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PubMed1982

Graft rejection in sponges. Genetic structure of accepting and rejecting populations.

Graft rejection frequencies in a population of the sponge Ectyoplasia ferox are reported in relation to the complexity of the histocompatibility system in this species. The frequency of graft acceptance is high but we show that, despite assumptions in the literature to the contrary, this does not imply that sponges accepting each other's grafts are genetically identical. This paper reports that graft-accepting pairs of sponges can have dissimilar plasmalemmal proteins. In addition, a theoretical analysis is presented of the types of histocompatibility systems that would account for the present results and those of others. We concluded that there is no evidence that sponges have highly polymorphic histocompatibility systems. The paper also reports on the histology of graft rejection and discusses some of the ecological relevance of the findings.

Alleles↗
PubMed2002

Genetic structure of the Ards Peninsula, Northern Ireland: evidence from civil registers of marriage 1840-1911.

This paper uses marital migration data transcribed from the Civil Registers of Marriage 1840-1911 to estimate kinship from migration matrices and isonymy in the Ards Peninsula, Northern Ireland. The distribution of religious denominations (Presbyterian, Episcopalian, and Roman Catholic) varies systematically throughout the region, with up to 77% Roman Catholic in the south and 81% Presbyterian in the north. Portavogie, a fishing village on the east coast, is exclusively Protestant, with a population 93% Presbyterian. Comparison of migration and isonymy with geographical distance by multidimensional scaling and the MATFIT procedure show Portavogie to be an outlier, more distantly related to other areas than its geographical position would predict. We suggest that this discrepancy is due to settlement history and occupational and religious isolation. Mantel tests show that marital migration is significantly related to geographical distance (rMG = 0.4257), as is the distribution of religious denominations (rRG = 0.5548) through settlement history. Migration is dependent on religion (rMR = 0.3674), and isonymy is dependent on migration (rIM= 0.2531) but not on geography or religion. With Portavogie omitted from the analysis, the dependence of migration on geography and on religion increases (rMG = 0.5583, rMR = 0.5646), as does the correlation between religion and geography (rRG = 0.7213). The dependence of isonymy on migration increases (rIM = 0.5103), and significant correlations between isonymy and religion (rIR = 0.4135) and isonymy and geography (rIG = 0.4660) appear. We argue that a full explanation of population structure requires geographical distance, settlement history, and the influence of religion and occupation to be taken into account.

Christianity↗
PubMed2004

Genetic structure of fragmented populations of a threatened endemic percid of the Rhône river: Zingel asper.

Zingel asper is an endemic percid of the Rhône basin considered to be critically endangered. This species was continuously distributed throughout the Rhône in 1900, but today only occupies 17% of its initial area. In the present study, five microsatellite loci were used to assess the level of genetic variability within and among populations localized in different sub-basins. Contrasting results were obtained for the three main populations from the Rhône. A reduced allelic diversity was observed for the two populations displaying the lowest patch sizes (length of the river system occupied); of these, a recent genetic bottleneck was detected for the population showing a particularly low density. However, the third population was characterized by a relatively large spatial extent, high local fish concentrations and an allelic diversity that was twice as high and associated with an equilibrium between mutation and drift. Thus, this population shows an apparently better evolutionary potential for long-term survival. Since 1930, a marked fragmentation of the whole Rhône system has appeared, related to the development of dams, and we assume that the significant genetic differentiation detected between the populations could mainly reflect the impact of this fragmentation. The high turnover of the Z. asper populations, and the major role of dispersal in population persistence (highlighted in a recent population dynamics study), indeed suggest that the differentiation observed could mainly have arisen from habitat fragmentation in recent history.

Alleles↗
PubMed2003

Genetic structure of a Japanese allotetraploid loach of the genus Cobitis (Osteichthyes, Cobitidae).

