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PubMed1988

Free fitness that always increases in evolution.

I here introduce a free fitness function in population biology, which monotonically increases with time and takes its maximum at the evolutionary equilibrium. By suitably defining an "index" for each state, the free fitness is expressed as the average index plus an entropy term. In many cases, the index has a biologically clear meaning, such as the logarithmic population mean fitness. The technique is applicable to any Markov process model (either continuous or discrete) with a positive steady state. I discuss four examples from various branches of population biology: (1) one-locus-two-allele system of population genetics with mutation, selection, and random genetic drift; (2) evolutionary dynamics of quantitative characters; (3) a molecular evolution model; and (4) an ecological succession model. Introducing free fitness clarifies the balance between systematic forces (e.g. natural selection or successional trend toward the climax) and disturbing processes (e.g. random drift).

Animals↗
PubMed1981

Estimating genetic divergence and genetic variability with restriction endonucleases.

Restriction endonucleases cut DNA at specific sites determined by the local nucleotide sequence. By comparing related DNA segments with respect to where such cuts are made, one can estimate the extent of sequence homology between the segments. Empirical methods are presented here for using these data to measure the proportion of mismatches between two sequences, the proportion of polymorphic positions in a series of sequences, or the degree of heterozygosity in a population. These methods do not require any assumptions concerning the evolutionary or population genetic processes involved. One can also use the data to calculate the precision of each of these estimates. When the positions of the cuts are not determined, these estimates can be made, using only the lengths of the resulting DNA fragments, by means of a maximum likelihood procedure. Several examples demonstrate the usefulness of these methods to study genetic differences in regions of the genome not amenable to study by other methods.

DNA↗
PubMed1980

Conservation and variation of nucleotide sequences in Escherichia coli strains isolated from nature.

A group of Escherichia coli isolates from nature were compared with one another and with laboratory strains of E. coli with respect to size distribution of chromosomal restriction endonuclease fragments and differences in nucleotide sequences in selected small portions of the genomes. The estimated frequency of base substitutions in nucleotide sequences in and near the trp operons of 26 of the 28 E. coli strains examined ranged from 0.008 to 0.066. Nucleotide sequences in or near lambda prophage homologs were significantly more variable than the sequences in or near trp, tnaA, and thyA genes. Thus, the lambda-homologous regions may have a significant horizontal component in their evolutionary histories, having undergone genetic exchange, whereas the trp, tnaA, and thyA regions may have solely vertical evolutionary histories. The relatedness of the E. coli strains in the genetic regions studied indicated that laboratory strains are not more closely related to one other than they are to isolates from nature. The isolates from natural populations did not form groups related either by host taxa or by geographical region of isolation.

Bacteriophage lambda↗
PubMed1989

Sociobiology and the structural stability of behavior patterns.

A structural stability approach to population-genetic systems and to dynamic evolutionary games is attempted in order to examine the theoretical significance of sociobiological selection models. A criterion of weak selection is derived that is not restricted to differential reproduction in polymorphic systems but describes possible directions of evolutionary change in time scales governed by genetic mutation rates. The criterion applies to the problems of how the initial mutational basis of an adaptive trait may be established and how this may happen, for analogous traits, independently in different species. Two basic sociobiological concepts are reconsidered with reference to the criterion. It is shown that W. D. Hamilton's condition of increases in inclusive fitness due to altruistic interactions among kin expresses the structural instability of populations against the evolution of altruistic behavior. Using the dynamic approach to evolutionary game theory, it is demonstrated that if a behavioral phenotype is an evolutionarily stable strategy, it is structurally stable against perturbations of the fitness payoffs, provided selection is weak. These results are applied to material problems of the evolution of animal social behavior.

Animals↗
PubMed2003

Block structure and stability of the genetic code.

