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PubMed2006

Differential patterns of morphological and molecular hybridization between Fraxinus excelsior L. and Fraxinus angustifolia Vahl (Oleaceae) in eastern and western France.

We examined large-scale patterns of morphology, genetic structure and ecological correlates of Fraxinus excelsior and the closely related species Fraxinus angustifolia in France, in order to determine the degree of hybridization between them. We sampled 24 populations in two putative hybrid zones (Loire and Saône), and five control populations of each species. We measured foliar characteristics of adult trees and used five nuclear microsatellites as molecular markers. Canonical discriminant analysis indicated that the two species differ in morphology, but that intermediate types are common in the Loire region but less frequent in the Saône region. Bayesian population assignment identified one F. angustifolia and two F. excelsior gene pools. Most Loire individuals clustered genetically with the F. angustifolia gene pool. In contrast, the Saône region presented individuals belonging mostly to F. excelsior pools, although the F. angustifolia type was frequent in certain populations. The lowest F(ST) values were found between the Loire and F. angustifolia controls that also exhibited no significant isolation by distance. The proportion of the F. angustifolia gene pool in each locality was negatively correlated with winter temperatures, suggesting that a cold climate may be limiting. Hybridization is probably favoured by the intermediate climatic conditions in the Loire region that allow both species to occur, but is somewhat hampered by the harsher winters in the Saône area where morphological introgression has apparently not yet occurred.

Alleles↗
PubMed2000

Mitochondrial DNA sequences in prehistoric human remains from the Alps.

The spread of agriculture that started in the Near East about 10 000 years ago caused a dramatic change in the European archaeological record. It is still unclear if that change was caused mostly by movement of people or by cultural transformations. In particular, there is disagreement on what proportion of the current European gene pool is derived either from the pre-agricultural, paleolithic and mesolithic people, or from neolithic farmers immigrating from the south-east. To begin to characterise the mtDNA gene pool of prehistoric Europe we examined five human remains from the Eastern Italian Alps, dated between 14 000 and 3000 years ago. Three of them yielded sufficient amount of mtDNA for analysis. DNA extracts were prepared in two independent laboratories, and PCR products from the first hypervariable segment of the mtDNA control region were cloned and sequenced. Together with the 5200 year old 'ice man', these DNA sequences show that European mtDNA diversity was already high at the beginning of the neolithic period. All the neolithic sequences have been observed in contemporary Europeans, suggesting genealogical continuity between the neolithic and present-day European mtDNA gene pool. The mtDNA sequence from a 14 000 year-old specimen was not observed in any contemporary Europeans, raising the possibility of a lack of continuity between the mesolithic and present-day European gene pools.

Agriculture↗
PubMed2006

Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution.

The extent of 5S and 45S ribosomal DNA (rDNA) variation was investigated in wild and domesticated common beans (Phaseolus vulgaris) chosen to represent the known genetic diversity of the species. 5S and 45S rDNA probes were localized on mitotic chromosomes of 37 accessions by fluorescent in situ hybridization (FISH). The two 5S rDNA loci were largely conserved within the species, whereas a high variation in the number of 45S rDNA loci and changes in position of loci and number of repeats per locus were observed. Domesticated accessions from the Mesoamerican gene pool frequently had three 45S rDNA loci per haploid genome, and rarely four. Domesticated accessions from Andean gene pool, particularly from the race Peru, showed six, seven, eight or nine loci, but seven loci were found in all three races of this gene pool. Between three and eight loci were observed in accessions resulting from crosses between Andean and Mesoamerican genotypes. The presence of two to eight 45S rDNA loci in wild common beans from different geographic locations indicates that the 45S rDNA amplification observed in the Andean lineage took place before domestication. Our data suggest that ectopic recombination between terminal chromosomal regions might be the mechanism responsible for this variation.

Biological Evolution↗
PubMed2001

Selective recovery of founder genetic diversity in aquacultural broodstocks and captive, endangered fish populations.

