[Stable cytological and histological peculiarities of the structure of the liver and other organs and tissue in various groups of vertebrates].
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Anatomy, Comparative↗
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[Comparative gene mapping and human karyotype evolution].
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Animals↗
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks.
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
Animals↗
[A comparative study of the difference in the evolution of refraction in the two eyes in patients with convergent strabismus (author's transl)].
In 329 cases of concomitant convergent strabismus, the alterations of refraction in the two eyes were compared over periods ranging from 10 to 30 years. In the group with unilateral strabismus (245 cases), a significant difference between the two eyes was observed. The change of refraction, if any, in the non-fixing eye (emmetropization or myopization) clearly lagged behind that in the fixing eye. This difference was particularly pronounced in the cases showing myopization. In the group with equivalent function of both eyes--alternating strabismus and cases with complete normalization, including functional normalization--a total of 84 cases, any emmetropization or myopization was found to run practically parallel in the two eyes. This shows that it is true of refraction, also that the genetically determined evolutive pattern may be modified by a functional abnormality.
Aging↗
Neuropeptides and the evolution of social behavior.
Comparative studies over the past year have revealed two new insights into the role of neuropeptides in the evolution of social behaviors. First, across vertebrate taxa, certain neuropeptide effects appear to be gender-specific. Second, species variations in receptor gene structure can alter neuropeptide receptor distribution and thereby contribute to species differences in social behavior.
Animals↗
Embryonic recapitulation, coenogenesis and heterochrony. An attempt at a comparative analysis of the relationships between embryogenesis and evolution.
The relationships between embryogenesis and the scale of living beings have been the subject of long-dated observations. It is well known that Haeckel, going back and codifying this data, has divided it into two large groups called palingenesis and coenogenesis. He has only mentioned the concept of heterochrony to which we give much more importance nowadays. We will look over these questions and link them up with some aspects of modern genetics.
Animals↗
Aneuploidy vs. gene mutation hypothesis of cancer: recent study claims mutation but is found to support aneuploidy.
For nearly a century, cancer has been blamed on somatic mutation. But it is still unclear whether this mutation is aneuploidy, an abnormal balance of chromosomes, or gene mutation. Despite enormous efforts, the currently popular gene mutation hypothesis has failed to identify cancer-specific mutations with transforming function and cannot explain why cancer occurs only many months to decades after mutation by carcinogens and why solid cancers are aneuploid, although conventional mutation does not depend on karyotype alteration. A recent high-profile publication now claims to have solved these discrepancies with a set of three synthetic mutant genes that "suffices to convert normal human cells into tumorigenic cells." However, we show here that even this study failed to explain why it took more than "60 population doublings" from the introduction of the first of these genes, a derivative of the tumor antigen of simian virus 40 tumor virus, to generate tumor cells, why the tumor cells were clonal although gene transfer was polyclonal, and above all, why the tumor cells were aneuploid. If aneuploidy is assumed to be the somatic mutation that causes cancer, all these results can be explained. The aneuploidy hypothesis predicts the long latent periods and the clonality on the basis of the following two-stage mechanism: stage one, a carcinogen (or mutant gene) generates aneuploidy; stage two, aneuploidy destabilizes the karyotype and thus initiates an autocatalytic karyotype evolution generating preneoplastic and eventually neoplastic karyotypes. Because the odds are very low that an abnormal karyotype will surpass the viability of a normal diploid cell, the evolution of a neoplastic cell species is slow and thus clonal, which is comparable to conventional evolution of new species.
Aneuploidy↗
Evolution of mammalian genome organization inferred from comparative gene mapping.
Comparative genome analyses, including chromosome painting in over 40 diverse mammalian species, ordered gene maps from several representatives of different mammalian and vertebrate orders, and large-scale sequencing of the human and mouse genomes are beginning to provide insight into the rates and patterns of chromosomal evolution on a whole-genome scale, as well as into the forces that have sculpted the genomes of extant mammalian species.
Animals↗
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile.
