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PubMed1988

Speculation on the evolution of insulin-dependent diabetes genes.

A hypothesis about the evolution of insulin-dependent diabetes mellitus (IDDM)-susceptibility alleles is proposed. IDDM is known to be associated with two HLA-DR alleles, DR3 and DR4. DR3 is associated with IDDM in all ethnoracial groups including populations in which IDDM is rare, such as African and Asian populations, as well as whites in whom IDDM is common. However, in general, DR4 is associated with IDDM only in populations with white ancestry with high rates of IDDM. IDDM in American blacks illustrates the evolutionary patterns of the two diabetes alleles. The frequency of IDDM in American blacks relative to that in American whites (20% to 30%) approximates the frequency of the American black gene pool that is white-derived (also 20% to 30%), and DR4 is associated with IDDM in American blacks but not in African blacks. These data are consistent with the infusion of a dominant white-derived DR4-associated diabetes allele into the black gene pool. Recent studies of mitochondrial DNA suggest that modern humans evolved in Africa 200,000 to 300,000 years ago and that repeated migrations populated the world. The DR-population:IDDM-frequency relationships suggest that the DR3-associated diabetes allele evolved early (greater than or equal to 100,000 years ago) in Africa, whereas the DR4-associated diabetes allele evolved later (less than 15,000 years ago) in northern Europe. Recent data from studies of IDDM in families and populations which suggest that the DR4-associated allele has dominant characteristics and the DR3-associated allele has recessivelike characteristics fit into this hypothesis.

Alleles↗
PubMed2004

ISSR profiling of genetic variability in the ecotypes of Antheraea mylitta Drury, the tropical Tasar silkworm.

Antheraea mylitta, Drury, the semi-wild silk-producing lepidopteran insect commonly known as tasar silkworm is unique to India and is distributed over a wide tropical forest range covering the states of Andhra Pradesh, Bihar, Chhattisgarh, Madnya Pradesh, Maharashtra, Orissa and Uttaranchal. The populations found in different areas are know by their specific local names and are considered as different ecotypes, but it is difficult to separate the populations on the basis of morphological and life-cycle traits and thus molecular characterization was attempted. The present communication relates to the results obtained from the analysis of polymorphism unraveled by twelve ISSR primers for 11 populations of A. mylitta belonging to six ecotypes and 41 individuals of "Railey"--ecotype collected from five zones of Dandakarnya forest in Madnya Pradesh. This communication, further, presents molecular evidences on genetic differences between eleven ecotype populations and highlights the genotypic diversification of a single ecotype into further separate discrete gene pools. The canonical discriminant function analysis revealed grouping of the five populations of Railey ecotype into two "clumps", while accessions of other ecotypes stood separated from each other. Thr "Railey" populations on detailed study, further, revealed separation of two (Tokapal and Nangur) populations into discrete gene pools and the other three (Kondagaon, Darba and Tongpal) populations, in spite of larger geographic distance between them, overlapped one on the other. The analysis also identified nine markers, which can be utilized to characterize specific population and will be of help to follow the ongoing genetic changes triggered by various ecological factors and human influences on the "Railey" ecotype.

Animals↗
PubMed2002

The genetical history of humans and the great apes.

When and where did modern humans evolve? How did our ancestors spread over the world? Traditionally, answers to questions such as these have been sought in historical, archaeological, and fossil records. However, increasingly genetic data provide information about the evolution of our species. In this review, we focus on the comparison of the variation in the human gene pool to that of our closest evolutionary relatives, the great apes, because this provides a relevant perspective on human genetical evolution. For instance, comparisons to the great apes show that humans are unique in having little genetic variation as well as little genetic structure in their gene pool. Furthermore, genetic data indicate that humans, but not the great apes, have experienced a period of dramatic growth in their early history.

Animals↗
PubMed2003

Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm.

