Genetic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel.

This study investigated allele size constraints and clustering, and genetic effects on microsatellite (simple sequence repeat, SSR) diversity at 28 loci comprising seven types of tandem repeated dinucleotide motifs in a natural population of wild emmer wheat, Triticum dicoccoides, from a shade vs sun microsite in Yehudiyya, northeast of the Sea of Galilee, Israel. It was found that allele distribution at SSR loci is clustered and constrained with lower or higher boundary. This may imply that SSR have functional significance and natural constraints. Genetic factors, involving genome, chromosome, motif, and locus significantly affected SSR diversity. Genome B appeared to have a larger average repeat number (ARN), but lower variance in repeat number (sigma(ARN)(2)), and smaller number of alleles per locus than genome A. SSRs with compound motifs showed larger ARN than those with perfect motifs. The effects of replication slippage and recombinational effects (eg, unequal crossing over) on SSR diversity varied with SSR motifs. Ecological stresses (sun vs shade) may affect mutational mechanisms, influencing the level of SSR diversity by both processes.

Climatic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel.

Microsatellite (SSR) diversity at 28 loci comprising seven types of tandem dinucleotide repeated motifs was analyzed in 105 individual plants of wild emmer wheat, Triticum dicoccoides, from a microsite in Yehudiyya, northeast of the Sea of Galilee, Israel. The study area was less than 1000 m(2) and involved 12 paired plots distributed in a mosaic pattern. Each experiment involved very close (a few meters apart), but sharply divergent, microclimatic niches in the open park forest of Tabor oak: (1) sun, between trees, and (2) shade, under tree canopy. Significant microclimatic divergence characterized many loci displaying asymmetric and non-random distribution of repeat numbers. Niche-specific and niche-unique alleles and linkage disequilibria were found in the two sub-populations. Microsatellite diversity at both single- and two-locus levels is affected by microclimatic environment. The evidence reflects effects of ecological stresses and natural selection on SSR diversity, resulting presumably in adaptive structures.

Biological clock in total darkness: the Clock/MOP3 circadian system of the blind subterranean mole rat.

Blind subterranean mole rats retain a degenerated, subcutaneous, visually blind but functionally circadian eye involved in photoperiodic perception. Here we describe the cloning, sequence, and expression of the circadian Clock and MOP3 cDNAs of the Spalax ehrenbergi superspecies in Israel. Both genes are relatively conserved, although characterized by a significant number of amino acid substitutions. The glutamine-rich area of Clock, which is assumed to function in circadian rhythmicity, is expanded in Spalax compared with that of humans and mice, and is different in amino acid composition from that of rats. We also show that MOP3 is a bona fide partner of Spalax Clock and that the Spalax Clock/MOP3 dimer is less potent than its human counterpart in driving transcription. We suggest that this reduction in transcriptional activity may be attributed to the Spalax Clock glutamine-rich domain, which is unique in its amino acid composition compared with other studied mammalian species. Understanding Clock/MOP3 function could highlight circadian mechanisms in blind mammals and their unique pattern as a result of adapting to life underground.

Extraordinary multilocus genetic organization in mole crickets, Gryllotalpidae.

Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization.

Microsatellite diversity correlated with ecological-edaphic and genetic factors in three microsites of wild emmer wheat in North Israel.

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.

Molecular evolution of cytochrome b of subterranean mole rats, Spalax ehrenbergi superspecies, in Israel.

We describe the molecular evolution of cytochrome b of blind subterranean mole rats. We examined 12 individuals for nucleotide differences in the region of 402 base pairs of mitochondrial cytochrome b. Each individual represents a different population from the entire ecological and speciational range of the four chromosomal species in Israel (2n = 52, 54, 58, and 60) belonging to the Spalax ehrenbergi superspecies. Our results indicate the following. (i) There are seven first-position transitional differences, compared to 34 variable third positions, with no observed second-position substitutions. (ii) A maximum of four amino acids differences occurs across the range. (iii) Within-species diversity increases southward. Only 1 autoapomorphic substitution characterizes either 2n = 52 or 2n = 54, but 6-11 substitutions characterize 2n = 58, and 9-13 substitutions characterize 2n = 60. (iv) Both parsimony and maximum-likelihood trees suggest two monophyletic groups: (a) 2n = 52 and 54, and (b) 2n = 58 and 60, as identified earlier by other protein and DNA markers. (v) Mitochondrial cytochrome b heterogeneity is significantly correlated with climatic factors (rainfall) and biotic factors (body size and allozymes). We hypothesize that two selective regimes direct cytochrome b evolution in the S. ehrenbergi superspecies: (i) purifying selection in the flooded, mesic, hypoxic northern range of 2n = 52 and 54 and (ii) diversifying selection in the climatically spatiotemporal, xeric, and variable southern range of 2n = 58 and 60. Thus, the molecular evolution of mitochondrial cytochrome b in S. ehrenbergi is explicable by opposite selective stresses across the range of S. ehrenbergi in Israel, associated with the ecological adaptive radiation of the complex.

