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Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans.

The consequences of mutation for population-genetic and evolutionary processes depend on the rate and, especially, the frequency distribution of mutational effects on fitness. We sought to approximate the form of the distribution of mutational effects by conducting divergence experiments in which lines of a DNA repair-deficient strain of Caenorhabditis elegans, msh-2, were maintained at a range of population sizes. Assays of these lines conducted in parallel with the ancestral control suggest that the mutational variance is dominated by contributions from highly detrimental mutations. This was evidenced by the ability of all but the smallest population-size treatments to maintain relatively high levels of mean fitness even under the 100-fold increase in mutational pressure caused by knocking out the msh-2 gene. However, we show that the mean fitness decline experienced by larger populations is actually greater than expected on the basis of our estimates of mutational parameters, which could be consistent with the existence of a common class of mutations with small individual effects. Further, comparison of the total mutation rate estimated from direct sequencing of DNA to that detected from phenotypic analyses implies the existence of a large class of evolutionarily relevant mutations with no measurable effect on laboratory fitness.

Amino Acid Substitution↗

A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.

Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant <&#x2009;50&#x2009;bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319&#x2009;bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.

Animals↗

Directions in evolutionary biology.

In order to understand both the past and future directions of research in evolutionary biology we need to begin by understanding in what way these programs of research differ from the model of most scientific work. The study of evolutionary processes and, in particular, the genetics of the evolutionary process must confront special difficulties in both the conceptual and the methodological aspects of research. On the conceptual side, unlike for molecular, cellular, and developmental biology, there is no basic mechanism that evolutionists are attempting to elucidate. There is no single cause of the evolutionary change in the properties of members of a species. Natural selection may be involved but so are random events, patterns of migration and interbreeding, mutational events, and horizontal transfer of genes across species boundaries. The change in each character of each species is a consequence of a particular mixture of these causal pathways.

Animals↗

Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances.

Self-incompatibility systems in plants are genetic systems that prevent self-fertilization in hermaphrodites through recognition and rejection of pollen expressing the same allelic specificity as that expressed in the pistils. The evolutionary properties of these self-recognition systems have been revealed through a fascinating interplay between empirical advances and theoretical developments. In 1939, Wright suggested that the main evolutionary force driving the genetic and molecular properties of these systems was strong negative frequency-dependent selection acting on pollination success. The empirical observation of high allelic diversity at the self-incompatibility locus in several species, followed by the discovery of very high molecular divergence among alleles in all plant families where the locus has been identified, supported Wright's initial theoretical predictions as well as many of its later developments. In the last decade, however, advances in the molecular characterization of the incompatibility reaction and in the analysis of allelic frequencies and allelic divergence from natural populations have stimulated new theoretical investigations that challenged some important assumptions of Wright's model of gametophytic self-incompatibility. We here review some of these recent empirical and theoretical advances that investigated: (i) the hypothesis that S-alleles are selectively equivalent, and the evolutionary consequences of genetic interactions between alleles; (ii) the occurrence of frequency-dependent selection in female fertility; (iii) the evolutionary genetics of self-incompatibility systems in subdivided populations; (iv) the evolutionary implications of the self-incompatibility locus's genetic architecture; and (v) of its interactions with the genomic environment.

Alleles↗

Coincident development of sesamoid bones and clues to their evolution.

Sesamoid bones form within tendons in regions that wrap around bony prominences. They are common in humans but variable in number. Sesamoid development is mediated epigenetically by local mechanical forces associated with skeletal geometry, posture, and muscular activity. In this article we review the literature on sesamoids and explore the question of genetic control of sesamoid development. Examination of radiographs of 112 people demonstrated that the relatively infrequent appearances of the fabella (in the lateral gastrocnemius tendon of the knee) and os peroneum (in the peroneus longus tendon of the foot) are related within individuals (P < 0.01). This finding suggests that the tendency to form sesamoids may be linked to intrinsic genetic factors. Evolutionary character analyses suggest that the formation of these sesamoids in humans may be a consequence of phylogeny. These observations indicate that variations of intrinsic factors may interact with extrinsic mechanobiological factors to influence sesamoid development and evolution.

