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.

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Climate change is a major environmental stress threatening biodiversity and human civilization. The best hope to secure staple food for humans and animal feed by future crop improvement depends on wild progenitors. We examined 10 wild emmer wheat (Triticum dicoccoides Koern.) populations and 10 wild barley (Hordeum spontaneum K. Koch) populations in Israel, sampling them in 1980 and again in 2008, and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time and simple sequence repeat allelic turnover. The revealed evolutionary changes imply unrealized risks present in genetic resources for crop improvement and human food production.climate warming | phenotypic and genotypic diversity | plant genetic resources I n recent decades there have been increasing concerns about the future of food production influenced by climate change (1-7) to feed a fast growing world population reaching 9-10 billion by 2050 (8). Aridization has alarmingly increased in summer, resulting in dry regions of wheat growing areas, particularly in the Americas, Asia, and Africa, and in the area of origin and diversity of wild emmer wheat in the Near East (9). Cultivated wheat, the number one world food staple, is genetically impoverished by long-term selective breeding (10). The wild progenitors of cultivated cereals, especially wild emmer wheat Triticum dicoccoides Koern. (TD) (9) and wild barley Hordeum spontaneum K. Koch (HS) (11), have become eroded by urbanization and agriculture (12). Both progenitors are rich in genetic resources adapted to abiotic (e.g., solar radiation, temperature, drought, and mineral poverty) and biotic (e.g., pathogens and parasites) stresses. These progenitors are the best genetic hope for improving genetically impoverished cultivars for human food production (9-17). Thus, it is crucial to evaluate the evolutionary adaptation in natural populations of the progenitors under climate change and to understand the hidden risk in human food security. Here we examined 10 TD populations and 10 HS populations in Israel from 1980 and again in 2008 and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time (FT) and simple sequence repeat (SSR) allelic turnover. ResultsPhenotypic Analysis. In a greenhouse experiment, we compared the time from germination until flowering of ∼800 genotypes in 20 natural populations from different habitats and climates that were subjected to 28 y of climate change. The sampled populations (16, 17) were distributed across 350 km of their Israeli range (SI Appendix, Fig. S1 and Table S1). A total of 57 independent pair-wise comparisons were made under dry (300 mm) and wet (600 mm) irrigation regimes. Dramatically, in all TD and HS populations, without exception, the 2008 populations reached FT earlier than those collected in 1980 (Sign test, P < 1...

The Near East Fertile Crescent is well recognized as a primary center of barley origin, diversity, and domestication. A large number of wild barleys have been collected from the Tibetan Plateau, which is characterized by an extreme environment. We used genome-wide diversity array technology markers to analyze the genotypic division between wild barley from the Near East and Tibet. Our results confirmed the existence of Tibetan wild barley and suggested that the split between the wild barleys in the Near East and those in Tibet occurred around 2.76 million years ago (Mya). To test the concept of polyphyletic domestication of barley, we characterized a set of worldwide cultivated barley. Some Chinese hulless and six-rowed barleys showed a close relationship with Tibetan wild barley but showed no common ancestor with other cultivated barley. Our data support the concept of polyphyletic domestication of cultivated barley and indicate that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. The current results may be highly significant in exploring the elite germplasm for barley breeding, especially against cold and drought stresses.adaptation | evolution | harsh environment