Wheat storage proteins: glutenin DNA diversity in wild emmer wheat, Triticum dicoccoids, in Israel and Turkey. 3. Environmental correlates and allozymic associations.

The diversity of high-molecular-weight (HMW) and low-molecular-weight (LMW) glutenin subunits in the tetraploid wild progenitor of wheat, Triticum dicoccoides, was studied at the DNA level by the polymerase chain reaction (PCR). The DNA diversity of HMW and LMW glutenins was shown to be correlated to environmental physical and biotic factors (climate, soil and pathogen resistance) and to allozyme variation. We conclude that glutenin DNA diversity is nonrandomly distributed and could be more optimally sampled in nature for future breeding programmes to improve bread quality.

Wheat storage proteins: glutenin diversity in wild emmer, Triticum dicoccoides, in Israel and Turkey. 2. DNA diversity detected by PCR.

Germplasm of Triticum dicoccoides collected from different environments in Israel was evaluated by using the PCR as a molecular marker. Two pairs of primers were used in the PCR in amplifying the DNA tracts coding the high-and low-molecular-weight glutenin subunits. Analyses reveal great variability within and between populations indicating the high values of this germplasm for future breeding programs to improve the protein quality in wheat.

Chromosome translocations in wild populations of tetraploid emmer wheat in Israel and Turkey.

Translocation frequencies (as compared to the standard chromosome arrangement typified by that in 'Chinese Spring') in 9 or more genotypes from each of 15 populations of Triticum dicoccoides in Israel were determined. Data also were obtained from 2 genotypes of the southernmost population (Jaba). A single population from Turkey was also investigated. There were 119 genotypes with translocations in the sample of 171 genotypes investigated (70%). The frequency of translocations in different populations varied from 0.27 to 1.00, and all populations had 1 or more genotypes with one or more translocations. Some populations such as Qazrin appeared to be homogeneous for translocations, but most populations were heterogeneous. A sample of 17 genotypes from 12 of the populations were crossed with the Langdon D-genome disomic substitutions to determine the identity of the chromosomes involved in the translocations. There were nine genotypes with translocations and with the exception of a 2A/2B translocation, none of them involved the same chromosomes. The B-genome chromosomes were involved in translocations more frequently than the A-genome chromosomes. Translocation frequencies (TF) of the various populations were correlated with environmental variables, primarily with water availability and humidity, and possibly also with soil type. In general, TF was higher in peripheral populations in the ecologically heterogeneous frontiers of species distribution than in the central populations located in the catchment area of the upper Jordan valley.

Chromosomal speciation and adaptive radiation of mole rats in Asia Minor correlated with increased ecological stress.

The evolutionary forces causing chromosomal speciation and adaptation are still enigmatic. Here we tested the Israel evolutionary model of positive association of diploid chromosome number (2n) and genetic diversity with aridity stress in subterranean mole rats, on a 30-times-larger scale in Asia Minor. We analyzed both karyotype and allozyme diversity across Turkey, based on 37 allozymic loci in 20 localities of the Spalax leucodon and 4 localities of the Spalax ehrenbergi superspecies. We found extensive chromosomal speciation in S. leucodon (2n = 38, 40, 50, 54, 60, and 62) and in S. ehrenbergi (2n = 52, 56, and 58), presumably representing from 14 to > 20 additional biological species. Genetic diversity indices were low, but, like the chromosome number (2n), positively correlated with aridity stress, increasing centripetally from the periphery toward geologically young, arid, and climatically unpredictable central Anatolia. Nei's genetic distance D across all populations averaged 0.174 (range 0.002-0.422), supporting, combined with 2n and ecogeography, the biological species status of most tested populations. Chromosome evolution is the basis of speciation and adaptation in Spalax; it provides both postmating reproductive isolation, as well as higher levels of recombination with increased 2n. A mathematical model shows that a Robertsonian fission of a single metacentric considerably increases haplotype diversity. This haplotype diversity may contribute to population adaptation to climatic stress and ecological unpredictability in space and time. The increase in diversity corroborates the nichewidth genetic-variation hypothesis.

