Population analysis of the GLB1 gene in South Brazil

Infantile GM1 gangliosidosis is caused by the absence or reduction of lysosomal beta-galactosidase activity. Studies conducted in Brazil have indicated that it is one of the most frequent lysosomal storage disorders in the southern part of the country. To assess the incidence of this disorder, 390 blood donors were tested for the presence of two common mutations (1622-1627insG and R59H) in the GLB1 gene. Another group, consisting of 26 GM1 patients, and the blood donors were tested for the presence of two polymorphisms (R521C and S532G), in an attempt to elucidate whether there is a founder effect. The frequencies of the R59H and 1622-1627insG mutations among the GM1 patients studied were 19.2% and 38.5%, respectively. The frequency of polymorphism S532G was 16.7%, whereas R521C was not found in the patients. The overall frequency of either R59H or 1622-1627insG was 57.7% of the disease-causing alleles. This epidemiological study suggested a carrier frequency of 1:58. Seven different haplotypes were found. The 1622-1627insG mutation was not found to be linked to any polymorphism, whereas linkage disequilibrium was found for haplotype 2 (R59H, S532G) (p < 0.001). These data confirm the high incidence of GM1 gangliosidosis and the high frequency of two common mutations in southern Brazil.     

Estimation of genetic variability of the founder population in a conservation scheme using microsatellites

In a conservation programme with genealogical records it is possible to estimate the amount of variability of the founder population from a measure of the similarity among the individuals in the current population based on microsatellite markers. Here we compare three available methods and we shown that the one based on the molecular coancestry coefficient should be preferred.     

Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus

Aflatoxins are toxic and carcinogenic polyketides produced by several Aspergillus species that are known to contaminate agricultural commodities, posing a serious threat to animal and human health. Aflatoxin (AF) biosynthesis is almost fully characterized and involves the coordinated expression of approximately 25 genes clustered in a 70-kb DNA region. Aspergillus parasiticus is an economically important and common agent of AF contamination. Naturally occurring nonaflatoxigenic strains of A. parasiticus are rarely found and generally produce O-methylsterigmatocystin (OMST), the immediate precursor of AF. To elucidate the evolutionary forces acting to retain AF and OMST pathway extrolites (chemotypes), we sequenced 21 intergenic regions spanning the entire cluster in 24 A. parasiticus isolates chosen to represent the genetic diversity within a single Georgia field population. Linkage disequilibrium analyses revealed five distinct recombination blocks in the A. parasiticus cluster. Phylogenetic network analyses showed a history of recombination between chemotype-specific haplotypes, as well as evidence of contemporary recombination. We performed coalescent simulations of variation in recombination blocks and found an approximately twofold deeper coalescence for cluster genealogies compared to noncluster genealogies, our internal standard of neutral evolution. Significantly deeper cluster genealogies are indicative of balancing selection in the AF cluster of A. parasiticus and are further corroborated by the existence of trans-species polymorphisms and common haplotypes in the cluster for several closely related species. Estimates of Ka/Ks for representative cluster genes provide evidence of selection for OMST and AF chemotypes, and indicate a possible role of chemotypes in ecological adaptation and speciation.     

Recombination and lineage‐specific gene loss in the aflatoxin gene cluster of Aspergillus flavus

