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PubMed2004

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae).

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

Bayes Theorem↗
PubMed1993

[Population-genetic characteristic of the rural population of southern Tajikistan].

The results of genetic and demographic study of the inhabitants in south Tadjikistan are presented. It had been shown that the population studied is a typical rural population of Middle Asia and is characterized by the extended reproductive capacity, homogeneity of national composition and a high proportion of consanguineous marriages. Genetic variation in blood groups (AB0, MN, Rh-D, P1), serum proteins and red cell enzyme systems (Tf, Gc, Hp, PGM1, PGD, EsD, AcP1) was examined. A comparative analysis of gene frequencies in the population studied and some other Middle Asia populations has been carried out.

Adolescent↗
PubMed1975

Population genetic studies in bees (APIDAE, Hymenoptera). I. Genetic load.

Three populations of Apis mellifera each predominantly of a different subspecies (mellifera, ligustica and adansonii) and 7 species of stingless bees (Meliponinae, Apidae) were manipulated for applying the MORTON, CROW & MULLER's methodology in order to estimate the lethal equivalents (B) of each population. A total of 249 queens were used, 27 being meliponids and 222 Apis mellifera. The populations of Apis have a B that does not differ significantly when they are compared to each other (1.29, 1.36, 1.32) and the balanced average equals 1.33. When the x-alleles are not considered, this balanced value is 0.262. The figures for B in the seven species of stingless bees ranged between 0.104 and 0.159 with balanced average of 0.132. The main reason for this smaller load in meliponids may rest in their effective population numbers, which are smaller than those of Apis. The average mortality for diploid females (0.141) and for haploid males (0.163) allows the estimation of the total elimination (sigma E = 0.073). Since for haplo-diploid systems the total mutation rate is sigma mu = 2 sigma E divided by 3 the figure 0.048 is obtained. Since about 15% of the genes in Apis mellifera are sex limited, this value of sigma mu should be added of 0.0072 (that is 0.15 X 0.048) and then, the total mutation rate becomes 0.055. Using a quite different method, the one by MORTON, CROW & MULLER, the figure 0.076 was obtained. If a mutation rate of 10(-5) is assumed, the number of genes in Apis mellifera that can make a contribution to the genetic load would vary between 5,500 and 7,600.

Animals↗
PubMed2006

Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus.

We investigated the distributions of genetic and phenotypic variation for two Yellowstone National Park populations of the heterocyst-forming cyanobacterium Mastigocladus (Fischerella) laminosus that exhibit dramatic phenotypic differences as a result of environmental differences in nitrogen availability. One population develops heterocysts and fixes nitrogen in situ in response to a deficiency of combined nitrogen in its environment, whereas the other population does neither due to the availability of a preferred nitrogen source. Slowly evolving molecular markers, including the 16S rRNA gene and the downstream internal transcribed spacer, are identical among all laboratory isolates from both populations but belie considerable genetic and phenotypic diversity. The total nucleotide diversity at six nitrogen metabolism loci was roughly three times greater than that observed for the human global population. The two populations are genetically differentiated, although variation in performance on different nitrogen sources among genotypes could not be explained by local adaptation to available nitrogen in the respective environments. Population genetic models suggest that local adaptation is mutation limited but also that the populations are expected to continue to diverge due to low migratory gene flow.

Cyanobacteria↗
PubMed1999

Population genetic data on loci LDLR, GYPA, HBGG, D7S8 and GC in the Bangkok population compared with rural Thais from Trat province.