Adult↗

The dynamics of quantifiable homeostasis. III: a linear model of certain metrical diseases.

A generalization of the linear, lagged, homeostatic process shows that whether a displacement of the trait function dies out with time, continues indefinitely, or shows a steadily amplifying (wild) oscillation depends on the value assumed by the product of the lag time and the restoration constant. Moreover, it is shown that if a steady displacing force is used rather than an instantaneous displacement, a new homing value results which is given by the ratio of the displacing force to the restoration coefficient. Combining these two developments furnishes grounds for determining whether or not an overshoot will occur when administration of a drug is stopped (for instance, the rebound thrombosis on discontinuing heparin). Further developments of these ideas show how the diabetes that begins in mature patients can be wholly accounted for by the well-known prolongation of the lag in insulin response that occurs in that disorder. If wild oscillation is to be avoided as the lag time increases, the restoration constant must be weakened (evidently by a systematic reduction in insulin receptors) and this weakening means that the homing value is displaced. Thus the hyperglycemia in this diabetes is to be seen as the price paid for avoiding wild oscillation. Provided that the therapeutic use of exogenous insulin is systematic and regular, rather than cybernetic, its success where endogenous (cybernetic) insulin secretion has failed is readily understood. The point is illustrated by a familiar analogy of a car driver with slow responses. The genetic and evolutionary implications of these ideas are outlined.

Cybernetics↗

Partial N-terminal amino acid sequence analyses and comparative tryptic peptide maps of murine Ia molecules encoded by the I-A subregion.

The partial N-terminal amino acid sequences and tryptic peptide maps of I-A subregion products from the H-2b, H-2d, H-2k and H-2s haplotypes demonstrate that haplotype-associated differences are present in both alpha and beta polypeptides. The genetic and evolutionary implications of these multiple amino acid substitutions and the homology relationships among Ia molecules from human, guinea pig and the I-E subregion of the mouse are discussed.

Alleles↗

Life in unusual environments: progress in understanding the structure and function of enzymes from extreme halophilic bacteria.

Extreme halophilic archaea are saturated with salt and the intracellular electrolyte concentration exceeds that of the extracellular environment. Enzymes and other proteins from extreme halophilic archaea have been purified for many years and studied by biochemical and biophysical solution methodologies. They are active and stable at multimolar salt concentrations and denature below 2 to 3 M NaCl or KCl. Adaptation to these high concentrations of salt, genetic and evolutionary aspects, and the possibility of biotechnological applications are problems of considerable interest. Since the status of this fascinating field of research was reviewed in 1992, malate dehydrogenase from Haloarcula marismortui, now known to be a tetramer, was sequenced, its gene was cloned and expressed in active form, and its physical properties were redefined. A single mutation of Arg100 (in the enzyme active site) to Gln switched the enzyme specificity from malate to lactate dehydrogenase. Recent determination of its molecular structure by X-ray crystallography (O. Dym et al., in press) provides an exciting basis for the understanding of the structure and function of extreme halophilic enzymes. A major problem which so far has not been tackled in the study of extreme halophilic archaea is the understanding of protein nucleic acid interactions which are essential for the performance of biological function. Whereas the stability and activity of enzymes and other proteins can be modified to perform at high salt concentrations by use of currently known structural concepts, the existence of meaningful protein nucleic acid interactions in physiological concentrations of 4 to 5 M KCl constitutes an unsolved enigma worth intensive investigation.

Environment↗

The effects of gene conversion control factors on conversion-induced changes in allele frequencies in populations and on linkage disequilibrium.

Conversion control factors (ccfs) are widespread. They control conversion properties at their target loci, affecting the conversion frequency and the amount and even the direction of gene conversion disparity. Three major types of ccf can be recognised. Experimental studies of the effects of ccfs have been combined with theoretical studies and modelling to examine the effects of ccfs on the evolutionary population genetics of alleles at the target locus. The ccf alleles present can greatly affect the rate and the direction of conversion-induced changes in target locus allele frequencies. Gene conversion can both cause and remedy linkage disequilibrium, with causation being related to polymorphism for ccfs. Disparity in conversion direction does not by itself necessarily cause linkage disequilibrium.

