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Significance of habitat type for the genetic population structure of Panonychus citri (Acari: Tetranychidae).

Restricted migration and habitat fragmentation promote genetic differentiation between populations. Because most of the hosts of Panonychus citri are woody plants, mainly citrus trees that are usually planted at intervals of several metres, this mite likely faces more risks (e.g., starvation) by dispersing between host plants, compared to other spider mite species that infest both herbaceous and woody plants, such as Tetranychus urticae. Such a limited gene flow between patches (host plants) can lead to differentiation of populations even within a small area. Therefore, we hypothesize that P. citri populations are genetically differentiated not only between distant populations but also within small areas, such as within a grove. To test this hypothesis, we investigated the divergence of P. citri populations in Japanese citrus groves according to a hierarchical arrangement of geographical distance, ranging from distant populations (10 groves distributed throughout different areas in two major Japanese islands; this level of analysis is referred to as 'geographic') to local populations (different trees in a specific grove; 'local'). Three molecular markers were used: an esterase locus, one microsatellite and a point mutation in the mitochondrial cytochrome oxidase subunit I. At a local level acaricide susceptibility tests were also performed using two acaricides: fenpyroximate (25 ppm) and etoxazole (3.33 ppm). At a broad geographic level the gene diversity decreased with decreasing area size and distance between populations. By contrast, at the local level, populations maintained a significant level of variation between trees within groves, and the divergence within groves was higher than between groves. Whereas no statistical difference of the mortalities was detected among groves for the two acaricides tested, the difference was statistically significant among trees within groves in fenpyroximate (ANOVA, p<0.025) and marginal in etoxazole (0.1<p<0.05). We concluded that P. citri populations maintain a higher level of variation between trees (or patches of trees) within groves than between groves at the local level, though the gene diversity tended to be smaller with decreasing distance between populations at the geographical level. Results are discussed in relation to the dispersal behaviour of spider mites.

Animals↗

A computer simulation study of VNTR population genetics: constrained recombination rules out the infinite alleles model.

Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. We show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. We use sampling theory to confirm the intrinsically poor fit to the infinite alleles model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations.

Alleles↗

Population genetic structure of Titanotrichum oldhamii (Gesneriaceae), a subtropical bulbiliferous plant with mixed sexual and asexual reproduction.

BACKGROUND AND AIMS: Titanotrichum oldhamii is a monotypic genus distributed in Taiwan, adjacent regions of China and the Ryukyu Isands of Japan. Its conservation status is vulnerable as most populations are small and widely scattered. Titanotrichum has a mixed system of reproduction with vegetative bulbils and seeds. The aim of this study was to understand the population genetic structure of Titanotrichum in relation to its specific reproductive behaviour and to determine possible implications for conservation strategies. METHODS: After an extensive inventory of most wild populations of Titanotrichum in East Asia, samples from 25 populations within its major distribution were carried out utilizing RAPD and inter-SSR molecular fingerprinting analysis. KEY RESULTS: The findings support the conclusion that many populations reproduce predominantly asexually but that some genetic variation still exists within populations. However, significant amounts of variation exist between populations, perhaps reflecting population differentiation by drift. This partitioning of genetic diversity indicates that the level of inter-population gene exchange is extremely low. These findings are consistent with field observations of very limited seed production. The Chinese populations are similar to those of Northern Taiwan, while the Ryukyu populations fall within the range of variation of the north-central Taiwan populations. The Taiwanese populations are relatively variable and differentiation between north, east and south Taiwan is evident. CONCLUSIONS: The distribution of Titanotrichum seems to be consistent with a former land connection between China, Taiwan and the Ryukyu Islands at a glacial maximum during the Quaternary, followed by progressive fragmentation of the populations. North-central Taiwan is the centre of genetic diversity, possibly due to the proximity of the former land bridge between the regions, together with the variety of suitable habitats in north Taiwan. The significance of these findings for conservation is discussed.

Base Sequence↗

Comparative population genetic structures and local adaptation of two mutualists.

Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

Adaptation, Biological↗

Hydrography and population genetic structure in brook charr (Salvelinus fontinalis, Mitchill) from eastern Canada.

Despite the abundance of studies of genetic diversity in freshwater fishes, few have specifically addressed the role of habitat structure in partitioning genetic variance within and among populations. In this study, we analysed the variability of six microsatellite loci among 24 brook charr population samples in order to correlate hydrographic structure with genetic organization. These populations originated from three Canadian National parks (Kouchibouguac, Fundy and Forillon) that showed distinct hydrographic structure. Considering the general characteristics of these habitats, we formulated specific hypotheses in regard to genetic structure, which were principally based on the potential for gene flow and population size associated with each habitat. The hierarchical analysis of molecular variance and the genetic distances computed among populations revealed that habitat structure analyses constitute an important, but insufficient, predictor of genetic structure. We discuss the importance of habitat complexity on genetic structure in the context of management and conservation.