It has been argued that the level of genetic diversity in the modern durum wheat ( Triticum turgidum L. var. durum) elite germplasm may have declined due to the high selection pressure applied in breeding programs. In this study, 58 accessions covering a wide spectrum of genetic diversity of the cultivated durum wheat gene pool were characterized with 70 microsatellite loci (or simple sequence repeats, SSRs). On average, SSRs detected 5.6 different allelic variants per locus, with a mean diversity index (DI) equal to 0.56, thus revealing a diversity content comparable to those previously observed with SSRs in other small-grain cereal gene pools. The mean genetic similarity value was equal to 0.44. A highly diagnostic SSR set has been identified. A high variation in allele size was detected among SSR loci, suggesting a different suitability of these loci for estimating genetic diversity. The B genome was characterized by an overall polymorphism significantly higher than that of the A genome. Genetic diversity is organised in well-distinct sub-groups identified by the corresponding foundation-genotypes. A large portion (92.7%) of the molecular variation detected within the group of 45 modern cvs was accounted for by SSR alleles tracing back to ten foundation-genotypes; among those, the most recent CIMMYT-derived founders were genetically distant from the old Mediterranean ones. On the other hand, rare alleles were abundant, suggesting that a large number of genetic introgressions contributed to the foundation of the well-diversified germplasm herein considered. The profiles of recently released varieties indicate that the level of genetic diversity present in the modern durum wheat germplasm has actually increased over time.

Alleles↗
PubMed2004

Genetic characterization of the population of Grande Comore Island (Njazidja) according to major blood groups.

The Comorian population is historically considered a blend of influences from African Bantus, Arabs, and possibly Austronesians. In this study we present the first genetic data on the current Comorian population. Serologic analysis of the six major blood group systems (ABO, RH, KEL, FY, JK, and MNS) was performed on 164 individuals from Grande Comore Island (Njazidja). In addition, Duffy genotypes were determined by polymerase chain reaction using allele-specific primers. Our findings establish a high frequency of the Fy(a- b-) phenotype (86%), presenting the same genetic background as in sub-Saharan Africa. Analysis of genetic frequencies, distances, and admixture with other populations indicates that African Bantus made the main contribution to the gene pool (73.2%+/-15.5%). The Arab contribution from the Arabian peninsula was smaller (24.2%+/-7%) and the Indonesian contribution was minor (2.6%+/-9%). The major Bantu contribution was commensurate with the Bantu cultural influence. The contribution from the Arabian peninsula seemed in relation to its permeating religious and linguistic influence. As with the language, the Indonesian contribution to the Comorian gene pool was small. These results are in agreement with historical, sociological, and linguistic data.

Alleles↗
PubMed1993

The establishment of underdominant chromosomal rearrangements in multi-deme systems with local extinction and colonization.

The fate of an underdominant chromosomal mutant was investigated in multideme models with high rates of local extinction and colonization. Four models with different patterns of colonization (number of colonists and place of origin of colonists) were studied by performing a large number of computer simulations with the Monte Carlo method for several sets of values of the following parameters: coefficient of selection against the heterozygote, extinction rate of each deme, deme size, and number of demes. The probability of the newly arisen rearrangement being established in the multi-deme system depends strongly on the pattern of colonization, other things being equal. In the three models in which there is absent or scarce mixing of gene pools of different demes when a new deme is founded, the fixation probability of the new chromosomal rearrangement is rather close to that calculated by R. Lande (1979, Evolution 33, 234-251; 1985, Heredity 54, 323-332), which is equal to the corresponding probability in a single deme divided by the number of demes. In the model with extensive mixing of gene pools of demes, the corresponding probability is lower (considerably in some cases). Furthermore, in the models where the fixation probability is higher, the analysis of the time of the process leads to the conclusion that in systems consisting of a large number of demes, overlapping of several different processes of fixation of chromosomal rearrangements occurs.

Animals↗
PubMed2026

Genome-Wide SNP Characterisation of Three Kazakh Sheep Breeds: Kazakh Fat-Tailed Coarse-Wool, Degeres, and Etti Merino.

