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PubMed2003

Normal linear models with genetically structured residual variance heterogeneity: a case study.

Normal mixed models with different levels of heterogeneity in the residual variance are fitted to pig litter size data. Exploratory analysis and model assessment is based on examination of various posterior predictive distributions. Comparisons based on Bayes factors and related criteria favour models with a genetically structured residual variance heterogeneity. There is, moreover, strong evidence of a negative correlation between the additive genetic values affecting litter size and those affecting residual variance. The models are also compared according to the purposes for which they might be used, such as prediction of 'future' data, inference about response to selection and ranking candidates for selection. A brief discussion is given of some implications for selection of the genetically structured residual variance model.

Analysis of Variance↗
PubMed2001

Genetic structure of the saxicole Pitcairnia geyskesii (Bromeliaceae) on inselbergs in French Guiana.

South American inselbergs constitute singular and fragmented habitats in the tropical rain forest. Pitcairnia geyskesii is restricted to these habitats and exhibits both sexual and asexual reproduction. The genetic structure of populations on three inselbergs in French Guiana is examined by analysis of ten isozyme loci. All analyzed populations show high levels of genetic variation. On average, 63.3% of loci per population were polymorphic, with a mean number of 2.21 alleles per polymorphic locus, and mean observed and expected heterozygosities of 0.185 and 0.183, respectively. The analyses of genetic variability displayed at different levels (inselbergs, subpopulations, and mats) give different but complementary information. A significant multilocus disequilibrium was detected in one subpopulation, whereas none was observed within the whole populations sampled on the three inselbergs. Tests on spatial genetic structure indicate a patchy distribution of genotypes on two inselbergs. The data give some insights on the reproductive behavior of P. geyskesii. (1) Efficient sexual reproduction leads to seed recruitment at the level of the inselberg. (2) Both clonality and seed recruitment occur within mats. (3) Vegetative spread by fragmentation is involved in the establishment of new mats. There is substantial differentiation (F(ST) = 0.322) and low gene flow among inselbergs (Nm = 0.234). High genetic diversity within inselbergs appears as a consequence of the association of genet longevity induced by clonal replication and recruitment of new genets produced by sexual reproduction.

Journal Article↗
PubMed1998

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers.

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift-based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele-sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breeds assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.

Alleles↗
PubMed1998

Genetic structure of local populations of Lutzomyia longipalpis (Diptera: Psychodidae) in central Colombia.

Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of American visceral leishmaniasis in the New World tropics, has a broad but discontinuous geographical distribution from southern Mexico to Argentina. A baseline for population genetic structure and genetic variability for this species was obtained by analyzing 5 local, peridomestic populations at the approximate center of its distribution, the Magdalena River Valley of central Colombia. Three populations of L. longipalpis from El Callejón, a small rural community, were compared with 2 populations from neighboring areas 12 and 25 km distant for genetic variation at 15 isoenzyme loci. The mean heterozygosity ranged from 11 to 16%, with 1.2 to 2.3 alleles detected per locus. Nei's genetic distances among the populations were very low, ranging from 0.001 to 0.007. Gene flow estimates based on FST indicated high levels of gene flow among local L. longipalpis populations, with minimal population substructuring.

Alleles↗
PubMed2005

Hierarchical analysis of population genetic structure in the monogynous ant Cataglyphis cursor using microsatellite and mitochondrial DNA markers.

Despite having winged queens, female dispersal in the monogynous ant Cataglyphis cursor is likely to be restricted because colonies reproduce by fission. We investigated the pattern of population genetic structure of this species using eight microsatellite markers and a mitochondrial DNA (mtDNA) sequence, in order to examine the extent of female and nuclear gene flow in two types of habitat. Sampling was carried out at a large spatial scale (16 sites from 2.5 to 120 km apart) as well as at a fine spatial scale (two 4.5-km transects, one in each habitat type). The strong spatial clustering of mtDNA observed at the fine spatial scale strongly supported a restricted effective female dispersal. In agreement, patterns of the mtDNA haplotypes observed at large and fine spatial scales suggested that new sites are colonized by nearby sites. Isolation by distance and significant nuclear genetic structure have been detected at all the spatial scales investigated. The level of local genetic differentiation for mitochondrial marker was 15 times higher than for the nuclear markers, suggesting differences in dispersal pattern between the two sexes. However, male gene flow was not sufficient to prevent significant nuclear genetic differentiation even at short distances (500 m). Isolation-by-distance patterns differed between the two habitat types, with a linear decrease of genetic similarities with distance observed only in the more continuous of the two habitats. Finally, despite these low dispersal capacities and the potential use of parthenogenesis to produce new queens, no signs of reduction of nuclear genetic diversity was detected in C. cursor populations.

