Excess Of Rare Alleles Research Articles

Molecular analysis of olive (Olea europaea L.) in Iraq using the internal transcribed spacer (ITS) region

Olea is a genus of about 40 species in the Oleaceae family distributed in warm temperate and tropical areas of southern Europe, Africa, southern Asia, and Australia. The study aimed to use the variations in the Internal Transcribed Spacer 1 (ITS1) region to construct a phylogenetic tree for 12 Iraqi olive varieties with 15 ITS1 sequences downloaded from the NCBI database. Leaf samples were collected from 12 olive varieties grown in five geographical regions of the north of Iraq. Using the BLAST algorithm, 12 sequences were manually adjusted by chromatogram comparison and aligned with the NCBI GenBank database. Haplotype diversity ranged from zero in the Australian population to one in the Moroccan and Spanish populations. Nucleotide diversity ranged from 0.0 in the Australian population to 0.08 in the Algerian population and Tajima's D value was −0.940. Genetic differentiation values ranged from 0.0177 between Iraqi Moroccan and Iraqi Spanish populations to 0.6540 between Iraqi and Algerian populations. The average pairwise nucleotide diversity within populations was 0.9036 in Iraqi and Turkish olive populations to 0.8671 in Iraqi and Algerian populations. The phylogenetic tree formed 2 main clusters. The first cluster includes all Algerian varieties and the Iraqi varieties are grouped in second cluster. The negative Tajima test value in all populations indicates an excess of rare alleles. The high value of gene flow between the Iraqi and Australian populations may have been mediated by human transport and these varieties may have been originated from the same geographical region.

Population genetics and phenotypic differentiation of cotton leafhoppers (Hemiptera: Cicadellidae) from Pakistan

ABSTRACTThe cotton leafhopper, Amrasca biguttula (Ishida), a sucking insect pest of cotton and vegetables, is present throughout Southeast Asia. Patterns of molecular and morphological differentiation among A. biguttula populations collected from seven cotton growing areas of Punjab, Pakistan, were studied by sequencing the barcode region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene and by morphometrically analyzing wing shape. Molecular analysis revealed absence of isolation by distance (r = 0.075, P = 0.341) in spite of significant population differentiation (overall FST = 0.15 ± 0.06 (SE)). Also, haplotype diversity varied between populations, and neutrality tests indicated an excess of rare alleles in one of the seven areas. Although leafhopper populations are clearly shaped by genetic drift and possibly also by founder events, wing shape and size were conserved across the study area. These results have important implications for understanding the processes affecting patterns of molecular and morphological variations of pest insects that often are strongly controlled by agrochemical applications.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

BackgroundA genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.ResultsNucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.ConclusionsIn a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants

I describe a method for simulating samples from gene families of size two under a neutral coalescent process, for the case where the duplicate gene either has fixed recently in the population or is still segregating. When a duplicate locus has recently fixed by genetic drift, diversity in the new gene is expected to be reduced, and an excess of rare alleles is expected, relative to the predictions of the standard coalescent model. The expected patterns of polymorphism in segregating duplicates ("copy-number variants") depend both on the frequency of the duplicate in the sample and on the rate of crossing over between the two loci. When the crossover rate between the ancestral gene and the copy-number variant is low, the expected pattern of variability in the ancestral gene will be similar to the predictions of models of either balancing or positive selection, if the frequency of the duplicate in the sample is intermediate or high, respectively. Simulations are used to investigate the effect of crossing over between loci, and gene conversion between the duplicate loci, on levels of variability and the site-frequency spectrum.

Molecular assessment of the genetic integrity, distinctiveness and phylogeographic context of the Saltwater crocodile (Crocodylus porosus) on Palau

The saltwater crocodile (Crocodylus porosus) is the largest and most broadly distributed crocodilian species, and thus is of special conservation and economic interest. Similar to other parts of its range throughout the Indo-Pacific, C. porosus distributed in the Republic of Palau have experienced a severe population decline over the past century primarily due to commercial hunting and eradication campaigns. In addition, several thousand crocodiles of undocumented species and origin were imported into Palau during the 1930's for commercial farming purposes, potentially polluting the gene pool of the endemic saltwater crocodiles. Analysis of 39 individuals collected throughout the Republic of Palau revealed a single mitochondrial DNA control region haplotype shared by populations sampled in Sulawesi, Borneo and Australia. The mtDNA results, in combination with microsatellite genotypic data at six loci, detected no evidence for inter-specific hybridization between endemic Palauan C. porosus and potentially introduced Crocodylus species. There was no evidence for a genetic bottleneck in the Palauan population, however an excess of rare alleles was identified, indirectly suggesting a recent history of admixture potentially linked to introductions of non-native C. porosus. Following from these findings, Palauan C. porosus should be included in the single ESU previously established for all saltwater crocodiles given the recovery of a fixed, but geographically widespread haplotype. Although Palauan C. porosus exhibited significant genetic differentiation relative to all other sampled populations, it's delineation as a distinct management unit is precluded at the present time by evidence that the genetic integrity of the population may have been compromised by the introduction of non-native saltwater crocodiles.

