Eviatar Nevo

Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review

Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.

Genetic variation in natural populations: Patterns and theory

Abstract Allozymic variation in natural populations of plants, animals, and humans based on studies published prior to early 1976 and involving 243 species, in which 14 or more loci were tested, is herein reviewed. Explanatory models are compared and contrasted in view of the evidence to see which theories best explain genetic variation in natural populations. The analysis suggests that the amounts of genetic polymorphism and heterozygosity vary nonrandomly between loci, populations, species, habitats, and life zones, and are correlated with ecological heterogeneity. Natural selection, in some form, may often be the major determinant of genetic population structure and differentiation. Yet precise critical experiments must be designed to test possible alternative hypotheses, to establish direct cause-effect relationships between ecological and genetic profiles, and to assay the contribution of single and multilocus structures to fitness.

The Evolutionary Significance of Genetic Diversity: Ecological, Demographic and Life History Correlates

The evolutionary significance of genetic diversity of proteins in nature remains controversial despite the numerous protein studies conducted electrophoretically during the last two decades. Ironically, the discovery of extensive protein polymorphisms in nature (reviewed by Lewontin, 1974; Powell, 1975; Selander, 1976; Nevo 1978, 1983b; Hamrick et al., 1979; Nelson and Hedgecock, 1980), did not resolve the disagreement between the die ho torn ou s explanatory models of selection (e.g., Ayala, 1977; Milkman, 1978; Clarke, 1979; Wills, 1981) versus neutrality (Kimura, 1968; Kimura and Chta, 1971; Nei, 1975; and modifications in Kimura, 1979atb). The more general problem of the relative importance of the evolutionary forces interacting in genetic population differentiation at the molecular levels of proteins and DNA, i.e., mutation, migration, natural selection and genetic drift, remains now as enigmatic as ever.

Evolution of genome–phenome diversity under environmental stress

The genomic era revolutionized evolutionary biology. The enigma of genotypic-phenotypic diversity and biodiversity evolution of genes, genomes, phenomes, and biomes, reviewed here, was central in the research program of the Institute of Evolution, University of Haifa, since 1975. We explored the following questions. (i) How much of the genomic and phenomic diversity in nature is adaptive and processed by natural selection? (ii) What is the origin and evolution of adaptation and speciation processes under spatiotemporal variables and stressful macrogeographic and microgeographic environments? We advanced ecological genetics into ecological genomics and analyzed globally ecological, demographic, and life history variables in 1,200 diverse species across life, thousands of populations, and tens of thousands of individuals tested mostly for allozyme and partly for DNA diversity. Likewise, we tested thermal, chemical, climatic, and biotic stresses in several model organisms. Recently, we introduced genetic maps and quantitative trait loci to elucidate the genetic basis of adaptation and speciation. The genome–phenome holistic model was deciphered by the global regressive, progressive, and convergent evolution of subterranean mammals. Our results indicate abundant genotypic and phenotypic diversity in nature. The organization and evolution of molecular and organismal diversity in nature at global, regional, and local scales are nonrandom and structured; display regularities across life; and are positively correlated with, and partly predictable by, abiotic and biotic environmental heterogeneity and stress. Biodiversity evolution, even in small isolated populations, is primarily driven by natural selection, including diversifying, balancing, cyclical, and purifying selective regimes, interacting with, but ultimately overriding, the effects of mutation, migration, and stochasticity.

Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum

The replicative retrotransposon life cycle offers the potential for explosive increases in copy number and consequent inflation of genome size. The BARE-1 retrotransposon family of barley is conserved, disperse, and transcriptionally active. To assess the role of BARE-1 in genome evolution, we determined the copy number of its integrase, its reverse transcriptase, and its long terminal repeat (LTR) domains throughout the genus Hordeum. On average, BARE-1 contributes 13.7 × 103 full-length copies, amounting to 2.9% of the genome. The number increases with genome size. Two LTRs are associated with each internal domain in intact retrotransposons, but surprisingly, BARE-1 LTRs were considerably more prevalent than would be expected from the numbers of intact elements. The excess in LTRs increases as both genome size and BARE-1 genomic fraction decrease. Intrachromosomal homologous recombination between LTRs could explain the excess, removing BARE-1 elements and leaving behind solo LTRs, thereby reducing the complement of functional retrotransposons in the genome and providing at least a partial “return ticket from genomic obesity.”

Biochemical diversity and evolution in the genus Mus

Thirteen biochemical groups of wild mice from Europe, Asia, and Africa belonging to the genus Mus are analyzed at 22–42 protein loci. Phylogenetic trees are proposed and patterns of biochemical evolution are discussed, as well as the possible contribution of wild mice to the genetic diversity of laboratory stocks.

