High Genetic Homogeneity Research Articles

Reproductive ecology of the endangered Alpine species Eryngium alpinum L. (Apiaceae): phenology, gene dispersal and reproductive success.

Eryngium alpinum (Apiaceae) is an endangered perennial, characteristic of the Alpine flora. Because the breeding system influences both demographic (reproductive success) and genetic (inbreeding depression, evolutionary potential) parameters that are crucial for population maintenance, the reproductive ecology of E. alpinum was investigated. Specifically, the aims of the study were (1) to determine the factors (resources and/or pollen) limiting plant fitness; and (2) to assess the potential for gene flow within a plant, within a patch of plants, and across a whole valley where the species is abundant. Field experiments were performed at two sites in the Fournel valley, France, over three consecutive years. Studies included a phenological survey, observations of pollinators (visitation rates and flight distances), dispersal of a fluorescent powder used as a pollen analogue, the use of seed traps, determination of the pollen/ovule ratio, and an experiment to test whether seed production is limited by pollen and/or by resources. E. alpinum is pollinated by generalist pollinators, visitation rates are very high and seed set is resource- rather than pollen-limited. The short flights of honeybees indicate a high potential for geitonogamy, and low pollen and seed dispersals suggest strong genetic structure over short distances. These results are interpreted in the light of previous molecular markers studies, which, in contrast, showed complete outcrossing and high genetic homogeneity. S. The study highlights the usefulness of adopting several complementary approaches to understanding the dynamic processes at work in natural populations, and the conservation implications for E. alpinum are emphasized. Although the studied populations do not seem threatened in the near future, long-term monitoring appears necessary to assess the impact of habitat fragmentation. Moreover, this study provides useful baseline data for future investigations in smaller and more isolated populations.

High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast of the Americas

Phallusia nigra is a cosmopolitan solitary ascidian with a distinct niger-blue tunic that is considered to be an easy diagnostic feature, even in the field. The wide geographic distribution of this species may have been a result of the overconfidence of taxonomists and ecologists in the assignment of unknown specimens to this species, based on this simple diagnostic character. Indeed, there seems to be a correlation between cosmopolitanism and the presence of few, but very conspicuous diagnostic characters in benthic invertebrate species. Almost invariably, genetic studies have demonstrated that the cosmopolitanism of those species is artificial and that, rather, they are made up of groups of morphologically very similar, but genetically distinct, species. Thus, we decided to verify the specific status of Western Atlantic populations of P. nigra, from Miami (USA) to São Paulo (southeastern Brazil) by estimating genetic variation and population structure levels along the entire range of this ascidian in the Western Atlantic. The analysis of 10 allozyme systems shows high levels of mean heterozygosity ( H=0.28) so that P. nigra has genetic variation levels more related with other invertebrates than to their, phylogenetically closer, chordate relatives (that show lower levels of heterozygosity). The genetic structure of the population was relatively high ( F ST=0.083) for conspecific populations, but much lower than what would be expected if they belonged to different species. High levels of gene identity also indicate that the Western Atlantic population of P. nigra constitutes a single species. This result suggests an extremely high dispersal capability of the larvae of this ascidian or a relatively recent range expansion of its populations. Since this species is commonly found in harbors, the anthropogenic transport (p.e., in ballast water) may have contributed for the observed genetic homogeneity.

Genetic characterization of Erwinia amylovora strains by amplified fragment length polymorphism.

