GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals Changing Ploidy as a Strategy: The Irish Potato Famine Pathogen Shifts Ploidy in Relation to Its Sexuality

2017 ◽  
Vol 30 (1) ◽  
pp. 45-52 ◽  
Author(s):  
Ying Li ◽  
He Shen ◽  
Qian Zhou ◽  
Kun Qian ◽  
Theo van der Lee ◽  
...  
Keyword(s):  
Ploidy Level ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Global Food Security ◽  
Genome Wide ◽  
Key Factor ◽  
Potato Famine ◽  
Selection Of

The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high potential to adapt to various environments and great risk to break disease resistance genes in potato. As are other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of single nucleotide polymorphisms, nuclear DNA quantification, and microscopic counting of chromosome numbers, we assessed the ploidy level of a comprehensive selection of isolates. All progenies from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level may be a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1843-1854 ◽  
Author(s):  
Nancy N FitzSimmons ◽  
Craig Moritz ◽  
Colin J Limpus ◽  
Lisa Pope ◽  
Robert Prince
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Green Turtle ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Chelonia Mydas ◽  
Single Copy ◽  
Microsatellite Data ◽  
Ecological Data ◽  
Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Associations between Oxytocin Receptor Gene Polymorphisms, Empathy towards Animals and Implicit Associations towards Animals

Animals ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. 140 ◽  
Author(s):  
Melanie Connor ◽  
Alistair Lawrence ◽  
Sarah Brown
Keyword(s):  
Social Behaviour ◽  
Allelic Variation ◽  
Receptor Gene ◽  
Oxytocin Receptor ◽  
Implicit Associations ◽  
Nucleotide Polymorphisms ◽  
Psychological Variables ◽  
Oxytocin Receptor Gene ◽  
Receptor Gene Polymorphisms ◽  
Human Social Behaviour

Oxytocin has been well researched in association with psychological variables and is widely accepted as a key modulator of human social behaviour. Previous work indicates involvement of oxytocin receptor gene (OXTR) single nucleotide polymorphisms (SNPs) in human-human empathy, however little is known about associations of OXTR SNPs with empathy and affective reactions of humans towards animals. Five OXTR SNPs previously found to associate with human social behaviour were genotyped in 161 students. Empathy towards animals and implicit associations were evaluated. A General Linear Model was used to investigate the OXTR alleles and allelic combinations along with socio-demographic variables and their influence on empathy towards animals. Empathy towards animals showed a significant association with OXTR SNP rs2254298; homozygous G individuals reported higher levels of empathy towards animals than heterozygous (GA). Our preliminary findings show, for the first time, that between allelic variation in OXTR and animal directed empathy in humans maybe associated, suggesting that OXTRs social behaviour role crosses species boundaries, warranting independent replication.

scholarly journals The Variability of Puroindoline-Encoding Alleles and Their Influence on Grain Hardness in Modern Wheat Cultivars Cultivated in Poland, Breeding Lines and Polish Old Landraces (Triticum aestivum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1075
Author(s):  
Mateusz Przyborowski ◽  
Sebastian Gasparis ◽  
Maciej Kała ◽  
Wacław Orczyk ◽  
Anna Nadolska-Orczyk
Keyword(s):  
Triticum Aestivum ◽  
System Analysis ◽  
Allelic Variation ◽  
Triticum Aestivum L ◽  
Nucleotide Polymorphisms ◽  
Wheat Cultivars ◽  
Grain Hardness ◽  
Wild Type ◽  
Breeding Lines ◽  
Modern Wheat

Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour and the final product quality. The objective of the study was to analyze the mutation frequency in both Pin genes and their influence on grain hardness in 118 modern bread wheat cultivars and breeding lines cultivated in Poland, and 80 landraces from Poland. The PCR products containing the Pin gene coding sequences were sequenced by the Sanger method. Based on detected the SNPs (single-nucleotide polymorphisms) we designed CAPS (cleaved amplified polymorphic sequence) markers for the fast screening of Pinb alleles in a large number of genotypes. All analyzed cultivars, breeding lines, and landraces possess the wild-type Pina-D1a allele. Allelic variation was observed within the Pinb gene. The most frequently occurring allele in modern wheat cultivars and breeding lines (over 50%) was Pinb-D1b. The contribution of the remaining alleles (Pinb-D1a, Pinb-D1c, and Pinb-D1d) was much less (approx. 15% each). In landraces, the most frequent allele was Pinb-D1a (over 70%), followed by Pinb-D1b (21% frequency). Pinb-D1c and Pinb-D1g were found in individual varieties. SKCS (single-kernel characterization system) analysis revealed that grain hardness was strictly connected with Pinb gene allelic variation in most tested cultivars. The mean grain hardness values were significantly greater in cultivars with mutant Pinb variants as compared to those with the wild-type Pinb-D1a allele. Based on grain hardness measured by SKCS, we classified the analyzed cultivars and lines into different classes according to a previously proposed classification system.

Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup.

Genetics ◽  
1988 ◽  
Vol 118 (4) ◽  
pp. 671-683
Author(s):  
A Caccone ◽  
G D Amato ◽  
J R Powell
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Hybridization ◽  
Nuclear Dna ◽  
Single Copy ◽  
Rate Of Change ◽  
Drosophila Genome ◽  
Island Species ◽  
Drosophila Melanogaster Subgroup ◽  
Chromosomal Data ◽  
Group 2

Abstract Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.

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