Prior to the introduction of any DNA marker as a tool for person identification and paternity test in certain ethnic groups, a population genetic database should be constructed. Using multiplex primers in single tube polymerase chain amplification, 5 loci of unrelated genes in the PM Amplitype kit (Perkin Elmer) were studied in two Thai population groups: 228 DNA samples were extracted from blood collected at the Borai rural area in Trat province; another 123 DNA samples were collected at the outpatient clinic, Department of Forensic Medicine, King Chulalongkorn Memorial Hospital, Bangkok. Analysis of alleles and genotypes was performed after reversed dot blot hybridization of PCR products to allelic sequence specific probes immobilized on the membrane strip followed by nonradioisotopic detection according to the manufacturer's protocol. Population genetic statistic parameters including discrimination power (DP), the probability of matching (PM), power of exclusion for trio (PE trio) and typical paternity index (PI typical) were computed. Both Thai population groups showed no significant deviation from the Hardy Weinberg Expectation (HWE). The combined DP of all 5 loci in the PM Amplitype markers was 0.993636 for rural Thais and 0.994409 for Thais from Bangkok. The combined PM for rural Thais and those living in Bangkok was 0.006364 and 0.005591, respectively. The combined PE trio was 0.696825 and 0.698875 in both Thai population groups and the combined PI typical values were < 1.0. In conclusion, person identification using PM Amplitype DNA markers was efficient and satisfactory within certain limits. Hence, the application of PM Amplitype DNA markers for paternity tests should be cautiously considered and applied in combination with other parameters.

Alleles↗
PubMed2000

Inferring infection processes of a parasitic nematode using population genetics.

The distribution of genetic differentiation in a population of the parasitic nematode Strongyloides ratti divided between rat hosts was determined. We applied population genetic theory to these data to determine the source of new infections. We estimate the rate at which a rat acquires a new infection from (a) the existing subpopulation of parasites within that rat ('self-reinfection') versus (b) the wider environment ('immigration'). We find that the observed levels of genetic diversity and differentiation in the study population are consistent with low to moderate rates of self-reinfection and inconsistent with high rates of self-reinfection.

Animals↗
PubMed2001

Population genetics from an information perspective.

Some basic effects of population genetics are derived governing the occurrences of alleles A(i)and genotypes A(i)A(j)among its members. A principle of extreme physical information (EPI) is used. These effects are (1) the equation of genetic change, (2) Fisher's theorem of partial change, (3) a new uncertainty principle, and (4) the monotonic decrease of Fisher information with time, indicating increased disorder for the population. General conditions of population change are allowed: fitness coefficients w(ij)generally changing with time [except in effect (2)], population randomly or non-randomly mating, and a general number of loci present within each chromosome. EPI is a practical tool for deriving probability laws. It is an outgrowth of a physical process that occurs during any act of measurement. Here the measurement is the random observation of a genotype A(i)A(j). This observation is to be used to estimate the time of the observation, called "evolutionary time". The measurement activity incurs errors in the estimated observation time and fitness value of the observed genotype. By the Cramer-Rao inequality, the product of the two uncertainties must exceed unity [effect (3)]. The Fisher information I in data space is postulated to originate in the space of the genotype where it had some generally larger value J. The EPI principle extremizes the loss of information (I--J) with I=1/2 J. The solution gives rise to effects (1) and (2). Finally, it is shown that effect (4) holds when the population approaches an equilibrium state, e.g. for time values greater than a threshold if fitness coefficients w(ij)are constant. EPI provides a common framework for deriving physical laws and laws of population genetics. The new effects (3) and (4) are confirmed through computer simulation.

Animals↗
PubMed2006

Population genetics models of common diseases.

The number and frequency of susceptibility alleles for common diseases are important factors to consider in the efficient design of disease association studies. These quantities are the results of the joint effects of mutation, genetic drift and selection. Hence, population genetics models, informed by empirical knowledge about patterns of disease variation, can be used to make predictions about the allelic architecture of common disease susceptibility and to gain an overall understanding about the evolutionary origins of such diseases. Equilibrium models and empirical studies suggest a role for both rare and common variants. In addition, increasing evidence points to changes in selective pressures on susceptibility genes for common diseases; these findings are likely to form the basis for further modeling studies.

Genetic Predisposition to Disease↗
PubMed1995

Population genetics of induced mutations.