Erwinia amylovora is one of the most important pathogens of pear and apple and is subject to strict quarantine regulations worldwide, although its patterns of dispersal are largely unknown. Previous attempts to fingerprint E. amylovora strains by molecular techniques have detected very little polymorphism because of the high genetic homogeneity of this bacterium. Our aim was to establish and test a typing method to quantify genetic diversity among strains of this plant pathogen. Twenty-two strains from different hosts and geographical locations were examined by PCR fingerprinting with four primers and by amplified fragment length polymorphism (AFLP) with four selected combinations of primers with a single base extension. PCR fingerprinting revealed little polymorphism producing the same amplification patterns for 17 strains, while the combined AFLP patterns yielded 78 polymorphic bands (34% of total bands) and allowed the differentiation of all but two strains. Clustering of strains in the resulting dendrogram was not correlated with host, year or country of isolation, and questions previous genealogies based on PFGE patterns. The AFLP technique allowed the detection of an unprecedented number of genetic markers in E. amylovora and proved to be the most useful tool so far for discriminating among strains of this pathogen. The results obtained in this study strongly suggest the occurrence of multiple introductions of the pathogen in Spain and other European countries. A major limitation in understanding the ecology of fire blight is the lack of typing techniques with a high power of discrimination. This study demonstrates the high resolution and the usefulness of the AFLP technique to differentiate among E. amylovora strains.

Behavioural differences between Aphidius ervi populations from two tritrophic systems are due to phenotypic plasticity

AbstractThe Palaeoarctic parasitoid Aphidius ervi Haliday (Hymenoptera, Aphidiidae) parasitises legume aphids in its region of origin. In Chile, it parasitises both legume and cereal aphids. This special situation was studied at two levels: (i) the host searching behaviour of A. ervi from two different tritrophic systems (Acyrthosiphon pisum on alfalfa and Sitobion avenae on wheat) was investigated in dual choice tests in a wind tunnel between odours from both A. pisum‐alfalfa host plant complex (HPC) and S. avenae‐wheat HPC, and (ii) the genetic structure of A. ervi populations from both sources using molecular markers. Responses of A. ervi females to volatile olfactory cues emanating from A. pisum‐alfalfa HPC and S. avenae‐wheat HPC were significantly higher towards the HPC on which they were reared during the last generation before experimentation, regardless of the origin of the parasitoid. As previously described for this parasitoid species, oviposition experience was also of major relevance in the preferences of female parasitoids. On the other hand, variation in mitochondrial DNA segments and RAPD‐PCR polymorphism using total DNA showed the absence of host‐based population structure and a high genetic homogeneity between these A. ervi populations. These results reject the possible existence of different host‐strains of this parasitoid in Chile.

RAPD Analysis of Maize Somaclones

The genetic difference between maize line A188 and A188-derived somaclones was assessed via analysis of randomly amplified polymorphic DNA (RAPD). In total, 17 decanucleotide primers used each allowed amplification of 2–17 fragments ranging 200–2000 bp. The RAPD patterns did not differ between individual plants of line A188, which demonstrated again its high genetic homogeneity. The difference between the initial line and the somaclones was high, ranging 64–74%. On evidence of the genetic divergence, the somaclones formed two clusters. The distribution of somaclones between these clusters was consistent with their origin.

Salinity tolerance of Darwinula stevensoni (Crustacea, Ostracoda)

Relatively few laboratory tests of the effect of salinity on ostracod species exist. Here we report the results of acute and chronic bioassay tests to study the effects of six different salinities (deionised water, 22, 120, 922, 9600 μS‐cm‐1, and marine water) on survival and reproductive parameters (number of eggs and hatching). The test was carried out on individuals of Darwinula stevensoni from different localities characterised by different salinity (from 111 μS‐cm‐1 at Monate, Italy, to 3440 μS‐cm‐1 at Hollandersgatkreek, Belgium). Individuals belonging to three life cycle stages were used (pre‐adult, adult, ovigerous). Surprisingly low mortality was observed in all treatments and for all life stages, independently of population of provenance. Only in marine water was mortality noticeable although reproductive parameters were hardly affected. Given the high genetic homogeneity of the species, our results seem to support the hypothesis of high phenotypic plasticity for salinity tolerance in D. stevensoni.

