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Genetic variation and population genetic structure in Trifolium pratense.

Trifolium pratense (red clover) is a short-lived herbaceous plant native to southeastern Europe and Asia Minor. Widel used in agriculture, T. pratense is cultivated as an annual, winter annual, or biennial. It blooms from mid-spring to early fall and is insect pollinated and self-incompatible. Seeds are mammal and bird dispersed. Naturalized populations of T. pratense occur along roadsides and in old fields as well as native grasslands. Allozyme diversity and population genetic structure were determined for nine populations of T. pratense. Results from 13 allozyme loci indicate that genetic diversity is higher and population divergence is lower than expected based on the life-history characteristics of the species. We conclude that the high levels of genetic diversity found within populations of T. pratense suggest that these are not newly established founder populations, and that the low levels of genetic divergence seen among populations are probably due to high rates of gene flow among populations as a result of seed and pollen movement.

Chi-Square Distribution↗
PubMed1997

Antigenic and genetic structure of Borrelia burgdorferi.

Lyme borreliosis is a disease caused by the spirochaetes Borrelia burgdorferi, Borrelia afzelii and Borrelia garinii and it is transmitted by ticks. Most of the proteins (outer surface proteins, flagellar proteins and other uncertain location proteins) have a strong antigenic variability. Osp A protein genetic and serological studies facilitated the differentiation of seven serotypes strongly correlated with the known genospecies. The genetic structure of these spirochaetes included a large linear chromosome, several linear microchromosomes as well as a number of circular plasmids.

Antigenic Variation↗
PubMed1982

Genetic structure and transforming sequence of avian sarcoma virus UR2.

We have recently shown that a newly isolated avian sarcoma virus, UR2, is defective in replication and contains no sequences homologous to the src gene of Rous sarcoma virus. In this study, we analyzed the genetic structure and transforming sequence of UR2 by oligonucleotide fingerprinting. The sizes of the genomic RNAs of UR2 and its associated helper virus, UR2AV, were determined to be 24S and 35S, respectively, by sucrose gradient sedimentation. The molecular weight of the 24S UR2 genomic RNA was estimated to be 1.1 x 10(6), corresponding to 3,300 nucleotides, by gel electrophoresis under the native and denatured conditions. RNase T1 oligonucleotide mapping indicated that UR2 RNA contains seven unique oligonucleotides in the middle of the genome and shares eight 5'- and six 3'-terminal oligonucleotides with UR2AV RNA. From these data, we estimated that UR2 RNA contains a unique sequence of about 12 kilobases in the middle of the genome, and contains 1.4 and 0.7 kilobases of sequences shared with UR2AV RNA at the 5' and 3' ends, respectively. Partial sequence analysis of the UR2-specific oligonucleotides by RNase A digestion revealed that there are no homologous counterparts to these oligonucleotides in the RNAs of other avian sarcoma and acute leukemia viruses studied to date. UR2-transformed non-virus-producing cells contain a single 24S viral RNA which is most likely the message coding for the transforming protein of UR2. On the basis of the uniqueness of the transforming sequence, we concluded that UR2 is a new member of the defective avian sarcoma viruses.

Alpharetrovirus↗
PubMed2004

The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor.

In most heterothallic mushroom species, inbreeding is avoided by an incompatibility system determined by two loci each with multiple alleles (the A and B mating-type loci). In this study we investigated the genetic structure of the mating-type loci in the tropical oyster mushroom Pleurotus djamor using both positional cloning and degenerate PCR methods. DNA sequences from genomic regions cosegregating with the mating-type loci of P. djamor revealed homeodomain transcription factors (A) and pheromone receptors (B), suggesting the genetic basis for mating-type determination in P. djamor is the same as in the model mushroom species. Three pheromone receptors were detected in a single homokaryotic isolate of P. djamor. Only one pair of homeodomain genes was detected in the A mating-type region. It is hypothesized that the A mating-type locus of P. djamor is comprised of only one homeodomain pair, which may explain the lower number of A mating-type alleles relative to other mushroom species.

Amino Acid Sequence↗
PubMed2003

Population genetic structure of the malaria vector Anopheles minimus A in Vietnam.

