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PubMed1977

Enzyme polymorphisms of Ideles populations (Ahaggar, Algeria) and the Iwellemeden Kel Kummer Twaregs (Menaka, Mali).

Surveys dealing with enzyme polymorphisms have recently been conducted in the Sahara. Results from two populations are reported here: 227 inhabitants of Ideles village (Ahaggar, Algeria); 285 nomads of a genetic isolate, the Kel Kummer Twareg tribe (Menaka, Mali). The four classical molecular variants of G6PD:A+, A-, B+, B-, are found in Ideles. The frequency of the G6PD A+ Negroid variant reaches 15% in Ideles and 7.7% among the Kel Kummer. However, gene frequencies will have to be recalculated after a study of the genetic transmission through families. The PGDC gene of 6PGD is especially frequent in the Kel Kummer where 10 'Canning' phenotypes have been observed. The PGM distribution of alleles at locus 1 in Ideles is the same as in the Mediterranean populations. The pa gene of acid phosphatase, relatively frequent in Ideles, has been excluded by drift from the Kel Kummer gene pool. AK and LDH enzymes have also been studied in both samples. The abnormal Ea1 mutation of serum pseudocholinesterase exists in Ideles and in the Kel Kummer as in other populations of the Sahara; the C5 esterase component was revealed by electrophoresis in 5% of the Kel Kummer people.

Acid Phosphatase↗
PubMed2002

When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum.

Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox.

Bacteriophages↗
PubMed2003

Genetic differentiation at nuclear and mitochondrial loci among large white-headed gulls: sex-biased interspecific gene flow?

We measured genetic differentiation among species of large white-headed gulls using mitochondrial (cytochrome b haplotypes) and nuclear (microsatellites) markers. Additional information was added using a previously published study of allozymes on the same species. Levels of differentiation among species at nuclear markers are much lower than would be expected for avian species and are not concordant with the level of differentiation in mitochondrial markers. This discrepancy is best explained by a combination of recent species origin and interspecific gene flow after speciation. The data also suggest that female-mediated gene flow is reduced compared to male-mediated gene flow, either due to behavioral bias or due to stronger counterselection of female hybrids in accordance with Haldane's rule for ZW species. Whatever the reasons for the low differentiation of the species' nuclear gene pools, the extensive similarity of their nuclear genome demonstrates that selection on a limited number of characters is an important factor in establishing and maintaining clear-cut phenotypic differences between these species and suggests that the number of loci involved in this process is quite low. This situation may not be exceptional in birds, indeed a number of studies have found similarly low level of differentiation in nuclear markers among congeneric bird species, although usually based on a single set of markers. Because hybridization is a widespread phenomenon in birds, many of these cases might be due to interspecific gene flow.

Animals↗
PubMed1978

Ethnic communities in Israel: the genetic blood markers of the Babylonian Jews.

One hundred eighty-eight Jewish individuals who either they or whose both parents were born in Iraq were typed for 7 blood groups (ABO, MNS, Rh, Kell, Duffy, P and Kidd), 12 red cell enzyme systems and 2 serum proteins. Iraqi Jews are characterized by a high frequency of A (in ABO), N (in MNS), low cde (Rh) and low Hp-1. Several rare electrophoretic variants were encountered: PGM1 6-1, PHI 3-1 and PHI 2-1, and an unidentified AK phenotype. No evidence of Negroid admixture was found in their gene pool. Comparisons with results previously obtained in Iraqi Jews show general similarities in frequencies while comparisons with neighboring non-Jewish populations suggest divergence in most systems investigated. The difficulties of assessing relationships on the basis of a few selected differences and the need for careful interpretations of similarities are emphasized.

Blood Group Antigens↗
PubMed1996

Clusters of identical new mutation in the evolutionary landscape.