The Japanese allotetraploid spined loach of the genus Cobitis "yamato complex" sensu SAITOH et al. (2000), distributed in Western Japan, originated from hybridization between C. biwae on the maternal side and C. striata (Kyushu form) on the paternal side. Mitochondrial (mt) and nuclear DNA were analyzed in order to determine the genetic relationships among 15 populations spanning the entire range of the yamato complex. PCR-RFLP analysis of the ND1 mtDNA gene indicated that the yamato complex contains two divergent types of mtDNA: type A, consisting of one haplotype observed only in the Fukagawa River and type B consisting of 12 haplotypes found in the entire area. Phylogenetic analysis based on the cytochrome b mtDNA gene corroborated RFLP analysis, and indicated that type A was closely related to a different species, C. biwae (Kochi group) and C. striata (large race), rather than type B. The results of RAPD analysis on the Fukagawa River individuals, where types A and B sympatrically existed suggested that no reproductive isolation occurs between them. The existence of two distinct mtDNA types within the yamato complex suggest either multiple maternal origin at the speciation (tetraploidization) time or mtDNA introgression from other species afterwards.

Animals↗
PubMed2004

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci.

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.

Animals↗
PubMed1987

[Molecular-genetic structure and incompatibility of the nonconjugative enterobacterial R plasmids pKMR281 and pKMR285].

Physical maps of Enterobacteriaceae nonconjugative plasmids pKMR281 (Sm, Su, molecular weight of 6 kb) and pKMR285 (Sm, Su Tc, molecular weight of 9 kb) were constructed for endonucleases EcoRI, PstI, EcoRV, SmaI, BglII, SalI and PvuII. The genes controlling production of aminoglycoside-3''-phosphotransferase and dihydropteroate synthetase of type II and the genetic tetracycline resistance determinant of class A were localized on the plasmids. Heteroduplex analysis of plasmids pKMR281 and pKMR285 showed that plasmid pKMR281 was completely homologous to plasmid pKMR285. The site of plasmid pKMR285 nonhomology with respect to plasmid pKMR281 corresponded to the area containing the tetracycline resistance determinant. Plasmids pKMR281 and pKMR285 were compatible with the tester plasmids of 25 incompatibility groups of Enterobacteriaceae and probably constitute a new incompatibility group. It was shown that pKMR281 and pKMR285 type plasmids were widely distributed in clinical strains of E. coli and Shigella spp. isolated in the Krasnodar Region.

Chromosome Mapping↗
PubMed2004

Genetic structure and outcrossing rates in Flourensia cernua (Asteraceae) growing at different densities in the South-western Chihuahuan Desert.

BACKGROUNDS AND AIMS: Flourensia cernua is a partially self-incompatible, wind-pollinated shrub that grows in two scrub types of contrasting densities. It was anticipated that differences in plant density would affect the amount of genotype availability, and thus higher outcrossing rates and less genetic differentiation would be found at high-density sites. METHODS: At five high-density sites and at five low-density sites, 11 allozyme loci were analysed in adults. Outcrossing rates were estimated using five allozyme loci sampled from eight families from each scrub type. KEY RESULTS: High levels of genetic variation were found at all sites (ranging from P = 82-100 %, He = 0.33-0.45, and Ho = 0.4-0.59). Heterozygotes were found in excess (FIS = -0.15 +/- 0.06 s.d.), suggesting that natural selection favours heterozygosity, and there was little differentiation between sites (FST = 0.08 +/- 0.02 s.d.). Life history attributes, such as long-lived habit and wide geographic distribution, as well as the presence of a self-incompatibility system may explain these results. Outcrossing rates did not differ from 1.0 in both scrub types, and there was no genetic differentiation between scrub types (FST = -0.01 +/- 0.004 s.d.). CONCLUSIONS: The high rate of outcrossing favoured by partial incompatibility may generate unrestricted gene flow between scrub types and thus may explain the lack of differentiation between them. High heterozygosity could be expected in long-lived plants of arid zones as they confront a variable and stressing environment.

Algorithms↗
PubMed2005

Genetic structure in populations of an ancient woodland sedge, Carex sylvatica Hudson, at a regional and local scale.