Dispersal Pattern of Black-Billed Magpies (Pica Hudsonia) Measured by Molecular Genetic (Rapd) Analysis

AbstractBlack-billed Magpies (Pica hudsonia) are a relatively sedentary corvid, with greater dispersal of females than males. To genetically confirm that dispersal pattern, 29 reproductively active adults were captured over two years and were scored for primer-specific random amplified polymorphic DNA (RAPD) bands (53 polymorphic bands in 1996 and 104 in 1997). In both years, we captured more previously banded males than females, and individuals recaptured were more often the heaviest nestling in their brood from the previous years. Genetic distances between all possible adult pairs were calculated and degree of genetic similarity between pair-wise comparisons was assessed using the Mantel test. In the pair-wise comparison of genetic distances, data for both years showed that genetic distances between males were significantly less (P < 0.05) than those for other adult combinations (male–female and female–female). Using the same analytical approach, we found that females were no more genetically similar to one another (P > 0.05) than were random pairs of adults. Group-distance analysis using the computer package RAPD also showed higher genetic similarity among males than among females. We suggest that a plausible hypothesis to account for the relatively high genetic homogeneity of the breeding male population compared to the female population is that a long-lasting intraclutch dominance hierarchy exists among siblings. That hierarchy is sufficiently long-lasting to influence the breeding population, resulting in alpha males remaining in the natal area, whereas lower ranking birds, including females, are forced to disperse.

Is the Guadeloupean racoon (Procyon minor) really an endemic species? New insights from molecular and chromosomal analyses

The Guadeloupean racoon has been chosen as the emblematic species of the Parc National de Guadeloupe because of its supposed endemic specificity. However, its taxonomic position is not clearly defined. At what period did this animal colonize Guadeloupe and how it reached the island remain unsolved questions. To clarify these points, insular and continental individuals (Procyon lotor), coming from five localities and belonging to three subspecies, were compared using molecular (sequencing of a 294-bp of the left domain of the mtDNA control region) and chromosomal (C, G and R karyotypes) analyses. Genetic distance between the Guadeloupean racoon and lotor subspecies from Virginia and Maryland was very short (mean sequence divergence between haplotypes equals to 1.46%). A four times higher distance was found between P. l. lotor and P. l. pallidus, a continental subspecies inhabiting Arizona than between P. l. lotor and Procyon minor. A neighbour-joining phenogram is proposed; the Guadeloupean haplotype is on a branch close to the one clustering P. l. lotor from the East coast whereas the haplotype from Arizona diverged earlier. These results strongly suggest that the Guadeloupean racoon is included in the P. lotor species. Moreover, no differences were found between P. lotor and P. minor karyotypes, again suggesting a high genetic homogeneity between the two taxa. Furthermore, comparison of the control region variability within Procyon with intra- and interspecific variability observed in other Carnivores, clearly strengthens the hypothesis that P. minor is conspecific with P. lotor. These results imply that the taxonomic status of the Guadeloupean racoon should be revised. In a biogeographic perspective, it is suggested that the racoon has been recently introduced in Guadeloupe by man with individuals coming from the east coast of the USA. The consequences of these results for conservation of the racoon in Guadeloupe, and more generally, the definition and the use of the subspecies as a unit of conservation are discussed.