The contribution of induced mutations to the burden of genetic disease in the context of population genetics is considered. A clear distinction is made between the effects of genetic disease and mutational events. Much of the existing burden of genetic disease is a consequence of mutations that occurred in the past. The problem of distinguishing between spontaneous and induced mutations is discussed. Molecular genetics techniques are blurring the definitions of these terms. Classical population genetics shows that the frequency of affected individuals will reach an equilibrium depending on the mutation rate and the selective pressure against affected individuals. Increasing the mutation rate or reducing the selective pressures would result in a new equilibrium with an increase in the frequency in subsequent generations of affected individuals with dominant and X-linked mutant alleles. The increase in the number of recessive mutant alleles would be much slower and take many generations to reach the new equilibrium level. One assumption behind such equilibria is random mating. Changes in human demography with a rapid increase in population size, the breakup of small, relatively inbred subpopulations, and relaxed selective pressures will lead to a new equilibrium for recessive genes at probably higher frequencies. These factors will be the major contributors to increasing the burden of recessive genetic disease by increasing the total numbers of cases. The proportion of the population with a genetic disease will also continue to grow as a greater proportion of the population survives to late middle age and succumbs to diseases associated with old age, such as cancer, circulatory disease, dementias, and diabetes, each of which is likely to have a genetic component.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic Diseases, Inborn↗
PubMed2004

Molecular population genetics and the search for adaptive evolution in plants.

The first papers on plant molecular population genetics were published approximately 10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these studies focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding the detection of selection, with focus on plant populations, and we also summarize the empirical plant molecular population genetics literature. At face value, the literature suggests that a history of balancing or positive selection in plant genes is rampant. In two well-studied taxa (maize and Arabidopsis) over 20% of studied genes have been interpreted as containing the signature of selection. We argue that this is probably an overstatement of the prevalence of natural selection in plant genomes, for two reasons. First, demographic effects are difficult to incorporate and have generally not been well integrated into the plant population genetics literature. Second, the genes studied to date are not a random sample, so selected genes may be overrepresented. The next generation of studies in plant molecular population genetics requires additional sampling of local populations, explicit comparisons among loci, and improved theoretical methods to control for demography. Eventually, candidate loci should be confirmed by explicit consideration of phenotypic effects.

Evolution, Molecular↗
PubMed1985

Population bottlenecks and nonequilibrium models in population genetics. III. Genic homozygosity in populations which experience periodic bottlenecks.

The amount of variability in a population that experiences repeated restrictions in population size has been calculated. The restrictions in size occur cyclically with a fixed cycle length. Analytical formulas for describing the gene identity at any specific time in the expanded and restricted phases of the cycle, and for the average and second moment of the gene identity, have been derived. It is shown that the level of genetic diversity depends critically on the two parameters that account for the population size, mutation rate and the time of duration for each of the two phases in the cycle. If one or both of these composite parameters are small, the gene diversity will be much reduced, and population gene diversity will then be predictable from knowledge of the harmonic mean population size over the entire cycle. If these parameters take on intermediate values, diversity changes constantly during the cycle, fluctuating steadily from a high to a low value and back again. If these parameters are large, gene diversity will fluctuate rapidly between extreme values and will stay at the extremes for long periods of time.

Gene Frequency↗
PubMed2006

Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity.

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

Animals↗
PubMed2003

[Analysis of population genetic structure and molecular identification of Changium smyrnioides and Chuanminshen violaceum with ISSR marker].

OBJECTIVE: To assess the population genetic diversity and genetic structure and screen species-specific bands for identification of Changium smyrnioides and Chuanminshen violaceum. METHOD: Seven wild populations of Changium smyrnioides and one cultivated population of Chuanminshen violaceum were studied by ISSR analysis. The population genetic diversity and population genetic structure were assessed by using POPGENE software. RESULT: A total of 152 ISSR markers were scored, among which 136 (90.8%) were polymorphic. The values of Gst tended to be high (mean Gst = 0.575). The level of genetic divesity of Changium smyrnioides (A = 1.272; P = 27.26%; I = 0.132; H = 0.087) was higher than that of Chuanminshen violaceum (A = 1.217; P = 21.7; I = 0.103; H = 0.067). CONCLUSION: The genetic variation of Changium smyrnioides is high and the majority of genetic variation occur among populations. Substantial genetic divergence is shown by cluster analysis (UPGMA) to befound between Changium smyrnioides and Chuanminshen violaceum at DNA level. In addition, one species-specific marker has been obtained in Chuanminshen violaceum. The phylogenetic relationship of two species has also been discussed.