In contrast to the common assumption that each new mutant results from a unique, independent mutation event, clusters of identical premeiotic mutant alleles are common. Clusters can produce large numbers of related individuals carrying identical copies of the same new genetic change. By entering the gene pool in multiple copies at one time, clusters can influence fundamental processes of population genetics. Here we report evidence that clusters can increase the arrival and fixation probabilities and can lengthen the average time to extinction of new mutations. We also suggest it may be necessary to reconsider other fundamental elements of population genetic theory.

Animals↗
PubMed2006

Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae.

Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline B. henselae strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the B. henselae population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.

Animals↗
PubMed1976

Genetic variation and the ecological parameter "food medium" in cage populations of Drosophila melanogaster.

Impressive effects of the ecological factor "food medium" upon the frequencies of the lethal-bearing second chromosomes in Drosophila melanogaster were found in cage populations originated from a common gene pool. Allozyme frequencies for two second enzyme loci were also determined. The lethal frequencies found were higher when the environmental was restrictive than when it was favorable. Moreover, the lethal frequencies were higher in populations of smaller size than in those of greater. The role of the lethal genetic variants in the structure of populations is discussed.

Alcohol Oxidoreductases↗
PubMed2004

Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.

BACKGROUND: The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools. RESULTS: The data indicate that Fusobacterium has a core genome of a very different nature to other bacterial lineages, and branches out at the base of Firmicutes. However, depending on the method used, 35-56% of Fusobacterium genes appear to have a xenologous origin from bacteroidetes, proteobacteria, spirochaetes and the Firmicutes themselves. A high number of hypothetical ORFs with unusual codon usage and short lengths were found and hypothesized to be remnants of transferred genes that were discarded. Some proteins and operons are also hypothesized to be of mixed ancestry. A large portion of the Gram-negative cell wall-related genes seems to have been transferred from proteobacteria. CONCLUSIONS: Many instances of similarity to other inhabitants of the dental plaque that have been sequenced were found. This suggests that the close physical contact found in this environment might facilitate horizontal gene transfer, supporting the idea of niche-specific gene pools. We hypothesize that at a point in time, probably associated to the rise of mammals, a strong selective pressure might have existed for a cell with a Clostridia-like metabolic apparatus but with the adhesive and immune camouflage features of Proteobacteria.

Bacterial Proteins↗
PubMed2026

Adaptive genomic evolution and WD40-regulated temporal dynamics of anthocyanins support leaf photoplasticity in Parrotia subaequalis.

BACKGROUND: Parrotia subaequalis, a Tertiary relict endemic to China, plays a significant role in phylogeny and adaptive evolution as a key species in the early differentiation of angiosperms. It has abundant leaf colors and great potential as an ornamental tree. RESULTS: This study assembled the first chromosome-level genome of P. subaequalis (Contig N50 = 2.15 Mb), revealing transposable element proliferation, key paleopolyploid events and dynamic gene family evolution, including the expansion of secondary metabolite transport and synthesis genes (such as WD40, 2OG-FeII_Oxy) and the contraction of gene families related to flower morphogenesis (such as F-box-like, K-box). Through integrative transcriptomics and targeted metabolomics approaches, we further revealed that the color transition of young leaves from red to green was driven by temporal accumulation differences of malvidin-3,5-O-diglucoside, whose biosynthesis is progressively down-regulated during leaf development. WGCNA revealed that a subset of WD40 genes (light-signaling, TTG1/HOS15-like, etc.) coexpresses with anthocyanin biosynthetic genes, like 4CLL9, GT1, in anthocyanin-related modules enriched for auxin signaling and hydrolase activity, suggesting a potential link between WD40 expansion and photoprotective plasticity. Relevant regulatory networks were found to complement the species-specific gene pool related to leaf color regulation. CONCLUSION: This genomic resource of P. subaequalis advanced our understanding of early angiosperm adaptation through neofunctionalized regulatory networks and established a foundation for molecular breeding aimed at enhancing environmental resilience while preserving ornamental traits.

Anthocyanins↗
PubMed2003

[Analysis of genetic diversity of population of Northern Eurasia from autosomal microsatellite loci].