Gynogenic lines of onion (Allium cepa L.): evidence of their homozygosity

Haploid induction via gynogenesis offers the possibility of using doubled haploid (DH) inbred lines in onion breeding. A first DH line that originated from the open-pollinated (OP) cultivar 'Dorata di Parma' was obtained after overcoming difficulties associated with the haploidy of the regenerants. Spontaneous chromosome doubling occurs seldom in onion. The first DH line obtained was cloned and selfed to produce sufficient seeds for genetic studies. The homozygosity of the DH gynogenic line was revealed on the basis of the low standard deviations of the bulb traits polar diameter, shape index and weight with respect to those of the S1 line or the OP cultivar. In the DH line, moreover, segregation of RAPD and alpha esterase markers was not noted. Out of four primers revealing polymorphism at 16 ge-netic loci in the OP cultivar 'Dorata di Parma', none produced polymorphism in the DH gynogenic line. The Est-1 locus, homozygous in 22 plants (Est-1 (1/1) in 3 and Est-1 (2/2) in 19) and heterozygous (Est-1 (1/2)) in 11 plants of the OP cultivar, always carried the same alleles in the DH line. We also tested genetic stability during micropropagation of a second halpoid line obtained via gynogenesis from var. 'Senshyu Yellow'. Seventeen plants of this line were tested to detect changes occurring during the tissue culture process. Again no polymorphism was observed. The high genetic homogeneity observed in the two gynogenic lines of onion could be related to the absence of the callus phase during the gynogenic process.

Genetic variation and differentiation in the lizard, Podarcis wagleriana (Reptilia: Lacertidae)

Abstract The electrophoretic variation at 26 presumptive gene loci was investigated in populations of Podarcis wagleriana from Sicily, the Aegadian Islands, and the Aeolian Islands. For interspecific comparison, samples of the closely related lizard P. sicula from the same geographic area were also used. Population heterogeneity analyses carried out by the estimation of F -statistics and Nei's standard genetic distance, showed a high genetic homogeneity within P. sicula , but a noticeable genetic differentiation within P. wagleriana . In the latter species, Nei's D ranged from 0 to 0.212, and this is because the Aeolian populations were quite distinct from those inhabiting Sicily and the Aegadian Islands. Fixed differences identified at three loci ( Ck, Ada, Gp-4 ) contributed to a relatively high value of Nei's standard genetic distance between the two population groups ( D = 0.147). This value is very similar to those found comparing pairs of well-recognized biological species included in the genera Podarcis and Lacerta . Estimation of the time of evolutionary divergence shows that the Aeolian and Sicilian populations of P. wagleriana have been isolated geographically for a long time (0.7 Myr according to Nei's formula; 2 Myr according to Sarich's calibration), indicating evolutionary divergence at the species level. Based on genetic and biogeographic data, it is suggested the recognition of full specific status for the Aeolian populations, for which the name P. raffonei comb. nova (Aeolian wall lizard) is proposed. Electrophoretic data and comparative species distributions suggest that (1) Podarcis sicula recently colonized the Aeolian Islands, and (2) it has competed successfully with P. raffonei in this area, greatly reducing the range of the latter and causing the extinction of most of its populations. In fact, P. sicula is widespread in the Aeolian Archipelago, while P. raffonei is confined at present to one large island (Vulcano) and three tiny islands (Strombolicchio, Scoglio Faraglione, La Canna). This can be considered a classic example of competitive exclusion of a native form ( P. raffonei ) by a species accidentally introduced by man ( P. sicula ).

Genetic variation and differentiation in the lizard, Podarcis wagleriana (Reptilia: Lacertidae)

The electrophoretic variation at 26 presumptive gene loci was investigated in populations of Podarcis wagleriana from Sicily, the Aegadian Islands, and the Aeolian Islands. For interspecific comparison, samples of the closely related lizard P. sicula from the same geographic area were also used. Population heterogeneity analyses carried out by the estimation of F -statistics and Nei's standard genetic distance, showed a high genetic homogeneity within P. sicula, but a noticeable genetic differentiation within P. wagleriana. In the latter species, Nei's D ranged from 0 to 0.212, and this is because the Aeolian populations were quite distinct from those inhabiting Sicily and the Aegadian Islands. Fixed differences identified at three loci (Ck, Ada, Gp-4) contributed to a relatively high value of Nei's standard genetic distance between the two population groups (D = 0.147). This value is very similar to those found comparing pairs of well-recognized biological species included in the genera Podarcis and Lacerta. Estimation of the time of evolutionary divergence shows that the Aeolian and Sicilian populations of P. wagleriana have been isolated geographically for a long time (0.7 Myr according to Nei's formula; 2 Myr according to Sarich's calibration), indicating evolutionary divergence at the species level. Based on genetic and biogeographic data, it is suggested the recognition of full specific status for the Aeolian populations, for which the name P. raffonei comb. nova (Aeolian wall lizard) is proposed. Electrophoretic data and comparative species distributions suggest that (1) Podarcis sicula recently colonized the Aeolian Islands, and (2) it has competed successfully with P. raffonei in this area, greatly reducing the range of the latter and causing the extinction of most of its populations. In fact, P. sicula is widespread in the Aeolian Archipelago, while P. raffonei is confined at present to one large island (Vulcano) and three tiny islands (Strombolicchio, Scoglio Faraglione, La Canna). This can be considered a classic example of competitive exclusion of a native form (P. raffonei) by a species accidentally introduced by man (P. sicula).

