Sesquiterpene lactone and diterpene constituents of helianthus annuus

One new furanoheliangolide derivative, 4,5-dihydroniveusin A, as well as the known compounds niveusin B and argophyllin A and B, were isolated from a Texas population of Helianthus annuus. Three previously characterized diterpene acids, grandifloric acid, ciliaric acid and 17-hydroxy-ent-isokaur-15(16)-en-19-oic acid were the principal constituents of this population.     

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus)

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (N_e) are much smaller than those expected in a fishes with large population census sizes (N_c). Estimates of N_e indicate low effective population sizes, even before the population collapse. The ratio N_e/N_e ranged between 10⁻⁶ and 10⁻⁸, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.     

Life history aspects of the mayfly Siphlonurus typicus (Ephemeroptera: Siphlonuridae) with a new application for measuring nymphal development and growth

Little is known about the life history of mayflies that inhabit temporary ponds. The purpose of this study was to observe and quantify life histories attributes of Siphlonurus typicus, which is known to reside in temporary ponds. Weekly samples of nymphs were taken from two temporary ponds in eastern Connecticut from March to June, 1999. Individuals were graded into 11 maturity classes, based on developmental characteristics, as a means of predicting population maturity rates. Head capsule widths (HCWs) were used to determine if growth occurred between maturity classes. Degree days were found to be an excellent predictor for population maturity (r ²=0.963, p<0.0001). Nymphs that hatched earlier in the year had larger HCWs than nymphs that hatched later in the year, possibly because of different temperature regimes. The University of Connecticut Forest pond (UCF) population matured faster than the Merrow Meadows pond (MER) population, but both sexes of the UCF population tended to be smaller than their counter parts from the MER population. Sex ratios were female bias for the UCF population (1.35:1), but were not different for the MER population. Adult emergence and mating occurred from 27 May to 21 June. There was a positive relationship between number of eggs per female and female body length. Oviposition at both sites occurred directly on the ponds, pond inlets, and outlets, indicating that pond populations were the result of local migrants as well as permanent residents. Temperature was a determining factor of maturity and fecundity for Siphlonurus typicus.     

Development of simple sequence repeat markers for the Japanese population of the Asian citrus psyllid,Diaphorina citri (Hemiptera: Psyllidae)

We developed nine simple sequence repeat (SSR) markers for the Japanese population of Diaphorina citri Kuwayama, which is known as the vector for citrus greening disease or huanglongbing, for use in population genetic studies. Analysis of 50 individuals collected from Tokunoshima Island showed that allelic diversity ranged from 5 to 24 alleles per locus, and observed and expected heterozygosities ranged from 0.100 to 0.939 and from 0.222 to 0.926, respectively. These SSR markers can be used to understand the population genetics of D. citri, and the obtained information may be useful in the estimation of population genetic structure, gene flow and invasion routes of D. citri.     

Increasing temperature weakens the positive effect of genetic diversity on population growth

Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species’ thermal optimum (i.e., the temperature at which population growth is maximal, or T _opt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G) in r, plastic changes in population growth across temperatures (E), and strong G × E interactions underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world.     

Prediction of identity by descent probabilities from marker-haplotypes

The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (i.e. all information came from the marker genotypes), and the situation where, say T, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.     

Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland

Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500–1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (N_E), a marked bottleneck event at 1400–1500 and a decrease in N_E in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.     

Molecular Variability in North Indian Isolates of Cylindrocladium quinquieseptatum Causing Eucalyptus Leaf and Seedling Blight

Cylindrocladium quinqueseptatum has been considered as the most destructive pathogen of Eucalyptus nurseries and plantations in north India. Genetic resistance has not been determined against this disease in Eucalyptus and genetic diversity among the fungal population in northern India is not known. Seventy three isolates from infected leaves and twigs of Eucalyptus were collected from different northern Indian state and analyzed through RAPD-PCR for screening genetic diversity. The UPGMA cluster analysis score of 284 loci permitted identification of 11 population lines and an outlier. This molecular variability prevalent among the north Indian population of the pathogen can used in identifying Cylindrocladium leaf and seedling blight resistant Eucalyptus germplasm.     