Hatchery broodstocks used for genetic conservation or aquaculture may represent their ancestral gene pools rather poorly. This is especially likely when the fish that found a broodstock are close relatives of each other. We re-analysed microsatellite data from a breeding experiment on red sea bream to demonstrate how lost genetic variation might be recovered when gene frequencies have been distorted by consanguineous founders in a hatchery. A minimal-kinship criterion based on a relatedness estimator was used to select subsets of breeders which represented the maximum number of founder lineages (i.e., carried the fewest identical copies of ancestral genes). UPGMA clustering of Nei's genetic distances grouped these selected subsets with the parental gene pool, rather than with the entire, highly 'drifted' offspring generation. The selected subsets also captured much of the expected heterozygosity and allelic diversity of the parental gene pool. Independent pedigree data on the same fish showed that the selected subsets had more contributing parents and more founder equivalents than random subsets of the same size. The estimated mean coancestry was lower in the selected subsets, meaning that inbreeding in subsequent generations would be lower if they were used as breeders. The procedure appears suitable for reducing the genetic distortion due to consanguineous and over-represented founders of a hatchery gene pool.

Alleles↗
PubMed2000

Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada.

Microsatellite DNA markers from 13 simple sequence repeat (SSR) loci were used to compare genetic diversity between preharvest pristine and postharvest residual gene pools of two adjacent virgin, old-growth ( approximately 250 years) stands of eastern white pine (Pinus strobus L.) in Ontario. There was concurrence in genetic diversity changes in the postharvest gene pools of the two stands. The total and mean numbers of alleles detected in each stand were reduced by approximately 26% after tree density reductions of approximately 75%. Approximately 18 and 21% of the low-frequency (0. 25 > P > or = 0.01) alleles and 76 and 92% of the rare (P < 0.01) alleles were lost from residual stands A and B, respectively, after harvesting. Multilocus gametic diversity was reduced by 38 and 85% and genotype additivity by approximately 50% in the residual stands after harvesting. Latent genetic potential of each stand was reduced by approximately 40%. Although heterozygosity was reduced (1-5%) in the postharvest residual stands, the reductions were not substantial and not comparable to those using other genetic diversity measures. The reductions in genetic diversity measures were slightly higher than those theoretically expected in postbottleneck populations according to drift theory. In the absence of substantial gene migration that could ameliorate the genetic losses, the ability of the postharvest white pine gene pools to adapt to changing environmental and disease conditions may have been compromised. The microsatellite DNA results for genetic effects of harvesting in old-growth eastern white pine stands were similar to those that we reported earlier from allozyme analysis (Buchert et al. 1997). The results indicate that silvicultural practices should ensure that the gene pools of remaining pristine old-growth stands are reconstituted in the regenerating stands.

Alleles↗
PubMed1998

[Genogenography of the aboriginal population of Marii El (from data on immunobiochemical polymorphism)].

The geographic distribution of the frequencies of genes related to the immunological and biochemical polymorphism was studied in the Maris, who are the indigenous population of the Marii El Republic. Data on the frequencies of 33 alleles of 10 loci (ABO, TF, GC, PI, HP, AHS, F13B, ACP1, PGM1, and GLO1) in five raions (districts) of Marii El were obtained. Computer interpolation maps were constructed for all alleles. The maps allows to predict the distribution of the alleles throughout Marii El. A map of the reliability of the cartographic prediction was drawn. For the first time, the reliability of predicted gene frequencies were taken into account in constructing and interpreting the maps of gene frequencies. For the entire set of the studied genes, parameters of heterozygosity (HS) and gene diversity (GST) were estimated. Cartographic correlation analysis was performed to reveal the relationship between gene frequencies and geographic coordinates. It was found that 42% of the studied genes predominantly correlated with latitude and 9% with longitude. It was assumed that the genetic structure of Mari populations had been mainly determined by latitude-related factors. A map of Nei's genetic distances between the overall Mari gene pool and the local populations revealed a central core, which was close to the "average Mari" gene pool, and a periphery, which was genetically distant from it. Suggestions on the microevolution of the Mari gene pool were advanced. Maps of the genes with the most characteristic genetic relief (ABO*B, ACP*A, TF*D, GC*1F, PI*M2, HP*1F, and F13B*3) are shown. These maps exhibit a high correlation with the maps of principal components.

