Changes In Genotypic Composition Research Articles

Changes in Genotype Composition and Morphology at an Experimental Site of Common Reed (Phragmites australis) Over a Quarter of a Century

The cultivation of common reed (Phragmites australis) is one of the most promising practices of paludiculture on fen peatlands. This highly productive grass has a high adaptation capacity via high levels of genetic diversity and phenotypic plasticity. In this study, a reed experimental site established on a degraded fen in 1996/97 with a mixture of monoclonally (meristematically propagated plantlets) and polyclonally (pre-grown seedlings) planted plots was investigated by microsatellite genotyping. All nine genotypes of the monoclonal planted plots were recovered and could be genetically characterized; invasion by other genotypes was negligible. Similarly, the polyclonal plots sustained high clonal diversity with no prevalence of a single genotype. The growth characteristics of the five quantitatively investigated genotypes significantly differed from each other (α = 0.05): dry biomass per stem 5–18 g, panicles per m2 20–60, average stem diameter 3.5–6 mm, height 170–250 cm. Similarly, the persistence of genotypes at the planted plots and their invasiveness (ability to invade neighboured plots) varied. These results show that common reed stands are extremely persistent even if established with genotypes that are likely not to be locally adapted. Their genetic structure remained stable for at least 24 years regardless of the planting density (1, 4, and 10 plants per m2). Our results indicate that farmers may be able to maintain favourable genotypes for many years, thus the selection and breeding of common reed as a versatile crop for rewetted peatlands is a promising objective for paludiculture research.

Ecological Dynamics of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa.

Microcystis aeruginosa is predicted to interact and coexist with diverse broad- and narrow-host-range viruses within a bloom; however, little is known about their affects on Microcystis population dynamics. Here, we developed a real-time PCR assay for the quantification of these viruses that have different host ranges. During the sampling period, total Microcystis abundance showed two peaks in May and August with a temporary decrease in June. The Microcystis population is largely divided into three phylotypes based on internal transcribed sequences (ITS; ITS types I to III). ITS I was the dominant phylotype (66% to 88%) except in June. Although the ITS II and III phylotypes were mostly less abundant, these phylotypes temporarily increased to approximately equivalent abundances of the ITS I population in June. During the same sampling period, the abundances of the broad-host-range virus MVGF_NODE331 increased from April to May and from July to October with a temporary decrease in June, in which its dynamics were in proportion to the increase of total Microcystis abundances regardless of changes in host ITS population composition. In contrast, the narrow-host-range viruses MVG_NODE620 and Ma-LMM01 were considerably less abundant than the broad-host-range virus and generally did not fluctuate in the environment. Considering that M. aeruginosa could increase the abundance and sustain the bloom under the prevalence of the broad-host-range virus, host abundant and diverse antiviral mechanisms might contribute to coexistence with its viruses. IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa interacts with diverse broad- and narrow-host-range viruses. However, the dynamics of the Microcystis population (at the intraspecies level) and viruses with different host ranges remain unknown. Our real-time PCR assays unveiled that the broad-host-range virus gradually increased in abundance over the sampling period, in proportion to the increase in total Microcystis abundance regardless of changes in genotypic composition. The narrow-host-range viruses were considerably less abundant than the broad-host-range virus and did not generally fluctuate in the environment. The expansion and maintenance of the Microcystis bloom even under the increased infection by the broad-host-range virus suggested that highly abundant and diverse antiviral mechanisms allowed them to coexist with viruses under selective pressure. This paper expands our knowledge about the ecological dynamics of Microcystis viruses and provides potential insights into their coexistence with their host.

Company matters: The presence of other genotypes alters traits and intraspecific selection in an Arctic diatom under climate change.

Arctic phytoplankton and their response to future conditions shape one of the most rapidly changing ecosystems on the planet. We tested how much the phenotypic responses of strains from the same Arctic diatom population diverge and whether the physiology and intraspecific composition of multistrain populations differs from expectations based on single strain traits. To this end, we conducted incubation experiments with the diatom Thalassiosira hyalina under present‐day and future temperature and pCO2 treatments. Six fresh isolates from the same Svalbard population were incubated as mono‐ and multistrain cultures. For the first time, we were able to closely follow intraspecific selection within an artificial population using microsatellites and allele‐specific quantitative PCR. Our results showed not only that there is substantial variation in how strains of the same species cope with the tested environments but also that changes in genotype composition, production rates, and cellular quotas in the multistrain cultures are not predictable from monoculture performance. Nevertheless, the physiological responses as well as strain composition of the artificial populations were highly reproducible within each environment. Interestingly, we only detected significant strain sorting in those populations exposed to the future treatment. This study illustrates that the genetic composition of populations can change on very short timescales through selection from the intraspecific standing stock, indicating the potential for rapid population level adaptation to climate change. We further show that individuals adjust their phenotype not only in response to their physicochemical but also to their biological surroundings. Such intraspecific interactions need to be understood in order to realistically predict ecosystem responses to global change.

DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). In particular, we investigated the long-term (100 yr) diversity and dynamics of Synechococcus,, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided the ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR; quantitative Polymerase Chain Reaction) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus, (fraction of Synechococcus, in total cyanobacteria). The diversity of Synechococcus, in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and the following internally transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, the study of ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (in temperature and phosphorus concentration) affected Synechococcus, community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus, clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

Effect of Crop Rotations on Rotylenchulus reniformis Population Structure.

Rotylenchulus reniformis is a highly variable nematode species and an economically important pest in many cotton fields across the south-eastern United States. Rotation with resistant or poor host crops is a method for management of reniform nematode. We studied the effect of six planting schemes covering four 120-day planting cycles on the predominant genotype of R. reniformis. Rotations used were: (i) cotton to corn; (ii) susceptible soybean to corn; (iii) resistant soybean to cotton; (iv) corn to cotton; (v) continuous susceptible soybean; (vi) continuous cotton. After each 120-day cycle, amplified fragment length polymorphisms (AFLPs) produced from four primer pairs were used to determine the effect of crop rotation on the predominant genotype of reniform nematode. A total of 279 polymorphic bands were scored using four primer combinations. Distinct changes in genotype composition were observed following rotations with resistant soybean or corn. Rotations involving soybean (susceptible and resistant) had the greatest effect on population structure. The characterization of field population variability of reniform nematode and of population responses to host plants used in rotations can help extend the durability of resistant varieties and can help identify effective rotation schemes.

Irreversible microevolutionary changes in genotypic composition of sika deer Cervus nippon populations in response to vegetation degradation and food shortage

The present study deals with changes in important skull characteristics of the sika deer Cervus nippon Temminck, 1838 in response to changes in food supply. Moderate food shortage results mainly in a linear reduction in skull size, while severe food shortage results in changes in skull shape. In the deer that returned to habitats with sufficient food supply, some skull parameters recovered to, or even exceeded, normal values, whereas other parameters remained stressed resulting in retention or enhancement of skull distortions. Differences in skull parameters among the populations studied were comparable to those between some cervid species, eg, the Siberian roe deer Capreolus pigargus Pallas, 1771 and European roe deer Capreolus capreolus Linnaeus, 1758 and other deer subspecies. In the introduced sika deer populations, skull distortions were apparently caused by interspecific hybridization. Descendants of the escaped deer have not reverted to the normal phenotype, even over several generations, providing a recent case of true evolutionary changes. This occurred by a change in the ratio of different morphotypical groups, probably due to their different responses to food shortage. Thus sufficient food supply may account for changes in a population’s genotypic composition through selection of characteristics that favour passing on genetic material when food is limited.

EVIDENCE FOR NEGATIVE FREQUENCY-DEPENDENT SELECTION DURING EXPERIMENTAL COEVOLUTION OF A FRESHWATER SNAIL AND A STERILIZING TREMATODE

Host-parasite coevolution is often suggested as a mechanism for maintaining genetic diversity, but finding direct evidence has proven difficult. In the present study, we examine the process of coevolution using a freshwater New Zealand snail (Potamopyrgus antipodarum) and its common parasite (the sterilizing trematode, Microphallus sp.) Specifically, we test for changes in genotypic composition of clonal host populations in experimental populations evolving either with or without parasites for six generations. As predicted under the Red Queen model of coevolution, the initially most common host genotype decreased in frequency in the presence, but not the absence, of parasitism. Furthermore, the initially most common host genotype became more susceptible to infection by the coevolving parasite populations over the course of the experiment. These results are consistent with parasite-meditated selection leading to a rare advantage, and they indicate rapid coevolution at the genotypic level between a host and its parasite.

Changes in genotypic composition of Myzus persicae (Hemiptera: Aphididae) on tobacco during the past two decades in Japan.

Ninety-nine and 476 clones of Myzus persicae (Sulzer) were sampled on tobacco at Kyoto (Shimogamo) (1996-2000) and at 23 other localities (1998-1999) in Japan, respectively. The clones were classified into colour-esterase forms, distinguished by combinations of body colour and electrophoretically detectable esterases, to verify the changes in genotypic composition during the past two decades. Fifteen and 31 colour-esterase forms were found at Kyoto (Shimogamo) and at 23 other localities, respectively. Fourteen (representing c. 95% of the total clones sampled) and 24 (c. 44%) colour-esterase forms, respectively, were different from those found on tobacco during 1978-1985. The frequency of the green form and the very highly insecticide-resistant form increased. More than half of the colour-esterase forms found in the present survey were newly detected. The factors associated with these changes are discussed.

