Clonal variation in life-history traits and feeding rates in the gastropod, Potamopyrgus antipodarum: performance across a salinity gradient

1. Parthenogenetic species are often geographically more widely distributed than their sexual relatives. This success in colonizing can be explained either by dispersal of one or a few clones of wide physiological tolerance or by the distribution of many locally adapted clones.
2. Here we compare the influence of salinity on reproductive output, feeding rate, growth rate and size at birth between two genotypes of Potamopyrgus antipodarum to address the questions (i) Do these traits vary in response to changing salinity? (ii) Does the response to a salinity gradient differ between genotypes? (iii) Can the patterns of variation, in relation to salinity, contribute to explaining the geographical distribution of P. antipodarum in Europe?
3. Our results demonstrate that genetic variation among populations of P. antipodarum is reflected in differences in life-history traits and feeding rates in response to a salinity gradient. The phenotypic differences between the genotypes are consistent with the geographical distribution of P. antipodarum clones in Europe.
4. The overall response to salinity of both genotypes of P. antipodarum suggests an optimum at ≈ 5‰ S; however, both genotypes showed a broad salinity tolerance and were able to feed, grow and reproduce over the entire salinity range tested (0–15‰ S). The broad environmental tolerance of both genotypes together with their widespread geographical distribution across Europe provide evidence consistent with the general-purpose genotype hypothesis.     

Embryo production in a parthenogenetic snail (Potamopyrgus antipodarum) is negatively affected by the presence of other parthenogenetic females

Abstract. Stimuli associated with copulatory behavior are often needed to maximize reproductive output in internally fertilized sexual taxa. Although non-pseudogamous parthenogenetic females have no need for sperm, parthenogens descended from sexual ancestors may still require copulatory stimuli to reach their full reproductive potential. Retention of physiological dependence on copulation in parthenogens could facilitate the maintenance of sexual reproduction in species where sexual and parthenogenetic individuals coexist if parthenogens do not receive enough copulatory stimuli to achieve maximal daughter production. A laboratory experiment was conducted to determine whether embryo production in parthenogenetic female snails ( Potamopyrgus antipodarum ) is dependent on male presence. Rather than male presence, this experiment showed that embryo production is affected by the number of coexisting parthenogens. Specifically, parthenogens housed with fewer other parthenogens produced significantly more embryos than parthenogens housed with a greater number of other parthenogens, regardless of male presence and total population size. This result indicates that copulatory dependence is not likely to contribute to the maintenance of sex in P. antipodarum . Instead, it demonstrates that females of P. antipodarum negatively affect each other's reproduction, and suggests that females of P. antipodarum may exert a larger competitive influence than males of P. antipodarum . Moreover, this finding raises the possibility that highly parthenogenetic and consequently female-dense populations of P. antipodarum may experience decreased reproductive output when population size is large and resources are limiting.     

Genomic variation in parthenogenetic lizard Darevskia armeniaca: evidence from DNA fingerprinting data

Microsatellites, or short tandem repeats, are abundant across genomes of most organisms. It is evident that the most straightforward and conclusive way of studying mutations in microsatellite-containing loci is to use clonally transmitted genomes or DNA sequences inherited in multigeneration pedigrees. At present, little is known about the origin of genetic variation in species that lack effective genetic recombination. DNA fingerprinting in 43 families of the parthenogenetic lizard species Darevskia armeniaca (131 siblings), using (GACA)(4), (GGCA)(4), (GATA)(4), and (CAC)(5) probes, revealed mutant fingerprints in siblings that differed from their mothers in several restriction DNA fragments. In some cases, the mutant fingerprints detected in siblings were also found in population samples. The mutation rate for new restriction fragment length estimated by using multilocus probes varied from 0.8 x 10(-2) to 4.9 x 10(-2) per band/per sibling. Probably, the most variations detected as restriction fragment length polymorphism have germ-line origin, but somatic changes of (CAC)(n) fingerprints in adult lizards were also observed. These results provide new evidence of existing unstable regions in genomes of parthenogenetic vertebrate animals, which provide genetic variation in unisexual populations.     

Biodiversity of Asian rice gall midge (Orseolia oryzae Wood Mason) from five countries examined by AFLP analysis.