It is known that different codons may be unified into larger groups related to the hierarchical structure, approximate hidden symmetries, and evolutionary origin of the universal genetic code. Using a simplified evolutionary motivated two-letter version of genetic code, the general principles of the most stable coding are discussed. By the complete enumeration in such a reduced code it is strictly proved that the maximum stability with respect to point mutations and shifts in the reading frame needs the fixation of the middle letters within codons in groups with different physico-chemical properties, thus, explaining a key feature of the universal genetic code. The translational stability of the genetic code is studied by the mapping of code onto de Bruijn graph providing both the compact visual representation of mutual relationships between different codons as well as between codons and protein coding DNA sequence and a powerful tool for the investigation of stability of protein coding. Then, the results are extended to four-letter codes. As is shown, the universal genetic code obeys mainly the principles of optimal coding. These results demonstrate the hierarchical character of optimization of universal genetic code with strictly optimal coding being evolved at the earliest stages of molecular evolution. Finally, the universal genetic code is compared with the other natural variants of genetic codes.

Amino Acids↗
PubMed2001

Evolution and genetics of root hair stripes in the root epidermis.

Root hair pattern develops in a number of different ways in angiosperm. Cells in the epidermis of some species undergo asymmetric cell divisions to form a smaller daughter cell from which a hair grows, and a larger cell that forms a non-hair epidermal cell. In other species any cell in the epidermis can form a root hair. Hair cells are arranged in files along the Arabidopsis root, located in the gaps between underlying cortical cell files. Epidermal cells overlying a single cortical cell file develop as non-hair epidermal cells. Genetic analysis has identified a transcription factor cascade required for the formation of this pattern. WEREWOLF (WER) and GLABRA2 (GL2) are required for the formation of non-hair epidermal cells while CAPRICE (CPC) is required for hair cell development. Recent analyses of the pattern of epidermal cells among the angiosperms indicate that this striped pattern of cell organization evolved from non-striped ancestors independently in a number of diverse evolutionary lineages. The genetic basis for the evolution of epidermal pattern in angiosperms may now be examined.

Biological Evolution↗
PubMed1999

Short sequence repeats in microbial pathogenesis and evolution.

Repetitive DNA is ubiquitous in microbial genomes. Different classes of short sequence repeats (SSRs) have been identified and demonstrated to be generally heterogeneous in a locus-dependent manner, reflected in variation in the number of repeat units present at a given genomic site or by sequence heterogeneity among individual units. Both types of variability can be used to assess intra-species genetic diversity. Repeat variability often affects the coding potential of the region in which the repetitive element is located. This implies that determination of the primary structure of variable numbers of tandem repeats can be used for epidemiological identification purposes, and also for the analysis of gene function. Precise assessment of SSR structure can also generate insight into the regulation of gene expression. Together, DNA repeat analysis in microbial species provides information on both functional and evolutionary aspects of genetic diversity among microbial isolates.

Candida albicans↗
PubMed1988

On the evolution of genetic incompatibility systems. IV. Modification of response to an existing antigen polymorphism under partial selfing.

A 2-locus model of the evolution of self-incompatibility in a population practicing partial selfing is presented. An allele is introduced at a modifier locus which influences the strength of the rejection reaction expressed by the style in response to antigens recognized in pollen. Two causes of inbreeding depression are investigated. First, offspring viability depends solely on the source (self or non-self) of the fertilizing pollen. Second, offspring viability declines with the expression of recessive deleterious alleles, segregating at a third (disease) locus, which exhibit an imperfect association with antigen alleles. Evolutionary changes occurring at the disease locus are not considered in this study. The condition under which a modifier allele that intensifies the incompatibility reaction increases when rare depends upon the number of antigens, the frequency of recessive deleterious alleles at the disease locus, and the level of association between the antigen locus and the disease locus. It is the improvement of viability among offspring derived by outcrossing, rather than the prevention of self-fertilization, that may represent the primary evolutionary function of genetic incompatibility systems.

Biological Evolution↗
PubMed1998

Complex limiting behaviour of multilocus genetic systems in cyclical environments.

