Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium

Abstract Population genetic data are presented which should contribute to evaluation of the hypothesis that the extraordinary evolutionary patterns observed at the b locus of the rabbit immunoglobulin light chain constant region can be the outcome of overdominance-type selection. The analysis of allele correlations in natural populations revealed an excess of heterozygotes of about 10% at the b locus while heterozygote excess was not observed at loci determining the immunoglobulin heavy chain. Data from the published literature, where homozygote advantage was suggested, were reevaluated and found in agreement with data here presented. Gene diversity was evenly distributed among populations and showed similarities with patterns reported for histocompatibility loci. Analysis of genotypic disequilibria revealed strong digenic associations between the leading alleles of heavy and light chain constant region loci in conjunction with trigenic disequilibria corresponding to a preferential association of b locus heterozygosity with the predominant allele of the heavy chain e locus. It is argued that this may indicate compensatory or nonadditive aspects of a putative heterozygosity enhancing mechanism, implying that effects at the light chain might be more pronounced in populations fixed for the heavy chain polymorphism.

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Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽

10.1099/mic.0.038224-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2080-2091 ◽

Cited By ~ 28

Author(s):

Anne-Laure Michon ◽

Fabien Aujoulat ◽

Laurent Roudière ◽

Olivier Soulier ◽

Isabelle Zorgniotti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Diversity ◽

Natural Populations ◽

Variable Region ◽

Housekeeping Gene ◽

Single Copy ◽

Population Based ◽

Rrna Gene ◽

Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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RAPD ANALYSIS OF GENETIC VARIATION IN NATURAL POPULATIONS OF AEGILOPS SP. FROM SOUTH ADRIATIC

AGROFOR ◽

10.7251/agreng1801035d ◽

2018 ◽

Vol 3 (1) ◽

Author(s):

Miodrag DIMITRIJEVIĆ ◽

Sofija PETROVIĆ ◽

Borislav BANJAC ◽

Goran BARAĆ

Keyword(s):

Genetic Variation ◽

Food Production ◽

Rapd Markers ◽

Rapd Analysis ◽

Gene Diversity ◽

Rapd Marker ◽

Natural Populations ◽

Genetic Structuring ◽

Potential Source ◽

Novel Approach

New challenges that food production is facing, requires novel approach inagricultural strategy. The scissors of growing demand for food and the limits of theEarth's resources are forcing plant breeders to run for the new borders, utilizing allthe available genetic variation in order to create fruitful and economically soundcultivars. Aegilops sp. (Poaceae) is a potential source of genetic variation for wheatimprovement. RAPD marker analysis was used in order to distinguish and evaluatedifferent genotypes of Aegilops sp. population samples from the collectiongathered during few years’ expeditions in South Adriatic, along the coastal, littoraland the inland parts of Montenegro. Ten randomly amplified polymorphic DNAmarkers (RAPDs) were tested: OPA-05, OPA-08, OPB-06, OPA-02, OPA-07,OPA-25, OPB-07, OPB-18, OPC-06, OPC-10 to examine genetic structuring on 18samples of 6 populations of different Aegilops sp. According to global AMOVA,75% of total gene diversity was attributable mostly to diversity within population(ΦPT =0.205 p=0.001), indicating that the groups of studied goat grass populationswere seemingly to differing genetically. In contrast, 25% of the variation camefrom variation among populations. According to PCoA, the distribution of 18 goatgrass accessions by Principal Coordinate Analysis shows 3 distinct groups. PCoaxis 1, PCo axis 2, and PCo axis 3 account for 20.8%, 18.2% and 14.1% of thevariation, respectively. The results showed that RAPD markers could be aconvenient tool for investigating genetic variation and for detecting geneticstructuring of populations. Genetic variability formed under natural selection wasentrenched.

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Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽

10.1139/cjb-2013-0029 ◽

2013 ◽

Vol 91 (10) ◽

pp. 653-661 ◽

Cited By ~ 4

Author(s):

Anochar Kaewwongwal ◽

Arunee Jetsadu ◽

Prakit Somta ◽

Sompong Chankaew ◽

Peerasak Srinives

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Allelic Richness ◽

Gene Diversity ◽

In Situ Conservation ◽

Natural Populations ◽

Microsatellite Variation ◽

Genetic Clusters ◽

Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

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Taxonomic and conservation implications of ecological speciation in Nesospiza buntings on Tristan da Cunha

Bird Conservation International ◽

10.1017/s095927090800004x ◽

2008 ◽

Vol 18 (1) ◽

pp. 20-29 ◽

Cited By ~ 6

Author(s):

Peter G. Ryan

Keyword(s):

Species Conservation ◽

Natural Populations ◽

Morphological Diversity ◽

Ecological Speciation ◽

Conservation Priority ◽

Evolutionary Processes ◽

Natural Processes ◽

Tristan Da Cunha ◽

Conservation Implications

AbstractIn addition to protecting species, conservation also includes the maintenance of evolutionary processes, but this aspect is often overlooked. Nesospiza buntings provide a good case study of the need to conserve evolutionary processes. They are endemic to the South Atlantic Tristan da Cunha archipelago, and traditionally have been treated as two species, with each having different subspecies on Nightingale and Inaccessible Islands. Both species are listed as Vulnerable because of their small ranges (<20 km2) and the threat posed by the possible introduction of alien organisms such as mice or rats. The two species differ markedly in size, especially bill size, related to dietary differences. However, recent research suggests that morphological diversity evolved independently on Nightingale and Inaccessible Islands, necessitating a revision of the taxonomy within the genus. I recommend that five taxa be recognized, with two endemic to Nightingale and three to Inaccessible Island. N. wilkinsi and N. questi on Nightingale are well-defined species, but there is considerable hybridization between taxa on Inaccessible Island. These three taxa may be incipient species, but are perhaps best treated as subspecies: N. acunhae acunhae, N. a. dunnei and N. a. fraseri (nom. nov.). All three species qualify as threatened, with N. acunhae and N. questi Vulnerable and N. wilkinsi Endangered. With fewer than 200 individuals, N. wilkinsi has one of the smallest natural populations of any bird. A reassessment of its population size is a conservation priority, following the 2001 storm that damaged many Phylica trees on Nightingale Island. Improved biosecurity quarantine measures are also needed for Nightingale Island. Care should be taken not to disrupt the natural processes occurring among bunting taxa on Inaccessible Island.