Aflatoxins produced by Aspergillus flavus are potent carcinogens that contaminate agricultural crops. Recent efforts to reduce aflatoxin concentrations in crops have focused on biological control using nonaflatoxigenic A. flavus strains AF36 (=NRRL 18543) and NRRL 21882 (the active component of afla‐guard^®). However, the evolutionary potential of these strains to remain nonaflatoxigenic in nature is unknown. To elucidate the underlying population processes that influence aflatoxigenicity, we examined patterns of linkage disequilibrium (LD) spanning 21 regions in the aflatoxin gene cluster of A. flavus. We show that recombination events are unevenly distributed across the cluster in A. flavus. Six distinct LD blocks separate late pathway genes aflE, aflM, aflN, aflG, aflL, aflI and aflO, and there is no discernable evidence of recombination among early pathway genes aflA, aflB, aflC, aflD, aflR and aflS. The discordance in phylogenies inferred for the aflW/aflX intergenic region and two noncluster regions, tryptophan synthase and acetamidase, is indicative of trans‐species evolution in the cluster. Additionally, polymorphisms in aflW/aflX divide A. flavus strains into two distinct clades, each harbouring only one of the two approved biocontrol strains. The clade with AF36 includes both aflatoxigenic and nonaflatoxigenic strains, whereas the clade with NRRL 21882 comprises only nonaflatoxigenic strains and includes all strains of A. flavus missing the entire gene cluster or with partial gene clusters. Our detection of LD blocks in partial clusters indicates that recombination may have played an important role in cluster disassembly, and multilocus coalescent analyses of cluster and noncluster regions indicate lineage‐specific gene loss in A. flavus. These results have important implications in assessing the stability of biocontrol strains in nature.     

Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses

The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationship are compared and shown to be closely related. Together, they provide an estimate of the amount of genetic variation which existed in founder animals. This study confirms the narrow genetic base of the breed and provides comprehensive analysis of contributions of founder animals. Seventy-eight percent of alleles in the current population are derived from 30 founders, 27 of these male. Ten founder females account for 72% of maternal lineages, while one founder stallion is responsible for 95% of paternal lineages.     

Estimating the minimum rate of genetic transformation in bacteria

Extensive data from multilocus electrophoresis are available for many bacterial populations. In some cases, for example Neisseria gonorrhoeae, these data are consistent with the population being in linkage equilibrium. This raises the following question. What frequency of transformation, or other means of genetic recombination, is needed, relative to mutation, to produce apparent panmixis? Simulation of a finite-population model suggests that, if transformation is at least twenty times as frequent as mutation, the population structure will be indistinguishable from a panmictic one, using the best available data sets. That is, relatively infrequent transformation is sufficient to produce approximate linkage equilibrium.     

Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

Theory predicts that naturally occurring hybrid zones between genetically distinct taxa can move over space and time as a result of selection and/or demographic processes, with certain types of hybrid zones being more or less likely to move. Determining whether a hybrid zone is stationary or moving has important implications for understanding evolutionary processes affecting interactions in hybrid populations. However, direct observations of hybrid zone movement are difficult to make unless the zone is moving rapidly. Here, evidence for movement in the house mouse Mus musculus domesticus × Mus musculus musculus hybrid zone is provided using measures of LD and haplotype structure among neighbouring SNP markers from across the genome. Local populations of mice across two transects in Germany and the Czech Republic were sampled, and a total of 1301 mice were genotyped at 1401 markers from the nuclear genome. Empirical measures of LD provide evidence for extinction and (re)colonization in single populations and, together with simulations, suggest hybrid zone movement because of either geography-dependent asymmetrical dispersal or selection favouring one subspecies over the other.     

Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by T_m the mth coalescent time, when m + 1 lineages coalesce into m lineages, and A_n(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, A_n(t), and the coalescence times, T_m, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n − A_n(t) follows a Poisson distribution, and as m → n, n(n ? 1)T_m/2N(0) follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.     

A striking example of the founder effect in the mollusc Littorina saxatilis

Two South African populations of Littorina saxatilis were examined by starch-gel electrophoresis at 16 enzyme loci and compared with 13 populations of North Atlantic saxatilis from both American and European coasts, and with six British populations of the closely related species Littorina arcana. The South African animals showed a severely reduced heterozygosity (– 0.052) compared with Atlantic populations of saxatilis ( = 0.181), and the mean genetic distance between the two areas was high ( = 0.203) compared with distances within the North Atlantic saxatilis populations (D = 0.034). In fact, the saxatilis from South Africa were genetically more distant from the North Atlantic samples of L. saxatilis than were the arcana from British shores. The reduced genetic heterozygosity and genetic divergence of the South African populations is attributed to founder effects following a postulated recent introduction by man.     

