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Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum.

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.

Amino Acid Sequence↗

Colonization history and introduction dynamics of capsella bursa-pastoris (Brassicaceae) in north america: isozymes and quantitative traits

Multilocus isozyme genotypic composition for aspartate aminotransferase (AAT), leucine aminopeptidase (LAP) and glutamate dehydrogenase (GDH) was studied for Capsella in the source continent, Europe (9000 plants from 593 populations), and in the colonized continent, North America (2700 plants from 88 populations). North America was depauperate in the number of genotypes (by approximately 50%), but in terms of frequencies, a few genotypes were common and shared by both continents. Although some, very rare, genotypes were, however, unique for North America, our data provided no evidence to indicate that the introduced gene pools were reconstructed on a multilocus genetic basis after introduction. Instead, they argued for a considerable number of independent introduction events. Geographical distribution patterns of multilocus genotypes in Europe and North America were pronounced and enabled us to trace the colonization history of Californian Capsella back to Spanish ancestral populations and those of temperate North America back to temperate European gene pools. A random-block field experiment with 14 Californian populations from different climatic regions revealed that variation patterns of quantitative traits reflect ecotypic variation, and the ecological amplitude of Capsella in North America is similar to that in Europe, which can be traced back to the introduction of preadapted genotypes. It appears that certain multilocus isozyme genotypes are associated with certain ecotypes. The variable European gene pool of Capsella was essentially introduced into North America without major genetic changes.

Journal Article↗

Genetic identification of wild and domestic cats (Felis silvestris) and their hybrids using Bayesian clustering methods.

Crossbreeding with free-ranging domestic cats is supposed to threaten the genetic integrity of wildcat populations in Europe, although the diagnostic markers to identify "pure" or "admixed" wildcats have never been clearly defined. Here we use mitochondrial (mt) DNA sequences and allelic variation at 12 microsatellite loci to genotype 128 wild and domestic cats sampled in Italy which were preclassified into three separate groups: European wildcats (Felis silvestris silvestris), Sardinian wildcats (Felis silvestris libyca), and domestic cats (Felis silvestris catus), according to their coat color patterns, collection localities, and other phenotypical traits, independently of any genetic information. For comparison, we included some captive-reared hybrids of European wild and domestic cats. Genetic variability was significantly partitioned among the three groups (mtDNA estimate of F(ST) = 0.36; microsatellite estimate of R(ST) = 0.30; P < 0.001), suggesting that morphological diversity reflects the existence of distinct gene pools. Multivariate ordination of individual genotypes and clustering of interindividual genetic distances also showed evidence of distinct cat groups, partially congruent with the morphological classification. Cluster analysis, however, did not enable hybrid cats to be identified from genetic information alone, nor were all individuals assigned to their populations. In contrast, a Bayesian admixture analysis simultaneously assigned the European wildcats, the Sardinian wildcats, and the domestic cats to different clusters, independent of any prior information, and pointed out the admixed gene composition of the hybrids, which were assigned to more than one cluster. Only one putative Sardinian wildcat was assigned to the domestic cat cluster, and one presumed European wildcat showed mixed (hybrid) ancestry in the domestic cat gene pool. Mitochondrial DNA sequences indicated that three additional presumed European wildcats might have hybrid ancestry. These four cats were sampled from the same area in the northernmost edge of the European wildcat distribution in the Italian Apennines. Admixture analyses suggest that wild and domestic cats in Italy are distinct, reproductively isolated gene pools and that introgression of domestic alleles into the wild-living population is very limited and geographically localized.

Alleles↗

Origins of U.S. Hispanics. Implications for diabetes.

