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PubMed2001

Can mixed strategies be stable in asymmetric games?

Selten (1980, J. theor. Biol. 84, 93(N)/01) has shown that mixed strategies cannot be evolutionarily stable in asymmetric games. Because every interaction features some asymmetry, this result apparently precludes mixed strategies in an evolutionary setting. In Maynard Smith's Hawk-Dove game (1982, Evolution and the theory of games (UP-Cambridge), for example, Selten's result restricts attention to pure-strategy evolutionarily stable outcomes in which the animals use the ability to condition their actions on asymmetries to coordinate, with one playing Hawk and one playing Dove, and with conflicts in which both animals play Hawk never arising. This result contrasts with the intuition that the mixed equilibrium of the Hawk-Dove game captures important aspects of many animal interactions, including the possibility of conflict. In this paper, we follow Eshel and Sansone (1995, J. theor. Biol. 177, 341-356) in enriching Selten's model to incorporate an important aspect of animal interactions, namely that payoffs and asymmetries may both be imperfectly observed. In the richer model, we find conditions under which effectively mixed strategies are stable in asymmetric games, as well as conditions under which they are not stable. Behavior will be conditioned on asymmetries, leading to pure-strategy equilibria in which conflict is avoided, when there are relatively large, observable asymmetries and small observable variations in payoffs. Under opposite conditions, evolutionarily stable equilibria will appear that are effectively mixed, including the potential for conflict.

Animals↗
PubMed1998

Molecular evidence for parallel evolution of adaptive syndromes in fig-breeding Lissocephala (Drosophilidae).

Afrotropical Lissocephala (Drosophilidae) breed strictly in syconia (figs) of Ficus (Moraceae) and have accordingly evolved specific features including modified female and eggshell morphologies, ovipositing, larval foraging, and mating behaviors. These various traits may exist as two or three alternative states. Each species displays a specific suite of traits so closely coordinated with one another that alternative states of the overall suites of traits can be seen as "adaptive syndromes." Three clear-cut adaptive syndromes can be recognized while two taxonomic lineages (juncta and sanu species groups) are traditionally accepted on the basis of male terminalia. A crucial evolutionary question results from the consideration that ecological clusters and taxonomic groups have conflicting compositions: the three syndromes are found in the juncta group while two of them occur in the sanu group. To resolve this conflict, we present molecular data which provide a robust phylogeny: mitochondrial DNA (12S + 16S ribosomal DNA and cytochrome b) sequence data are in agreement with one another regardless of the algorithm used. All molecular data consistently support male terminalia dichotomy. Such a level of consistency unambiguously indicates that parallel evolution of adaptive syndromes occurred. Thus, homoplasy may affect morphological and behavioral traits concomitantly when these are involved in a network of functional relationships.

Adaptation, Physiological↗
PubMed2006

Get the balance right: mitofusins roles in health and disease.

Mitochondria are highly dynamic organelles exhibiting an elaborate morphology and fine structure. Fusion and fission processes contribute to the maintenance and dynamics of mitochondrial morphology. The Mitofusins, a class of evolutionary conserved GTPases of the mitochondrial outer membrane, are essential for the controlled fusion of mitochondrial membranes. Genetic and biochemical data propose a model in which functional domains, such as the GTPase domain and the C-terminally located coiled coil structure, act in an orchestrated manner to coordinate the tethering and mitochondrial outer membrane fusion. In addition, recent reports shed new light on the physiological importance of Mitofusin function suggesting a role in mitochondrial metabolism, apoptosis as well as cellular signalling. Mutations identified in the human Mfn2 gene from patients with the peripheral neuropathy Charcot-Marie-Tooth Type 2A invoke a direct correlation between mitochondrial morphology and function.

Adaptor Proteins, Signal Transducing↗
PubMed1987

Physiologic versus pathologic hypertrophy and the pressure-overloaded myocardium.