GENETIC DIVERSITY AND ENVIRONMENTAL ASSOCIATIONS OF WILD BARLEY, HORDEUM SPONTANEUM , IN ISRAEL

The levels and patterns of adaptive genetic variation in natural populations of the wild progenitors of cultivated plants are still largely unknown. Yet such knowledge would contribute substantially to three important areas of inquiry. These are (1) the general static and dynamic properties of genetic variation in natural populations, (2) the evolutionary process of domestication, and (3) the utility of wild gene pools in future plant breeding. Thus Lewontin (1974), among others, has drawn attention to the advantages that natural plant populations possess as experimental materials; and Harlan (1975a, b) and Zohary (1969), for example, have stressed the need to collect and study the wild progenitors of crop plants from the viewpoints of domestication and exploitation. There are several reasons why wild barley, Hordeum spontaneum , is an ideal species for such studies. First, this species is the recognized progenitor of cultivated barley with which it can yield fully fertile hybrids (see Zohary, 1969). Second, it has the technical advantages of diploidy (2n = 14), predominant self-pollination, and an annual life cycle. Third, its ecology and distribution are already well known. It is widespread in the Near East Fertile Crescent where it occupies primary habitats as well as man-made, secondary formations. It constitutes an important component of open plant communities characteristic of the summer dry hilly belt arcing the Euphrates Basin and the Jordan Rift Valley (Harlan and Zohary, 1966, Zohary, 1969). In Israel, H. spontaneum is abundant,

High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat

The naked mole rat (Heterocephalus glaber) displays exceptional longevity, with a maximum lifespan exceeding 30 years. This is the longest reported lifespan for a rodent species and is especially striking considering the small body mass of the naked mole rat. In comparison, a similarly sized house mouse has a maximum lifespan of 4 years. In addition to their longevity, naked mole rats show an unusual resistance to cancer. Multi-year observations of large naked mole-rat colonies did not detect a single incidence of cancer. Here we identify a mechanism responsible for the naked mole rat’s cancer resistance. We found that naked mole-rat fibroblasts secrete extremely high-molecular-mass hyaluronan (HA), which is over five times larger than human or mouse HA. This high-molecular-mass HA accumulates abundantly in naked mole-rat tissues owing to the decreased activity of HA-degrading enzymes and a unique sequence of hyaluronan synthase 2 (HAS2). Furthermore, the naked mole-rat cells are more sensitive to HA signalling, as they have a higher affinity to HA compared with mouse or human cells. Perturbation of the signalling pathways sufficient for malignant transformation of mouse fibroblasts fails to transform naked mole-rat cells. However, once high-molecular-mass HA is removed by either knocking down HAS2 or overexpressing the HA-degrading enzyme, HYAL2, naked mole-rat cells become susceptible to malignant transformation and readily form tumours in mice. We speculate that naked mole rats have evolved a higher concentration of HA in the skin to provide skin elasticity needed for life in underground tunnels. This trait may have then been co-opted to provide cancer resistance and longevity to this species.

Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce.

Resistance Gene Candidate2 (RGC2) genes belong to a large, highly duplicated family of nucleotide binding site–leucine rich repeat (NBS-LRR) encoding disease resistance genes located at a single locus in lettuce (Lactuca sativa). To investigate the genetic events occurring during the evolution of this locus, ∼1.5- to 2-kb 3′ fragments of 126 RGC2 genes from seven genotypes were sequenced from three species of Lactuca, and 107 additional RGC2 sequences were obtained from 40 wild accessions of Lactuca spp. The copy number of RGC2 genes varied from 12 to 32 per genome in the seven genotypes studied extensively. LRR number varied from 40 to 47; most of this variation had resulted from 13 events duplicating two to five LRRs because of unequal crossing-over within or between RGC2 genes at one of two recombination hot spots. Two types of RGC2 genes (Type I and Type II) were initially distinguished based on the pattern of sequence identities between their 3′ regions. The existence of two types of RGC2 genes was further supported by intron similarities, the frequency of sequence exchange, and their prevalence in natural populations. Type I genes are extensive chimeras caused by frequent sequence exchanges. Frequent sequence exchanges between Type I genes homogenized intron sequences, but not coding sequences, and obscured allelic/orthologous relationships. Sequencing of Type I genes from additional wild accessions confirmed the high frequency of sequence exchange and the presence of numerous chimeric RGC2 genes in nature. Unlike Type I genes, Type II genes exhibited infrequent sequence exchange between paralogous sequences. Type II genes from different genotype/species within the genus Lactuca showed obvious allelic/orthologous relationships. Trans-specific polymorphism was observed for different groups of orthologs, suggesting balancing selection. Unequal crossover, insertion/deletion, and point mutation events were distributed unequally through the gene. Different evolutionary forces have impacted different parts of the LRR.

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

The central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach (“ecotype simulation”) to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the “Evolution Canyons” of Israel. This approach has identified multiple ecotypes within traditional species, with each predicted to be an ecologically distinct lineage; many such ecotypes were confirmed to be ecologically distinct, with specialization to different canyon slopes with different solar exposures. Ecotype simulation provides a long-needed natural foundation for microbial ecology and systematics.