Anopheles minimus A, a major malaria vector in Southeast Asia, is the main target of vector control in this area. The impact of these control measures can be influenced by the population structure of the target species. In rural areas, An. minimus breeds along the banks of small clear-water streams, yet in the suburbs of Hanoi, northern Vietnam, there is an An. minimus population whose immature stages develop in water tanks. This study uses allozyme data (1) to assess the population structure of An. minimus A and (2) to evaluate the taxonomic status of the urban An. minimus population from Hanoi. The population from the suburbs of Hanoi was identified as An. minimus A. Although significant genetic differentiation was observed between rural and urban An. minimus A populations, they have not differentiated substantially by genetic drift. Limited macrogeographical differentiation was observed between two rural populations at distances of more than 1000 km. Consequently, geographical distance is not the primary factor in differentiating An. minimus A populations having the typical breeding ecology. The estimated effective population size is consistent with the moderate macrogeographical differentiation. Furthermore, no genetic structuring was observed between adult mosquitoes having different behaviour. The macrogeographical population structure indicates that genes may spread over large areas, whereas the presence of an 'urban' An. minimus A population shows the ability of this species to adapt to anthropogenic environmental changes.

Animals↗
PubMed2004

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA.

Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.

Africa↗
PubMed2026

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics↗
PubMed2000

Clonal and spatial genetic structure in Eurya emarginata (Theaceae).

Eurya emarginata (Thunb.) Makino (Theaceae) is a dioecious, insect-pollinated tree, which combines sexual reproduction and clonal spread. It is narrowly distributed in coastal areas from southern China, along southern Korea, and extending to central and southern Japan. We used allozyme loci and spatial autocorrelation statistics to examine the clonal structure and the spatial distribution of allozyme polymorphisms of sexually reproduced individuals in a study population (70 m x 120 m area) in Korea. The population maintains moderate levels of allozyme variability (mean He=0.133), and multilocus genotypic diversity is high (mean DG=0. 992). The frequency of clones was 0.377 (90/239), and the mean clone-pair distance was very large (35.06 m +/- 1.91 m [SE]), indicating that clones can form at long distances away from their ancestors. In addition, it was found that genetic patch width was at least 24 m. However, join-count statistics for the total number of unlike joins showed that, contrary to expectation for such species, clonal reproduction does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the whole population. In contrast, limits to seed and pollen dispersal create substantial levels of genetic structure.

Alleles↗
PubMed1997

Genetic structure of populations of the threatened eastern massasauga rattlesnake, Sistrurus c. catenatus: evidence from microsatellite DNA markers.

Throughout its distribution in North America, the threatened eastern massasauga rattlesnake (Sistrurus c. catenatus) persists in a series of habitat-isolated disjunct populations of varying size. Here, we use six microsatellite DNA loci to generate information on the degree of genetic differentiation between, and the levels of inbreeding within populations to understand how evolutionary processes operate in these populations and aid the development of conservation plans for this species. Samples were collected from 199 individuals from five populations in Ontario, New York and Ohio. Our results show that all sampled populations: (i) differ significantly in allele frequencies even though some populations are < 50 km apart, and may contain genetically distinct subpopulations < 2 km apart; (ii) have an average of 23% of alleles that are population specific; and (iii) have significant FIS values (mean overall FIS = 0.194) probably due to a combination of Wahlund effects resulting from fine-scale genetic differentiation within populations and the presence of null alleles. Our results imply that massasauga populations may be genetically structured on an extremely fine scale even within continuous populations, possibly due to limited dispersal. Additional information is needed to determine if dispersal and mating behaviour within populations can account for this structure and whether the observed differentiation is due to random processes such as drift or to local adaptation. From a conservation perspective, our results imply that these massasauga populations should be managed as demographically independent units and that each has high conservation value in terms of containing unique genetic variation.

Animals↗
PubMed2006

Genetic structure of Galitzkya macrocarpa and G. potaninii, two closely related endemics of central Asian mountain ranges.

UNLABELLED: BACKGROUND AND AIMS Habitats in mountains are often isolated. Plants growing in these sites face severe dispersal limitations, but also difficulties for recruitment. The focus was laid on the magnitude of genetic differences among populations but also on the size of potentially occurring clones. METHODS: RAPD fingerprints were obtained from 23 populations in southern Mongolia. Sampling covered the entire distribution range of Galitzkya macrocarpa; samples of G. potaninii represented only the Mongolian part of its mainly northern Chinese range. KEY RESULTS: The Mongolian endemic G. macrocarpa showed moderately strong population differentiation (Phi ST = 0.251), and limited evidence for isolation by distance. Local genetic diversity was not positively correlated to habitat size, and not reduced in peripheral populations. Clonal growth is possible, but most plants originate from sexual reproduction. In contrast, populations of G. potaninii were highly differentiated (Phi ST = 0.550); and the most remote outposts had reduced genetic diversity. In these areas, isolation is expected to date back to glacial times. CONCLUSIONS: Effects of natural fragmentation differ among species. Both are rare, but G. macrocarpa appears to be able to maintain genetic diversity over its range. Clonal growth is an option in its mixed reproduction strategy and allows survival under harsh conditions. In contrast, genetic structure in G. potaninii gives reason for concern, and further studies on population dynamics are needed.