The myocardium consists of myocytes and capillaries embedded in a connective tissue matrix. Myocardial mass, which is predominantly a function of myocyte size, is determined by systolic tension; when systolic pressure is gradually elevated above the normal range, mass will increase. The hypertrophic process is a continuum consisting of subtle transitions that take place within the muscular, collagenous, and vascular compartments; these transitions, however, need not be temporarily concordant. We would identify three phases to the hypertrophic process. First, there is an evolutionary phase, whereby the structural and biochemical remodeling of the various compartments of the myocardium is in transition, with each compartment having its own rate of adjustment. During this evolutionary phase, myocardial contractility, as reflected by stress-length and stress-velocity relations, may or may not be normal, but ventricular pump function and O2 delivery are preserved. Second, there is a physiologic phase during which the structural and biochemical remodeling of the compartments reaches a coordinated balance. The myocardial stress-length relation and ventricular function are each normal, but rate-dependent indices of contractility may be abnormal. During the physiologic phase of hypertrophy, the remodeled myocardium will revert to normal when the abnormal loading condition is removed. Finally, there is a pathologic phase. In this phase, compartment remodeling is no longer balanced (e.g., the ratio of structural versus maintenance proteins), and length and rate-dependent indices of myocardial contractility are depressed. Ventricular pump function is also abnormal in the pathologic phase; consequently. O2 delivery to the tissues is impaired. This imbalance in O2 demand and supply may be apparent at rest in more advanced expressions of disease or may appear during the physiologic stress of exercise in less severe disease. In the latter case, the patient's aerobic capacity is reduced to the extent that it can be used to grade the severity of heart failure and to predict the cardiac reserve. During the pathologic phase of hypertrophy, the structural and biochemical remodeling of the myocardium may be irreversible, although this may not be the case for each compartment. Finally, it is important to distinguish cardiac (or myocardial) failure from the clinical syndrome of congestive heart failure. The latter arises from congested organs and hypoperfused tissues; its clinical manifestations are dependent on the activation of the adrenergic nervous and renin-angiotensin-aldosterone systems and the presence of a salt-avid kidney. Congestive heart failure is a late clinical feature of chronic pressure overload and pathologic hypertrophy.

Animals↗
PubMed2005

Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains.

SBP-domain proteins are plant-specific putative transcription factors. They all contain the highly conserved 76 amino acid residue SBP-domain, shown to bind specifically to related motifs in the Antirrhinum majus SQUA promoter and the orthologous Arabidopsis thaliana AP1 promoter. The structural basis for this sequence-specific binding of DNA are two Zn-finger like structures formed by the coordination of two zinc ions by conserved cysteine and histidine residues. Amino acid exchanges of the cysteine residues involved revealed that each of the Zn(2+)-coordinating structures is essential for DNA binding. By random target-site selection studies, it is shown that the palindromic GTAC core motif is essential for efficient DNA binding with additional nucleotides preferred by different SBP-domain proteins. Despite their different functions and origin from plants at different evolutionary distances, the mode of DNA binding is conserved from the single-cell algae Chlamydomonas reinhardtii to the moss Physcomitrella patens and higher plants. At the C-terminal end of the SBP-domain, a putative bipartite nuclear localization signal is located, which overlaps with the DNA-binding domain, in particular with the second Zn(2+)-binding structure. By immunolocalization of SPL3 and transient expression of SBP-green fluorescent protein fusion proteins in plant cells, it is shown that this nuclear localization signal is functional. Exchange of a highly conserved serine next to the nuclear localization signal by aspartate, which may mimic phosphorylation, resulted in a decreased nuclear import (SPL8), while DNA binding in vitro was abolished completely. In contrast, exchange by alanine increased nuclear import and left DNA binding intact. This suggests that the function of SBP-domain proteins is also regulated by post-translational modification on the levels of nuclear import and DNA binding.

Active Transport, Cell Nucleus↗
PubMed2004

Order and disorder in bacterial genomes.

The availability of sequenced bacterial genomes allows a deeper understanding of their organizational features that are related with fundamental cellular processes such as coordinated gene expression, chromosome replication and cell division. Nevertheless, recent genome comparisons and experimental work highlighted the fluidity of bacterial chromosomes, including genome rearrangements that imperil the selective features of chromosome order. As a result, the clash between elements generating rearrangements and chromosome organization is a classic case of evolutionary conflict.

Bacteria↗
PubMed2002

Identification and cloning of human polynucleotide phosphorylase, hPNPase old-35, in the context of terminal differentiation and cellular senescence.