The Mitochondrial Genome of Arctica islandica; Phylogeny and Variation

Arctica islandica is known as the longest-lived non-colonial metazoan species on earth and is therefore increasingly being investigated as a new model in aging research. As the mitochondrial genome is associated with the process of aging in many species and bivalves are known to possess a peculiar mechanism of mitochondrial genome inheritance including doubly uniparental inheritance (DUI), we aimed to assess the genomic variability of the A. islandica mitochondrial DNA (mtDNA). We sequenced the complete mitochondrial genomes of A. islandica specimens from three different sites in the Western Palaearctic (Iceland, North Sea, Baltic Sea). We found the A. islandica mtDNA to fall within the normal size range (18 kb) and exhibit similar coding capacity as other animal mtDNAs. The concatenated protein sequences of all currently known Veneroidea mtDNAs were used to robustly place A. islandica in a phylogenetic framework. Analysis of the observed single nucleotide polymorphism (SNP) patterns on further specimen revealed two prevailing haplotypes. Populations in the Baltic and the North Sea are very homogenous, whereas the Icelandic population, from which exceptionally old individuals have been collected, is the most diverse one. Homogeneity in Baltic and North Sea populations point to either stronger environmental constraints or more recent colonization of the habitat. Our analysis lays the foundation for further studies on A. islandica population structures, age research with this organism, and for phylogenetic studies. Accessions for the mitochondrial genome sequences: KC197241 Iceland; KF363951 Baltic Sea; KF363952 North Sea; KF465708 to KF465758 individual amplified regions from different speciemen     

The gut microbiome composition and degradation enzymes activity of black Amur bream (Megalobrama terminalis) in response to breeding migratory behavior

Black Amur bream (Megalobrama terminalis), a dominant species, resides in the Pearl River basin, known for its high plasticity in digestive ability. During spawning season, M. terminalis individuals with large body size and high fertility undergo a spawn migratory phase, while other smaller individuals prefer to settlement over migration. It is well known that gut microbial community often underpins the metabolic capability and regulates a wide variety of important functions in fish. However, little was known about how the gut microbiomes affect fish breeding migration. To investigate the variations in the gut microbiome of M. terminalis during the migration, we used high‐throughput 16S rRNA gene sequencing to reveal the distinct composition and diversity of the whole gut microbiome of migrated and nonmigrated population during period of peak reproduction, respectively. Our results indicated that nonmigrated population in estuary had a higher alpha diversity than that of migrated population in main stem. Additionally, an obvious abundant taxa shift between the gut microbiota community of nonmigrated and migrated M. terminalis was also observed. Change of dominant gut taxa from nonmigrated to migrated population was thought to be closely related to their degradation enzymes. Our results suggested that amino acid metabolism and lipid metabolism in migrated population were higher than that in nonmigrated population, providing a line of evidence for that M. terminalis change from partial herbivorous to partial carnivorous diet during breeding migration. We further concluded that, in order to digest foods of higher nutrition to supply energy to spawning migration, M. terminalis regulate activities of the gut microbiome and degradation enzymes, considered to be a key physiological strategy for reproduction.     

Molecular Evidence for Lessepsian Invasion of Soritids (Larger Symbiont Bearing Benthic Foraminifera)

The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF) that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea) and from a known hotspot in Shikmona (northern Israel) that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.     