The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip

We have used linkage disequilibrium (LD) to identify single nucleotide polymorphisms (SNPs) on the Illumina Equine SNP50 BeadChip, which may be incorrectly positioned on the genome map. A total of 1201 Thoroughbred horses were genotyped using the Illumina Equine SNP50 BeadChip. LD was evaluated in a pairwise fashion between all autosomal SNPs, both within and across chromosomes. Filters were then applied to the data, firstly to identify SNPs that may have been mapped to the wrong chromosome and secondly to identify SNPs that may have been incorrectly positioned within chromosomes. We identified a single SNP on ECA28, which showed low LD with neighbouring SNPs but considerable LD with a group of SNPs on ECA10. Furthermore, a cluster of SNPs on ECA5 showed unusually low LD with surrounding SNPs. A total of 39 SNPs met the criteria for unusual within-chromosome LD. The results of this study indicate that some SNPs may be misplaced. This finding is significant, as misplaced SNPs may lead to difficulties in the application of genomic methods, such as homozygosity mapping, for which SNP order is important.     

The Eskimo isolate of Scoresbysund—an example of the founder effect in anthropology

The east coast of Greenland is inhabited in only two places: in Angmagssalik live the direct descendants of the 413 Eskimo discovered in 1884; 1000 km further north, a small isolated settlement, Scoresbysund, was founded in 1925 by 70 Eskimo from Angmagssalik.Several biological features were studied both on the parent population and its descendants and the founders themselves and their progeny. Moreover, detailed and periodically maintained genealogical records from the time of their discovery provide exceptional complete information on these two groups and make them particularly favourable for the study of certain anthropological and genetic problems.Regarding various hereditary anthropological characteristics (blood groups, finger patterns, anthropometric measurements), the isolate shows certain particularities compared to the parent population. There is a much greater ressemblance between the settlement's founders and their present descendants than between these two groups and the parent population and its descendants. A set of converging elements indicate that this isolate represents a good example of the founder effect for various anthropological characteristics.     

Linkage disequilibrium between the fragile X mutation and two closely linked CA repeats suggests that fragile X chromosomes are derived from a small number of founder chromosomes

In order to investigate the origin of mutations responsible for the fragile X syndrome, two polymorphic CA repeats, one at 10 kb (FRAXAC2) and the other at 150 kb (DXS548) from the mutation target, were analyzed in normal and fragile X chromosomes. Contrary to observations made in myotonic dystrophy, fragile X mutations were not strongly associated with a single allele at the marker loci. However, significant differences in allelic and haplotypic distributions were observed between normal and fragile X chromosomes, indicating that a limited number of primary events may have been at the origin of most present-day fragile X chromosomes in Caucasian populations. We propose a putative scheme with six founder chromosomes from which most of the observed fragile X–linked haplotypes can be derived directly or by a single event at one of the marker loci, either a change of one repeat unit or a recombination between DXS548 and the mutation target. Such founder chromosomes may have carried a number of CGG repeats in an upper-normal range, from which recurrent multistep expansion mutations have arisen.     

Distribution of beta-globin haplotypes among the tribes of southern Gujarat,India

The present study was carried out in Indo-European speaking tribal population groups of southern Gujarat (India) to elucidate the allelic and haplotypic content of β-globin system in individuals with HbAA genotypes. 6 neutral restriction sites of the β-globin system were analysed and various statistical parameters were estimated to draw meaningful interpretations. All the 6 sites were found to be polymorphic and most were in Hardy–Weinberg Equilibrium in the studied group. Haplotypes were constructed using two different combinations of the 6 restriction sites analysed. Analysis of the 5 sites revealed a set of three predominant haplotypes, ‘+−−−−’, ‘−++−+’ and ‘−+−++’; and haplotypes ‘+−−’, ‘++−’ and ‘+++’ were found to be the most frequent when the 3 sites were used to construct the haplotypes. Haplotypic heterozygosity levels (> 83%) observed in the present study group were comparable to those observed in African and Afro-American populations and greater than other world populations. All the ancestral haplotypes, +−−−−−, −++−+, −+−++ and −−−−+ were found in the study group. The distribution pattern of various haplotypes was consistent with the global pattern. The paucity of comparable data from other Indian populations restricted one from making interpretations about the study group's relationships with other Indian populations but the results were indicative of older population histories or experience of gene flow by the study group and their affinities with populations of southern India.     

