Upon comparison of the TBII values among the three groups, the highest basal values corresponded to Group III with significant differences being found versus Group I (p < 0.05) and Group II (p < 0.001). TBII concentrations in the three groups studied remained high at 6 and 12 months with no significant differences being observed. Negativization was shown in the TBII at 24 months in Group II with a significant difference being seen versus Group I and III. At 36 months negativization was seen in the TBII in Group I with significant differences with respect to Group II. CONCLUSIONS: The rate of reactivation following antithyroid treatment is greater to that obtained in groups treated with iodine or surgery. The earliest negativization of TBII was obtained with radioiodine.

Adolescent↗
PubMed2001

Automatic method for evaluating the activity of sourdough strains based on gas pressure measurements.

A new method is proposed for the evaluation of the activity of sourdough strains, based on gas pressure measurements in closed air-tight reactors. Gas pressure and pH were monitored on-line during the cultivation of commercial yeasts and heterofermentative lactic acid bacteria on a semi-synthetic medium with glucose as the major carbon source. Relative gas pressure evolution was compared both to glucose consumption and to acidification and growth. It became obvious that gas pressure evolution is related to glucose consumption kinetics. For each strain, a correlation was made between maximum gas pressure variation and amount of glucose consumed. The mass balance of CO2 in both liquid and gas phase demonstrated that around 90% of CO2 was recovered. Concerning biomass production, a linear relationship was found between log colony-forming units/ml and log pressure for both yeasts and bacteria during the exponential phase; and for yeasts, relative gas pressure evolution also followed optical density variation.

Carbon Dioxide↗
PubMed2026

Comparative genomic characterization and antimicrobial resistance of bacteremia-causing Enterococcus faecium and Enterococcus faecalis in a Chinese hospital.

Enterococci are common commensals of the human gut and important opportunistic pathogens, with Enterococcus faecium and Enterococcus faecalis being the most clinically prevalent species. A significant epidemiological shift has emerged with an increasing clinical burden of E. faecium. To compare genomic evolution of E. faecium and E. faecalis, we performed whole-genome sequencing on 93 E. faecium and 32 E. faecalis isolates causing bloodstream infections at a single hospital (2022-2024). Analysis of patient demographics revealed that E. faecium infections originated from fewer sources than E. faecalis, with a higher proportion deriving from intra-abdominal infections. Multilocus sequence typing identified ST78 and ST789 as the predominant sequence types for E. faecium, whereas ST16 and ST179 were most common for E. faecalis. E. faecium carried more antimicrobial resistance genes and putative virulence marker (PVM)-type virulence genes than E. faecalis, with vancomycin resistance predominantly mediated by vanHAX (33/93, 35.5%) and a single E. faecalis isolate also carrying vanHAX (1/32, 3.1%); the structurally incomplete vanHMX gene cluster was detected in 11 E. faecium isolates. Pan-genome analysis indicated a larger core genome in E. faecalis compared to E. faecium, consistent with greater plasmid replicon diversity in the latter. Intra-host comparisons showed that two E. faecalis pairs from the same patient were clonally related, with one isolate acquiring a vanHAX plasmid conferring vancomycin resistance. In contrast, E. faecium isolates exhibited marked genomic diversity even among clonally related pairs. These findings suggest that E. faecium possesses greater genomic plasticity and adaptive potential to the clinical environment.IMPORTANCEThis study provides a detailed comparison of clinical and genomic features between Enterococcus faecium and Enterococcus faecalis from the same hospital setting. We show that E. faecium isolates, mainly ST78/ST789, carry more antimicrobial resistance genes and a higher number of putative virulence marker (PVM) genes than E. faecalis, reflecting their hospital-adapted nature. E. faecium also exhibits a smaller core genome and greater diversity of plasmid replicon types, indicating higher genomic plasticity and capacity for horizontal gene transfer. By contrast, E. faecalis retains a larger core genome and a set of classical virulence factors, and its within-host isolates are clonally related. These distinct genomic profiles help to understand how the two species adapt to clinical environments and may inform more targeted infection control strategies and resistance surveillance.

Enterococcus faecium↗
PubMed2003

Sexual isolation evolves faster than hybrid inviability in a diverse and sexually dimorphic genus of fish (Percidae: Etheostoma).

Theory predicts that sexual (or behavioral) isolation will be the first form of reproductive isolation to evolve in lineages characterized by sexual selection. Here I directly compare the rate of evolution of sexual isolation with that of hybrid inviability in a diverse and sexually dimorphic genus of freshwater fish. The magnitude of both sexual isolation and hybrid inviability were quantified for multiple pairs of allopatric species. Rates of evolution were inferred by comparing genetic distances of these species pairs with the magnitude of each form of reproductive isolation: the slope of the regression of genetic distance on the magnitude of reproductive isolation represents the rate of evolution. Of the two forms of isolation, the magnitude of sexual isolation exhibited the steeper slope of regression, indicating that sexual isolation will tend to evolve to completion earlier than hybrid inviability, strictly as a by-product of evolution in geographically isolated populations. Additional evidence from the literature is used to qualitatively compare rates of evolution of sexual isolation with that of other forms of reproductive isolation. Preliminary comparisons support the prediction that sexual isolation will evolve more rapidly than other forms. Because Etheostoma is characterized by striking sexual dimorphism, these results are consistent with the hypothesis that sexual selection for exaggerated mate-recognition characters causes the relatively rapid evolution of sexual isolation.

Animals↗
PubMed1990

The comparative biology of second sex ratio evolution within a natural population of a parasitic wasp, Nasonia vitripennis.

Correlation and regression analyses indicate that isofemale strains extracted from a population of the parasitic wasp, Nasonia vitripennis, differ in the fit of their second sex ratios (those produced in previously parasitized hosts) to the predictions of the theory of optimal facultative sex ratio adjustment. Under the theory's simple assumptions about population structure, there is significant heterogeneity of fitnesses among the isofemale strains. The reasons underlying these types of heterogeneity must be understood before we can make statements about the nature of sex ratio evolution in this species. These results suggest that comparative analyses are essential for testing the qualitative predictions of optimality models.

Animals↗
PubMed1998

Different evolution of simian immunodeficiency virus in a natural host and a new host.

To address the mechanisms of host-virus adaptation and pathogenesis of lentiviral infections, we compared the evolution of the same isolate of simian immunodeficiency virus (SIVsmm9) in two different situations: nonpathogenic infection of its natural host, the sooty mangabey, and AIDS-inducing infection of a new host, the rhesus macaque. Samples were obtained at 6, 12, and 23 or 30 months postinfection from three animals of each species. Sequences were derived from the V1 and V2 domains of the surface glycoprotein. In the macaques, we observed specific variations absent from all mangabey samples, indicating that different host species select different virus variants. In the macaques, we also observed a different shape in the phylogenetic tree, a lower divergence of sibling sequences, and a lower synonymous/nonsynonymous change ratio than in the mangabeys. This suggests that the viral population is larger and submitted to weaker selection pressures when host-virus adaptation is achieved, such as in the mangabey.

Adaptation, Physiological↗