The paper presents the results of analysis of the gene pools of several North Eurasian ethnic groups (Buryats, Evenks, Altaians, Russians, Kyrgyzes, Tuvinians, Tatars, and Ukrainians) examined using a panel of autosomal microsatellite markers (D4S397, D5S393, D7S640, D8S514, D9S161, D10S197, D11S1358, D12S364, and D13S173) mapped on different chromosomes and represented by the (CA)n dinucleotide repeats. In the group of populations examined the proportion of genetic variability at microsatellite loci explained by interpopulation differences was about 2.5%, while genetic differences between the individuals within a population accounted for 97.5% of this variability. Analysis of genetic relationships among the populations revealed substantial differences between the populations belonging to the Indo-European and Altaic linguistic families in gene diversity at microsatellite loci.

Asia↗
PubMed2005

Restriction fragment length polymorphisms of type I collagen locus 2 (COL1A2) in two communities of African ancestry and other mixed populations of northwestern Ecuador.

Restriction fragment length polymorphisms are good anthropological markers for discriminating geographically distinct populations at both the allele and the haplotype level. Two communities of African ancestry and ladinos, mestizos, and mulattoes living in the Esmeraldas province in northwestern Ecuador were analyzed for three RFLPs (EcoRI, RsaI, and MspI) of the COL1A2 gene. Also, the same markers were studied in a population sample from Spain to compare the allele and haplotype frequencies of the Esmeraldas populations with those of their representative European parental population. Data for the native American and sub-Saharan African founder components were available from the literature. No significant levels of differentiation between the two African Ecuadoran communities emerged from either the frequency analysis of each single marker and all three RFLP markers together or from the AMOVA. The ladinos and mestizos also showed a rather similar distribution of allele and haplotype frequencies, confirming that the two ethnic terms do not correspond to genetically different populations. The comparison with the supposed founding European, sub-Saharan African, and native American populations indicated a large presence of African genes in the gene pool of both communities, with a higher proportion of the Amerindian component in Viche than in Rio Cayapas. The present findings confirm the previous genetic admixture estimates based on nuclear and mitochondrial DNA markers and the demographic data.

Alleles↗
PubMed1981

The impact of random and lineal fission of the genetic divergence of small human groups: a case study among the Yanomama.

Most of the genetic divergence that currently separates populations of Homo sapiens must have arisen during that long period when the local village (or band) was the basic unit of biological evolution. Studies of tribally intact Amerindian groups exhibiting such small-group organization have demonstrated marked genetic divergence between nearby villages. Some of this genetic radiation can be attributed to the effects of random genetic drift over time within these small demes. Some of it, however, might be better ascribed to the consequences of nonrandom genetic assortment at the time of village fission, a recurring event for such groups. Even random genetic assortment at the time of fission would lead to some genetic divergence, due to the finite size of the parent gene pool. We term the genetic consequences of random assortment the random fission effect. Routinely, village fission occurs along family lines, leading to even greater genetic divergence between the daughter villages. We use the term lineal fission effect to describe the genetic consequences of nonrandom assortment and contrast these results with those derived from random assortment--A formal treatment of random and lineal fission effects is developed, first for the single-locus case, then for the multiple-locus extension. Using this formulation, three Yanomama fission events were examined. Fission in the Yanomama often involves a great deal of mutual hostility between the two factions, so that subsequent gene flow between the two daughter villages is minimal. The first two examples are typical of the Yanomama behavior norm, and are accompanied by a minimum of subsequent gene flow between the daughter villages. In these two cases, the observed divergence values are very large and are also very unlikely under random fission. The lineal fission effect is pronounced. The net impact of lineal fission is to reduce the effective size of the village at the time of fission by a factor of four, relative to expectation from random fission. The third example, however, involved an unusually amicable split of a village, followed by free genetic exchange between the fission products. This "friendly fission" yields an observed divergence value not much in excess of the expectation from random fission.--The long-term consequences of such fission bottlenecks in effective population size are discussed for both intra- and inter-tribal genetic diversity. It appears that the rate of genetic divergence for tribal and subtribal groups may have been somewhat greater than would be expected from classical drift arguments.