ABO Blood-Group System↗
PubMed2006

Detection and quantification of the nifH gene in shoot and root of cucumber plants.

A real-time polymerase chain reaction (PCR) method was applied to quantify the nifH gene pool in cucumber shoot and root and to evaluate how nitrogen (N) supply and plant age affect the nifH gene pool. In shoots, the relative abundance of the nifH gene was affected neither by different stages of plant growth nor by N supply. In roots, higher numbers of diazotrophic bacteria were found compared with that in the shoot. The nifH gene pool in roots significantly increased with plant age, and unexpectedly, the pool size was positively correlated with N supply. The relative abundance of nifH gene copy numbers in roots was also positively correlated (r = 0.96) with total N uptake of the plant. The data suggest that real-time PCR-based nifH gene quantification in combination with N-content analysis can be used as an efficient way to perform further studies to evaluate the direct contribution of the N2-fixing plant-colonizing plant growth promoting bacteria to plant N nutrition.

Bacteria↗
PubMed1995

Pork characteristics as affected by two populations of swine and six crude protein levels.

Previous research has investigated the effect of genetic line and dietary CP on gilt growth and carcass composition. The aim of this research was to characterize lean tissue composition, color, tenderness, and water-holding capacity as affected by protein level and genetic lines. Thirty-six Gene Pool pigs, a population with low lean growth potential, and 36 Hampshire pigs, a population with a high lean growth potential, had ad libitum access to diets consisting of 10, 13, 16, 19, 22, or 25% CP. Longissimus muscles of Hampshire pigs were lighter, more red, and more yellow than those from Gene Pool pigs (P< .01). Redness and yellowness of longissimus muscles decreased linearly (P < .01) as protein level increased. Chops from Hampshire pigs required less force and less total energy to shear but had lower cooking yields and water-holding capacity than chops from Gene Pool pigs (P < .01). Chops from pigs fed 19 and 22% protein required greater force (quadratic, P < .01) and more total energy (quadratic, P < .05) to shear. Objective color differences revealed that restructured, cured hams from Hampshire pigs were lighter, less red, and had less intense cured color (P < .01). The Hampshire line of gilts produced pork muscle that was leaner, more pale in color, more tender, and lower in water-holding capacity than the Gene Pool line. Level of dietary CP caused alterations in tenderness and lean composition, especially when diets contained less protein.

Animals↗
PubMed2026

Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).

Seed coat color and patterning are key quality traits in common bean (Phaseolus vulgaris L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter-market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high-throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene-specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (G, B, V, J, Rk, T, and Z) and two patterning genes (CPi and CSt), together with a previously reported marker associated with the postharvest seed coat darkening locus (Psd). An additional PACE marker targeting the Phaseolin (Phs) locus was developed to distinguish Middle American (S-type) and Andean (T-type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat-specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%-100%). However, for loci such as J, V, Rk, T, and Z, allele-specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background-specific interactions. Collectively, these results provide a comprehensive set of high-resolution, gene-anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker-assisted selection for market class-specific seed coat traits and accelerating genetic improvement.

Phaseolus↗
PubMed2001

High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula.