The purpose of this article was to characterize the origins of the United States Hispanic population and discuss the implications of these origins in the context of diabetes risk. Particular attention was focused on the genetic origins of the three major U.S. Hispanic groups, i.e., Mexican Americans, Puerto Ricans, and Cubans. The U.S. Census figures provided basic demographic information. Genetic marker data for ancestral populations were taken from a review of the literature and compendia. Genetic marker data for the Puerto Rican and Cuban populations were extracted from the literature. Genetic markers determined on approximately 1000 randomly selected Mexican Americans from Starr County, Texas, were taken as representative of the Mexican-American population. The Hispanic population is the second largest and fastest growing minority in the U.S. Estimates of the Hispanic population in 1988 indicated some 19.4 million residents, of whom 62% were classified as Mexican, 13% as Puerto Rican, and the remaining 25% as Cubans and others. Various lines of evidence can be used to characterize the Hispanic population and its origins. These include ethnohistory, self-assessment of ancestry, surname distributions, speech and cultural characteristics, quantitative traits, and genetic structure. Genetic data were used to estimate the contribution of putative ancestral populations to the contemporary gene pool. For Mexican Americans, 31% of the contemporary gene pool is estimated to be Native American derived, whereas 61 and 8% are Spanish and African derived, respectively. In Puerto Rico, the percentage of contributions of Spanish, Native American, and African admixture to the population are 45, 18, and 37%, respectively. For Cuba, the parallel estimates are 62, 18, and 20%. The high frequency of Native American-derived genes in the contemporary Hispanic population predict a higher frequency of non-insulin-dependent diabetes mellitus (NIDDM) under the assumption that genes are important in NIDDM etiology. Our results are consistent with the finding of the significant role of genes in determining risk.

Adolescent↗

Osteoporosis, sedentary lifestyle, and increasing hip fractures: pathogenic relationship or differential survival bias.

Osteoporosis, although a disorder of antiquity, has become more prevalent in developed countries and is a major risk factor for skeletal fracture. Accordingly, the increasing incidence of hip fracture among the elderly within developed nations has been attributed to an increased prevalence of osteoporosis. An increasingly sedentary lifestyle has been suggested as a significant contributing factor for the increased prevalence of osteoporosis. However, differential survival, reflecting changing competing mortality risks, will alter the gene pool of a surviving population cohort. Thus, the gene pool (and hence, disease susceptibilities) of 70-year-old individuals in 1990, for example, should not implicitly be assumed to be the same as 70-year-old individuals in 1950. Consequently, differences in the prevalence of osteoporosis or incidence of hip fracture between current and past elderly cohorts do not necessarily imply differences in environmental risk factors such as levels of physical activity. Instead, variation in competing mortality risks over time may produce differential survival with selection bias and "naturally" lead to increases in the incidence and prevalence of some aging-related disorders such as osteoporosis.

Aged↗

The common, Near-Eastern origin of Ashkenazi and Sephardi Jews supported by Y-chromosome similarity.

About 80 Sephardim, 80 Ashkenazim and 100 Czechoslovaks were examined for the Y-specific RFLPs revealed by the probes p12f2 and p49a,f on TaqI DNA digests. The aim of the study was to investigate the origin of the Ashkenazi gene pool through the analysis of markers which, having an exclusively holoandric transmission, are useful to estimate paternal gene flow. The comparison of the two groups of Jews with each other and with Czechoslovaks (which have been taken as a representative source of foreign Y-chromosomes for Ashkenazim) shows a great similarity between Sephardim and Ashkenazim who are very different from Czechoslovaks. On the other hand both groups of Jews appear to be closely related to Lebanese. A preliminary evaluation suggests that the contribution of foreign males to the Ashkenazi gene pool has been very low (1% or less per generation).

Adult↗

Genetic basis for broad interspecific compatibility in Solanum verrucosum.