In mammalian genomes, linked genes show similar rates of evolution, both at fourfold degenerate synonymous sites (K4) and at nonsynonymous sites (KA). Although it has been suggested that the local similarity in the synonymous substitution rate is an artifact caused by the inclusion of disparately evolving gene pairs, we demonstrate here that this is not the case: after removal of disparately evolving genes, both (1) linked genes and (2) introns from the same gene have more similar silent substitution rates than expected by chance. What causes the local similarity in both synonymous and nonsynonymous substitution rates? One class of hypotheses argues that both may be related to the observed clustering of genes of comparable expression profile. We investigate these hypotheses using substitution rates from both human-mouse and mouse-rat comparisons, and employing three different methods to assay expression parameters. Although we confirm a negative correlation of expression breadth with both K4 and KA, we find no evidence that clustering of similarly expressed genes explains the clustering of genes of comparable substitution rates. If gene expression is not responsible, what about other causes? At least in the human-mouse comparison, the local similarity in KA can be explained by the covariation of KA and K4. As regards K4, our results appear consistent with the notion that local similarity is due to processes associated with meiotic recombination.
Animals↗
Effect of hydrogen ion buffers on photosynthetic oxygen evolution in the blue-green alga, Agmenellum quadruplicatum.
The photosynthetic oxygen evolution capacity of Agmenelium quadruplication suspended in four hydrogen ion buffers (pH 7.4, 0.05 M) and its synthetic marine growth medium was measured with an oxygen electrode. High rates of oxygen evolution were obtained in the growth medium and N-tris(hydroxymethyl)-methylglycine (Tricine) buffer. Compared to oxygen evolution in the growth medium, rates in phosphate buffer and N-tris(hydroxymethyl)-2-aminoethanesulphonic acid (TES) buffer were sometimes reduced by up to 30% and rates in tris (hydroxymethyl) amino-methane (Tris) were consistently reduced by 50%. An incubation-rinsing procedure caused inhibition of oxygen evolution in TES, phosphate, and Tris by 50 to 100%. Oxygen evolution could be restored to cells rinsed in TES or phosphate by resuspension in growth medium or in buffer plus magnesium and calcium ions. Bezoquinone-supported oxygen evolution was not affected by rinsing with any buffer tested except Tris. Ferricyanide was photoreduced at a low rate by cells rinsed in Tes but at a high rate in TES plus magnesium and calcium ions. We interpreted our results to mean that, in Agmenellum quadruplicatum, inhibition of photosynthetic oxygen evolution by Tris occurs at the level of photosystem 2 while the effects of TES and phosphate are on electron-transport occurring after the rate-limiting reaction.
Buffers↗
[Obesity in Chilean preschool children: anthropometric evolution and socioeconomic determinants].
BACKGROUND: The prevalence of obesity among low-income preschool children has increased in Chile. AIM: To compare the anthropometric evolution of obese and non obese children from birth and to determine the influence of maternal body composition and socioeconomic variables with childhood obesity. SUBJECTS AND METHODS: Using a case control design, 237 obese, 449 normal and 54 overweight 4 year old low income children, attending 8 public outpatient clinics in Santiago, were studied. Anthropometric data since birth to the moment of the study was gathered from the clinical charts at the clinics. RESULTS: Z scores for height/age and weight/height were significantly higher at all ages, excepting height/age in boys at the moment of birth. At the moment of the study, obese and overweight children were four and one cm taller than the normal weight controls. Maternal body mass index (odds ratio 3.07), being a first child, having a working mother, to have a telephone at home and birth weight were the variables significantly associated with obesity, according to an adjusted effects analysis. CONCLUSIONS: The strong association of maternal and offspring obesity implies that the prevention of childhood obesity must consider health actions directed towards mothers as well.
Analysis of Variance↗
Microbial genome evolution: sources of variability.
Comparative genome analyses of close relatives have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. The genomes of free-living bacteria often carry phages and repetitive sequences that mediate genomic rearrangements in contrast to the small genomes of obligate host-associated bacteria. This suggests that genomic stability correlates with the genomic content of repeated sequences and movable genetic elements, and thereby with bacterial lifestyle. Genes with unknown functions present in a single species tend to be shorter than conserved, functional genes, indicating that the fraction of unique genes in microbial genomes has been overestimated.
Bacteria↗
Are Drosophila melanogaster populations under a stable geographical differentiation due to the presence of P elements?