Genetic polymorphisms in subterranean mammals (Spalax ehrenbergi superspecies) in the near east revisited: patterns and theory.

Allozyme diversity in the superspecies Spalax ehrenbergi has been revisited by studying 36 gene loci in 241 subterranean mole rats from 22 populations and nine chromosomal species, four from Turkey (2n = 52E (east), 52W (west), 56 and 58), four from Israel (2n = 52, 54, 58 and 60), and one from Egypt (2n = 60). The following results were indicated. (1) Genetic patterns: 11 of the 36 loci analysed (30.5 per cent) were monomorphic across the range, fifteen (41.7 per cent) were weakly polymorphic and the remaining 10 loci (27.8 per cent) were strongly polymorphic. (2) Heterozygosity: the average H was 0.051, range 0.00-0.098. In Israel, H increased with aridity and climatic unpredictability towards the northern Negev Desert, and was remarkably high in small steppic semi-isolates and desert isolates. (3) Species discrimination: some of the S. ehrenbergi species can be discriminated qualitatively. (4) Genetic distances (D): between species these values averaged 0.077, range 0.001-0.269, with the highest D between the ancestor Turkish and descendant Israeli and Egyptian species. The phylogenetic tree supports the Turkish origin of the Israeli Spalax ehrenbergi species, and the recent speciation of the Egyptian Spalax. (5) Genetic diversity is mostly (58 per cent) within populations. (6) Allozyme correlates: allozyme diversity was significantly correlated with the external physical (both climatic and edaphic) and biotic (parasite infection and plant cover) environment. (7) Spatial autocorrelation of allozyme frequencies suggests that migration is not influential. (8) Gametic phase disequilibria were significant in four out of five species tested, and were associated with climatic and edaphic factors. These results support the environmental selection hypothesis of genetic diversity including the niche-width variation hypothesis in space and time. Natural selection appears to play a major role in genetic differentiation of proteins in adaptive radiation and speciation.

Genetic polymorphisms of α- and ß-amylase isozymes in wild emmer wheat, Triticum dicoccoides, in Israel.

α- and ß-amylase isozyme diversity was studied electrophoretically by thin-layer polyacrylamide gel isoelectrofocusing in the tetraploid wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats. We analyzed 225 plants from 23 populations encompassing the ecological spectrum of T. dicoccoides in Israel. The results were as follows: (a) Band and multilocus genotype polymorphisms abound and vary within and between the four amylase components: malt, green (α-amylases), and dry and germinating seeds (ß-amylases). (b) The number of bands of malt, green, and dry and germinating seeds were 20, 6, 11 and 13, respectively, generating 40, 6, 51, and 51 patterns or multilocus genotypes (MGP), respectively. The MGPs vary drastically within and between populations, from monomorphic in some populations with a single pattern to highly polymorphic ones, (c) Mean H e values for malt, green, and germinating and dry seeds are 0.053, 0.055, 0.088, and 0.077, respectively; mean number of bands per individual was 11.8, 4.4, 7.6, and 4.0, respectively, (d) The percentages of 50 bands and 148 multilocus genotype patterns (MGP) (in parenthesis) were classified into widespread, sporadic, and localized: 84.4 (10.8), 8.9 (12.2), 6.7 (77.0), respectively. Notably, 89.2% of the patterns were not widespread, but sporadic and localized, (e) The mean value of genetic distances among populations (Nei's D) for the four amylase groups is D = 0.136, 0.175, 0.288 and 0.307, respectively, not displaying geographical correlates. (f) Most of the α- and ß-amylase diversity is between populations (G st = 68-75%). (g) Significant environmental correlates occur between either bands or patterns and climatic diversity (water and primarily temperature factors). (h) Significant associations of multilocus amylase bands occur across Israel. Like-wise, significant gametic phase disequilibria, D, occur within populations and are positively correlated with climatic variables, primarily that of temperature, (i) Discriminant analyses correctly classified (95-100%) the 23 wild emmer populations into their ecogeographical region and soil type. (j) Autocorrelation analysis showed that there is no correlation between bands and geographic distance and excluded migration as a major factor of amylase differentiation.These results suggest that diversifying climatic and edaphic natural selection rather than stochastisity or migration is the major evolutionary force driving amylase differentiation at both the single and multilocus levels. Furthermore, wild emmer harbors high levels of α- and ß-amylase diversity both as single bands and as multilocus adaptive genetic patterns. These are exploitable both as genetic markers for quantitative loci (QTLs) and as adaptive genetic resources to improve wheat germination and growth through classical breeding and/or biotechnology.