Kazakhstan's sheep portfolio underpins much of the country's mutton and wool production, yet several of its principal breeds remain genomically uncharacterised. The aim of this study was to characterise the genomic diversity, population structure, and global phylogenetic placement of three economically important Kazakh breeds and to determine whether they constitute separate gene pools requiring independent management. We present the first genome-wide SNP characterisation to include the Degeres (DE), the Etti Merino (EM), and the Kazakh fat-tailed coarse-wool (KKG) breeds simultaneously. A total of 1497 animals (DE = 354, EM = 642, KKG = 501) sampled across seven production households were genotyped and, after quality control, analysed at 42,279 SNPs, of which 22,766 LD-pruned markers were used for principal component analysis and AMOVA. We applied principal component analysis (PCA), pairwise FST, analysis of molecular variance (AMOVA), neighbour-joining phylogenetics, model-based ancestry estimation (ADMIXTURE), and Hill-number diversity profiling, and projected the breeds against the global Ovine SNP50 HapMap panel (74 reference breeds, 2819 animals; 37,685 shared SNPs). All three breeds retained uniformly high within-breed diversity (expected heterozygosity 0.413-0.417) with fixation indices at or near zero. AMOVA partitioned 94.03% of variance within breeds (&#x3a6;ST = 0.060, p < 0.001). PCA, phylogeny, and ADMIXTURE concordantly resolved three breed-specific clusters at K = 3, with a maximum interbreed FST of 0.038 within the study dataset. Against the global panel, EM was genetically closest to Merino and Merino-derived reference breeds (pooled FST = 0.017) and substantially more distant from Southwest Asian sheep (FST = 0.045), whereas DE and KKG showed the reciprocal pattern (FST = 0.027 and 0.020 to Southwest Asia, 0.052 to the Merino group). DE additionally displayed the heterozygote excess and partial admixture expected of an incompletely consolidated composite. These results delineate three distinct gene pools and carry direct implications for breed management and the conservation of genomic diversity in Kazakhstani sheep.

ADMIXTURE↗
PubMed1991

General introduction and epidemiology of trichinellosis.

All studies on trichinellosis have been based on the assumption that there is only one cosmopolitan agent of human and animal trichinellosis; Trichinella spiralis (Owen, 1835). In the past, swine and only a few synanthropic animals were considered reservoirs, and the presence of the parasite in sylvatic animals was considered rare. Breeding experiments before, and then biochemical approaches (isoenzymes and DNA analysis), showed the presence of a high genetic variability inside this genus, suggesting it be considered as polyspecific. At present, eight gene pools, named from T1 to T8, have been identified in the genus Trichinella. T1 (T. spiralis s str) is the etiological agent for the domestic cycle, with a cosmopolitan distribution related to swine breeding and human habits. However, in some areas this parasite passes from domestic to sylvatic animals and vice versa. Six gene pools are the agents for the sylvatic cycle at different latitudes, mainly in carnivores. T2 (T. nativa) is present in terrestrial mammals and seldom in sea mammals of arctic and subarctic regions. T3, T5, and T8 are present mainly in Canidae (T3), Ursidae (T5), Hyaenidae and Felidae (T8) of temperate-subtropical areas of Palearctic, Nearctic and South African regions, respectively. T6 is present in carnivores in the subarctic-temperate area of the Nearctic region; and T7 (T. nelsoni) in Hyaenidae and Felidae of Equatorial Africa. Only T4 (T. pseudospiralis) can infect both mammals and birds, and it shows a cosmopolitan distribution. Probably trichinellosis is present world-wide, but unknown in those areas where it has not been sought.

Animals↗
PubMed2002

Short-term changes in bacterial community fingerprints and potential activities in an alfisol supplemented with solid waste leachates.

We investigated the effect on soil functioning of adding leachates from municipal solid waste incinerator (MSWI) ashes to laboratory columns (bare soil) and to field experimental plots (bare soil or grass cover). Leachate of MSWI-solidified air pollution control residues (SAPCr) contained more salts but less heavy metals than did MSWI-bottom ash (BA) leachate. Leachate-supplemented soils (BA soil, SAPCr soil) and control (water added) soil (W) were analyzed after 30 days. Potential denitrifying activity (PDA) and potential N2 fixation (acetylene reduction assay, ARA) were measured in controlled conditions. PDA was significantly lower in SAPCr soil than in W soil, both in the laboratory (-45%) and in bare soil in the field (-31%). ARA values were lower in bare SAPCr soil (-54%) and in bare BA (-25%) soil. Both activities remained unaffected by leachate supplementation in soil under permanent grass cover. Automated ribosomal intergenic spacer analysis (A-RISA) fingerprints and RFLP of nifH gene pools were used to assess changes in the structure of bacterial community. Multivariate analysis of these fingerprints revealed that SAPCr leachate had a stronger effect than BA leachate on the total and N2-fixing bacterial communities. Similar results were obtained for laboratory and bare soil field plots, but leachates did not affect nifH gene pools from soil under permanent grass cover. The stronger impact of SAPCr leachate on both structure of bacterial communities and activities supports the conclusion that observed effects would result from the abundance of salts rather than from heavy metal toxicity.