Revealing the demographic histories of species using DNA sequences

Various methodological approaches using molecular sequence data have been developed and applied across several fields, including phylogeography, conservation biology, virology and human evolution. The aim of these approaches is to obtain predictive estimates of population history from DNA sequence data that can then be used for hypothesis testing with empirical data. This recent work provides opportunities to evaluate hypotheses of constant population size through time, of population growth or decline, of the rate of growth or decline, and of migration and growth in subdivided populations. At the core of many of these approaches is the extraction of information from the structure of phylogenetic trees to infer the demographic history of a population, and underlying nearly all methods is coalescent theory. With the increasing availability of DNA sequence data, it is important to review the different ways in which information can be extracted from DNA sequence data to estimate demographic parameters.     

Microsatellite variation in simulated and natural founder populations of the Laysan finch (Telespiza cantans)

Historical and demographic data were used in a computer model tosimulate neutral genetic change in populations of the Laysanfinch (Telespiza cantans), an insular passerine bird that hasundergone documented founder events at Pearl and Hermes reef(PHR). Measures of genetic variation in the natural PHRpopulations generally matched those in the simulated populations,except that heterozygosity on Southeast Island was lower than themodel predicted, and the heterozygote excess in the naturalpopulations had a low probability of occurrence in the simulatedpopulations. The estimate of effective population size (N _e) fromthe stochastic demographic model matched the estimate fromgenetic data for two populations, but the demographic estimatewas higher than the genetic estimate for Southeast Island. Smallfounder number was rejected as a possible explanation for thereduced genetic variation on Southeast. We suggest that N _e wasoverestimated in part because we assumed seasonal variance inreproductive success. Additional variance components need to bemeasured in the field and incorporated into the model. Accounting for the heterozygote excess also requires furthertheoretical and field investigations. Possible explanations forthe excess include inbreeding depression, incest avoidance, andthe effect of polygyny on heterozygote excess in smallpopulations. We concluded that the Pearl and Hermes reefpopulation will continue to lose genetic variation at a highrate, and translocations from the native population on Laysan maybe required to maintain a viable population on the reef.     

Linkage disequilibrium and founder effect analysis of the NF1 gene in French Canadians from the Quebec population

We genotyped 19 neurofibromatosis type 1 (NF1) families from French Canadians of the Quebec population with four intragenic microsatellites (IVS26-2.3, IVS27AC28.4, IVS27AC33.1, and IVS38GT53.0). Linkage analysis of the four microsatellite markers among the 19 NF1 families indicates that the four microsatellites are strongly linked with NF1 disease (LOD = 2.76-3.64). The four markers are associated (P = 0-0.077) except marker pair IVS26-2.3/IVS27AC33.1 (P = 0.18 or 0.17). However, perhaps due to the high mutation rate of the NF1 gene, no founder effect for NF1 was detected in the Quebec French Canadians.     

Estimation of migration from a perturbation experiment in natural populations of Drosophila buzzatii Patterson & Wheeler

In order to estimate migration and gene flow, allele frequencies in populations at two sites separated by 120 m were differentially perturbed by the continuous release over 413 days of flies homozygous at particular allozyme loci. The effects of perturbation were determined by genotype assay at two collections prior to, thirteen during and nine after the perturbation period. Maximum likelihood methods were developed to estimate migration into the two populations from the homozygous releases, and migration between the two populations. The successful perturbation of allele frequencies in a natural population is demonstrated. A plateau in allele frequencies during perturbation and a return to original frequencies following cessation of perturbation was most likely due to selection during development against recessive alleles concurrently introduced into the populations by the released flies. There is unequivocal evidence for short distance gene flow between the two populations. The migration rates estimated at ten times over a nine month period were extremely variable, but with higher population density at one site positively related with migration from that site to the other.