Terminal differentiation and cellular senescence display common properties including irreversible growth arrest. To define the molecular and ultimately the biochemical basis of the complex physiological changes associated with terminal differentiation and senescence, an overlapping-pathway screen was used to identify genes displaying coordinated expression as a consequence of both processes. This approach involved screening of a subtracted cDNA library prepared from human melanoma cells induced to terminally differentiate by treatment with fibroblast IFN and mezerein with mRNA derived from senescent human progeria cells. This strategy identified old-35, which encodes an evolutionary conserved gene, human polynucleotide phosphorylase (hPNPase(old-35)), that is regulated predominantly by type I IFNs. The hPNPase(OLD-35) protein localizes in the cytoplasm of human cells and induces RNA degradation in vitro, as does its purified bacterial protein homologue. Ectopic expression of hPNPase(old-35) in human melanoma cells reduces colony formation, confirming inhibitory activity of this RNA-degradation enzyme. Identification of hPNPase(old-35), an IFN-inducible 3'-5' RNA exonuclease, provides additional support for a relationship between IFN action and RNA processing and suggests an important role for this gene in growth control associated with terminal differentiation and cellular senescence.

Amino Acid Sequence↗
PubMed2001

Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.

The tRNA splicing endoribonuclease EndA from Methanococcus jannaschii is a homotetramer formed via heterologous interaction between the two pairs of homodimers. Each monomer consists of two alpha/beta domains, the N-terminal domain (NTD) and the C-terminal domain (CTD) containing the RNase A-like active site. Comparison of the EndA coordinates with the publicly available protein structure database revealed the similarity of both domains to site-specific deoxyribonucleases: the NTD to the LAGLIDADG family and the CTD to the PD-(D/E)XK family. Superposition of the NTD on the catalytic domain of LAGLIDADG homing endonucleases allowed a suggestion to be made about which amino acid residues of the tRNA splicing nuclease might participate in formation of a presumptive cryptic deoxyribonuclease active site. On the other hand, the CTD and PD-(D/E)XK endonucleases, represented by restriction enzymes and a phage lambda exonuclease, were shown to share extensive similarities of the structural framework, to which entirely different active sites might be attached in two alternative locations. These findings suggest that EndA evolved from a fusion protein with at least two distinct endonuclease activities: the ribonuclease, which made it an essential "antitoxin" for the cells whose RNA genes were interrupted by introns, and the deoxyribonuclease, which provided the means for homing-like mobility. The residues of the noncatalytic CTDs from the positions corresponding to the catalytic side chains in PD-(D/E)XK deoxyribonucleases map to the surface at the opposite side to the tRNA binding site, for which no function has been implicated. Many restriction enzymes from the PD-(D/E)XK superfamily might have the potential to maintain an additional active or binding site at the face opposite the deoxyribonuclease active site, a property that can be utilized in protein engineering.

Binding Sites↗
PubMed2005

Oblique decision trees for spatial pattern detection: optimal algorithm and application to malaria risk.

BACKGROUND: In order to detect potential disease clusters where a putative source cannot be specified, classical procedures scan the geographical area with circular windows through a specified grid imposed to the map. However, the choice of the windows' shapes, sizes and centers is critical and different choices may not provide exactly the same results. The aim of our work was to use an Oblique Decision Tree model (ODT) which provides potential clusters without pre-specifying shapes, sizes or centers. For this purpose, we have developed an ODT-algorithm to find an oblique partition of the space defined by the geographic coordinates. METHODS: ODT is based on the classification and regression tree (CART). As CART finds out rectangular partitions of the covariate space, ODT provides oblique partitions maximizing the interclass variance of the independent variable. Since it is a NP-Hard problem in RN, classical ODT-algorithms use evolutionary procedures or heuristics. We have developed an optimal ODT-algorithm in R2, based on the directions defined by each couple of point locations. This partition provided potential clusters which can be tested with Monte-Carlo inference. We applied the ODT-model to a dataset in order to identify potential high risk clusters of malaria in a village in Western Africa during the dry season. The ODT results were compared with those of the Kulldorff' s SaTScan. RESULTS: The ODT procedure provided four classes of risk of infection. In the first high risk class 60%, 95% confidence interval (CI95%) [52.22-67.55], of the children was infected. Monte-Carlo inference showed that the spatial pattern issued from the ODT-model was significant (p < 0.0001). Satscan results yielded one significant cluster where the risk of disease was high with an infectious rate of 54.21%, CI95% [47.51-60.75]. Obviously, his center was located within the first high risk ODT class. Both procedures provided similar results identifying a high risk cluster in the western part of the village where a mosquito breeding point was located. CONCLUSION: ODT-models improve the classical scanning procedures by detecting potential disease clusters independently of any specification of the shapes, sizes or centers of the clusters.

Africa, Western↗
PubMed2005

Hand preferences for unimanual and coordinated bimanual tasks in baboons (Papio anubis).