The dynamics of gynodioecy in Plantago lanceolata L. I. Frequencies of male-steriles and their cytoplasmic male sterility types

The maintenance of a gynodioecious breeding system (hermaphrodites and male-steriles) was studied in Plantago lanceolata. Cytoplasmic-nuclear inheritance is important in the maintenance of male-steriles. The male-sterile trait is cytoplasmically based (CMS), and male fertility can be restored by nuclear genes. Male-sterile frequencies differ among populations. Several hypotheses can be considered. (1) In each population a different equilibrium could be optimal because of environmentally dependent fitnesses. (2) None of the populations has reached an equilibrium (yet). (3) The populations are in different phases of a dynamic equilibrium, i.e. limit cycles. The last two explanations both predict a dynamic process, a continuous change within populations. Sex phenotype frequencies and their underlying gene frequencies were assessed. Sex phenotype frequencies changed over years within populations. We showed that these changes resulted from changes in genotype composition, which favours the two hypotheses (2 and 3) that predict a dynamic process. CMS-type frequencies were estimated using mtDNA markers. Among populations, CMS types differed in frequencies. CMSI and CMSIII seemed to exclude each other, and CMSII types occurred in all populations. In all populations, CMSI appeared to be less restored than the other CMS types. This was not expected on the basis of either of the two theoretical models that included dynamics (hypotheses 2 and 3).

Genetic structure of an aphid studied using microsatellites: cyclic parthenogenesis, differentiated lineages and host specialization.

In a previous study, samples of the grain aphid Sitobion avenae (F.) were collected from wheat and adjacent cocksfoot hosts in a population thought to be primarily parthenogenetic, and DNA from individual aphids was analysed with a multilocus technique. Here we have applied single-locus microsatellites and a mitochondrial DNA marker to a subset of the same DNA extracts, and have made several additional inferences about important genetic and population processes in S. avenae. Microsatellite analysis indicated very high levels of genic and genotypic variation. S. avenae fell into three genotypic groups inferred to be almost noninterbreeding, while analysis of linkage and Hardy-Weinberg equilibria suggested high levels of sexual recombination within each genotypic group. Host specialization was evident: one lineage was found only on wheat, and one (bearing many alleles inferred to be introgressed from the blackberry-grass aphid S. fragariae (Walker)) was found only on cocksfoot. The third group of interrelated genotypes was found commonly on both hosts. Although most genotypes were found only once, some were much more numerous in the sample than expected from the frequency of the alleles they contained. This, and rapid temporal changes in genotypic composition of samples, indicates strong selective differences between genotypes and lineages. In the major genotypic group, the commonest genotypes were significantly more homozygous than were rare ones: thus these data may help to explain the frequent observation of homozygous excess in aphid allozymes. The genotype group showing S. avenae-like as well as S. fragariae-like alleles also carried S. fragariae-like mitochondrial DNA in at least 25/31 cases, indicating gender-asymmetrical hybridization.

The dynamics of gynodioecy in Plantago lanceolata L. I. Frequencies of male-steriles and their cytoplasmic male sterility types

The maintenance of a gynodioecious breeding system (hermaphrodites and male-steriles) was studied in Plantago lanceolata. Cytoplasmic-nuclear inheritance is important in the maintenance of male-steriles. The male-sterile trait is cytoplasmically based (CMS), and male fertility can be restored by nuclear genes. Male-sterile frequencies differ among populations. Several hypotheses can be considered. (1) In each population a different equilibrium could be optimal because of environmentally dependent fitnesses. (2) None of the populations has reached an equilibrium (yet). (3) The populations are in different phases of a dynamic equilibrium, i.e. limit cycles. The last two explanations both predict a dynamic process, a continuous change within populations. Sex phenotype frequencies and their underlying gene frequencies were assessed. Sex phenotype frequencies changed over years within populations. We showed that these changes resulted from changes in genotype composition, which favours the two hypotheses (2 and 3) that predict a dynamic process. CMS-type frequencies were estimated using mtDNA markers. Among populations, CMS types differed in frequencies. CMSI and CMSIII seemed to exclude each other, and CMSII types occurred in all populations. In all populations, CMSI appeared to be less restored than the other CMS types. This was not expected on the basis of either of the two theoretical models that included dynamics (hypotheses 2 and 3).

Temporal, Spatial, and Age-Specific Changes in Genotypic Composition of Mule Deer

Spatial, temporal, and age-specific genetic variation is described for a mule deer ( Odocoileus hemionus ) herd from northwestern Colorado during 1983—1986. Little genetic differentiation was observed between major migratory herd subdivisions, although spatial structuring and inbreeding within subdivisions is indicated during some years. Significant differences in common allele frequencies at six of 11 variable loci and changes in apportionment of genetic variance among individuals within and among locations occurred during 4 years of study. Common allele frequencies increased with year of study. Significant differences in allele frequencies also were observed between fawns and adult females. Temporal and age-specific genetic differences probably were influenced most by changes in breeding structure.