Alleles↗

The pvB370 BamHI satellite DNA family of the Drosophila virilis group and its evolutionary relation to mobile dispersed genetic pDv elements.

The pvB370 BamHI tandemly repeated satellite DNA family was isolated and analyzed in eight species of the Drosophila virilis group and is probably common to all its members. Unexpectedly, the satellite DNA family showed similar levels of intra- and interspecific sequence variability. An EMBL gene-bank search revealed a high degree of similarity between the members of the pvB370 BamHI satellite DNA sequence family and the direct terminal repeats of the mobile dispersed genetic pDv elements described in D. virilis and other species of the group. However, no similarity was observed to the transcribed and translated part of the pDv elements. It is suggested that the satellite DNA repeats are phylogenetically older than the mobile dispersed genetic pDv element and that the functional pDv elements might have derived from the satellite DNA family through an insertion of a tandemly repeated 36-bp transcription unit.

Animals↗

The structure and position of mouse centromeric heterochromatin in BrdU-labelled chromosomes and diplochromosomes stained by the pH 10.4 method.

A mouse cell line of C57Bl/6J spontaneous melanoma (clone PG 19), and a C-type virus transformed cell line (G-8 clone 124) originating from normal Balb/c mice were used in a study of the centromeric heterochromatin region of BrdU-labelled chromosomes stained by the Giemsa pH 10.4 method. Three possible explanations for the generation of compound lateral asymmetry within the centromeric heterochromatin region of the laboratory mouse are discussed: 1) inverted translocation; 2) centric fusion followed by paracentromeric fission and 3) inversion of part of the centromeric satellite DNA. These processes could be of considerable genetic and evolutionary significance. The non-random spatial position of unstained and dark stained C-bands in BrdU-labelled diplochromosomes of endoreduplicated cells can be explained as being due to the localization of the old and new DNA chains in a unineme chromatid model. The late replicating regions are shown to be located on the inside of the half-chromatid close to the axial symmetry axis of the metaphase chromosome.

Animals↗

Present status of the ovine gene map (Ovis aries); comparison with the bovine map (Bos taurus).

The status of the sheep map to the end of June 1993 is presented. Mapping information is available for a total of 107 loci comprising 16 anonymous DNA segments. This is an increase of 66 loci since 1990. No loci have been mapped on 10 of the 26 autosomes. Comparison of the cattle (350 loci) and sheep maps confirms their close evolutionary and genetic relationship and will reduce the effort required for their gene mapping.

Animals↗

Genomic and Structural Analysis of Gamete Recognition Proteins in a Broadcast Spawning Echinoderm Mesocentrotus franciscanus.

Gamete recognition proteins are expressed on the surfaces of sperm and eggs, where they mediate interactions between gametes. The genetic basis for gamete recognition proteins, as well as their structure and interactions, have yet to be fully resolved. Using a new high-quality de novo genome assembly for the sea urchin Mesocentrotus franciscanus, we investigated the genomic structure, expression, and protein forms of several gamete recognition proteins: sperm bindin, egg receptor for sperm (HSP110), and egg bindin receptor (EBR1), as well as the receptor for egg jelly (REJ) and its paralogs. To inform future population genetic and evolutionary studies, we resolve the genomic structure of the large EBR1 protein, identifying fewer tandem CUB-TSP1 repeats in EBR1 compared to the initial characterization of this protein. As expected for an egg receptor for sperm, EBR1 is highly expressed in female reproductive tissues (eggs and female gonad), compared to other tissues. In contrast, HSP110 shows similar levels of expression across male and female reproductive tissues, as well as across non-reproductive tissues and development stages. HSP110 might be a pleiotropic gene that in part influences fertilization. Using protein structural modeling and functional domain predictions, we propose hypotheses about potential interactions among EBR1, bindin, and HSP110 proteins that may provide insight into sperm-egg interactions in sea urchins. Resolving the genomic structure of genes encoding gamete recognition proteins, in combination with functional annotations and protein structural modeling, enables deeper investigation into the consequences of variation in gamete recognition proteins and the evolution of reproductive isolation.