Bacteria↗
PubMed2000

Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.).

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine--Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands.

DNA, Chloroplast↗
PubMed2003

[Genetic differentiation of residents of Central Asia from autosomal marker data].

The gene pool of five ethnic groups of the Central Asian population was characterized using nine human-specific polymorphic insertion/deletion loci (ACE, PLAT, APOA1, PV92, F13B, A25, B65, CD4, Mt-Nuc). It has been shown for the first time that at the CD4 locus, the frequency of Alu(-) is inversely related to the Mongoloid component of the population. For the Central Asian populations, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Dungans (0.04), immigrants from China, and Tajiks (0.15). The coefficient of gene differentiation in the Central Asian populations for all the genes was 2.8%, which indicates a relatively low level of population genetic subdivision in this region. The unity of the gene pool of the Central Asian Caucasoids was shown.

Alleles↗
PubMed2000

Identifying conservation units within captive chimpanzee populations.

One of the primary objectives in the captive management of any endangered primate is to preserve as much as possible the genetic diversity that has evolved and still exists in wild gene pools. The rationale for this is based on the theoretical understanding of the relationship between genetic diversity and fitness in response to selection. There remains little consensus, however, as to the type of genetic data that should be used to monitor captive populations. In order to develop a deeper understanding of the degree and nature of genetic diversity among "wild" chimpanzee gene pools, as well as to determine if one type of genetic data is more useful than others, DNA sequence data were generated at three unlinked, nonrepetitive nuclear loci, one polymorphic microsatellite, and the mitochondrial D-loop for 59 unrelated common and pygmy chimpanzees. The results suggest that: 1) data from nuclear loci can be used to differentiate common chimpanzee subspecies; 2) pygmy chimpanzees may have less genetic diversity than common chimpanzees; 3) shared microsatellite alleles do not always indicate identity by descent; and 4) nonrepetitive loci provide unique insights into evolutionary relationships and provide useful information for captive management programs.

Animals↗
PubMed2006

Possible ancestral structure in human populations.

Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p approximately 10(-7)), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

Animals↗
PubMed2001

DNA diversity and population admixture in Anatolia.

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51-200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic-speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y-chromosome loci. That (admittedly approximate) figure is compatible both with a substantial immigration accompanying the arrival of the Turkmen armies (which is not historically documented), and with continuous gene flow from Asia into Anatolia, at a rate of 1% for 40 generations. Because a military invasion is expected to more deeply affect the male gene pool, similar estimates of admixture for female- and male-transmitted traits are easier to reconcile with continuous migratory contacts between Anatolia and its Asian neighbors, perhaps facilitated by the disappearance of a linguistic barrier between them.

Adult↗
PubMed2005

Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups.

In search of the ancestors of Native American mitochondrial DNA (mtDNA) haplogroups, we analyzed the mtDNA of 531 individuals from nine indigenous populations in Siberia. All mtDNAs were subjected to high-resolution RFLP analysis, sequencing of the control-region hypervariable segment I (HVS-I), and surveyed for additional polymorphic markers in the coding region. Furthermore, the mtDNAs selected according to haplogroup/subhaplogroup status were completely sequenced. Phylogenetic analyses of the resulting data, combined with those from previously published Siberian arctic and sub-arctic populations, revealed that remnants of the ancient Siberian gene pool are still evident in Siberian populations, suggesting that the founding haplotypes of the Native American A-D branches originated in different parts of Siberia. Thus, lineage A complete sequences revealed in the Mansi of the Lower Ob and the Ket of the Lower Yenisei belong to A1, suggesting that A1 mtDNAs occasionally found in the remnants of hunting-gathering populations of northwestern and northern Siberia belonged to a common gene pool of the Siberian progenitors of Paleoindians. Moreover, lineage B1, which is the most closely related to the American B2, occurred in the Tubalar and Tuvan inhabiting the territory between the upper reaches of the Ob River in the west, to the Upper Yenisei region in the east. Finally, the sequence variants of haplogroups C and D, which are most similar to Native American C1 and D1, were detected in the Ulchi of the Lower Amur. Overall, our data suggest that the immediate ancestors of the Siberian/Beringian migrants who gave rise to ancient (pre-Clovis) Paleoindians have a common origin with aboriginal people of the area now designated the Altai-Sayan Upland, as well as the Lower Amur/Sea of Okhotsk region.