Genetic diversity of an endangered aquatic plant, Potamogeton lucens subspecies sinicus

The genetic diversity of the species, Potamogeton lucens subsp. sinicus var. teganumensis, which is critically endangered in Japan, was investigated. This species now occurs in only two known localities in Japan. One is a native population (Oitoike population), but the other (Teganuma-Okahotto population) is found in a small artificial pond that was dug in 1998. It is considered that the Teganuma-Okahotto population grew from a soil seed bank. Based on RAPD variation, we compared the genetic diversity of the two populations of P. lucens var. teganumensis in Japan and one population of P. lucens subsp. sinicus var. sinicus in China. The Teganuma-Okahotto population showed RAPD variation, suggesting that it may be derived from more than one seed buried in old sediments. This population also had the highest value of Shannon's Information Index among the three study populations. This finding suggests that seeds buried in sediments can contain genetic variability, and may be used to conserve the genetic diversity of rare and endangered plants.     

Functional response of Euseius concordis to densities of different developmental stages of the cassava green mite

Both prey density and developmental stage of pests and natural enemies are known to influence the effectiveness of biological control. However, little is known about the interaction between prey density and population structure on predation and fecundity of generalist predatory mites. Here, we evaluated the functional response (number of prey eaten by predator in relation to prey density) of adult females and nymphs of the generalist predatory mite Euseius concordis to densities of different developmental stages of the cassava green mite Mononychellus tanajoa, as well as the fecundity of adult females of the predator. We further assessed the instantaneous rate of increase, based on fecundity and mortality, of E. concordis fed on eggs, immatures and adults of M. tanajoa. Overall, nymphs and adults of E. concordis feeding on eggs, immatures and females of M. tanajoa had a type III functional response curve suggesting that the predator increased prey consumption rate as prey density increased. Both nymphs and adult females of the predator consumed more eggs than immatures of M. tanajoa from the density of 20 items per leaf disc onwards, revealing an interaction between prey density and developmental stage in the predatory activity of E. concordis. In addition, population growth rate was higher when the predator fed on eggs and immatures in comparison with females. Altogether our results suggest that E. concordis may be a good candidate for the biological control of M. tanajoa populations. However, the efficiency of E. concordis as a biological control agent of M. tanajoa is contingent on prey density and population structure.     

High intraspecific genetic and morphological variation in the pioneer lichen Cladonia rei colonising slag dumps

This study investigates the genetic and morphological variability of the lichen Cladonia rei inhabiting strongly contaminated postsmelting slag dumps in southern Poland. Altogether, 27 C. rei samples were analysed, including 17 from a single population in one dump. The phylogenetic analysis includes samples of C. rei, outgroup species, and external sequences of Cladonia section representatives from GenBank. Comparative analysis of the internal transcribed spacer (ITS) rDNA sequences revealed the presence of 19 C. rei haplotypes overall, including several of the most frequent, of which 11 are represented by single individuals only. As many as 12 haplotypes were recorded within a single population. Three strongly supported monophyletic clades comprised of specimens from different geographical regions were recovered. Morphometric analysis showed great phenotypic variability within particular clades. Apart from a full range of previously known morphological forms of the species, an additional specific morphotype was recognised in the dumps; however, its representatives do not create a monophyletic group. High genetic variability within a single population suggests that C. rei has a great potential for colonising anthropogenic habitats. This attribute emphasises the role of this lichen as an essential pioneer in the early stages of natural regeneration of such sites.     

Demography and population models of ticks of the genus Ixodes with long-term life cycles

The most important parameters necessary for creation of population models for three-host species with long-term life cycles are discussed by the example of the ticks Ixodes persulcatus and I. ricinus. In these species, specimens of the same biological age may belong to different age cohorts and their calendar age may differ by several months or even years. Accurate estimation of the calendar age of singular individuals is difficult; it is based on the extrapolation by its possible biological age and by belonging to the certain age cohort of a natural population. In order to possess a prognostic value, the population models must predict a single-moment population density of activated hungry specimens of all the three developmental stages and the probability of host-finding in hungry ticks during the questing period. The daily mortality of ticks of different developmental stages and phases of each stage (questing, feeding, preparation for molting, and diapause) should also be known. The population density of questing hungry ticks in the ecosystem is determined by the balance between the recruitment of new individuals into the population, their removal from the population by hosts, the dying of ticks from starvation, and the consumption of ticks by predators. At present, unfortunately, only some of these parameters are sufficiently known.     