Wood sedge (Carex sylvatica) is a well-known ancient woodland species with a long-term persistent seed bank and a caespitose growth habit. All thirteen isolated Carex sylvatica populations in the Dutch Rhine floodplain (including the river branches Waal and IJssel) were mapped in detail and analysed for genetic variation at a large number of AFLP loci and one microsatellite locus. Across all populations, only 40 % of the sampled individuals (n=216) represented a unique genotype. A high number of the studied patches (spatial clusters of tussocks, 2-10 m in diameter) within populations contained only one or a few genotypes. Identical plants (tussocks) were also found 20-500 m apart and in one case even 1000 m apart. Observed heterozygosity levels (H(O)=0.029) were low, indicating low levels of gene flow, which is in agreement with the selfing nature of other caespitose sedges. Although the number of genotypes in populations is low, these genotypes are genetically very distinct and variation within populations accounted for 55% of the total variation. The absence of a correlation between genetic and geographic distances among populations, and the scattered distribution of genotypes among patches within woodlands, support our hypothesis of rare establishments and subsequent local dispersal within woodlands in this forest floor species, which may benefit from and partly depend on human land use and forest management activities.

Carex Plant↗
PubMed2006

ISSR-PCR: tool for discrimination and genetic structure analysis of Plutella xylostella populations native to different geographical areas.

The diamondback moth (DBM), Plutella xylostella (L.) is considered as the most destructive pest of Brassicaceae crops world-wide. Its migratory capacities and development of insecticide resistance in many populations leads to more difficulties for population management. To control movement of populations and apparitions of resistance carried by resistant migrant individuals, populations must be identified using genetic markers. Here, seven different ISSR markers have been tested as a tool for population discrimination and genetic variations among 19 DBM populations from Canada, USA, Brazil, Martinique Island, France, Romania, Austria, Uzbekistan, Egypt, Benin, South Africa, Réunion Island, Hong Kong, Laos, Japan and four localities in Australia were assessed. Two classification methods were tested and compared: a common method of genetic distance analyses and a novel method based on an advanced statistical method of the Artificial Neural Networks' family, the Self-Organizing Map (SOM). The 188 loci selected revealed a very high variability between populations with a total polymorphism of 100% and a global coefficient of gene differentiation estimated by the Nei's index (Gst) of 0.238. Nevertheless, the largest part of variability was expressed among individuals within populations (AMOVA: 73.71% and mean polymorphism of 94% within populations). Genetic differentiation among the DBM populations did not reflect geographical distances between them. The two classification methods have given excellent results with less than 1.3% of misclassified individuals. The origin of the high genetic differentiation and efficiency of the two classification methods are discussed.

Algorithms↗
PubMed1999

Effect of insect-mediated dispersal on the genetic structure of postglacial water mite populations

Assaying population structure in species that differ in dispersal ability can help to determine whether population differentiation is dependent on the movement of individuals between populations. Here, allozyme variation is analysed in over 1100 individuals from nine species and two species complexes of Arrenurus water mites collected throughout north-eastern North America. As larvae, eight taxa are obligate parasites of winged adult insects that provide the primary opportunity for dispersal. Three additional species have lost the ability to parasitize insects and do not disperse in this manner. Consistent with the glaciated history of the region, very low allozyme heterozygosity was found in these taxa (Ho = 0.00-0.12), near panmixia in five out of seven species for which population differentiation was calculated and no patterns of isolation by distance over spatial scales up to several hundred kilometres. Nonetheless, in two out of three comparisons between sister species with and without parasitic larvae, parasitism was significantly associated with higher heterozygosity. Population differentiation could also be contrasted for two of these sister species pairs; in each case, lower estimates of FST were found in the mites able to disperse on insects. The statistical significance of these contrasts was dependent on the method used to estimate variance. At the scale of the genus, behavioural differences among insect vectors allows for broader hypotheses that relate water mite genetic diversity to dispersal ability. For the genus, rank correlations of dispersal ability with direct count heterozygosity (n = 11) and population differentiation (n = 7) were not significantly different from zero. These results are consistent with the hypothesis that allozyme population structure is primarily the result of historical patterns in these regions. However, comparisons between sister species suggest a limited role for dispersal in homogenizing populations genetically, even when drift-gene flow equilibrium has not been achieved.