Evolution of the Phosphoglycerate mutase Processed Gene in Human and Chimpanzee Revealing the Origin of a New Primate Gene

Processed genes are created by retroposition from messenger RNA of expressed genes. The estimated amount of processed copies of genes in the human genome is 10,000-14,000. Some of these might be pseudogenes with the expected pattern for nonfunctional sequences, but some others might be an important source of new genes. We have studied the evolution of a Phosphoglycerate mutase processed gene (PGAM3) described in humans and believed to be a pseudogene. We sequenced PGAM3 in chimpanzee and macaque and obtained polymorphism data for human coding region. We found evidence that PGAM3 likely produces a functional protein, as an example of addressing functionality for human processed pseudogenes. First, the open reading frame was intact despite many deletions that occurred in the 3' untranslated region. Second, it appears that the gene is expressed. Finally, interspecies and intraspecies variation for PGAM3 was not consistent with the neutral model proposed for pseudogenes, suggesting that a new functional primate gene has originated. Amino acid divergence was significantly higher than synonymous divergence in PGAM3 lineage, supporting positive selection acting in this gene. This role of selection was further supported by the excess of rare alleles in a population genetic analysis. PGAM3 is located in a region of very low recombination; therefore, it is conceivable that the rapid fixation events in this newly arising gene may have contributed to a selective sweep of variation in the region.

Chromosomal effects of rapid gene evolution in Drosophila melanogaster.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.

SNP frequencies in human genes: an excess of rare alleles and differing modes of selection

Regions flanking (3’ and 5’) the protein-coding region of a gene that are transcribed but not translated (stands for untranslated region).

PHYLOGEOGRAPHY OF THE SARDINES (SARDINOPSSPP.): ASSESSING BIOGEOGRAPHIC MODELS AND POPULATION HISTORIES IN TEMPERATE UPWELLING ZONES

Sardines (Sardinops spp.) occupy temperate upwelling zones in the coastal regions of the Indian and Pacific Oceans, including locations in Japan, California, Chile, Australia, and South Africa. East and West Pacific populations are separated by vast expanses of open ocean, and northern and southern hemisphere populations are separated by tropical waters which are lethal to sardines. The relative importance of these barriers has been the focus of a longstanding debate between vicariance and dispersal schools in biogeography. Comparisons of a 500 bp fragment of the mitochondrial (mt) DNA control region reveal strong geographic structuring of mtDNA lineages but shallow divergence both within and between regional populations. Regional populations are related to one another in a stepping-stone pattern, the apparent result of a series of Pleistocene dispersal events around the continental margins of the Indian-Pacific Basin. These mtDNA data, combined with an electrophoretic survey of variability at 34 nuclear loci (Grant and Leslie 1996), indicate that the five regional forms of Sardinops (considered separate taxa by most authorities) probably diverged within 500,000 years BP, a much shorter timeframe than predicted by vicariance models based on plate tectonics. High mtDNA haplotype diversity, coupled with an excess of rare alleles in the protein electrophoretic dataset, may indicate exponential growth from a small ancestral population. The mtDNA and allozyme data are concordant with climate records and fossil evidence in portraying regional populations as recent, unstable, and ephemeral. Regional populations of sardines have probably been extinguished and recolonized over short evolutionary timescales in response to changes in climate and the oceanography of coastal upwelling zones.

THE IMPACT OF ELECTROPHORETIC GENOTYPE ON LIFE HISTORY TRAITS IN PINUS TAEDA.

Reports of positive associations between allozymic heterozygosity and measures of fitness are routine, but it has not been possible to distinguish between the two preeminent explanations of the phenomenon, dominance and overdominance. We tested several of the assumptions of these hypotheses in our study of the relationship between electrophoretic genotype and three life history traits in loblolly pines (Pinus taeda L.). Traits examined included the survival and growth of selfed and outcrossed progeny of 45 maternal trees, and maternal fecundity, measured as the number of surviving progeny per mother tree. Inbreeding depression was severe; the relative fitness of the selfed progeny was only 8% that of the outcrossed progeny. We found a heterozygote fecundity advantage, which should have resulted in an excess of rare alleles in the progeny. Instead, there was evidence of severe survival selection against rare alleles in both heterozygous and homozygous forms. The deficit of rare alleles averaged 69 and 50% in the selfed and outcrossed progeny, respectively. The one allele in the sample that we should have suspected of being maintained by overdominance (a PGI2 mid-frequency allele) appeared to be overdominant for outcrossed height growth and probably for fecundity as well. Multiple-locus genotype explained very little of the variation in growth, however, and rather than seeing evidence for overdominance as a force in maintaining most of the observed polymorphism, we were left to explain, in the face of the severe survival selection, why the rare alleles were present at all. Projection of the stand into the future through computer simulation showed how balancing selection acting on differential growth, fecundity, and mortality among genotypes could, over the life of the stand, account for the maintenance of the rare alleles in the population.