Asia, Central↗
PubMed1999

Selection of a nucleopolyhedrovirus for control of Spodoptera frugiperda (Lepidoptera: Noctuidae): structural, genetic, and biological comparison of four isolates from the Americas.

Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is the principal pest of maize in tropical and subtropical regions of the Americas. Larvae of this species are susceptible to a nucleopolyhedrovirus (NPV) which has attracted interest as a potential biocontrol agent. Four strains of NPV isolated from infected S. frugiperda larvae in the United States, Nicaragua, and Argentina were subjected to a structural, genetic, and biological comparison to select a candidate isolate for use in biocontrol experiments in Mexico and Honduras. All isolates had an occlusion body polyhedrin protein of 32 kDa, but the virions of each isolate differed subtly in the pattern and abundance of certain structural polypeptides revealed by SDS-PAGE analysis. Restriction endonuclease analysis of viral DNA confirmed that these isolates were strains of a single virus species but showed that they were not genetically homogeneous; each isolate could be differentiated from the others using common restriction enzymes. Droplet feeding bioassays indicated that an isolate from Nicaragua (Sf-NIC) and an isolate from the United States (Sf-US) had the highest infectivity when tested against 2nd instars originating from a Honduran S. frugiperda colony. No significant differences were detected in the speed of kill of Sf-NIC (102.7 h), Sf-US (102.3 h) and Sf-AR (103.4 h), whereas that of Sf-2 (97.3 h) was significantly shorter. Additional bioassays of the Sf-NIC isolate against 2nd to 6th instars demonstrated that LC50 values increased with larval stage from 2.03 x 10(5) OBs/ml for 2nd instars to 1.84 x 10(8) OBs/ml for 5th instars. The concentration required to elicit a lethal infection of 6th instars was so high that a reliable estimate of LC50 could not be obtained. The mean time to death for each stage challenged with the Sf-NIC isolate increased with instar from an average of 102.7 h in 2nd instars to 136.9 h in 5th instars.

Analysis of Variance↗
PubMed2001

River basin-related genetic structuring in an endangered fish species, Chondrostoma lusitanicum, based on mtDNA sequencing and RFLP analysis.

Chondrostoma lusitanicum is a Portuguese endemic cyprinid with a restricted distribution and reduced numbers in some basins, justifying its status as a threatened species. We examined genetic population structure using samples from throughout its geographical range in Portugal, using sequencing of b cytochrome and restriction fragment length polymorphism analysis of the NADH subunits 5 and 6. There was reduced within-population genetic variability but considerable among-population differentiation, particularly marked between both the Mira and Arade basins in the extreme south and other populations. These results confirm phylogeographic relationships suggested by previous fragmentary allozyme studies for C. lusitanicum, and are in accordance with allozyme and mitochondrial DNA data on phylogeography of coexisting cyprinid species of the genus Leuciscus. The levels of genetic divergence revealed by sequence and RFLP data showed strongly concordant patterns: geographical genetic structuring, with the definition of three distinct groups, was observed. The high values of nucleotide divergence and pairwise sequence divergence of the Mira and Arade groups, when compared with all other samples, support a distinct taxonomic status probably at the species level. Results are also discussed in relation to conservation of this highly fragmented species, in terms of Evolutionary Significant Units and Management Units.

Analysis of Variance↗
PubMed2002

Population genetic structure of two rare tree species (Colubrina oppositifolia and Alphitonia ponderosa, Rhamnaceae) from Hawaiian dry and mesic forests using random amplified polymorphic DNA markers.

Hawaiian dry and mesic forests contain an increasingly rare assemblage of species due to habitat destruction, invasive alien weeds and exotic pests. Two rare Rhamnaceae species in these ecosystems, Colubrina oppositifolia and Alphitonia ponderosa, were examined using random amplified polymorphic DNA (RAPD) markers to determine the genetic structure of the populations and the amount of variation relative to other native Hawaiian species. Relative variation is lower than with other Hawaiian species, although this is probably not a consequence of genetic bottleneck. Larger populations of both species contain the highest levels of genetic diversity and smaller populations generally the least as determined by number of polymorphic loci, estimated heterozygosity, and Shannon's index of genetic diversity. Populations on separate islands were readily discernible for both species as were two populations of C. oppositifolia on Hawai'i island (North and South Kona populations). Substructure among Kaua'i subpopulations of A. ponderosa that were ecologically separated was also evident. Although population diversity is thought to have remained at predisturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Recovery efforts must focus on control of alien species if these and other endemic dry and mesic forest species are to persist.