In the present study we have analyzed 44 Y-chromosome biallelic polymorphisms in population samples from northwestern (NW) Africa and the Iberian Peninsula, which allowed us to place each chromosome unequivocally in a phylogenetic tree based on >150 polymorphisms. The most striking results are that contemporary NW African and Iberian populations were found to have originated from distinctly different patrilineages and that the Strait of Gibraltar seems to have acted as a strong (although not complete) barrier to gene flow. In NW African populations, an Upper Paleolithic colonization that probably had its origin in eastern Africa contributed 75% of the current gene pool. In comparison, approximately 78% of contemporary Iberian Y chromosomes originated in an Upper Paleolithic expansion from western Asia, along the northern rim of the Mediterranean basin. Smaller contributions to these gene pools (constituting 13% of Y chromosomes in NW Africa and 10% of Y chromosomes in Iberia) came from the Middle East during the Neolithic and, during subsequent gene flow, from Sub-Saharan to NW Africa. Finally, bidirectional gene flow across the Strait of Gibraltar has been detected: the genetic contribution of European Y chromosomes to the NW African gene pool is estimated at 4%, and NW African populations may have contributed 7% of Iberian Y chromosomes. The Islamic rule of Spain, which began in a.d. 711 and lasted almost 8 centuries, left only a minor contribution to the current Iberian Y-chromosome pool. The high-resolution analysis of the Y chromosome allows us to separate successive migratory components and to precisely quantify each historical layer.

Africa South of the Sahara↗
PubMed1992

Allozyme analysis of Trichinella isolates from various host species and geographical regions.

Allozyme analysis was carried out on 152 Trichinella isolates from synanthropic and wild animals and from humans; the isolates were collected from 5 continents. The analysis, involving 27 enzymes, revealed the presence of 8 distinct gene pools, termed T1-T8. Four of the genetic groups represent the 4 previously proposed species: Trichinella spiralis sensu stricto (T1), Trichinella nativa (T2), Trichinella nelsoni (T7), and Trichinella pseudospiralis (T4). The other 4, T3, T5, T6, and T8 are distinct from previously described species. The absence of allozymic hybrid patterns among even sympatric groups indicates a lack of gene flow among the groups. Principal component analysis and the unweighted pair group method of analysis were used to assemble allozyme patterns of the 152 isolates into discrete groups and to show their relative relationships. Both analyses indicated the presence of 8 primary clusters that correlated with the gene pools revealed by direct allozyme profile analysis. The absence of evidence of gene flow among the gene pools and the high level of allozymic differentiation between the cluster groups support the concept that the genus Trichinella is composed of several sibling species.

Animals↗
PubMed1992

Evolution and ecology of influenza A viruses.

In this review we examine the hypothesis that aquatic birds are the primordial source of all influenza viruses in other species and study the ecological features that permit the perpetuation of influenza viruses in aquatic avian species. Phylogenetic analysis of the nucleotide sequence of influenza A virus RNA segments coding for the spike proteins (HA, NA, and M2) and the internal proteins (PB2, PB1, PA, NP, M, and NS) from a wide range of hosts, geographical regions, and influenza A virus subtypes support the following conclusions. (i) Two partly overlapping reservoirs of influenza A viruses exist in migrating waterfowl and shorebirds throughout the world. These species harbor influenza viruses of all the known HA and NA subtypes. (ii) Influenza viruses have evolved into a number of host-specific lineages that are exemplified by the NP gene and include equine Prague/56, recent equine strains, classical swine and human strains, H13 gull strains, and all other avian strains. Other genes show similar patterns, but with extensive evidence of genetic reassortment. Geographical as well as host-specific lineages are evident. (iii) All of the influenza A viruses of mammalian sources originated from the avian gene pool, and it is possible that influenza B viruses also arose from the same source. (iv) The different virus lineages are predominantly host specific, but there are periodic exchanges of influenza virus genes or whole viruses between species, giving rise to pandemics of disease in humans, lower animals, and birds. (v) The influenza viruses currently circulating in humans and pigs in North America originated by transmission of all genes from the avian reservoir prior to the 1918 Spanish influenza pandemic; some of the genes have subsequently been replaced by others from the influenza gene pool in birds. (vi) The influenza virus gene pool in aquatic birds of the world is probably perpetuated by low-level transmission within that species throughout the year. (vii) There is evidence that most new human pandemic strains and variants have originated in southern China. (viii) There is speculation that pigs may serve as the intermediate host in genetic exchange between influenza viruses in avian and humans, but experimental evidence is lacking. (ix) Once the ecological properties of influenza viruses are understood, it may be possible to interdict the introduction of new influenza viruses into humans.