Racial variation in the distribution of Ha‐ras‐1 alleles

Restriction fragment length polymorphism analyses of the Ha-ras-1 proto-oncogene were undertaken in white and black populations residing in the Baltimore-Washington metropolitan area to address whether specific rare alleles of the Ha-ras-1 proto-oncogene locus vary in their distribution among different racial groups. High-molecular-weight genomic DNA samples from the lungs of 80 lung cancer patients and 92 accident victims were digested with appropriate restriction enzymes and subjected to Southern analysis using the 6.6-kb BamHI human Ha-ras-1 recombinant fragment from the plasmid pEC. Thirty allelomorphs of different sizes were detected among the 172 study subjects. An association was observed between race and specific alleles. Rare alleles were more frequent in black cancer patients and trauma victims than in whites. Within each racial category, lung cancer patients had an excess of rare alleles. These data indicate the importance of controlling for racial variation when designing studies to determine human cancer risk factors.

Genetic profile of cosmopolitan populations: Effects of hidden subdivision

Natural populations of many organisms exhibit excess of rare alleles in comparison with the predictions of the neutral mutation hypothesis. It has been shown before that either a population bottleneck or the presence of slightly deleterious mutations can explain this phenomenon. A third explanation is presented in this work, showing that hidden subdivision within a population can also lead to an excess of rare alleles in the total population when the expectations of the neutral model are based on the allele frequency profile of the entire population data. With two examples (mitochondrial DNA-morph distribution and isozyme allele frequency distributions), it is shown that most cosmopolitan human populations exhibit excess of rare as well as total allele counts, when these are compared with the expectations of the neutral mutation hypothesis. The mitochondrial data demonstrate that such excesses can be detected from genetic variation at a single locus as well, and this is not due to stochastic error of allele frequency distributions. Contrast of the present observations with the allele frequency profiles in agglomerated tribal populations from South and Central America shows that even when the neutral expectations hold for individual subpopulations, if all subpopulations are grouped into a single population, the pooled data exhibit an excess of total number of alleles that is mainly due to the excess of rare alleles. Therefore, a primary cause of the excess number of rare alleles could be the hidden subdivision, and the magnitude of the excess indicates the extent of substructuring. The two components of hidden subdivision are: 1) Number of subpopulations, and 2) the average genetic distance among them. The implications of this observation in estimating mutation rate are discussed indicating the difficulties of comparing mutation rates from different population surveys.

MAINTENANCE OF GENETIC VARIABILITY UNDER THE JOINT EFFECT OF MUTATION, SELECTION AND RANDOM DRIFT

Formulae are developed for the distribution of allele frequencies (the frequency spectrum), the mean number of alleles in a sample, and the mean and variance of heterozygosity under mutation pressure and under either genic or recessive selection. Numerical computations are carried out by using these formulae and Watterson's (1977) formula for the distribution of allele frequencies under overdominant selection. The following properties are observed: (1) The effect of selection on the distribution of allele frequencies is slight when 4Ns </= 4, but becomes strong when 4Ns becomes larger than 10, where N denotes the effective size and s the selective difference between alleles. Genic selection and recessive selection tend to force the distribution to be U-shaped, whereas overdominant selection has the opposite tendency. (2) The mean total number of alleles in a sample is much more strongly affected by selection than the mean number of rare alleles in a sample. (3) Even slight heterozygote advantage, as small as 10(-5), increases considerably the mean heterozygosity of a population, as compared to the case of neutral mutations. On the other hand, even slight genic or recessive selection causes a great reduction in heterozygosity when population size is large. (4) As a test statistic, the variance of heterozygosity can be used to detect the presence of selection, though it is not efficient when the selection intensity is very weak, say when 4Ns is around 4 or less. A model, which is somewhat similar to Ohta's (1976) model of slightly deleterious mutations, has been proposed to explain the following general patterns of genic variation: (i) There seems to be an upper limit for the observed average heterozygosities. (ii) The distribution of allele frequencies is U-shaped for every species surveyed. (iii) Most of the species surveyed tend to have an excess of rare alleles as compared with that expected under the neutral mutation hypothesis.

Role of very slightly deleterious mutations in molecular evolution and polymorphism

Several models of multiple slightly deleterious alleles are reviewed and theoretical consequences of slightly negative selection are discussed in conjunction with evolution and variation at the molecular level. Facts are organized which may be satisfactorily explained by the hypothesis of very slightly deleterious mutations. They are: (1) There appears to be an upper limit in heterozygosity for protein loci as measured by electrophoresis. (2) The excess of rare alleles is more pronounced in Drosophila than in man. (3) Correlation of heterozygosities at a locus among sibling species of the Drosophila willistoni group is too high compared to what is expected by the strict neutral theory, while it is not so among human races and between man and chimpanzee. (4) The rate of protein divergence is exceptionally high in Hawaiian Drosophila.