Amplified fragment length polymorphism (AFLP) analysis was used to assess the biodiversity of one of the most important dipteran pests of cereals, the Asian rice gall midge (Orseolia oryzae Wood Mason). Larvae and pupae were collected at 15 locations in five Asian countries and preserved in 95% ethanol for storage, shipment, and DNA extraction using cetyltrimethylammonium bromide (CTAB). Although only approximately 1 microg of DNA was extracted from a single pupa or larva, the use of several AFLP primers in various combinations meant that this amount of DNA was sufficient to allow many DNA fingerprints to be made per individual. Fingerprints were sufficiently reproducible, especially during selective amplification, to allow the genetic diversity within a field population to be characterized. Extraction of DNA from a pool of 20 insects yielded AFLP fingerprints in which variation among individuals was sacrificed in favor of detecting differences among populations. For each location, pooled DNA was amplified with three primer pairs. A total of 261 distinct AFLP bands were identified for the 45 fingerprints. Cluster analysis, performed by the unweighted pair-group method (UPGMA), separated the populations into two distinct groups. Group I included two populations from Guangdong province of southern China and one each from Laos and Imphal in northeastern India, while group II was comprised of eleven populations from elsewhere in India (Assam, Orissa, Madhya Pradesh, Andhra Pradesh, and Kerala) and from Nepal and Sri Lanka. AFLP analysis provided insight into the origins of gall midge biotypes. In 1992, the prevailing biotype in Imphal changed from Indian biotype 3 to a new biotype 3M. Our data show that biotype 3M belongs to group I and did not arise by a recent mutation from biotype 3, which belongs to group II. By contrast, Indian biotypes 2 and 4 are likely to have diverged through recent mutation and selection, as are Chinese biotypes 1 and 4. The almost simultaneous emergence of new biotypes in Kerala and Sri Lanka during 1985-1988 was most probably coincidental, because these biotypes are not closely related. AFLP fingerprints were also able to detect sexual dimorphism in the DNA of adult gall midges and to distinguish gall midge from its major parasite Platygaster oryzae.     

Genetic variation among populations of the Hessian fly Mayetiola destructor (Diptera: Cecidomyiidae) in Morocco and Syria

The RAPD-PCR technique was used to study genetic variation within and among geographical populations of the Hessian fly, Mayetiola destructor (Say), from Morocco and Syria, associated with the fly's ability to overcome resistance in three wheat cultivars containing H5, H13 and H22 resistance genes. Variation was detected both for the level of susceptibility of the cultivars and RAPD profiles of M. destructor populations. By the use of RAPD-PCR, high genetic variability was detected among individuals and populations of M. destructor within and between areas separated geographically. The DNA fingerprints of populations of M. destructor were area-specific with Nei's measures of genetic distance ranging from 0.156 (between Abda and Beni Mellal, Morocco) to 1.977 (between Marchouch, Morocco and Lattakia, Syria). Cluster analysis of the genetic distances among the populations, identified the Syrian population as an outlier. A highly significant correlation (r = 0.81) observed between the genetic and geographic distances among the populations, provided genetic support for dispersal of the fly from its presumed origin in West Asia to Morocco.     

Genetic distances and taxonomic analysis of human populations of the Volga-Ural region based on data on DNA polymorphism]

DNA polymorphism was studied in the human diallelic loci MET and D7S23 linked to the cystic fibrosis gene, diallelic locus PAH (the phenylketonuria gene), polyallelic locus ApoB, and hypervariable DNA sequences identified by means of DNA fingerprinting with phage M13 DNA as a probe. The obtained data were used to calculate genetic distances and perform taxonomic analysis of populations of the Volga-Ural region (Turkic and Finno-Ugric ethnic groups). The DNA polymorphic systems studied were demonstrated to be highly informative; their advantages and disadvantages were revealed. According to the data obtained, the genetic distances that were calculated from DNA fingerprints more adequately reflected the genetic relationships between the populations studied than the distances calculated from the allelic frequencies of four DNA loci. It was also found that, in population studies, it would suffice to analyze only the 3.5-6 kb fingerprint fragment that is most suitable for reading, rather than the entire fingerprint obtained.     

The complex biogeographic history of a widespread tropical tree species

Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P < 0.001) and allele-size mutations contributed significantly (R(ST) > F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal.     