This study examined hand preference in baboons in a sample of 94 subjects for a unimanual task and in a sample of 104 subjects for a bimanual task. For the unimanual task, handedness was assessed by observing simple reaching for grains. For the bimanual task, tubes lined with peanut butter inside were presented to the baboons. The hand and the finger used to remove peanut butter were recorded. Population-level right-handedness was found for the bimanual but not the unimanual task. In addition, test-retest correlations showed consistency in hand use across time for the coordinated bimanual task but not the simple reaching task. No significant effects of age and sex on the direction and strength of hand preferences were found for either task. These are the first evidences of population-level handedness in baboons and the results are discussed in the context of evolutionary theories of cerebral dominance.

Analysis of Variance↗
PubMed1979

Population genetics of Drosophila amylase. II. Geographic patterns in D. pseudoobscura.

Morph frequencies of three related polymorphisms were determined in ten natural populations of Drosophila pseudoobscura. They are the well-known inversion polymorphism of the third chromosome and the polymorphism for alpha-amylase produced by the structural gene Amy (which resides on the third chromosome). The third polymorphism was for tissue-specific expression of Amy in adult midguts; a total of 13 different patterns of activity have been observed. The preceding paper (Powell and Lichtenfels 1979) reports evidence that the variation in Amy expression is under polygenic control. Here we show that the polymorphism for midgut patterns occurs in natural populations and is not an artifact of laboratory rearing.--From population to population, Amy allele frequencies and frequencies of inversions belonging to different phylads vary coordinately. The geographic variation in alpha-amylase midgut activity patterns is uncorrelated with that for the other two types of polymorphisms. Furthermore, no correlation was detected between activity pattern(s) and Amy genotype(s) when both were assayed in the same individual.--These results imply that whatever the evolutionary-ecological forces are that control frequencies of the structural gene variants, they are not the same factors that control the frequencies of polymorphic genetic factors responsible for the tissue-specific expression of the enzyme.

Alleles↗
PubMed2001

Adaptive design, selective history, and women's sexual motivations.

I have discussed an ongoing program of research designed to examine the nature of specific sexual selection pressures that have played a role in the evolution of human mating. I have suggested that the evidence tentatively be interpreted as consistent with the existence of female preferences for traits that indicate good genes. Nonetheless, more research is needed before definitive conclusions can be reached. At the outset, I discussed several points about the application of adaptationism to an understanding of human behavior. First, special-design arguments are often critical to evolutionary explanations. Special design is not only evidence that natural selection has been at work, it can also reveal the nature of selection pressures that have shaped the organism. Second, special design often cannot be readily "read off" the observed phenotype. A convincing special-design argument may require a coordinated, coherent explanation (a nomological network; Cronbach & Meehl, 1955) of multiple and varied observations. Third, observations that are "strange coincidences" if one's explanation is not correct, but expected if one's explanation is correct, are particularly informative pieces of evidence. The research on sexual selection illustrates these points. We have attempted to provide evidence for special design in females for preferring men who demonstrate developmental precision for the benefit of obtaining good genes. We can point to no one piece of evidence that directly demonstrates this special design. The explanation that women possess special design for preferring men who possess good genes in certain mating contexts (such as extra-pair sex), however, does provide a coherent account of a wide range of findings. At least one of these findings--that women prefer the scent of symmetrical men only when the probability of conception is high--was expected by this explanation, but has no obvious alternate explanation and hence appears to be a strange, peculiar coincidence if this explanation is wrong. By no means do we have a full and complete story here. The nomological network can and should be expanded in a number of ways and, thereby, the argument for special design tightened. Whether or not the special-design argument ultimately holds up to further scrutiny, however, I would like to think that our efforts to establish it have importantly contributed to an understanding of human mating.

Biological Evolution↗
PubMed2005

Evolutionary origin of cAMP-based chemoattraction in the social amoebae.