Solanum verrucosum Schlechtendal (2x&#x2009;=&#x2009;2n&#x2009;=&#x2009;24) is unique among the clade 4 Solanum Sect Petota species. In addition to being one of the only fully self-compatible diploid potato species, S. verrucosum is the only clade 4 species that lacks prezygotic interspecific reproductive barriers. This allows S. verrucosum to accept pollen from a broad range of Solanum species and thereby serving as a genetic "bridge" between the cultivated or primary potato gene pool and distantly related wild relatives in the tertiary gene pool. The genetic mechanisms underlying self-compatibility in Solanum often underpin interspecific compatibility interactions, which in S. verrucosum, has been attributed to the lack of S-RNase expression. Using an interspecific F2 mapping population (n&#x2009;=&#x2009;150), we investigated the genetic mechanisms responsible for the lack of interspecific reproductive barriers in S. verrucosum. This F2 population was evaluated for the ability to accept pollen from two clade 1, 1 EBN species (S. pinnatisectum and S. tarnii); from which two QTL for interspecific compatibility were identified on chromosomes 1 and 11, explaining 56.6% of the phenotypic variation observed. To identify the genetic basis of interspecific compatibility, we generated a chromosome-scale genome assembly of S. verrucosum MSII1813-2 and performed gene expression profiling of reproductive organs. Differential gene expression of S-RNase, located within the chromosome 1 QTL, confirmed the central role of the S-locus and specifically, S-RNase, in interspecific compatibility. Discovery of a non-S-locus QTL is consistent with previous findings that other non-S-locus factors are necessary for interspecific compatibility in S. verrucosum.

Solanum↗

Human V kappa immunoglobulin gene number: implications for the origin of antibody diversity.

To assess the relative contributions of germline versus somatically mutated genes in the human immune system, we have examined the size of the kappa light-chain variable region (V kappa) gene pool. Two cloned kappa subgroup 1 (V kappa 1) gene probes detected the same family of 15 to 20 crosshybridizing restriction fragments in human DNA, whereas flanking region probes detected fewer hybridizing fragments. Most of the hybridizing bands represent single-copy genes, as judged by a "'gene titration" experiment. Furthermore, the number of hybridization bands is a good estimate of the haploid gene number, since we observed little polymorphism of restriction sites in the V kappa locus of eight unrelated people. A cloned V kappa 3 probe hybridized to essentially the same 15--20 genes in human DNA as the V kappa 1 probes. These results strongly suggest that a discrete family of 15--20 genes constitutes a large proportion of the V genes from three of the four V kappa subgroups. The small number of V kappa genes in the human genome supports the idea that somatic mutation plays a major role in the origin of antibody diversity in man.

Antibody Diversity↗

Techniques for estimating genetic admixture and applications to the problem of the origin of the Icelanders and the Ashkenazi Jews.

A method is introduced for simultaneously using multiple loci to estimate admixture and test goodness of fit of the model of admixture. Deviation of observed frequencies from expectation caused by sources of error such as sampling and/or drift is allowed for all loci in all populations. This allows investigation of the effects of different assumptions about sources of error on the estimates. Admixture is then investigated for Icelanders and Ashkenazi Jews. Results indicate that the Icelanders have a large Norse contribution, and that the Jews may have a small to moderate contribution from the European gene pool. There are some indications that AB0 and G6PD give abnormal estimates of admixture compared to other loci, and that the Jewish gene pool may be derived from additional populations in addition to the populations considered.

ABO Blood-Group System↗

Sequence analyses and antigenic epitope mapping of the putative RNA-directed RNA polymerase of five U.S. bluetongue viruses.

We determined the complete nucleotide sequences of the cognate L1 double-stranded RNA segments of bluetongue virus (BTV) serotypes 2, 11, 13, and 17, which encode the putative RNA-directed RNA polymerase VP1. Each L1 gene contained 3944 nucleotides and was 10 bases shorter than the previously reported L1 gene of BTV 10. A single open reading frame which could encode the reported VP1 protein, 1302 amino acids in size, began with an initiation codon at nucleotides 12-14 and a termination codon at nucleotides 3918-3920. Analyses of the nucleotides of L1 genes and the deduced amino acid sequences of VP1 proteins of the five U.S. BTV serotypes indicated that the most recently isolated BTV-2 serotype from Florida was more distantly related than BTV-10, 11, 13, and 17, which were isolated primarily in the western U.S.A. The results are consistent with our hypothesis that BTVs-10, -11, -13, and -17 are derived from a single and common gene pool, and that BTV-2 belongs to a second, distinct gene pool. These genetic distinctions also reflected well with the known geographic distribution of the five U.S. BTV serotypes in North America. This putative RNA-directed RNA polymerase (149 KDa) was a basic protein, and the deduced amino acid sequences of the VP1 proteins contained seven highly conserved hydrophobic domains and many other sequence motifs which were also found in other known RNA polymerases. Four immunodominant but linear antigenic epitopes conserved among the VP1 of five U.S. BTVs were also been identified and mapped using monospecific oligoclonal antibodies.