Animals↗
PubMedDate not supplied

[Genetic peculiarity of the yakut population from the autosomal loci data].

The autosomal gene pool of Yakuts was analyzed with a panel of polymorphic Alu insertions. The observed allele frequencies were typical for other Asian ethnic groups. Genetic differentiation of three Yakut populations was relatively high, 2%. East Siberian ethnic groups were shown to have a common gene pool and to experience no intense gene flow from other populations. Development of the Yakut gene pool was assumed to involve no substantial genetic effect of neighboring populations. The results fit both autochthonous and southern origin hypotheses.

Alu Elements↗
PubMed2006

[Analysis of polymorphism at nine nuclear genome DNA loci in maris].

Population genetic survey of the indigenous populations of the Marii El Republic, represented by the two major ethnographic groups of Maris, Meadow (five samples from Morkinsk, Orshansk, Semursk, Sovetsk, and Zvenigovsk districts) and Mountain (one sample from Gornomariisk district) Maris, was carried out. All Mari groups were examined at nine polymorphic DNA loci of nuclear genome, VNTR(PAH) (N = 422), STR(PAH) (N = 152), VNTR(ApoB) (N= 294), VNTR(DAT1) (N = 363), VNTR(eNOS) (N = 373), ACE (N = 412), IVS6aGATT (N = 513), D7S23(KM.19) (N = 494), and D7S8 (N = 366). Allele and genotype frequency distribution patterns were obtained for individual samples and ethnographic groups, as well as for the ethnic group overall. In each of six Mari samples examined, the deficit of heterozygotes was observed, i.e., the mean observed heterozygosity was lower than the expected one. The indices of mean heterozygosity, Hs = 0.455, and interpopulation differentiation, FST = 0.0024, for the Mari gene pool were obtained using a set of DNA markers analyzed. Analysis of the genetic distances and between population differentiation (FST) showed that the main part of genetic diversity in Maris was determined by the differentiation between the populations of Meadow Maris. The contribution of the differences between the ethnographic groups of Mountain and Meadow Maris to the ethnic gene pool was small. It is suggested that the main role in the formation of the Mari gene pool is played by the geographic factor.

Alleles↗
PubMed2005

Epigenetic control of ovarian function: the emerging role of histone modifications.

The dynamic nature of the ovarian follicle makes it an ideal model to study the coordinated activation and inactivation of genes related to cell growth and differentiation. Much progress has been made in identifying transcription factors that promote the transcription of ovarian genes mediating gonadotropin action and steroidogenesis, but how these factors promote transcription in the context of chromatin is not well understood. Over the past 5 years, epigenetic regulation of ovarian genes through histone modifications has been the focus of an increasing number of studies. Several coactivators and corepressors associated with transcription factors are in fact histone acetyltransferases and histone deacetylases mediating the hyperacetylation and hypoacetylation of histones, respectively. Hyperacetylation of lysine residues in the core histone tails promotes chromatin alterations that favor transcription, whereas hypoacetylation of histones promotes gene silencing or repression. Not only does the acetylation status of the core histones determine whether chromatin remodeling occurs, but histone phosphorylation and methylation may serve equally important roles. For example, the combination of histone H3 phosphorylation and acetylation concertedly favors transcription. In addition, specific lysine methylations (e.g., K9 of histone H3) repress gene expression whereas other methylations promote gene expression. It is most likely the combination of histone modification events that regulate the initiation of transcription. Understanding how ovarian hormones control specific histone modifications will help us understand how follicular cells can switch from active gene pools governing cell proliferation to those gene groups controlling terminal differentiation. Progress in elucidating the ovarian specific regulation of histone modifying enzymes as well as identification of their target gene pools at different stages of the follicular cycle is expected in the next few years.