Mesocentrotus franciscanus↗

The major histocompatibility complex of the rat (Rattus norvegicus).

This review of the RT1 complex, the major histocompatibility complex (MHC) of the rat, focuses on genetic, genomic, evolutionary, and functional aspects at the molecular level. The class I, class II, and framework genes are listed. The physical map of the RT1 complex as revealed by analysis of clonal contigs is compared with the human and mouse MHC, and the degree of orthologous relationship is outlined. Elucidation of the RT1 complex provides important information for using the rat as a model of experimental transplantation and complex diseases.

Animals↗

Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein.

Recently, close relatives of class B floral homeotic genes, termed B(sister) genes, have been identified in both angiosperms and gymnosperms. In contrast to the B genes themselves, B(sister) genes are exclusively expressed in female reproductive organs, especially in the envelopes or integuments surrounding the ovules. This suggests an important ancient function in ovule or seed development for B(sister) genes, which has been conserved for about 300 million years. However, investigation of the first loss-of-function mutant for a B(sister) gene (ABS/TT16 from Arabidopsis) revealed only a weak phenotype affecting endothelium formation. Here, we present an analysis of two additional mutant alleles, which corroborates this weak phenotype. Transgenic plants that ectopically express ABS show changes in the growth and identity of floral organs, suggesting that ABS can interact with floral homeotic proteins. Yeast-two-hybrid and three-hybrid analyses indicated that ABS can form dimers with SEPALLATA (SEP) floral homeotic proteins and multimeric complexes that also include the AGAMOUS-like proteins SEEDSTICK (STK) or SHATTERPROOF1/2 (SHP1, SHP2). These data suggest that the formation of multimeric transcription factor complexes might be a general phenomenon among MIKC-type MADS-domain proteins in angiosperms. Heterodimerization of ABS with SEP3 was confirmed by gel retardation assays. Fusion proteins tagged with CFP (Cyan Fluorescent Protein) and YFP (Yellow Fluorescent Protein) in Arabidopsis protoplasts showed that ABS is localized in the nucleus. Phylogenetic analysis revealed the presence of a structurally deviant, but closely related, paralogue of ABS in the Arabidopsis genome. Thus the evolutionary developmental genetics of B(sister) genes can probably only be understood as part of a complex and redundant gene network that may govern ovule formation in a conserved manner, which has yet to be fully explored.

Alleles↗

Genetic identification of novel poxviruses of cetaceans and pinnipeds.

Novel poxviruses were identified in skin lesions of several species of cetaceans and pinnipeds using polymerase chain reaction targeting DNA polymerase and DNA topoisomerase I genes of members of the subfamily Chordopoxvirinae. With the exception of parapoxviruses, no molecular data of marine mammal poxviruses were available to infer genetic and evolutionary relatedness to terrestrial vertebrate poxviruses. Viruses were assigned to a cetacean poxvirus 1 (CPV-1) group based on nucleotide and amino acid identities of gene fragments amplified from skin lesions of Asian bottlenose (Tursiops aduncus), Atlantic bottlenose (Tursiops truncatus), rough-toothed (Steno bredanensis), and striped (Stenella coeruleoalba) dolphins. A different poxvirus was detected in skin lesions of a bowhead whale (Balaena mysticetus) and provisionally assigned to a CPV-2 group. These viruses showed highest identity to terrestrial poxviruses of the genera Orthopoxvirus and Suipoxvirus. A novel species-specific poxvirus was also identified in skin lesions of Steller sea lions (Eumetopias jubatus). None of these poxviruses were found to have amplifiable hemagglutinin gene sequences. Novel parapoxviruses were also identified in skin lesions of Steller sea lions and spotted seals (Phoca largha). A significant degree of divergence was observed in sequences of Steller sea lion parapoxviruses, while those of spotted seals and harbor seals (Phoca vitulina) were highly conserved.

Alaska↗