Diversification of HIV-1 strains after infection from a unique source.

In 1990, 7 hemophilia B patients were infected with human immunodeficiency virus type 1 (HIV-1) after exposure to a single common lot of clotting factor. The hypervariable regions V1 and V2 of the proviral env gene from the patients shared a homology between 97.5% and 100% at the time of seroconversion. To determine the in vivo diversification of these epidemiologically closely related virus strains, the patients were followed up in the early phase of HIV infection. Direct sequencing of the V1/V2 region in the env gene still revealed a very high degree of homology (96.5%-100%). In the case of the patient who showed the highest decrease of CD4+ cells, moderate genetic diversification of the virus was associated with a biological differentiation. The strain originally presenting two expressed substitutions displayed three more deviations 9 months after the first investigation (including one reversion to the consensus sequence). In addition, the virus that originally could not be cultivated could now be isolated as a low cytopathogenic agent. This study provides evidence that the high genetic homogeneity of HIV-1 observed at the time of seroconversion is maintained as a predominant consensus sequence in the following so-called latent phase of infection.

Direct determination of the point mutation rate of a murine retrovirus.

The point mutation rate of a murine leukemia virus (MuLV) genome (AKV) was determined under conditions in which the number of replicative cycles was carefully controlled and the point mutation rate was determined by direct examination of the RNA genomes of progeny viruses. A clonal cell line infected at a low multiplicity of infection (2 x 10(-3)) was derived to provide a source of virus with high genetic homogeneity. Virus stocks from this cell line were used to infect cells at a low multiplicity of infection, and the cells were seeded soon after infection to obtain secondary clonal cell lines. RNase T1-oligonucleotide fingerprinting analyses of virion RNAs from 93 secondary lines revealed only 3 base changes in nearly 130,000 bases analyzed. To obtain an independent assessment of the mutation rate, we directly sequenced virion RNAs by using a series of DNA oligonucleotide primers distributed across the genome. RNA sequencing detected no mutations in over 21,000 bases analyzed. The combined fingerprinting and sequencing analyses yielded a mutation rate for infectious progeny viruses of one base change per 50,000 (2 x 10(-5)) bases per replication cycle. Our results suggest that over 80% of infectious progeny MuLVs may be replicated with complete fidelity and that only a low percentage undergo more than one point mutation during a replication cycle. Previous estimates of retroviral mutation rates suggest that the majority of infectious progeny viruses have undergone one or more point mutations. Recent studies of the mutation rates of marker genes in spleen necrosis virus-based vectors estimate a base substitution rate lower than estimates for infectious avian retroviruses and nearly identical to our determinations with AKV. The differences between mutation rates observed in studies of retroviruses may reflect the imposition of different selective conditions.

Distribution of the necrosis and chlorosis genes in two wild tetraploid wheats, Triticum dicoccoides and T. araraticum.