Animals↗
PubMed2002

Population and colony genetic structure of the primitive termite Mastotermes darwiniensis.

The termite Mastotermes darwiniensis is the sole extant member of its family and occupies the basal position in the phylogeny of the eusocial order Isoptera. In this study, we investigated the micro- and macrogeographic genetic structure of M. darwiniensis in its native range in Australia. A total of 1591 workers were sampled from 136 infested trees in 24 locales. Each locale was separated by 2-350 km, and these locales were found within two broader geographic regions approximately 1500 km apart. The multilocus genotypes of all termites were assayed at six polymorphic microsatellite loci. The genetic data indicated that colonies typically fed on multiple trees within locales and extended over linear distances of up to 320 m. Single colonies were frequently headed by multiple reproductives. Workers were highly related (r = 0.40) and substantially inbred (f = 0.10). Thus, M. darwiniensis colonies are characterized by the input of alleles from multiple reproductives, which sometimes engage in consanguineous matings. Our analyses of population genetic structure above the level of the colony indicated that locales and regions were significantly differentiated (theta(locale) = 0.50, theta(region) = 0.37). Moreover, locales showed a pattern of genetic isolation by distance within regions. Thus, M. darwiniensis populations display restricted gene flow over moderate geographic distances. We suggest that the genetic patterns displayed by M. darwiniensis result primarily from selective pressures acting to maintain high relatedness among colonymates while allowing colonies to grow rapidly and dominate local habitats.

Animals↗
PubMed2003

Matrilineal genetic structure within and among populations of the cooperatively breeding common marmoset, Callithrix jacchus.

Common marmosets are members of the family Callitrichidae, South American primates characterized by highly social group living and cooperative breeding. In this study we analysed 1112 base pairs (bp) of the mitochondrial control region in 59 Callithrix jacchus individuals, sampled mainly from two geographically distinct field sites in N.E. Brazil. Analysis of molecular variation revealed a highly significant genetic structuring of haplotypes between social groups and between populations. Examination of matrilineal genetic structure within social groups revealed that seven of nine recorded breeding pairs were from different maternal lineages, indicating assortative mating and outbreeding. In addition to the breeders, at least six of 10 groups contained adult individuals from different matrilines, with five haplotypes present in one social group of nine animals. Groups of mixed lineages raise questions about potential reproductive conflicts of interest, and the extent of kin-selected altruism in the evolution and maintenance of cooperative breeding in this species.

Animals↗
PubMedDate not supplied

[Genetic structure of the Orlov trotter and the Russian trotter].

The genetic structures of Orlov's and Russian trotters for 16 biochemical systems have been comparatively analyzed. Polymorphism of 6 systems of these horse groups is revealed. The main genetic differentiation between Orlov's and Russian trotters is observed on the transferrin and phosphoglucomutase loci.

Animals↗
PubMed2003

Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae).

Cinnamomum insularimontanum Hayata (Lauraceae) is an insect-pollinated, broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, Wright's fixation index, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among four age-classes within a recently founded study population (60 x 100 m area) in southern Korea. There were no significant differences in expected heterozygosity among age classes. However, significant genetic differentiation among age classes was detected (P<0.0001). Fixation indices within age classes showed significant deficits of observed heterozygosity, which may be caused by partial selfing. The homogeneity of genetic structure among four age-classes may reflect similar spatial patterns of seed immigration from surrounding populations occurring year after year. Finally, the average Moran's I and coancestry estimates indicated essentially random spatial distributions of alleles for each of the four age-classes and between seedlings and 2-4 year juveniles vs adult trees. These findings are very similar to those observed in the same study area for another member of the Lauraceae, Neolitsea sericea, which has a very similar life history and ecological characteristics (ie, bird-dispersed fruits, insect pollination, and a similar age structure). Together, these results suggest that the fleshy drupes of lauraceous species represent an adaptation to aid in the independent dispersal of seed by birds, which in turn may increase the genetic diversity of founders colonizing new habitats.