Colubrina↗
PubMed2006

Genetic structure of Triatoma venosa (Hemiptera: Reduviidae): molecular and morphometric evidence.

Triatoma venosa presents a restricted geographical distribution in America and is considered as a secondary vector of Chagas disease in Colombia and Ecuador. A total of 120 adult insects were collected in domestic and peridomestic habitats in an endemic area of the department of Boyacá, Colombia, in order to determine their genetic structure through morphometric and molecular techniques. The head and wings of each specimen were used for the analyses of size, shape, and sexual dimorphism. A significant sexual dimorphism was found, although no differences in size among the studied groups were detected. Differences were found in the analyzed structures except for male heads. DNA was extracted from the legs in order to carry out the internal transcriber space-2 (ITS-2) amplification and the randon amplified polymorphic DNA (RAPD) analyses. Length polymorphisms were not detected in the ITS-2. Fst and Nm values were estimated (0.047 and 3.4, respectively). The high genetic flow found among the insects captured in the domicile and peridomiciliary environment does not permit a genetic differentiation, thus establishing the peridomicile as an important place for epidemiological surveillance.

Animals↗
PubMed2005

Measuring the genetic structure of the pollen pool as the probability of paternal identity.

Contemporary pollen flow in forest plant species is measured by the probability of paternal identity (PPI) for two randomly sampled offspring, drawn from a single female, and contrasting that with PPI for two random offspring, drawn from different females. Two different estimation strategies have emerged: (a) an indirect approach, using the 'genetic structure' of the pollen received by different mothers and (b) a direct approach, based on parentage analysis. The indirect strategy is somewhat limited by the assumptions, but is widely useful. The direct approach is most appropriate where a large majority of the true fathers can be identified exactly, which is sometimes possible with high-resolution SSR markers. Using the parentage approach, we develop estimates of PPI, showing that the obvious estimates are severely biased, and providing an unbiased alternative. We then illustrate the methods with SSR data from a 36-tree isolated population of Pinus sylvestris from the Meseta region of Spain, for which categorical paternity assignment was available for over 95% of offspring. For all the females combined, we estimate that PPI=0.0425, indicating uneven male reproductive contributions. Different (but overlapping) arrays of males pollinate different females, and for the average female, PPI=0.317, indicating substantial 'pollen structure' for the population. We also relate the direct measures of PPI to those available from indirect approaches, and show that they are generally comparable.

Genetic Variation↗
PubMed2006

Identification of a megaplasmid centromere reveals genetic structural diversity within the repABC family of basic replicons.

The basic replication unit of many plasmids and second chromosomes in the alpha-proteobacteria consists of a repABC locus that encodes the trans- and cis-acting components required for both semiautonomous replication and replicon maintenance in a cell population. In terms of physical genetic organization and at the nucleotide sequence level, repABC loci are well conserved across various genera. As with all repABC-type replicons that have been genetically characterized, the 1.4 Mb pSymA and 1.7 Mb pSymB megaplasmids from the plant endosymbiont Sinorhizobium meliloti encode strong incompatibility (inc) determinants. We have identified a novel inc sequence upstream of the repA2 gene in pSymA that is not present on pSymB and not reported in other repABC plasmids that have been characterized. This region, in concert with the repA and repB genes, stabilizes a test plasmid indicating that it constitutes a partitioning (par) system for the megaplasmid. Purified RepB binds to this sequence and binding may be enhanced by RepA. We have isolated 19 point mutations that eliminate incompatibility, reduce RepB binding or the stabilization phenotype associated with this sequence and all of these map to a 16-nucleotide palindromic sequence centred 330 bp upstream of the repA2 gene. An additional five near-perfect repeats of this palindrome are located further upstream of the repA2 gene and we show that they share some conservation with known RepB binding sites in different locations on other repABC plasmids and to two sequences found on the tumour inducing plasmid of Agrobacterium tumefaciens. These additional palindromes also bind RepB but one of them does not display obvious incompatibility effects. A heterogenic distribution of par sequences demonstrates unexpected diversity in the structural genetic organization of repABC loci, despite their obvious levels of similarity.

Bacterial Proteins↗