Selection for class II Mhc heterozygosity by parasites in subterranean mole rats.

Mhc organization and polymorphism have previously been studied in the four chromosomal species of the Spalax ehrenbergi superspecies in Israel, serologically, and at the DNA, RFLP and sequence levels of class I and class II genes. Here we demonstrate that the observed heterozygosity of Mhc class II genes P alpha 1 with 11 alleles, and Q beta, with at least 14 alleles, is positively and significantly correlated with infectivities of ectoparasites (gamasid mites) and endoparasites (helminths). Mhc heterozygosity is highest in the most infected area, which is in the most humid-warm region of the superspecies range, or where two zoogeographic regions overlap. We conclude that the evolutionary forces responsible for the Mhc class II two-gene polymorphisms include selection for increased heterozygosity as a defense strategy against ecto- and endoparasite infections.

Genetic divergence of heat production within and between the wild progenitors of wheat and barley: evolutionary and agronomical implications.

We compared and contrasted calorimetrically heat production in seedlings incubated at 5°C and 24°C using genotypes from cold and warm Israeli populations of the wild progenitors of barley (Hordeum spontaneum) and wheat (Triticum dicoccoides). The wild barley sample comprised 14 accessions, 7 from cold localities and 7 from warm localities. The wild emmer wheat sample consisted of 12 accessions, 6 from a cold locality, and 6 from a warm locality. Our results indicated that (1) heat production was significantly higher in the two wild cereals at 5 °C than at 24 °C; (2) interspecifically, wild barley generates significantly more heat than wild wheat at both 5 °C and 24 °C; (3) intraspecifically, wild barley from warm environments generates significantly more heat than wild barley from cold ones, at 24 °C. We hypothesize that both the inter- and intraspecific differences in heat production evolved adaptively by natural selection in accordance with the niche-width genetic variation hypothesis. These differences presumably enhance biochemical processes, hence growth, thereby leading to the shorter annual cycle of barley compared to that of wheat, and may explain the wider range of the wild and cultivated gene pools of barley, as compared with those of wheat. We propose that a shortening of the growth period through utilizing heat production gene(s) is feasible by classical methods of breeding and/or modern biotechnology.

Herbicide response polymorphisms in wild emmer wheat: ecological and isozyme correlations.

We demonstrate that the scores and frequencies of chlortoluron (CT) and metoxuron (MX) resistance and susceptible phenotypes of wild emmer wheat, Triticum dicoccoides, are correlated with ecological factors and allozyme markers. Some isozyme markers located on chromosome 6B (e.g. Adh,Est-4 and Got), which also harbours the CT and MX resistance gene, provide good genetic markers for herbicide resistance breeding. Significant correlations between herbicide and photosynthetic characters suggest that the evolution of herbicide resistance polymorphisms may be related to the process of photosynthesis in nature and predated domestication of cultivated wheat.

Photosynthetic performance in wild emmer wheat, Triticum dicoccoides: ecological and genetic predictability.

In a twin study, we have shown that wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats, harbours important genetic variation (Vg) in photosynthetic characteristics. This Vg resides within and between populations and ecogeographical regions in Israel, which is the center of origin and diversity of wild emmer wheat. Here we analyzed, by univariate and multivariate methods, the significant differentiation of variation in photosynthetic characteristics of 107 genotypes from 27 populations of wild emmer in Israel, distributed in three ecogeographical regions including central, xeric (northern cold and eastern warm) marginal, and mesic (western) marginal populations. The highest photosynthetic efficiency was displayed by populations of the xeric marginal region, but most variation for photosynthetic capacity occurs between accessions within ecogeographical regions and populations. Genotypes and populations of T. dicoccoides having high photosynthetic capacity can be identified by climatic factors and isozyme markers. The identification by genetic markers, if substantiated by testcrosses, can facilitate the maximization of conservation, in situ or ex situ, and utilization of these photosynthetic genetic resources for improvement of hexaploid wheat (T. aestivum).