Female↗
PubMed1999

The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis.

The extent to which recombination disrupts the bifurcating treelike phylogeny and clonal structure imposed by binary fission on bacterial populations remains contentious. Here, we address this question with a study of nucleotide sequence data from 107 isolates of the human pathogen Neisseria meningitidis. Gene fragments from 12 house-keeping loci distributed around the meningococcal chromosome were analyzed, showing that (1) identical alleles are disseminated among genetically diverse isolates, with no evidence for linkage disequilibrium; (2) different loci give distinct and incongruent phylogenetic trees; and (3) allele sequences are incompatible with a bifurcating treelike phylogeny at all loci. These observations are consistent with the hypothesis that meningococcal populations comprise organisms assembled from a common gene pool, with alleles and allele fragments spreading independently, together with the occasional importation of genetic material from other species. Further, they support the view that recombination is an important genetic mechanism in the generation new meningococcal clones and alleles. Consequently, for anything other than the short-term evolution of this species, a bifurcating treelike phylogeny is not an appropriate model.

Alleles↗
PubMed1986

Cryopreservation of chicken semen of inbred or specialized strains.

Pooled semen from several inbred special chicken strains was diluted with solutions containing glycerol or dimethylacetamide as a cryoprotectant. One-half milliliter samples in capped glass vials were frozen at 3 C/min to -35 C in a programmable freezer and stored in a nitrogen vapor tank. One vial of thawed semen was used to inseminate 4 hens by intravaginal, intrauterine, or intramagnal procedures. The intramagnal technique required minor surgery but always produced chicks in seven lines in contrast to the nonsurgical methods. Frozen semen of one strain stored for 29 weeks produced 12 to 14 chicks per vial when inseminated into 4 hens. This method, therefore, will reliably rescue gene pools from semen after long-term storage.

Animals↗
PubMed2004

Apolipoprotein E as a target for developing new therapeutics for Alzheimer's disease based on studies from protein, RNA, and regulatory region of the gene.

Alzheimer's disease (AD), the most common form of dementia, is a progressive, degenerative disorder of the central nervous system. The major hallmarks of AD include selective neuronal cell death and the presence of amyloid deposits and neurofibrillary tangles. Apolipoprotein E (ApoE) has also been shown to colocalize with these neuropathological lesions. Here is reviewed the role of ApoE in AD. The human ApoE gene has three alleles (epsilon2, epsilon3, epsilon4)-all products of the same gene. The epsilon3-allele accounts for the majority of the ApoE gene pool (approximately 70-80%), the epsilon4-allele accounts for 10-15% and the epsilon2 allele for 5-10%. Inheritance of the epsilon4-allele strongly increases the risk for developing AD at an earlier age. Functions of ApoE include cholesterol transport, neuronal repair, dendritic growth and anti-inflammatory activities. Putative pathological functions or "risk-factor activities" of ApoE-epsilon4 include its role in promoting amyloid accumulation, neurotoxicity, oxidative stress and neuro fibrillary tangles.ApoE mRNA is most abundant in the liver followed by the brain, where it is synthesized and secreted primarily by astrocytes. ApoE protein and mRNA are further detected in cortical and hippocampal neurons in humans. ApoE gene expression is induced by brain injury in some neurons and upregulated in astrocytes during aging. In AD, an increased ApoE mRNA was reported in the hippocampus. The risk for AD has been reported to correlate with transcriptional activity of the ApoE gene. Binding sites for putative transcriptional factors (TF), such as AP-1, AP-2 and NF-kappaB, are present in the ApoE promoter. The promoter also contains sites for the inflammatory response transcription factors IL-6 RE-BP, MED1, STAT1 and STAT2. A functional peroxisome-proliferator-activated receptor gamma (PPARgamma) has been detected in the ApoE/ApoCI intergenic region. ApoE mRNA levels were shown to be regulated by ciglitazone, a PPARgamma inducer. Certain statin drugs may also affect ApoE promoter activity. Two distal enhancers that specify ApoE gene expression in macrophages were identified. These results have implications for the regulation of ApoE gene expression, which plays an important role in the development of AD. The interaction of different transcription factors with the regulatory region of the ApoE gene is important to understand the neuroinflammatory process seen in AD.