In order to simulate the outcome of the P-M status of Eurasian populations of Drosophila melanogaster, the evolution of experimental mixed-strains was monitored for up to 50 generations. The results were compared with the evolution in natura of European populations sampled in 1981-83 and 1986-87 over a similar period of time. Different combinations of P and M' strains, Q and M' strains, M' and M' strains and M and M' strains were set up at 25 degrees C and duplicated at 13 degrees C night-21 degrees C day. The possibility of a change towards a P type only appeared with the introduction of the strong P strain Harwich into Eurasian strains. Strains with strength similar to that of Harwich are not currently found in wild populations. With the introduction of weak P and Q strains of the strength presently observed in western Europe, experimental populations evolved slowly towards a Q state or a weak M' state. M'-M' mixed populations resulted in strong M' strains, as was the case for M-M' populations. In these cases. P sequences were not eliminated. In wild populations both genetic and molecular analyses showed no significant differences, over a five year period, for GD sterility potentials, for total P copy number or for distribution of the full-sized and KP elements. Changes in Eurasian populations are probably taking place at a very low rate and may even have stopped, leading to a quasi-stable differentiation over the continent. During the different steps of progressive invasion of P transposable elements, several deleted elements developed and natural selection may have acted on them. The possibility of the selection of different types of regulatory mechanisms according to the presence of different kinds of derivative elements, leading to a world-wide differentiation between P-Q and M' strains is discussed.
Animals↗
A comparative test of a theory for the evolution of anisogamy.
Why are sperm small and eggs large? The dominant explanation for the evolution of gamete size dimorphism envisages two opposing selection pressures acting on gamete size: small gametes are favoured because many can be produced, whereas large gametes contribute to a large zygote with consequently increased survival chances. This model predicts disruptive selection on gamete size (i.e. selection for anisogamy) if increases in zygote size confer disproportional increases in fitness (at least over part of its size range). It therefore predicts that increases in adult size should be accompanied by stronger selection for anisogamy. Using data from the green algal order Volvocales, we provide the first phylogenetically controlled test of the model's predictions using a published phylogeny and a new phylogeny derived by a different method. The predictions that larger organisms should (i) have a greater degree of gamete dimorphism and (ii) have larger eggs are broadly upheld. However, the results are highly sensitive to the phylogeny and the mode of analysis used.
Animals↗
Plant comparative genetics after 10 years.
The past 10 years have seen the discovery of unexpected levels of conservation of gene content and gene orders over millions of years of evolution within grasses, crucifers, legumes, some trees, and Solanaceae crops. Within the grasses, which include the three 500-million-ton-plus-per-year crops (wheat, maize, and rice), and the crucifers, which include all the Brassica crops, colinearity looks good enough to do most map-based cloning only in the small genome model species, rice and Arabidopsis. Elsewhere, knowledge gained in a few major crops is being pooled and applied across the board. The extrapolation of information from the well-studied species to orphan crops, which include many tropical species, is providing a solid base for their improvement. Genome rearrangements are giving new insights into evolution. In fact, comparative genetics is the key that will unlock the secrets of crop plants with genomes larger than that of humans.
Arabidopsis↗
Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells.
The evolution of vesicular stomatitis virus (VSV) in a constant environment, consisting of either mammalian or insect cells, has been compared to the evolution of the same viral population in changing environments consisting in alternating passages in mammalian and insect cells. Fitness increases were observed in all cases. An initial fitness loss of VSV passaged in insect cells was noted when fitness was measured in BHK-21 cells, but this effect could be attributed to a difference of temperature during VSV replication at 37 degrees C in BHK-21 cells. Sequencing of nucleotides 1-4717 at the 3' end of the VSV genome (N, P, M and G genes) showed that at passage 80 the number of mutations accumulated during alternated passages (seven mutations) is similar or larger than that observed in populations evolving in a constant environment (two to four mutations). Our results indicate that insect and mammalian cells can constitute similar environments for viral replication. Thus, the slow rates of evolution observed in natural populations of arboviruses are not necessarily due to the need for the virus to compromise between adaptation to both arthropod and vertebrate cell types.
Adaptation, Physiological↗
Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica).
Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.
Fraxinus↗
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.
BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes. CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.
Algorithms↗