Here we demonstrate that complex limiting behaviour (supercycles and chaotic-like phenomena) may arise in a rather broad and natural class of multilocus systems, both haploid and diploid, experiencing stabilizing selection with cyclically varying optima over a short period. These include loci with purely additive, dominant, or semidominant effects, with different types of their chromosome distribution. The observed complex dynamics appeared to manifest a certain stability with respect to disturbances of parameters specifying the structure of the selected system and environmental characteristics. This mode of multilocus dynamics by far exceeds the potential attainable under ordinary selection models resulting in simple behaviour. It may represent a novel evolutionary mechanism increasing genetic diversity over long time periods. This novel mechanism could contribute to the observation that biological diversity has increased over geological time regardless of the well-known massive extinctions.

Animals↗
PubMed1999

A novel dnaK operon from Porphyromonas gingivalis.

The nucleotide sequence of the dnaK operon cloned from Porphyromonas gingivalis revealed that the operon does not contain homologues of either dnaJ or grpE. However, there were two genes which encode small heat shock proteins immediately downstream from the dnaK and they were transcribed together with dnaK as one unit. The ATPase activity of the P. gingivalis DnaK was synergistically stimulated up to 40-fold in the simultaneous presence of Escherichia coli DnaJ and GrpE. These results suggest that the DnaK homologue of P. gingivalis, with its unique genetic structure and evolutionary features, works as a member of the DnaK chaperone system.

Adenosine Triphosphatases↗
PubMed2006

Evolutionary insights into the high worldwide prevalence of MBL2 deficiency alleles.

Human mannose-binding lectin (MBL) is a member of the collectin protein family that binds a broad range of microorganisms and activates the lectin-complement pathway of innate immunity. Common alleles of MBL2 disrupt the MBL protein or modulate the amount of protein produced, resulting in MBL deficiency. The clinical manifestations of MBL deficiency have been extensively studied but the actual role of this lectin in immunity to infection remains a matter of strong debate. MBL is commonly thought to play a key role in protective immunity, because MBL deficiency has been associated with an increase in susceptibility to infectious diseases. However, the high worldwide prevalence of multiple MBL2 deficiency or low-producing alleles suggests the converse that MBL deficiency confers protection. To explore the underlying forces accounting for the high worldwide prevalence of MBL2 deficiency alleles, we characterized genetic diversity in and around the MBL2 genomic region in 1166 chromosomes from 24 worldwide populations. Our results clearly demonstrate that the patterns of MBL2 variation are compatible with neutral evolution, as opposed to negative, positive or balanced natural selection. The high worldwide frequencies of MBL2 alleles associated with the production of little or no protein therefore result exclusively from human migration and genetic drift. The evolutionary neutrality of MBL2 strongly supports the notion that MBL2 variation does not have strong effects on population fitness, suggesting, therefore, that this lectin is largely redundant in host human defences.

Alleles↗
PubMed2024

Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia.

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Humans↗
PubMed1987

Tryptophan synthase alpha subunit glutamic acid 49 is essential for activity. Studies with 19 mutants at position 49.

We have obtained a complete set of 20 variants of the alpha subunit of tryptophan synthase of Escherichia coli at position 49 in order to extend our previous studies on the effects of single amino acid replacements at position 49 on structure and function. Thirteen mutant alpha subunits have been newly constructed by site-directed mutagenesis using oligonucleotides. Six mutants were available from previous studies. We find that the wild type and all of the mutant alpha subunits form alpha 2 beta 2 complexes with the beta 2 subunit of tryptophan synthase with similar association constants and similarly stimulate the activity of the beta 2 subunit in the synthesis of L-tryptophan from L-serine and indole. Thus none of the changes at position 49 produces a change in the conformation of the alpha subunit which significantly interferes with normal subunit interaction. However, the 19 mutant alpha 2 beta 2 complexes are completely devoid of activity in reactions normally catalyzed by the active site of the alpha subunit. This is the first time that these several activities have been measured with a series of highly purified alpha subunits altered by mutation at a single site. Our finding that the mutant in which glutamic acid 49 is substituted by aspartic acid is totally devoid of alpha activity is especially significant and is strong evidence that glutamic acid 49 is an essential catalytic base in the reaction catalyzed by the alpha subunit. This result is consistent with the results of previous genetic studies, with evolutionary comparisons using sequence analysis, and with recent results from x-ray crystallography of the alpha 2 beta 2 complex of tryptophan synthase from Salmonella typhimurium.