Journal Article↗
PubMed2006

Does multiple hosts mean multiple parasites? Population genetic structure of Schistosoma japonicum between definitive host species.

Multi-host parasites, those capable of infecting more than one species of host, are responsible for the majority of all zoonotic, emerging or persistent human and animal diseases and are considered one of the major challenges for the biomedical sciences in the 21st century. We characterized the population structure of the multi-host parasite Schistosoma japonicum in relation to its definitive host species by genotyping miracidia collected from humans and domestic animals across five villages around the Yangtze River in Anhui Province, mainland China, using microsatellite markers. High levels of polymorphisms were observed and two main genetic clusters were identified which separated water buffalo, cattle and humans from goats, pigs, dogs and cats. We thereby believe that we present the first evidence of definitive host-based genetic variation in Schistosoma japonicum which has important epidemiological, evolutionary, medical and veterinary implications.

Animals↗
PubMed1999

Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK.

The relationships among 207 squirrels from 12 locations in the UK and three in mainland Europe were examined using mitochondrial DNA (mtDNA) control region sequence. Twenty-six haplotypes were detected, many of which were population specific. Eighty per cent of the populations analysed contained two or more haplotypes. Hierarchical analysis of molecular variance showed the majority of genetic variation to be partitioned among populations. Genetic diversity varied considerably within the UK, and conformed to no obvious geographical trend. The populations in Argyll and Spadeadam Forest showed the highest levels of variation in the UK. However, the greatest genetic diversity was seen in Bavaria, southern Germany where six unique alleles were detected in a sample of 10 individuals. Phylogenetic analysis revealed no evolutionary divergence between UK and mainland European haplotypes. We conclude that, within the UK, the genetic patterns observed are most likely to be explained by the effects of genetic drift which has occurred since the isolation of populations during the past few hundred years, hence we cannot detect any underlying phylogeographic pattern. Therefore, the use of larger, geographically distinct populations within the UK for augmentation of small isolated populations is unlikely to pose problems of genetic incompatibility. Further, the role that demographic factors may have in complicating the application of current genetically based management unit criteria is likely to need further attention.

Animals↗
PubMed1974

Genetic structure of a population occupying a circular habitat.

The geographical structure of a finite population distributed continuously and homogeneously along a circular habit is explored. Selection is supposed to be absent, and the analysis is restricted to a single locus with discrete, non-overlapping generations. Assuming every mutant is new to the population, the rate of decay of genetic variability is obtained, and the probability that two homologous genes separated by a given distance are different alleles is calculated. If moments of the migration function higher than second are neglected, the eigenvalue equation is shown to be a simple trigonometric one, and the Fourier series giving the transient and stationary probabilities of allelism are summed in terms of elementary functions. The proportion of homozygotes, the effective number of alleles maintained in the population, and the amount of local differentiation of gene frequencies are discussed.

Animals↗
PubMed1997

The genetic structure of Escherichia coli populations in feral house mice.

Escherichia coli was isolated from feral house mice (Mus domesticus) during the course of a mouse plague in the state of Victoria, Australia. Two farms were sampled over a period of 7 months and a total of 447 isolates were collected. The isolates were characterized using the techniques of randomly amplified polymorphic DNA and multi-locus enzyme electrophoresis. The mean genetic diversity of this E. coli population (H = 0.24) was found to be substantially lower than the diversity of an E. col population reported elsewhere for a single human host. Analysis of the allozyme data revealed that there were significant differences in the relative abundance of genotypes between the two localities sampled and among sample dates. Overall, however, spatial and temporal effects accounted for less than 5% of the genotypic diversity. Allele frequencies and the relative abundance of the more common genotypes did not differ between male and female hosts. The number of genotypes and genotype diversity increased as the age of the host increased, suggesting that the mice are continuing to acquire new E. coli clones throughout their life. The frequency of some alleles changed with respect to host age, which indicates that clone acquisition may not be a random process. It is argued that the low level of genetic diversity observed in this population of E. coli reflects the boom and bust nature of mouse population density in this region of Australia.

Alleles↗