Alleles↗

Ecotoxicology and population genetics: the emergence of "phylogeographic and evolutionary ecotoxicology".

Genetics of ecotoxicology has recently emerged as a priority research field. The advent of polymerase chain reaction and molecular population genetics has made it possible to examine the genetics in even the smallest individuals. Although a potentially powerful technique, current approaches oversimplify the relationship of change in gene frequency to contaminant exposure. Many of these approaches cannot control for random correlation or accessory abiotic factors that impinge on the system tested. Indeed, the gestalt approaches of laboratory exposure or natural field experiments may ignore significant genome-level interactions that are important within a given system. At the very least, these approaches would benefit by a biogeographic survey of genetic variation to understand geographic microevolutionary patterns, or phylogeography, within a species to reduce spurious correlations and erroneous conclusions. Other single locus approaches can be chosen to enhance this approach if genetic/environmental interactions have been characterized for laboratory populations or for other model systems.

Animals↗

Population genetics and identity of an introduced terrestrial slug: Arion subfuscus s.l. in the North-East USA (Gastropoda, Pulmonata, Arionidae).

Several European species of the terrestrial slug genus Arion have been introduced into North America. A case in point is the species complex A. subfuscus s.l. which has become one of the most abundant slug taxa in North America. In Europe this complex consists of at least two cryptic species, viz. A. fuscus and A. subfuscus s.s., the latter of which is further subdivided in five strongly divergent mtDNA lineages (A. subfuscus S1-S5). In order to determine which of these A. subfsucus s.l. taxa are present in the NE USA and in order to assess their population genetic structure, we compared mtDNA, nDNA and allozyme variation between populations from the NE USA and Europe. Our results show that (1) at least A. subfuscus S1 has become successfully established in the NE USA, (2) founder effects are the most likely explanation for the loss of a large amount of molecular genetic variation in populations from the NE USA (i.e. a loss of 96% of the 16S rDNA haplotypes, 67% of the ITS1 alleles and 46% of the alleles at polymorphic allozyme loci), and (3) part of the remaining genetic variation in NE USA populations was probably due to multiple introductions from the British Isles and the European mainland, and the hybrid structure of most of these source populations. Apparently, the extreme loss of molecular genetic variation in this introduced species has not prevented it from successfully establishing and spreading in novel environments.

Alleles↗

[The study of helminth population genetics].

Genetic markers including allozyme,mtDNA,RAPD/RFLP and micro DNA have been used in the research of helminth population genetics. Available data on helminth genetic variability have shown that most helminth populations exhibit different levels of genetic variation resulting mainly from the pattern of life cycle,geographical distribution and parasite-host interaction,and several hypotheses have been proposed to explain the genetic variation.

English Abstract↗

Population genetics of Escherichia coli in a natural population of native Australian rats.

Escherichia coli, a normal inhabitant of the intestinal tract of mammals and birds, is a diverse species. Most studies on E. coli populations involve organisms from humans or human-associated animals. In this study, we undertook a survey of E. coli from native Australian mammals, predominantly Rattus tunneyi, living in a relatively pristine environment in the Bundjalung National Park. The genetic diversity was assessed and compared by multilocus enzyme electrophoresis (MLEE), sequence analysis of the mdh (malate dehydrogenase) gene and biotyping using seven sugars. Ninety-nine electrophoretic types were identified from the 242 isolates analysed by MLEE and 15 sequences from the mdh genes sequenced from 21 representative strains. The Bundjalung isolates extend the diversity represented by the E. coli reference (ECOR) set, with new MLEE alleles found in six out of 10 loci. Many of the Bundjalung isolates fell into a discrete group in MLEE. Other Bundjalung strains fell into the recognized E. coli ECOR set groups, but tended to be at the base of both the MLEE and mdh gene trees, implying that these strains are derived independently from ancestral forms of the ECOR groups and that ECOR strains represent only a subset of E. coli adapted to humans and human-associated animals. Linkage disequilibrium analysis showed that the Bundjalung population has an 'epidemic' population structure. The Bundjalung isolates were able to utilize more sugars than the ECOR strains, suggesting that diet plays a prominent role in adaptation of E. coli.

Animals↗

[Population genetic analysis of Y-chromosomal single nucleotide polymorphism in six Chinese populations].

OBJECTIVE: To analyze the genetic polymorphism of 15 single nucleotide polymorphism (SNP) loci on the nonrecombining portion of the Y chromosome in 6 populations in China. METHODS: Allelic specific polymerase chain reaction and 2% agarose gel electrophoresis and 6% PAGE were used to analyze the genetic polymorphism of 343 unrelated males, representing 6 populations in China, including Fujian Hans, Sichuan Hans, Mongolian, Hezhen, Sibo and Hui from the South, Northeast and Northwest. RESULTS: Thirty haplogroups were observed, and 3 of them (H15, H16, H18) were seen in all of the six populations. Although the heterozygosity levels of the Hezhen, Mongolian, Sibo populations are similar and those of the other 3 populations (Fujian Hans, Sichuan Hans, Hui) are similar, the pairwise differences among haplogroups are significant. Analysis of molecular variance (AMOVA) and principal component (PC) analysis of the haplogroup distributions suggested highly different allele diversity between group I including Hezhen, Mongolian, Sibo and group II including Hui, Fujian Hans, Sichuan Hans. CONCLUSION: The above analyses show more significant variance components in Northeast/South populations and clearly reveal the geographic genetic relationship among the six populations in the Northeast/Northwest/South. These results confirm the complexity of the genetic structure of Chinese populations and make a significant contribution for constructing the contemporary human gene pool and tracing genetic dispersal trail from Chinese populations.