Genetic polymorphism of urine deoxyribonuclease I isomerases of subterranean mole rats, Spalax ehrenbergi superspecies, in Israel: ecogeographical patterns and correlates.

Genetic polymorphism of urine deoxyribonuclease I (DNase I) of mole rats was analyzed by isoelectric focusing in a thin-layer polyacrylamide gel (IEF-PAGE). One hundred and three subterranean mole rats, comprising 13 populations belonging to the four chromosomal species (2n = 52, 54, 58, 60) of the actively speciating Spalax ehrenbergi superspecies in Israel, were tested. The following results were indicated. (i) Spalax DNase I consisted of 6-12 major isozymes. (ii) Four phenotypes (numbers in parentheses) were 1 (92), 1-2 (5), 1-3 (4), and 2 (1). The decreasing order of genetic diversity, He, in the four species was 0.37, 0.13, 0.10, and 0.0 for 2n = 58, 52, 54, and 60, respectively. (iii) Spearman rank correlations and multiple regression analyses indicated associations of allele frequencies and genetic diversity with climatic and vegetation factors. We concluded that (a) climatic selection, either directly or indirectly through plant (i.e., food resources) diversity, plays an important role in DNase genetic differentiation and (b) no gene flow and introgression occur between the recent derivative of speciation (2n = 60) and its ancestor (2n = 58), suggesting the operation of reproductive isolation between both species despite natural hybridization.

Aldolase DNA polymorphism in subterranean mole-rats: genetic differentiation and environmental correlates.

We analysed the genetic diversity and environmental correlates of the aldolase A and B genes by means of restriction endonucleases (DNA RFLP analysis), in the four chromosomal species (2n = 52, 54, 58 and 60) of the actively speciating subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel. The results indicated that: (i) both aldolase genes are highly polymorphic; (ii) fragment frequencies and fragment profiles display geographical patterns and significant ecological correlates; (iii) discriminant analysis largely succeeded in separating the four chromosomal species on the basis of variation of aldolase RFLPs.

Genetic diversity and its ecological correlates in nature: comparisons between subterranean, fossorial, and aboveground small mammals.

We have reanalyzed the levels of observed heterozygosity based on old and new material of small mammals in attempt to retest the environmental theory of genetic diversity or the niche-width variation hypothesis. This study involves old and new material of 184 small mammalian species both insectivores and rodents; 111 living aboveground and 73 species living partly (fossorial, N = 28) or totally (subterranean, N = 45) underground. The results indicated that (i) in general, insectivores harbor significantly lower levels of heterozygosity than rodents, and (ii) both overall, and in insectivores and rodents separately, the narrow-niche fossorial and subterranean species displayed significantly lower levels of observed heterozygosity than small mammalian species living aboveground. This is true in almost all parametric and nonparametric analyses. Subterranean and fossorial small mammals are more homozygous in protein diversity, primarily isozymes, compared with aboveground species. This pattern corroborates the environmental theory or niche-width variation hypothesis of genetic diversity.

Adaptive variation in structure and function of kidneys of speciating subterranean mole rats.

We report on kidney structure and function in subterranean mammals of four chromosomal species (2n=52, 54, 58 and 60) belonging to the Spalax ehrenbergi superspecies, in relation to their speciation and adaptive radiation from mesic (2n=52) to xeric (2n=60) environments in Israel. Structural variables measured involved: (1) Relative Medullary Thickness, (RMT); (2) Relative Kidney Weight. (RKW); and (3) Percentage of Kidney out of Body Weight (PKW). Functional variables involved: (i) Urine Solid Concentration, (USC); and (ii) Urine Osmotic Concentration (UOC). The results for chromosomal species 2n=52, 54, 58 and 60 indicated nonsignificant increase southward for RMT, but displayed significant increase along the same transect for RKW, PKW, and USC. The UOC was significantly lower in mesic 2n=52 as compared to the other three species when experimental animals were fed in the laboratory on regular carrot food. However, protein stress food (soybean) and salt stress of 0.45 mol NaCl, caused significant, three and a half fold increase of UOC in 2n=52, 54 and 58; but four and a half fold increase in 2n=60, significantly higher than in the other three species. We conclude that both structurally and functionally, the kidneys differentiated adaptively during the Pleistocene evolution of S. ehrenbergi in Israel, in accordance with aridity stress and halophyte food resources towards the desert. Nevertheless, Spalax generally shows clear upper limits in kidney structural and functional capacities, preventing it from colonizing the true desert, south of the 100 mm isohyete.