Amino Acid Sequence↗

Renewal of genetic composition of a lancelet, Branchiostoma belcheri, in the Seto Inland Sea, Japan.

We studied renewal of genetic composition of a lancelet, Branchiostoma belcheri, at a station in the Seto Inland Sea, Japan, using random amplified polymorphic DNA (RAPD) technique. We detected a total of 49 DNA bands from 27 individuals of 5 seasonal samples. Among these, some were specific to individual or seasonal sample. There were no bands common to all individuals. We calculated the Band Sharing Index (BSI) values for each combination of individuals. BSI was in a wide range of 0.00-0.97 and the average BSI between the individuals of a sample was remarkably different from sample to sample (0.37-0.83). In cluster analysis on the basis of BSI, largely 3 clusters were constructed, which finally connected to a single cluster at as low as about 0.2 of BSI. Besides, many clusters were constructed exclusively by a seasonal sample. These results suggest a large gene pool of lancelets in this area, the remarkable differences in gene pool size among the samples and a seasonal renewal of genetic composition at a habitat.

Animals↗

Genetical ESS-models. I. Concepts and basic model.

Evolutionarily Stable Strategies (ESS) in phenotypic models are used to explain the evolution of animal interactive behaviour. As the behavioural features under consideration are assumed to be genetically determined, the question arises how underlying a genetical system might affect the results of phenotypic ESS-models. This question can be fully treated in terms of ESS-theory. A method of designing Genetical ESS-Models is proposed, which transfers the question of evolutionary stability to a "lower" level, the genetical basis. Genetical ESS-models - although nonlinear even in the simplest cases - can be analysed in a way that is familiar to ESS-theorists and yield immediate results on gene pool ESSs, which then may or may not maintain ESSs on the phenotypic level. Moreover, general results can be obtained to characterize evolutionarily stable gene pool states and their interrelation with commonsense, phenotypic ESSs. This part of the article presents the basic concepts and an outline of the method of genetical ESS-models. It gives, as a demonstration, a complete analysis for phenotypic two-strategy models (linear or nonlinear) based on a diploid, diallelic single-locus system under random mating. The results in this case suggest that a phenotypic ESS should indeed be expected to evolve but, maybe, only after passing through a succession of temporarily stable states.

Animals↗

High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations.

The extent and nature of southeastern Europe (SEE) paternal genetic contribution to the European genetic landscape were explored based on a high-resolution Y chromosome analysis involving 681 males from seven populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, and R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly Slavic, paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26) and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-Last Glacial Maximum R1a expansion from east to west, the Younger Dryas-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern Europe and SEE, and a rather weak extent of E3b1 diffusion toward regions nowadays occupied by Slavic-speaking populations.

Male↗

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains.

BACKGROUND: Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4 degrees C; 16 degrees C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Atmospheric Pressure↗

Three sibling species within Contracaecum osculatum (Nematoda, Ascaridida, Ascaridoidea) from the Atlantic Arctic-Boreal region: reproductive isolation and host preferences.