Variation of mini- and microsatellite DNA repeats in parthenogenetic lizard Darevskia armeniaca as revealed by DNA fingerprinting analysis

Population and family samples of two morphological forms (mutant and normal with respect to dorsal color) of pathogenetic lizard Darevskia armeniaca were examined by means of DNA fingerprinting using M13 mini- and (GATA)n and (TCC)n microsatellite DNA markers. The morphological forms examined were characterized by clonally inherited, species-specific patterns of the DNA markers, which were different from the species-specific DNA fingerprints of the other parthenogenetic species of the genus Darevskia (D. dahli. D. unisexualis, and D. rostombekovi). The mean index of similarity (S) obtained for a sample of 36 individuals from three isolated populations using three types of DNA markers was 0.966. This was similar to the variability level observed in D. dahli (0.962) (P > 0.05), but higher than that in D. unisexualis (0.950) (P < 0.05) and D. rostombekovi (0.875) (P < 0.01). Inheritance of M13 minisatellite and (TCC)n microsatellite DNA markers in the F1 offspring of parthenogenetic lizards was examined. It was shown that variability and clonal diversity of the fingerprint phenotypes observed in the populations and families of D. armeniaca could be at least partly explained by RFLP mutations in microsatellite repeats.     

Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation

Nested haplotype networks for three loci in a haploid, fungal plant pathogen, Sclerotinia sclerotiorum, in two natural, Norwegian populations of the woodland buttercup, Ranunculus ficaria, were extended with DNA fingerprints to determine fine-scale population divergence. To preserve the cladistic structure in the network for both nonrecombinant and postrecombinant haplotypes in highly recombinant clades, recombinant events were not removed ('peeled off'), but instead were examined in alternative (marginal) networks. Fungi from both sampling locations share a common origin with subsequent genetic divergence, consistent with expectations for metapopulation structure. Evidence for divergence includes (i) lack of shared fingerprints between the two locations, (ii) evolution of new fingerprints, via transposition and recombination, within 2 years on a fine spatial scale within one sampling location, and (iii) increase in the size of the intergenic spacer (IGS) in both sampling locations. Sites of microsatellite repeat expansion and of an insertion were consistent with the boundaries of two recombination blocks in the IGS. Both alternative networks based on the recombination blocks were essential to finding all associations of DNA fingerprints with IGS size, sampling site, sampling year and mycelial compatibility group. Variation in the elongation factor 1alpha and calmodulin loci supported the topologies and the recurrent, ongoing polarity of change in fingerprints and IGS size inferred from the IGS.     

GENETIC VARIABILITY WITHIN A POPULATION AND BETWEEN DIPLOID/HAPLOID TISSUE OF MACROCYSTIS PYRIFERA (PHAEOPHYCEAE)1

Multi-locus DNA fingerprints using an M13 probe were obtained for eight individuals of giant kelp Macrocystis pyrifera (L.) C. Ag. collected from Monterey Bay, California. For each individual, DNA was extracted from a diploid blade and from ca. 10⁹ haploid spores that were released from four to Jive sporophylls. Viable or swimming spores from one individual were pooled and referred to as a spore group. A total of 34 bands (4–19 kb) was detected in DNA fingerprints from the eight blades and eight spore groups, with individual blade or spore groups exhibiting 7–18 bands (mean = 12.6). One band (4.5 kb) was present in all 16 samples. Eight bands were detected in 11–14 of the 16 samples. Similarity indices were calculated for all pairwise comparisons of fingerprint bands among all possible combinations of blades and spore groups. Mean similarity indices for the eight blades (0.51, SE = 0.032) and spore groups (0.56, SE = 0.031) were significantly lower than for the eight comparisons of the blade and spore groups from a single individual (0.86, SE = 0.052). The data indicate that DNA fingerprints can be used to measure genetic variation within populations of M. pyrifera because variation of DNA fingerprints associated with meiotic products (spores) of a given individual is small relative to variation observed among individuals within the population. Additionally, fingerprint variation between diploid vegetative tissue and haploid meiotic products may be a measure of genetic change due to recombination or DNA turnover mechanisms.     

Assessment of genomic variability through DNA fingerprinting within and between chicken lines divergently selected for residual food consumption

DNA fingerprints obtained by multi-locus probes have been shown to be convenient tools to assess genetic variability and genetic distances in animal populations. This method has been applied in the present study to two Rhode Island Red lines of chickens divergently selected for residual food consumption (RFC) for 16 generations (R-: low RFC; R+: high RFC). Within each line, individuals were sampled from each tail of the phenotypic distribution of RFC for males and for females. The three probes used were two minisatellite probes, R18-1 and 33-6, and the endogenous avian retroviral element probe. Altogether, 101 bands were scored. Band-sharing levels obtained from analysis of pooled DNA were extremely high within-Line (> 0.9) and still high between the lines (0.82 to 0.86). When band frequencies were compared, correlation coefficients were lower between lines than between extreme groups within lines regardless of the performance level. Although the selected lines differed widely in the selected trait RFC and a few correlated traits, it was concluded that they are probably different by only a low proportion of their genome.     