Phenotypic novelties can arise if integrated developmental pathways are expressed at new developmental stages and then recruited to serve new functions. We analyze the origin of a novel developmental trait of Dictyostelid amoebae: the evolution of cAMP as a developmental chemoattractant. We show that cAMP's role of attracting starving amoebae arose through recruitment of a pathway that originally evolved to coordinate fruiting body morphogenesis. Orthologues of the high-affinity cAMP receptor (cAR), cAR1, were identified in a selection of species that span the Dictyostelid phylogeny. The cAR1 orthologue from the basal species Dictyostelium minutum restored aggregation and development when expressed in an aggregation-defective mutant of the derived species Dictyostelium discoideum that lacks high-affinity cARs, thus demonstrating that the D. minutum cAR is a fully functional cAR. cAR1 orthologues from basal species are expressed during fruiting body formation, and only this process, and not aggregation, was disrupted by abrogation of cAR1 function. This is in contrast to derived species, where cAR1 is also expressed during aggregation and critically regulates this process. Our data show that coordination of fruiting body formation is the ancestral function of extracellular cAMP signaling, whereas its derived role in aggregation evolved by recruitment of a preexisting pathway to an earlier stage of development. This most likely occurred by addition of distal cis-regulatory regions to existing cAMP signaling genes.

Amino Acid Sequence↗
PubMed2001

Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.

BACKGROUND: Ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. In prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. Duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. However, with the accumulation of numerous complete genome sequences of prokaryotes, several paralogous pairs of ribosomal protein genes have been identified. Here we analyze all such cases and attempt to reconstruct the evolutionary history of these ribosomal proteins. RESULTS: Complete bacterial genomes were searched for duplications of ribosomal proteins. Ribosomal proteins L36, L33, L31, S14 are each duplicated in several bacterial genomes and ribosomal proteins L11, L28, L7/L12, S1, S15, S18 are so far duplicated in only one genome each. Sequence analysis of the four ribosomal proteins, for which paralogs were detected in several genomes, two of the ribosomal proteins duplicated in one genome (L28 and S18), and the ribosomal protein L32 showed that each of them comes in two distinct versions. One form contains a predicted metal-binding Zn-ribbon that consists of four conserved cysteines (in some cases replaced by histidines), whereas, in the second form, these metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions, designated C+ and C-, respectively. Analysis of phylogenetic trees for these seven ribosomal proteins, combined with comparison of genomic contexts for the respective genes, indicates that in most, if not all cases, their evolution involved a duplication of the ancestral C+ form early in bacterial evolution, with subsequent alternative loss of the C+ and C- forms in different lineages. Additionally, evidence was obtained for a role of horizontal gene transfer in the evolution of these ribosomal proteins, with multiple cases of gene displacement 'in situ', that is, without a change of the gene order in the recipient genome. CONCLUSIONS: A more complex picture of evolution of bacterial ribosomal proteins than previously suspected is emerging from these results, with major contributions of lineage-specific gene loss and horizontal gene transfer. The recurrent theme of emergence and disruption of Zn-ribbons in bacterial ribosomal proteins awaits a functional interpretation.

Bacterial Proteins↗
PubMed1997

A rationale for the absolute conservation of Asn70 and Pro71 in mitochondrial cytochromes c suggested by protein engineering.

The absolutely conserved residues Asn70 and Pro71 of mitochondrial cytochrome c have been targeted for protein engineering by semisynthesis. Neither residue has even been implicated in mechanistic schemes, and we reasoned that the conservation of this dipeptide was to fulfill a crucial structural role. Semisynthesis was through condensation by autocatalytic fragment religation of natural fragment 1-65 (H) of the horse protein and synthetic 39-residue peptides containing noncoded amino acids prepared by solid-phase methods. High yields of the purified analogs, homoserine70 and norvaline71 cytochromes c, were obtained. Functional tests revealed minor destabilization of the Hse70-containing structure, with little adverse effect in in vitro assays, but [Nva71] cytochrome c was essentially devoid of activity in these systems. This appeared to be a consequence of a shift, more pronounced than any yet reported, in the conformational equilibrium between the active state III conformer and the inactive, 'alkaline' state IV. The results support our view that this dipeptide is optimal for, and rigidifies, the right-angle bend between two alpha-helices, thus determining the conformation of the 70s loop that terminates in the sixth ligand Met80, and 'forcing' the coordination of iron by thioether sulfur in the presence of the adjacent more avid amine ligands of state IV. Not only is [Nva71] cytochrome c inactive at pH 7, but it also proves to be an extremely potent inhibitor of electron transfer by native state III, thus providing the rationale for the evolutionary conservation of a high pK for the ligand exchange reaction.