Apiaceae↗
PubMed1993

A systematic and population genetic approach to the rabies problem in the yellow mongoose (Cynictis penicillata).

This paper reviews recent studies on the biology, systematics and population genetics of yellow mongoose populations in terms of possible implications for the epidemiology of rabies. Based on parallel studies, the existence of three distinct subspecies of yellow mongoose may have a direct bearing on rabies epidemiology; at least subspecific affiliation should be considered as a factor to be controlled for in rabies studies of the species. A direct correlation was found to exist between population genetics, social structure (and vagility) and aspects of the epidemiology of rabies in the yellow mongoose. The high frequency of enzyme polymorphisms restricted to single populations can be understood in terms of the well developed social structure and low vagility of yellow mongooses, which in turn explains the phenomenon of rabies outbreaks being restricted to highly localized foci which may flare up over a period of several years. Further research is required to establish whether predictable population genetic differences exist between high and low rabies-prone populations.

Animals↗
PubMed2005

Population genetics of the diamondback terrapin (Malaclemys terrapin).

We examined the population genetic structure of the diamondback terrapins (Malaclemys terrapin), within and among estuaries. Based on mark-recapture studies, these estuarine turtles have high site fidelity that is likely to make them vulnerable to local extinctions. We tested if observed site fidelity of adults would be reflected in intraestuarine population genetic structure of six highly polymorphic microsatellite loci (five tetranucleotide and one dinucleotide). No evidence was found for population structuring within the Charleston estuary nor among three different estuaries in South Carolina. We then examined four other terrapin populations from North Carolina to New York, as well as from the Florida Keys and from Texas. With increasing geographical distance, genetic differentiation increased from South Carolina through New York, but overall values were low. The dinucleotide locus contributed significantly more to the genetic differentiation of some population comparisons than any of the other loci. Interestingly, terrapins from South Carolina to New York were much more genetically similar to those from Texas (rho = 0.154) than to those from Florida (rho = 0.357). We attribute this pattern to extensive translocations of terrapins during the early 20th century to replenish diminished populations and to provide turtle farms with stocks. Terrapins collected in Texas were especially sought for shipment to the northeastern US because of their larger size. Our study indicates no population structure within or among adjacent estuaries. Thus, the mark-recapture information from adult and subadult feeding locations is a poor predictor of population genetic structure. Additionally, it appears that past human activities may have drastically altered the genetics of current populations. Finally, our data suggest that translocation of eggs or head starting of terrapins within estuaries or among adjacent estuaries is acceptable from a genetic standpoint.

Animals↗
PubMed1996

[Population genetics of spinal muscular atrophy].

A population genetic study of spinal amyotrophy (SMA) in six Russian and three Central Asian regions was carried out. In total, 29 patients with autosomal recessive (AR) infantile proximal SMA (SMA I-III) and four patients with rare SMA forms with an unspecified type of inheritance were revealed. In Russian populations, the prevalence of SMA I-III is similar (1.5-2.5/100000), it is one of the most common hereditary neurological diseases. A tendency toward nonuniform territorial SMA prevalence is observed in genetically subdivided populations. The lesser SMA I-III prevalence in Central Asian populations might be due in part to inbreeding depression. A segregation frequency of 0.21 is in accordance with AR inheritance; the proportion of sporadic cases is 3%. Clinical genealogical data support the genetic unity of forms I-III. The origin of pedigrees with SMA in distant relatives is discussed.

Asia, Central↗