Genetic variation within and between population samples from 22 locations of the Atlantic Arctic-Boreal region, including 1657 specimens morphologically assigned to Contracaecum osculatum, was electrophoretically analysed at 17 loci. Highly significant deviations from the Hardy-Weinberg equilibrium were found at various loci in several samples, owing to the existence of three distinct gene pools within C. osculatum (sensu lato) from the study area. These gene pools correspond to three biological species (provisionally designated A, B and C), characterized by distinct genotypes at several diagnostic loci. Reproductive isolation between C.osculatum A, B and C is confirmed by the lack of F1, recombinant, or backcross genotypes in sympatric areas, despite the occurrence of multiple infections. Mean heterozygosity per locus is on average 0.11 in species A, 0.10 in B and 0.07 in C. High levels of gene flow were found within each of the three species, the values of Nm (number of migrant individuals) ranging from 3.41 (C. osculatum C) to 5.77 (C. osculatum A). Average Nei's genetic distance is 0.46 between A and B, 0.50 between A and C and 0.77 between B and C. From these values, times of evolutionary divergence from 2 to 4 million years can be estimated. Genetic relationships among populations and species of the C. osculatum complex are illustrated by principal component analysis. The role of both geographical isolation and host preferences in the speciation of C. osculatum (sensu lato) is discussed. A morphological distinction of the three species has not yet been possible (sibling species). However, there is evidence that the name C. osculatum (sensu stricto) should be used for species C, which shows a geographical distribution and definitive host corresponding to the neotype of C. osculatum (sensu stricto). Finally, a comparison is made between the members of the C. osculatum complex from the Atlantic Arctic-Boreal region and those of the Pseudoterranova decipiens complex from the same area, as to: (i) times of evolutionary divergence, (ii) geographical distribution, and (iii) host preferences.

Alleles↗

The development and application of molecular markers for abiotic stress tolerance in barley.

This article represents some current thinking and objectives in the use of molecular markers to abiotic stress tolerance. Barley has been chosen for study as it is an important crop species, as well as a model for genetic and physiological studies. It is an important crop and, because of its well-studied genetics and physiology, is an excellent candidate in which to devise more efficient breeding methods. Abiotic stress work on cultivated gene pools of small grain cereals frequently shows that adaptive and developmental genes are strongly associated with responses. Developmental genes have strong pleiotropic effects on a number of performance traits, not just abiotic stresses. One concern is that much of the genetic variation for improving abiotic stress tolerance has been lost during domestication, selection and modern breeding, leaving pleiotropic effects of the selected genes for development and adaptation. Such genes are critical in matching cultivars to their target agronomic environment, and since there is little leverage in changing these, other sources of variation may be required. In barley, and many other crops, greater variation to abiotic stresses exists in primitive landraces and related wild species gene pools. Wild barley, Hordeum spontaneum C. Koch is the progenitor of cultivated barley, Hordeum vulgare L. and is easily hybridized to H. vulgare. Genetic fingerprinting of H. spontaneum has revealed genetic marker associations with site-of-origin ecogeographic factors and also experimentally imposed stresses. Genotypes and collection sites have been identified which show the desired variation for particular stresses. Doubled haploid and other segregating populations, including landrace derivatives have been used to map genetically the loci involved. These data can be used in molecular breeding approaches to improve the drought tolerance of barley. One strategy involves screening for genetic markers and physiological traits for drought tolerance, and the associated problem of drought relief-induced mildew susceptibility in naturally droughted fields of North Africa.

Adaptation, Physiological↗

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India.

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

Cluster Analysis↗

Genetic consequences of differential demographic behaviour in the Saguenay region, Québec.

Some rare inherited disorders are found with a high frequency in the population of the Saguenay region (Québec province, Canada, population 300,000). Inbreeding coefficients are too low to be an explanation for these high frequencies. In the first decades of settlement (1842-1870), most of the immigrants came from a small region called Charlevoix (east of Québec city). As most of the genetic disorders found in the Saguenay region are also found in the Charlevoix region, it is strongly suspected that the genes were introduced by these first settlers from Charlevoix. Using the BALSAC database (which contains linked information on the entire Saguenay population) to calculate the number of contemporary descendants and the genetic contribution of each founder to these descendants, we show that: (1) Founders who entered the population before 1870 contribute to 45% of the contemporary gene pool, despite the fact that they represent only 15% of all the 20,012 immigrants with descendants in the contemporary population (individuals born between 1950 and 1971). (2) Their genetic contribution is not homogenous in the contemporary population: 5% of the population have 100% of their gene pool coming from these first founders, while 10% have a zero to 5% contribution from these earliest founders. (3) Fifty percent of the genes introduced in the population were lost. (4) If only 68 immigrants among the first founders (2.0%) were carriers of the same gene, it could reach a frequency of 5% in the contemporary population, which is the frequency of most of the inherited disorders found in the population.

Alleles↗