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Evolutionary Meta-Analysis of Solanaceous Resistance Gene and Solanum Resistance Gene Analog Sequences and a Practical Framework for Cross-Species Comparisons

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-12-11-0318-r ◽

2012 ◽

Vol 25 (5) ◽

pp. 603-612 ◽

Cited By ~ 15

Author(s):

Edmund A. Quirin ◽

Harpartap Mann ◽

Rachel S. Meyer ◽

Alessandra Traini ◽

Maria Luisa Chiusano ◽

...

Keyword(s):

Comparative Genomics ◽

Resistance Gene ◽

Genome Sequence ◽

Gene Diversity ◽

Meta Analysis ◽

Solanum Species ◽

Plant Genome ◽

R Gene ◽

R Genes ◽

Protein Motifs

Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species—especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.

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HORDEIN VARIATION IN WILD (HORDEUM SPONTANEUM) AND CULTIVATED (H. VULGARE) BARLEY

Canadian Journal of Genetics and Cytology ◽

10.1139/g79-043 ◽

1979 ◽

Vol 21 (3) ◽

pp. 391-404 ◽

Cited By ~ 94

Author(s):

Hans Doll ◽

A. H. D. Brown

Keyword(s):

Linkage Disequilibrium ◽

Wild Species ◽

Storage Protein ◽

Natural Populations ◽

Hordeum Spontaneum ◽

Allele Frequencies ◽

Evolutionary Processes ◽

Highly Correlated ◽

The Individual ◽

Allozyme Loci

The storage protein hordein contains two major groups of polypeptides which are highly polymorphic in barley, and in its evolutionary progenitor Hordeum spontaneum Koch. Crosses between the two species showed that the complex electrophoretic phenotypes within the two groups of polypeptides are governed by codominant alleles at two corresponding loci, Hor-1 and Hor-2, which are moderately linked (11% ± 2). In natural populations of the wild species, the two complex hordein loci were much more polymorphic than the allozyme loci. Furthermore, the variation at these two loci was highly correlated so that individuals differ from one another at both loci much more frequently than expected from the allele frequencies at the individual loci. Considerable hordein variation was also present in Composite Cross XXI, and there was evidence of reassortment of patterns by the seventeenth generation. Thus the complex hordein loci, with their extreme diversity and linkage disequilibrium, are ideal markers for monitoring evolutionary processes in both natural, or composite cross populations.

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Gene diversity in natural populations of oak species

Annales des Sciences Forestières ◽

10.1051/forest:19930717 ◽

1993 ◽

Vol 50 (Supplement) ◽

pp. 186s-202s ◽

Cited By ~ 60

Author(s):

A Kremer ◽

RJ Petit

Keyword(s):

Gene Diversity ◽

Natural Populations

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Mitochondrial Gene Diversity Associated with the atp9 Stop Codon in Natural Populations of Wild Carrot (Daucus carota ssp. carota)

Journal of Heredity ◽

10.1093/jhered/esr142 ◽

2012 ◽

Vol 103 (3) ◽

pp. 418-425 ◽

Cited By ~ 16

Author(s):

Jennifer R. Mandel ◽

Edward V. McAssey ◽

Katherine M. Roland ◽

David E. McCauley

Keyword(s):

Daucus Carota ◽

Stop Codon ◽

Gene Diversity ◽

Mitochondrial Gene ◽

Natural Populations ◽

Wild Carrot

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Development of microsatellite markers for horse-chestnut (Aesculus hippocastanum), their polymorphism in natural Greek populations, and cross-amplification in related species

Dendrobiology ◽

10.12657/denbio.085.010 ◽

2021 ◽

pp. 105-116

Author(s):

Łukasz Walas ◽

Grzegorz Iszkuło ◽

Zoltan Barina ◽

Monika Dering

Keyword(s):

Microsatellite Markers ◽

Gene Diversity ◽

Natural Populations ◽

Illumina Miseq ◽

Balkan Peninsula ◽

Mean Value ◽

Aesculus Hippocastanum ◽

Horse Chestnut ◽

Nuclear Microsatellite ◽

Species Specific

New nuclear microsatellite markers (SSRs) were developed for Aesculus hippocastanum, a relict tree species from the Balkan Peninsula. The development of microsatellites was done using the Illumina MiSeq PE300 platform. Out of a set of 500 SSRs designed, a subset of 13 loci was tested using 290 individuals from seven natural populations. Twelve species-specific loci were polymorphic. The number of alleles per locus ranged from 2 to 17 and expected heterozygosity from 0.089 to 0.800 with a mean value of 0.484. The population of Kalampaka had the lowest value of allelic richness (2.63) and gene diversity in comparison to the remaining populations. STRUCTURE analysis confirmed isolation of population Mariolata from the southern edge of the species range and genetic similarity among populations from the Pindos Mts. Additionally, the utility of new SSRs in 29 individuals from nine other Aesculus taxa was tested. Eleven markers gave polymorphic products for all tested species. For 24 individuals, a high-quality product was obtained for each marker. Results confirmed the utility of specific markers for future population genetics studies.

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