Alleles↗

Population genetics of the wild yeast Saccharomyces paradoxus.

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.

Base Sequence↗

Population genetic studies of the Aka pygmies (Central Africa): a survey of red cell and serum enzymes.

Blood samples collected in a single Pygmy tribe, the Aka, living in Bokoka district (Central African Empire) were investigated with respect to the phenotype and gene frequencies of the following 12 enzyme systems: acid phosphatase, adenosine deaminase, adenylate kinase, carbonic anhydrase, esterase D, glucose-6-phosphate dehydrogenase, malate dehydrogenase, phosphoglucomutase 1, phosphoglucomutase 2, phosphogluconate dehydrogenase, superoxide dismutase and serum cholinesterase variants (locus E1 and E2). The data obtained in the study of genetic polymorphisms of this isolated and inbred population show a specific pattern with the following characteristics: the very low frequency of PGDB and pa alleles; the existence of two rare PGM variants at the PGM2 locus, typical PGM26Pyg (4.2%) and PGM29 (0.2%); the high frequency of the pr allele (10.8%) and CAII2 (8.22%) and ESD2 genes (18.4%). Furthermore, at the G6PD locus four distinct alleles have been found: the negroid GdA- (4%) and GdA+ (16%), the common GdB+ (79.2%)--, and the rare Gd+Ibadan Austin (0.7%). Cholinesterase typings disclosed the presence of the uncommon E1f and E1s genes distributed within a single breeding unit. The results are compared with other data previously reported on South African Khoisan and some Negroid populations; the particular genetic background of Pygmies is discussed.

Black People↗

Utilisation of population genetic and multivariate methods in the evaluation of results of cattle type traits judgement.

The results of the evaluation of linear type traits evaluation of Hungarian beef cattle populations were analysed by means of both traditional population genetic and multivariate biometric methods, i.e. by means of cluster analysis based on factor analysis. By using the multivariate methods it was possible to evaluate the different types of cattle with respect to type traits, reproductivity and productivity properties. It is proven by the results obtained that factor analysis is practicable in the judgement at the population level of the individual properties. A great number of type traits--27 or more--making an interrelating system can be analysed well by this method whilst the cluster analysis based on the factor analysis is suitable to classify the population on the basis of individual evaluation with simultaneous consideration of all type traits.

Animal Husbandry↗

The DNA revolution in population genetics.

Unprecedental clarity has come to our understanding of genetic variation by the analysis of DNA sequences. It is not surprising that the new DNA technologies are leading to a resurgence of interest in population genetics. In this review, I discuss recent progress and future directions towards reconstructing the history of human populations. There is increasing consensus on a recent 'Out of Africa' origin of modern humans, which explains why the greatest fraction of genetic diversity is found within populations, rather than between them. The comparison of Y chromosome and mitochondrial DNA data shows remarkable sex differences in geographic variation. The analysis of Neanderthal DNA has been a major breakthrough in the study of fossil DNA. Among major hopes for the future are application to polygenic diseases.

DNA↗

Population genetics in the forensic DNA debate.

The use of matching variable number of tandem repeat (VNTR) profiles to link suspects with crimes is potentially very powerful, but it has been quite controversial. Initial debate over laboratory procedures has largely given way to debate over the statistical and population genetic issues involved in calculating the frequency of a profile for a random member of a population. This frequency is used to weight the evidence of a match between suspect and crime scene material when the suspect denies responsibility for that material. A recent report from the National Research Council, intended to put to rest some of the issues, has instead raised further debate by advocating a procedure based on maximum frequencies of profile components over several different populations.

Alleles↗

Population genetic data on four STR loci in a Hungarian Romany population.

A population study of Hungarian Romanies was carried out on the STR loci HumLPL, HumF13B, HumFES and HumF1301. There was little evidence for association of alleles within/between the four STR systems. Allele frequency distributions were significantly different between the Romany and the previously reported Central Hungarian population databases. Population differentiation was estimated by computing F- and phi-statistics as well as frequency estimate differences of individual phenotypes for these two population samples. The results suggest that the population structure may have an effect on the interpretation of forensic DNA evidence in Hungary. Phylogenetic tree reconstruction with six populations from three major ethnic groups revealed a relatively distant genetic relationship of the Baranya Romanies with other Caucasian populations.

Alleles↗