5' Untranslated Regions↗
PubMed1989

Blood group gene frequencies of four population groups in the western Cape.

Blood group gene frequencies of 4 population groups in the western Cape region of South Africa were determined. The ABO, MNSs, Rhesus, Kell and Duffy blood group systems were studied in 2,094 non-Malay Cape Coloureds, 1,181 South African (SA) Negroes, 506 SA Caucasoids and 115 Cape Malays. The gene frequencies of these 4 population groups together with, for comparative purposes, previously published data on 3 others, namely Johannesburg Coloureds, Khoikhoi and San, were used to measure the genetic distances between them. In addition, multivariate analysis was used in an attempt to clarify whether the 2 coloured and the Cape Malay samples resemble each other, and to demonstrate the relationships between the 7 population groups. Although genetic distance measurements suggest that Johannesburg Coloureds have a greater SA Negro contribution to their gene pool than the Cape Coloureds, the results are in accordance with previous studies suggesting that coloureds in southern Africa form a relatively homogeneous group. The allele frequencies in the Rhesus and Duffy blood group systems suggest that Cape Malays, although similar in some respects to the Cape Coloureds, are a genetically distinct group.

ABO Blood-Group System↗
PubMed2025

Sex-Biased Admixture Followed by Isolation and Adaptive Evolution Shaped the Genomic and Blood Pressure Diversity of the LopNur People.

The LopNur people are an ethnic group living on the edge of the Taklamakan Desert, and they are believed to demonstrate a unique genetic makeup due to their isolation and limited contact with neighboring populations. However, a lack of genetic studies on the LopNur people has resulted in limited knowledge about their ancestral origins and demographic history. Here, we conducted the first whole-genome sequencing study of 164 LopNur individuals (LOP) to gain insight into their genetic history and adaptive evolution in an isolated desert area. Our analysis revealed that the present-day LOP have experienced a complex history of admixture followed by long-term isolation, with their ancestry derived from East Asia (∼41.46%), West Eurasia (∼26.43%), Siberia (∼24.27%), and South Asia (∼7.82%). Notably, a remarkable sex-biased admixture occurred between Western males and Eastern females. In addition to complex admixture followed by long-term geographic isolation and further recent migrations, adaptive evolution jointly formed the gene pool and phenotypic diversity of the present-day LOP. Intriguingly, our analysis suggests that the USP35-GAB2 region may be correlated with blood pressure in LOP, based on a joint analysis of genomics and blood pressure data. Moreover, we identified two variants, rs7387065, and rs2229437, located on CSMD1 and PRCP, respectively. These variants exhibited frequency differences between Asian and European populations and were reported to be associated with antihypertensive drug absorption. Our results provide new insight into the complex history of the LOP, an admixed and isolated ethnic group residing at the crossroads of East and West, a case with ancient admixture, long-term isolation, adaptive evolution, and sex-biased gene flow.

Female↗
PubMed1997

Partitioning of large and minichromosomes in Trypanosoma brucei.

The Trypanosoma brucei nuclear genome contains about 100 minichromosomes of between 50 to 150 kilobases and about 20 chromosomes of 0.2 to 6 megabase pairs. Minichromosomes contain nontranscribed copies of variant surface glycoprotein (VSG) genes and are thought to expand the VSG gene pool. Varying VSG expression allows the parasite to avoid elimination by the host immune system. The mechanism of inheritance of T. brucei chromosomes was investigated by in situ hybridization in combination with immunofluorescence. The minichromosome population segregated with precision, by association with the central intranuclear mitotic spindle. However, their positional dynamics differed from that of the large chromosomes, which were partitioned by kinetochore microtubules.

Animals↗