DNA, Mitochondrial↗
PubMed1993

[Unequal genetic contributions of parents to offsprings and their optimal control].

Due to the joint effects of natural and artificial selection, the proportions of genetic materials originating from different parents may vary in the gene pool of offsprings, and this creates a problem of unequal genetic contributions of parents to offsprings. It is shown that unequal genetic contribution substantially affects the genetic gain via realized selection differential and effective population size, and brings error to the empirical prediction formulae of selection response: R = i.sigma P.h2. The aim of breeding should be to select the genetically superior individuals and then to make more genetic contributions of better parents to offspring gene pool. However, the latter aspect has been ignored in theoretical study as well as in certain breeding practice. To deal with the problem, a method which takes maximizing genetic advance as general objective and considers some breeding restrictions, is suggested to control the percentage of genetic contributions. A numerical example from egg-type chicken breeding is used to demonstrate the effects of optimal control of unequal genetic contributions. The result indicates that at the same level of effective population size, the realized selection response for different traits under the optimal pattern of unequal genetic contributions could be 34.27-216.57% higher than that under the actual unequal pattern.

Animals↗
PubMed2003

The study of APOA1, APOC3 and APOA4 variability in healthy ageing people reveals another paradox in the oldest old subjects.

The genes coding for apolipoprotein A1 (APOA1), apolipoprotein C3 (APOC3) and apolipoprotein A4 (APOA4) are tandemly organised within a short region on chromosome 11q23-q24. Polymorphisms of these genes have been extensively investigated in lipoprotein disorders and cardiovascular diseases, but poorly investigated in healthy ageing. The aim of this study was to describe possible modifications of the APOA1, APOC3, and APOA4 gene pool by cross-sectional studies carried out in a healthy ageing population whose ages ranged from 18 to 109 years (800 subjects, 327 males and 473 females, free of clinically manifested disease, and with emato-chemical parameters in the norm). APOA1-MspI-RFLP (-75 nt from the transcription starting site), APOC3-SstI-RFLP (3'UTR, 3238 nt), and APOA4-HincII-RFLP (Asp127/Ser127) were analysed according to age and sex. A significant age-related variation of the APOA1 gene pool was observed in males. An analysis of the allele average effect exerted by APOA1-MspI-RFLP A/P alleles (Absence/Presence of the restriction site) on lipidemic parameters in 46-80 year old males showed that allele A decreased, while allele P significantly increased, serum LDL-cholesterol. Unexpectedly, the P allele was over-represented in the group of the oldest old subjects, thus giving evidence of another "genetic paradox of centenarians".

Adolescent↗
PubMedDate not supplied

Coadaptation revisited.

During the four decades or more since Dobzhansky introduced the term "coadaptation" to refer to the commonly observed selective superiority of inversion heterozygotes in populations of Drosophila pseudoobscura, the definition of the term has evolved, as have views concerning the rapidity with which coadaptation might occur. Indeed, the paucity of demonstrated instances of linkage disequilibrium in natural populations has led many to dismiss coadaptation as a factor in evolutionary change. The present article reviews the reasons why coadaptation (and the equivalent expression, "integration of gene pools") was proposed as a phenomenon occurring in local (or experimental) populations, offers supporting data obtained through a reanalysis of data on irradiated populations of D. melanogaster, and concludes that sound evidence supports coadaptation as a factor in the genetic change of populations.

Adaptation, Biological↗