Sympatric speciation has been controversial since it was first proposed as a mode of speciation. Subterranean blind mole rats (Spalacidae) are considered to speciate allopatrically or peripatrically. Here, we report a possible incipient sympatric adaptive ecological speciation in Spalax galili (2n = 52). The study microsite (0.04 km 2 ) is sharply subdivided geologically, edaphically, and ecologically into abutting barrier-free ecologies divergent in rock, soil, and vegetation types. The Pleistocene Alma basalt abuts the Cretaceous Senonian Kerem Ben Zimra chalk. Only 28% of 112 plant species were shared between the soils. We examined mitochondrial DNA in the control region and ATP6 in 28 mole rats from basalt and in 14 from chalk habitats. We also sequenced the complete mtDNA (16,423 bp) of four animals, two from each soil type. Remarkably, the frequency of all major haplotype clusters (HC) was highly soil-biased. HCI and HCII are chalk biased. HC-III was abundant in basalt (36%) but absent in chalk; HC-IV was prevalent in basalt (46.5%) but was low (20%) in chalk. Up to 40% of the mtDNA diversity was edaphically dependent, suggesting constrained gene flow. We identified a homologous recombinant mtDNA in the basalt/chalk studied area. Phenotypically significant divergences differentiate the two populations, inhabiting different soils, in adaptive oxygen consumption and in the amount of outsidenest activity. This identification of a possible incipient sympatric adaptive ecological speciation caused by natural selection indirectly refutes the allopatric alternative. Sympatric ecological speciation may be more prevalent in nature because of abundant and sharply abutting divergent ecologies.adaptation | ecological stress | radio-tracking | metabolism | microscale T he origin and nature of species, the mystery of mysteries (1) and "the most important single event in Evolution" (2), have always been problematic in evolutionary studies (2-7). We adhere to the Biological Species Concept (2), recognizing its merits and demerits (2). The recent resurgence in speciation studies highlights many past obscurities (4), including sympatric speciation (7-18). Nevertheless, many basic questions related to adaptation and speciation, including sympatric speciation, still await resolution based primarily on the genomic sequence studies, such as in Drosophila (8), or even in species that presumably originated sympatrically, such as in the fly Rhagolites (9) or cichlid fishes in Africa and Neotropical America (10).The mode of species origin is still a major focus of heated debate. Does speciation occur primarily in allopatry, i.e., requiring complete geographic isolation, or can it occur in parapatry and peripatry, where limited gene exchange operates, or even in sympatry, where free gene exchange occurs, as suggested by Darwin (1)? Darwin envisaged allopatric, parapatric, and sympatric modes of speciation, but neither he nor his followers estimated their proportions in nature, which remain enigmatic and limited (4). Moreover, no spe...

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Genetic diversity and structure of populations of the wild progenitor of barley, Hordeum spontaneum, from three countries, Israel, Turkey and Iran, in the Near East Fertile Crescent, are compared and contrasted. The analysis is based on electrophoretically discernible allozymic variation in proteins encoded by 27 shared loci in 2125 individuals representing 52 populations of wild barley. The results indicate that: (a) H . spontaneum in the Near East Fertile Crescent is very variable genetically; (b) genetic differentiation of populations includes some clinal but primarily regional and local patterns often displaying sharp geographic differentiation over short distances; (c) the average relative genetic dilferentiation (GJ was 540i0 within populations, 39O4 among populations, and 89, between the three countries; (d) allele distribution is characterized by a high proportion of unique alleles (51""), and a high proportion of common alleles that are distributed either locally or sporadically; (e) discriminant analysis by allele frequencies successfully clustered wild barley of each of thc three countries (960:, correct classification); ( f ) a substantial portion of the patterns of allozyme variation in the wild gene pool is significantly correlated with the environment and is predictable ecologically, chiefly by a combination of humidity and temperature variables; (g) natural populations of wild barley are, on the average, more variable than two composite crosses and land races of cultivated barley. The spatial patterns and environmental correlates and predictors of genetic variation of H . spontaneurn in the Fertile Crescent indicate that genetic variation in wild barley populations is not only rich but at least partly adaptive and predictable by ecology and allozyme markers. Consequently, conservation and utilization programmes should optimize sampling strategies by following the ecological-genetic factors and allozyme markers as effectively predictive guidelines.

This study was conducted to test the effects of internal (genetic) and external factors on allelic diversity at 27 dinucleotide microsatellite (simple sequence repeat [SSR]) loci in three Israeli natural populations of Triticum dicoccoides from Ammiad, Tabigha, and Yehudiyya, north of the Sea of Galilee. The results demonstrated that SSR diversity is correlated with the interaction of ecological and genetic factors. Genetic factors, including genome (A vs. B), chromosome, motif, and locus, affected average repeat number (ARN), variance in repeat number (sigma), and number of alleles (NA) of SSRs, but the significance of some factors varied among populations. Genome effect on SSR variation may result from different motif types, particularly compound (or imperfect) versus perfect motifs, which may be related to different evolutionary histories of genomes A and B. Ecological factors significantly affected SSR variation. Soil-unique and soil-specific alleles were found in two edaphic groups dwelling on terra rossa and basalt soils across macro- and microgeographical scales. The largest contributions of genetic and ecological effects were found for diversity of ARN and NA, respectively. Multiple regression indicated that replication slippage and unequal crossing over could be important mutational mechanisms, but their significance varied among motifs. Edaphic stresses may affect the probability of replication errors and recombination intermediates and thus control diversity level and divergence of SSRs. The results may indicate that SSR diversity is adaptive, channeled by natural selection and influenced by both internal and external factors and their interactions.