Base Sequence↗
PubMed2001

Adaptive life-history evolution in the livebearing fish Brachyrhaphis rhabdophora: genetic basis for parallel divergence in age and size at maturity and a test of predator-induced plasticity.

I document a genetic basis for parallel evolution of life-history phenotypes in the livebearing fish Brachyrhaphis rhabdophora from northwestern Costa Rica. In previous work, I showed that populations of B. rhabdophora that co-occur with predators attain maturity at smaller sizes than populations that live in predator-free environments. I also demonstrated that this pattern of phenotypic divergence in life histories was independently repeated in at least five isolated drainages. However, life-history phenotypes measured from wild-caught fish could be attributed to environmental effects rather than to genetic differences among populations. In the present study, I reared male fish from four populations (two that co-occur with predators and two from predator-free environments) under four sets of environmental conditions. The pattern of phenotypic divergence in maturation size documented in the field between populations collected from different predation environments persisted after two generations in the laboratory. I also found a genetic basis for differences between populations in the age at which males attain maturity and in growth rates. By rearing fish in four different common environments, I tested for phenotypic plasticity in male life-history traits in response to nonlethal exposure to predators. There was a significant delay in the onset of sexual maturity in fish exposed to predators relative to those in the control, but no differences among treatments in size at maturity or growth rates. These results, coupled with previous work on B. rhabdophora, demonstrate a repeated pattern of parallel evolutionary divergence among genetically isolated populations that is strongly associated with predation.

Adaptation, Physiological↗
PubMed2004

Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin.

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.

Animals↗
PubMed2006

Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.

The eubacterial genus Wolbachia comprises one of the most abundant groups of obligate intracellular bacteria, and it has a host range that spans the phyla Arthropoda and Nematoda. Here we developed a multilocus sequence typing (MLST) scheme as a universal genotyping tool for Wolbachia. Internal fragments of five ubiquitous genes (gatB, coxA, hcpA, fbpA, and ftsZ) were chosen, and primers that amplified across the major Wolbachia supergroups found in arthropods, as well as other divergent lineages, were designed. A supplemental typing system using the hypervariable regions of the Wolbachia surface protein (WSP) was also developed. Thirty-seven strains belonging to supergroups A, B, D, and F obtained from singly infected hosts were characterized by using MLST and WSP. The number of alleles per MLST locus ranged from 25 to 31, and the average levels of genetic diversity among alleles were 6.5% to 9.2%. A total of 35 unique allelic profiles were found. The results confirmed that there is a high level of recombination in chromosomal genes. MLST was shown to be effective for detecting diversity among strains within a single host species, as well as for identifying closely related strains found in different arthropod hosts. Identical or similar allelic profiles were obtained for strains harbored by different insect species and causing distinct reproductive phenotypes. Strains with similar WSP sequences can have very different MLST allelic profiles and vice versa, indicating the importance of the MLST approach for strain identification. The MLST system provides a universal and unambiguous tool for strain typing, population genetics, and molecular evolutionary studies. The central database for storing and organizing Wolbachia bacterial and host information can be accessed at http://pubmlst.org/wolbachia/.

Alleles↗
PubMed2026

Scaling up orphan crop research: genebank genetics highlight geographic structure in cultivated cowpea from 10 617 global accessions.

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical 'orphan crop', cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

Vigna↗
PubMed2006

Mitochondrial genome sequence evolution in Chlamydomonas.

The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.

Animals↗