Application of DNA fingerprints for cell-line individualization.

DNA fingerprints of 46 human cell lines were derived using minisatellite probes for hypervariable genetic loci. The incidence of 121 HaeIII DNA fragments among 33 cell lines derived from unrelated individuals was used to estimate allelic and genotypic frequencies for each fragment and for composite individual DNA fingerprints. We present a quantitative estimate of the extent of genetic difference between individuals, an estimate based on the percentage of restriction fragments at which they differ. The average percent difference (APD) among pairwise combinations from the population of 33 unrelated cell lines was 76.9%, compared with the APD in band sharing among cell lines derived from the same individual (less than or equal to 1.2%). Included in this survey were nine additional cell lines previously implicated as HeLa cell derivatives, and these lines were clearly confirmed as such by DNA fingerprints (APD less than or equal to 0.6%). On the basis of fragment frequencies in the tested cell line population, a simple genetic model was developed to estimate the frequencies of each DNA fingerprint in the population. The median incidence was 2.9 X 10(-17), and the range was 2.4 X 10(-21) to 6.6 X 10(-15). This value approximates the probability that a second cell line selected at random from unrelated individuals will match a given DNA fingerprint. Related calculations address the chance that any two DNA fingerprints would be identical among a large group of cell lines. This estimate is still very slight; for example, the chance of two or more common DNA fingerprints among 1 million distinct individuals is less than .001. The procedure provides a straightforward, easily interpreted, and statistically robust method for identification and individualization of human cells.     

Genetic variation in parthenogenetic Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca, L. unisexualis) analyzed by DNA fingerprinting

Multilocus DNA fingerprinting has been used to study the variability of some mini- and microsatellite sequences in parthenogenetic species of Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca and L. unisexualis). We demonstrate that these clonally reproducing lizards possess species-specific DNA fingerprints with a low degree of intra- and interpopulation variation. Mean indices of similarity obtained using M13 DNA, (GACA)4 and (TCC)50 as probes were 0.962 and 0.966 in L. dahli and L. armeniaca, respectively. The mean index of similarity obtained using M 13 and GATA probes in L. unisexualis was estimated to be 0.95. However, despite the high degree of band-sharing, variable DNA fragments were revealed in all populations with the microsatellite probes. An particularly high level of variability was observed for (TCC)n microsatellites in populations of L. unisexualis. In fact TCC-derived DNA fingerprints were close to being individual-specific, with a mean index of similarity of 0.824. Fingerprint analysis of parthenogenetic families of L. armeniaca showed that all maternal fragments were inherited together by the progeny, and no differences in fingerprint patterns were observed. On the other hand, while identical DNA fingerprints were obtained from L. unisexualis families with M13 and (GATA)4 probes, use of the (TCC)50 probe revealed remarkable intrafamily variation in this species. It is assumed that the genetic heterogeneity observed in parthenogenetic populations may be explained, at least in part, by the existence of genetically unstable microsatellite loci. Our data serve to illustrate processes of spontaneous mutagenesis and the initial stages of clonal differentiation in natural populations of the lizard species studied.     

Parentage determination in maize hybrids using the arbitrarily primed polymerase chain reaction (AP-PCR)

Summary Using a novel procedure based on the polymerase chain reaction, we have developed a rapid, efficient, and economical method for identifying plant genotypes. The arbitrarily primed polymerase chain reaction (AP-PCR) generates reproducible fingerprints from any organism, without the need for DNA sequence information. These fingerprints include DNA fragment polymorphisms that can be (1) used for varietal identification and parentage determination, (2) followed in segregating populations produced by crosses, (3) used as markers for the construction of genetic maps, and (4) used to generate dendograms of phylogenetic relationships, especially at the intraspecific level. AP-PCR requires only minute quantities of DNA (10–25 ng per reaction) and therefore can be used in situations in which DNA is limiting. We demonstrate the use of AP-PCR to identify inbred parents of hybrid maize plants in double-blind experiments.     

Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber

Patterns of genetic structure in eusocial naked mole-rat populations were quantified within and among geographically distant populations using multilocus DNA fingerprinting and mitochondrial DNA (mtDNA) sequence analysis. Individuals within colonies were genetically almost monomorphic, sharing the same mtDNA control region haplotype and having coefficients of band sharing estimated from DNA fingerprints ranging from 0.93 to 0.99. Family analysis of a hybrid captive colony of naked mole-rats with increased levels of genetic variability using multilocus DNA fingerprinting gave results consistent with Mendelian inheritance, and has revealed for the first time that multiple paternity can occur. In a survey of wild colonies from Ethiopia, Somalia and locations in northern and southern Kenya, we have examined mtDNA control region sequence variation in 42 individuals from 15 colonies, and together with multilocus DNA fingerprinting and mtDNA cytochrome- b sequence analysis in selected individuals have shown that these populations show considerable genetic divergence. Most of the variance in sequence divergence was found to be between geographical locations (Φ_ct= 0.68) and there was a significant correlation between sequence divergence and geographical separation of haplotypes. Six colonies from Mtito Andei in southern Kenya shared the same control region haplotype, suggesting a recent common maternal ancestor. In contrast, out of four colonies at Lerata in north Kenya, three haplotypes were identified, and phylogenetic analysis suggests that this area may be a zone where two distinct lineages are in close proximity. Genetic distances were maximal between Ethiopian and southern Kenyan populations at 5.8% for cytochrome- b , and are approaching interspecific values seen between other Bathyergids.     

Variability of GATA-microsatellite DNA in populations of the parthenogenetic species of lizard Lacerta unisexualis Darevsky

Multilocus DNA fingerprinting was used to analyze the genome variation of mini- and microsatellite DNA regions in parthenogenetic Caucasian rock lizard Lacerta unisexualis. The DNA fingerprints obtained with probe M13 were nearly identical in all populations examined (the average similarity index S = 0.992). The fingerprints obtained with probe (GATA)4 varied (S = 0.862). Polymorphic fragments were assumed to correspond to allelic variants of genetically unstable GATA loci. Comparison of the fingerprints of animals from four geographically isolated populations revealed several population-specific GATA microsatellite markers. Based on their distribution among the populations, the corresponding alleles were assumed to originate from a common ancestral allele.     

DNA fingerprinting: a tool for determining genetic distances between strains of poultry

Summary DNA fingerprinting, a technique based on the detection of hypervariable minisatellite regions in DNA restriction fragments, was tested for its applicability to conduct population genetics in poultry. Using MspI digestion and phage M13 DNA as a probe, between 25 and 35 minisatellite-containing DNA fragments were observed per bird. Comparison of the banding pattern of offspring with their parents revealed that the bands were inherited as stable genetic traits. The variability of the DNA fingerprinting pattern was reduced in inbred strains. DNA fingerprints of chickens from five well-defined populations of known genetic relationships were analyzed and indices of genetic distances were computed. They correctly reflected the history of these strains, indicating that DNA fingerprinting may be a powerful tool to characterize genetic relationships between different breeding populations of the same species.     

Relationships Among Genetic Makeup, Active Ingredient Content, and Place of Origin of the Medicinal Plant Gastrodia Tuber

Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers.     

Development of polymorphic simple sequence repeat markers for Pisolithus microcarpus

Six polymorphic simple sequence repeat (SSR) markers were developed for the ectomycorrhizal fungus Pisolithus microcarpus. A polymerase chain reaction (PCR)‐based technique was used in which random amplified polymorphic DNA (RAPD) fingerprints were probed with labelled SSR oligonucleotides by southern hybridization. The number of alleles per locus ranged from two to nine with expected heterozygosity values from 0.33 to 0.76. These loci will be potentially useful for genetic structure and gene flow studies of P. microcarpus populations. Cross‐species amplification with Pisolithus albus isolates at all loci was also observed.     

Random amplified polymorphic DNA analysis of Anopheles nuneztovari (Diptera: Culicidae) from Western and northeastern Colombia

Random amplified polymorphic DNA (RAPD) markers were used to analyze 119 DNA samples of three Colombian Anopheles nuneztovari populations to study genetic variation and structure. Genetic diversity, estimated from heterozygosity, averaged 0.34. Genetic flow was greater between the two populations located in Western Colombia (F ST: 0.035; Nm: 6.8) but lower between these two and the northeastern population (F ST: 0.08; Nm: 2.8). According to molecular variance analysis, the genetic distance between populations was significant (phi ST 0.1131, P < 0.001). The variation among individuals within populations (phi ST 0.8869, P < 0.001)was also significant, suggesting a greater degree of population subdivision, not considered in this study. Both the parameters evaluated and the genetic flow suggest that Colombian An. nuneztovari populations are co-specific.