Acetylation↗
PubMed2004

Genetic admixture of European FRDA genes is the cause of Friedreich ataxia in the Mexican population.

Friedreich ataxia accounts for approximately 75% of European recessive ataxia patients. Approximately 98% of pathogenic chromosomes have large expansions of a GAA triplet repeat in the FRDA gene (E alleles), and strong linkage disequilibrium among polymorphisms spanning the FRDA locus indicates a common origin for all European E alleles. In contrast, we found that only 14 of 151 (9.3%) Mexican Mestizo patients with recessive ataxia were homozygous for E alleles. Analysis of polymorphisms spanning the FRDA locus revealed that all Mestizo E alleles had the common European haplotype, indicating that they share a single origin. Genetic admixture levels were determined, which revealed that the relative contributions to the Mestizo FRDA gene pool by Native American and European genes were 76-87% and 13-24%, respectively, commensurate with the observed low prevalence of Friedreich ataxia in Mestizos. This indicates that Friedreich ataxia in Mexican Mestizos is due to genetic admixture of European mutant FRDA genes in the Native American gene pool that existed prior to contact with Europeans.

Adaptor Proteins, Signal Transducing↗
PubMed1995

Variability of the genetic contribution of Quebec population founders associated to some deleterious genes.

Relatively high frequencies of some rare inherited disorders can be found in the Saguenay Region (Quebec). To understand this phenomenon, a research project on the 17th-century founder effect that led to the formation of French Canadians' gene pool is being carried out. The focus of this study is on founders who contributed to the Saguenay gene pool and who are related to contemporary probands suffering from any one of five hereditary diseases: cystic fibrosis, tyrosinemia, hemochromatosis, Charlevoix-Saguenay spastic ataxia, and sensorimotor polyneuropathia with or without agenesis of the corpus callosum. A control group has been added for comparison purposes. Altogether, 545 ascending genealogies have been reconstructed, using the Interuniversity Institute for Population Research's RETRO database, leading to > 2,500 founders. The genetic contribution of each founder to each group has been measured. Results show that (1) nearly 80% of the individuals' gene pool come from founders who settled in Nouvelle-France in the 17th century, whatever the group; (2) 15% of the founders explain 90% of the total genetic contribution of the founders, but this pattern varies from one group to another; (3) there is no subgroup of founders more related to any given group of individuals.

Genes↗
PubMed2004

Mitochondrial DNA variation in the aboriginal populations of the Altai-Baikal region: implications for the genetic history of North Asia and America.

The discovery of mtDNA types common to Asians and Amerinds (types A, B, C, and D) forced investigators to search for those nations of Asia which, though not considered the ancestors of the Amerinds, have retained a close genetic resemblance with them. We collected samples and studied the gene pools of the Turkic-speaking nations of South Siberia: Altaians, Khakassians, Shorians, Tuvinians, Todjins, Tofalars, Sojots, as well as Mongolian-speaking Buryats. The data indicate that nearly all Turkic-speaking nations of Siberia and Central Asia, as well as the Buryats, have types A, B, C, and D in their gene pool. The highest total frequency of these types is observed in the Tuvinians and Sojots. They, as well as the Buryats, also have the lowest frequency of the europeoid types. The most mixed Asian-Europeoid gene pool examined turned out to be that of the Shorians. An important finding was the presence of type X in the Altaians, which had not yet been detected in Asia. As shown by computer analysis, this DNA sequence is not a late European admixture. Rather, the Altai variant X is ancient and can be close to the ancestral form of the variants of contemporary Europeans and Amerinds. The presented results prove that of all nations in Asia, the Turkic-speaking nations living between Altai and Baikal along the Sayan mountains are genetically closest to the Amerinds.

Americas↗