Biological Evolution↗
PubMed2005

Impact of insecticide-treated bed nets implementation on the genetic structure of Anopheles arabiensis in an area of irrigated rice fields in the Sahelian region of Cameroon.

Variation at 12 microsatellite loci was investigated to assess the impact of the implementation of insecticide-treated bed nets (ITNs) on the genetic structure of Anopheles arabiensis in Simatou, a village surrounded by irrigated rice fields in the Sahelian area of Cameroon. The An. arabiensis population of Simatou was sampled twice before ITN implementation, and twice after. Effective population size estimates (N(e)) were similar across each time point, except for the period closely following ITN introduction where a nonsignificant reduction was recorded. Hence, we believe that ITN implementation resulted in a temporary bottleneck, rapidly followed by a demographic expansion. The genetic diversity of the population was not significantly affected since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. Low estimates of genetic differentiation between the populations from Simatou and Lagdo, separated by 300 km, suggested extensive gene flow among populations of An. arabiensis in the Sahelian region of Cameroon. A decrease in the susceptibility to deltamethrin was observed following ITN introduction, but no kdr mutation was detected and a metabolic resistance mechanism is probably involved. The temporary effect of ITNs on the genetic structure of An. arabiensis population suggests that, to optimize the success of any control programme of this species based on ITNs, the control area should be very large and the programme should be implemented for a long period of time.

Animals↗
PubMed2004

Population genetic structure of the sugar beet cyst nematode Heterodera schachtii: a gonochoristic and amphimictic species with highly inbred but weakly differentiated populations.

The sugar beet cyst nematode Heterodera schachtii is a soil-dwelling phytoparasitic nematode that feeds on beet roots. It is an important pest in most sugar beet growing areas, and better knowledge of its genetic variability is an important step to preserve the durability of resistant sugar beet varieties. The population genetic structure of this species in northern France was studied using five microsatellite markers. A hierarchical sampling design was used to investigate spatial structuring at the scale of the region, the field and the plant. Multilocus genotypes were obtained for single individual second-stage larvae, using only one individual per cyst in order to avoid the analysis of closely allied individuals (larvae from the same cyst share at least the same mother). A consistent trend of heterozygote deficit at all loci was observed at all spatial scales. Heterozygote deficit at the level of individual plants argues against its generation through a Wahlund effect. Inbreeding could be due to very limited active dispersal of larvae in the soil, favouring mating between siblings, such as larvae emerging from the same cyst. Such behaviour could have important consequences for the evolution of virulence in increasing the production of homozygous virulent individuals. Moreover, an analysis of molecular variance (amova) reveals that only 1.6% of the genetic variability is observed among regions, 3.7% among fields of the same region and 94.6% within fields. The very low level of genetic differentiation among fields is also indicated by low values of FST (</= 0.105) even for fields 150 km apart. We suggest that long-distance gene flows occur due to passive transport of cysts by human activities, water or wind. As such mechanisms of gene flow would involve cysts and not larvae, the strong signals of inbreeding observed at the local scale should not be disrupted. To our knowledge, this study constitutes the first investigation of the genetic structure of a phytoparasitic nematode based on neutral codominant genetic markers scored in single individuals.

Analysis of Variance↗
PubMed2003

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China.

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.

China↗
PubMedDate not supplied

Genetic structure of Asian populations of Bombus ignitus (Hymenoptera: Apidae).

The genetic structure of seven mainland and island Asian populations of Bombus ignitus was investigated using nine microsatellite markers and the sequences of part of the mitochondrial cytochrome b (cytb) gene. While microsatellite markers showed high genetic variability, no sequence variation was found in the cytb gene fragment analyzed. The number of microsatellite alleles ranged from 9 to 24. Gene diversities per locus per population ranged from 0.378 to 0.992. Analysis of molecular variance (AMOVA) and most pairwise F(ST) values showed significant genetic differentiation between mainland and island populations. Cytb sequences data and microsatellite bottleneck tests indicated that almost all populations were subjected to recent bottlenecks. Our results suggest that B. ignitus populations diverged due to recent bottlenecks and geographic isolation.

Animals↗
PubMed2004

Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales.