Amino Acid Sequence↗
PubMed2004

Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

BACKGROUND: Cyclin-dependent kinases (CDKs) are a large family of proteins that function in a variety of key regulatory pathways in eukaryotic cells, including control over the cell cycle and gene transcription. Among the most important and broadly studied of these roles is reversible phosphorylation of the C-terminal domain (CTD) of RNA polymerase II, part of a complex array of CTD/protein interactions that coordinate the RNAP II transcription cycle. The RNAP CTD is strongly conserved in some groups of eukaryotes, but highly degenerate or absent in others; the reasons for these differences in stabilizing selection on CTD structure are not clear. Given the importance of reversible phosphorylation for CTD-based transcription, the distribution and evolutionary history of CDKs may be a key to understanding differences in constraints on CTD structure; however, the origins and evolutionary relationships of CTD kinases have not been investigated thoroughly. Moreover, although the functions of most CDKs are reasonably well studied in mammals and yeasts, very little is known from most other eukaryotes. RESULTS: Here we identify 123 CDK family members from animals, plants, yeasts, and four protists from which genome sequences have been completed, and 10 additional CDKs from incomplete genome sequences of organisms with known CTD sequences. Comparative genomic and phylogenetic analyses suggest that cell-cycle CDKs are present in all organisms sampled in this study. In contrast, no clear orthologs of transcription-related CDKs are identified in the most putatively ancestral eukaryotes, Trypanosoma or Giardia. Kinases involved in CTD phosphorylation, CDK7, CDK8 and CDK9, all are recovered as well-supported and distinct orthologous families, but their relationships to each other and other CDKs are not well-resolved. Significantly, clear orthologs of CDK7 and CDK8 are restricted to only those organisms belonging to groups in which the RNAP II CTD is strongly conserved. CONCLUSIONS: The apparent origins of CDK7 and CDK8, or at least their conservation as clearly recognizable orthologous families, correlate with strong stabilizing selection on RNAP II CTD structure. This suggests co-evolution of the CTD and these CTD-directed CDKs. This observation is consistent with the hypothesis that CDK7 and CDK8 originated at about the same time that the CTD was canalized as the staging platform RNAP II transcription. Alternatively, extensive CTD phosphorylation may occur in only a subset of eukaryotes and, when present, this interaction results in greater stabilizing selection on both CTD and CDK sequences. Overall, our results suggest that transcription-related kinases originated after cell-cycle related CDKs, and became more evolutionarily and functionally diverse as transcriptional complexity increased.

Amino Acid Sequence↗
PubMed1998

Coevolution of immunoglobulin heavy- and light-chain variable-region gene families.

The gene families encoding the immunoglobulin variable regions of heavy (VH) and light (VL) chains in vertebrates are composed of many genes. However, the gene number and the extent of diversity among VH and VL gene copies vary with species. To examine the causes of this variation and the evolutionary forces for these multigene families, we conducted a phylogenetic analysis of VH and VL genes from the species of amniotes. The results of our analysis showed that for each species, VH and VL genes have the same pattern of clustering in the trees, and, according to this clustering pattern, the species can be divided into two groups. In the first group of species (humans and mice), VH and VL genes were extensively intermingled with genes from other organisms; in the second group of species (chickens, rabbits, cattle, sheep, swine, and horses), the genes tended to form clusters within the same group of organisms. These results suggest that the VH and VL multigene families have evolved in the same fashion: they have undergone coordinated contraction and expansion of gene repertoires such that each group of organisms is characterized by a certain level of diversity of VH and VL genes. The extent of diversity among copies of VH and VL genes in each species is related to the mechanism of generation of antibody variety. In humans and mice, DNA rearrangement of immunoglobulin variable, diversity, and joining-segment genes is a main source of antibody diversity, whereas in chickens, rabbits, cattle, sheep, swine, and horses, somatic hypermutation and somatic gene conversion play important roles. The evolutionary pattern of VH and VL multigene families is consistent with the birth-and-death model of evolution, yet different levels of diversifying selection seem to operate in the VH and VL genes of these two groups of species.

Animals↗
PubMed1985

Subtype ayw variant of hepatitis B virus. DNA primary structure analysis.

The entire genome of human hepatitis B virus (HBV) occurring in Latvia was sequenced. This sequence, which is 3182 nucleotides long, was compared with the other previously published HBV genomes and was shown to share maximum homology with HBV subtype ayw DNA. The coordinates of 4 main open reading frames as well as hairpin structures are very well conserved in the two genomes. The distribution of nucleotide substitutions among different HBV genomes suggest that the open reading frames P and X can fulfil a coding function. On the basis of primary structure comparison for hepadnaviral DNAs several evolutionary conclusions can be drawn.

Amino Acid Sequence↗