Distributions of the Ne1 and Ne2 alleles for type 1 hybrid necrosis, and Ch1 allele for type 1 hybrid chlorosis in two wild tetraploid wheats, Triticum dicoccoides (wild emmer wheat) and T. araraticum (wild timopheevi wheat), have been investigated by crossing the collections of these species from their entire distribution areas with their appropriate testers. The frequencies of the Ne1 and Ch1 alleles were 53% and 13%, respectively, in T. dicoccoides; whereas they were 69% and 0% in T. araraticum. The Ne2 allele was not found in both species. The Ne1 allele of T. dicoccoides was mainly Ne1m, while that of T. araraticum was mainly Ne1w. The frequency of the Ch1 allele differed significantly between the two species. These facts indicate that the emmer and timopheevi groups of tetraploid wheat had been differentiated genetically before their domestication. On the frequencies of the Ne1 and Ch1 alleles, Israeli T. dicoccoides revealed high genetic homogeneity within local populations. While there was extreme variability among these populations, they showed no geographical inclination of their frequencies. These alleles are assumed to be neutral for selection and have been randomly fixed in most populations. A limited numbers of Sitopsis accessions of the genus Aegilops were tested for the two alleles, Ne1 and Ne2. None of them carried these alleles. Thus, the origin of the Ne1 alleles found in tetraploid wheats could not be traced back to any Sitopsis species.

DNA methylation in leprosy-associated bacteria: Mycobacterium leprae and Corynebacterium tuberculostearicum

The DNAs of two kinds of microorganisms from human leprosy lesion, Mycobacterium leprae and Corynebacterium tuberculostearicum (also known as "leprosy-derived corynebacterium" or LDC), have been analysed and compared with the genomes of reference bacteria of the CMN group (genera Corynebacterium, Mycobacterium and Nocardia). The guanine-plus-cytosine content (% GC) of DNA was determined by a double-labelling procedure, which is unaffected by the presence of modified and unusual bases (that alter both buoyant density and mid-melting-point determinations). Accordingly, the DNAs of seven LDC strains had GC values of 54-56 mol %, and that of armadillo-grown M. leprae a value of 54.8 +/- 0.9 mol %. Restriction patterns disclosed no methylated cytosine in the DNA sequences CCGG, GGCC, AGCT and GATC of either LDC or M. leprae DNA. N6-methyl adenine was present in the sequence GATC of all LDC strains, but was missing from the genomes of all others CMN organisms analysed, including M. leprae. By HPLC analysis of LDC-DNA hydrolysates, it was found that N6-methyladenine amounted to 1.8% of total DNA adenine, and was present exclusively within GATC sequences, which appeared all to be methylated. It is concluded that LDC represent a group of corynebacteria endowed with high genetic homogeneity and a unique restriction pattern, whereby their genome is easily distinguished from that of M. leprae, which has a similar base composition.

The genetic structure of Iceland.

Gene frequencies and parent-offspring migration data from nine geographic subdivisions in Iceland are analyzed. Estimated values of FST show high genetic homogeneity. Genetic maps are studied and the results are interpreted in the light of social and historical patterns. Actual road distances between subdivisions provide a slightly better indication of geographic isolation by distance than do straight-line distances. A high correlation between genetic structure predicted by migration data and the structure estimated from gene frequencies is obtained.

Etude d'un groupe nouveau d'Enterobacteriaceae (groupe H1) apparenté à l'espèce Enterobacter cloacae

A DNA-DNA hybridization study was carried out on a new group of enterobacteria (group H1) previously studied by numerical taxonomy work on the genus Enterobacter. This group showed a very high genetic homogeneity since the average relative binding ratio of nine analysed strains is equal to 91%. The taxonomic position of this group into the family of enterobacteria is discussed with the species E. cloacae (37 to 61%), K. pneumoniae (44 to 60%), K. oxytoca (57-58%), L. malonatica (syn. Citrobacter intermedius, a:46 to 54%), L. amalonatica (syn. C. intermedius, b: 51%), and the group H3 (52-61%). The group H1 is defined on phenotypic and genetic data.