Plague, the disease caused by the bacterium Yersinia pestis, has greatly impacted human civilization. Y. pestis is a successful global pathogen, with active foci on all continents except Australia and Antarctica. Because the Y. pestis genome is highly monomorphic, previous attempts to characterize the population genetic structure within a single focus have been largely unsuccessful. Here we report that highly mutable marker loci allow determination of Y. pestis population genetic structure and tracking of transmission patterns at two spatial scales within a single focus. In addition, we found that in vitro mutation rates for these loci are similar to those observed in vivo, which allowed us to develop a mutation-rate-based model to examine transmission mechanisms. Our model suggests there are two primary components of plague ecology: a rapid expansion phase for population growth and dispersal followed by a slower persistence phase. This pattern seems consistent across local, regional, and even global scales.

Animals↗
PubMed2006

Fine-scale spatial genetic structure of the distylous Primula veris in fragmented habitats.

In Flanders (northern Belgium), the distylous self-incompatible perennial herb Primula veris is common, but mainly occurs in fragmented habitats. Distyly, which favours disassortative mating, is characterized in P. veris by two genetically determined floral morph types (pin or thrum). Using 18 polymorphic loci, we investigated fine-scale spatial genetic structure (SGS) and spatial distribution of the morphs within four populations from two regions that differ in degree of habitat fragmentation. We studied the contributions made by sexual reproduction and clonal propagation and compared the SGS patterns between pin and thrum morph types. Clonal growth was very restricted to a few individuals and to short distances. One population showed a non-random spatial distribution of the morphs. Pin and thrum individuals differed in SGS patterns at a small scale, suggesting intrapin biparental inbreeding, also related to high plant densities. This may be explained by partial self-compatibility of the pin morph combined with restricted seed dispersal and pollinator behaviour. There is an indication of more pronounced SGS when populations occur in highly fragmented habitats. From our findings, we may hypothesize disruption of the gene flow processes if these large populations evolve into patchworks of small remnants, but also a possible risk for long-term population survival if higher intrapin biparental inbreeding leads to inbreeding depression. Our study emphasizes the need for investigating the interactions between the heterostylous breeding system, population demographic and genetic structure for understanding population dynamics in fragmented habitats and for developing sustainable conservation strategies.

Breeding↗
PubMed1995

Genetic structure of a lotic population of Burkolderia (Pseudomonas) cepacia.

The genetic structure of a population of Burkholderia (Pseudomonas) cepacia isolated from a southeastern blackwater stream was investigated by using multilocus enzyme electrophoresis to examine the allelic variation in eight structural gene loci. Overall, 213 isolates were collected at transect points along the stream continuum, from both the sediments along the bank and the water column. Multilocus enzyme electrophoresis analysis revealed 164 distinct electrophoretic types, and the mean genetic diversity of the entire population was 0.574. Genetic diversity values did not vary spatially along the stream continuum. From a canonical discriminant analysis, Mahalonobis distances (measurements of genetic similarity between populations) revealed significant differences among the subpopulations at the sediment sampling points, suggesting bacterial adaptation to a heterogeneous (or patchy) microgeographical environment. Multilocus linkage disequilibrium analysis of the isolates revealed only limited association between alleles, suggesting frequent recombination, relative to binary fission, in this population. Furthermore, the dendrogram created from the data of this study and the allele mismatch distribution are typical of a population characterized by extensive genetic mixing. We suggest that B. cepacia be added to the growing list of bacteria that are not obligatorily clonal.

Alleles↗
PubMed2000

Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations.

A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories.

Gene Frequency↗
PubMed2004

Genetic structure adds power to detect schizophrenia susceptibility at SLIT3 in the Chinese Han population.

The Chinese Han population, the largest population in the world, has traditionally been geographically divided into two parts, the Southern Han and Northern Han. In practice, however, these commonly used ethnic labels are both insufficient and inaccurate as descriptors of inferred genetic clustering, and can lead to the observation of "spurious association" as well as the concealment of real association. In this study, we attempted to address this problem by using 14 microsatellite markers to reconstruct the population genetic structure in 768 Han Chinese samples, including 384 Southern Han and 384 Northern Han, and in samples from Chinese minorities including 48 Yao and 48 BouYei subjects. Furthermore, with a dense set of markers around the region 5q34-35, we built fine-scale haplotype networks for each population/subpopulation and tested for association to schizophrenia susceptibility. We found that more variants in SLIT3 tend to associate with schizophrenia susceptibility in the genetically structured samples, compared to geographically structured samples and samples without identified population substructure. Our results imply that identifying the hidden genetic substructure adds power when detecting association, and suggest that SLIT3 or a nearby gene is associated with schizophrenia.

Adult↗