Enteroaggregative Escherichia coli Have Evolved Independently as Distinct Complexes within the E. coli Population with Varying Ability to Cause Disease

Enteroaggregative E. coli (EAEC) is an established diarrhoeagenic pathotype. The association with virulence gene content and ability to cause disease has been studied but little is known about the population structure of EAEC and how this pathotype evolved. Analysis by Multi Locus Sequence Typing of 564 EAEC isolates from cases and controls in Bangladesh, Nigeria and the UK spanning the past 29 years, revealed multiple successful lineages of EAEC. The population structure of EAEC indicates some clusters are statistically associated with disease or carriage, further highlighting the heterogeneous nature of this group of organisms. Different clusters have evolved independently as a result of both mutational and recombination events; the EAEC phenotype is distributed throughout the population of E. coli.     

Genetic characterization of grapevine-infecting Botrytis cinerea isolates from Argentina

BackgroundBotrytis cinerea is an ascomycete with a high genetic diversity and complex population structure, as reported from several hosts and sites. However, nothing is known about its genetic diversity in Argentina.AimsThe aim of this work is to estimate the genetic diversity of a local population of B. cinerea isolates obtained from grapevine in Argentina.MethodsIn this work, 35 strains that had been isolated from grapevines were genotyped for the presence of transposable elements and PCR-based RFLP molecular markers. The obtained results were compared with those from a large French population of the fungus, and used to perform a population genetics analysis using the Genepop software.ResultsAll the analysed isolates were classified as Group II (according to the most recent proposed classification) and showed a high degree of genetic diversity, with 14 different haplotypes. A significant difference in allele frequency was recorded between the local and French populations.ConclusionsThese comparisons between fungal populations, led to the detection of a high level of diversity and the differentiation between local and French groups of isolates. This was confirmed by an Fst value of 0.3332, which was higher than that reported for other pairwise comparisons of populations. This work constitutes the first report on the genetic diversity of B. cinerea isolates and their population structure in Argentina.     

Genetic diversity of an endangered aquatic plant,Potamogeton lucens subspecies sinicus

The genetic diversity of the species, Potamogeton lucens subsp. sinicus var. teganumensis, which is critically endangered in Japan, was investigated. This species now occurs in only two known localities in Japan. One is a native population (Oitoike population), but the other (Teganuma-Okahotto population) is found in a small artificial pond that was dug in 1998. It is considered that the Teganuma-Okahotto population grew from a soil seed bank. Based on RAPD variation, we compared the genetic diversity of the two populations of P. lucens var. teganumensis in Japan and one population of P. lucens subsp. sinicus var. sinicus in China. The Teganuma-Okahotto population showed RAPD variation, suggesting that it may be derived from more than one seed buried in old sediments. This population also had the highest value of Shannon's Information Index among the three study populations. This finding suggests that seeds buried in sediments can contain genetic variability, and may be used to conserve the genetic diversity of rare and endangered plants.     

Population Genetic Structuring in Opisthorchis viverrini over Various Spatial Scales in Thailand and Lao PDR

Khon Kaen Province in northeast Thailand is known as a hot spot for opisthorchiasis in Southeast Asia. Preliminary allozyme and mitochondrial DNA haplotype data from within one endemic district in this Province (Ban Phai), indicated substantial genetic variability within Opisthorchis viverrini. Here, we used microsatellite DNA analyses to examine the genetic diversity and population structure of O. viverrini from four geographically close localities in Khon Kaen Province. Genotyping based on 12 microsatellite loci yielded a mean number of alleles per locus that ranged from 2.83 to 3.7 with an expected heterozygosity in Hardy–Weinberg equilibrium of 0.44–0.56. Assessment of population structure by pairwise F_ST analysis showed inter-population differentiation (P<0.05) which indicates population substructuring between these localities. Unique alleles were found in three of four localities with the highest number observed per locality being three. Our results highlight the existence of genetic diversity and population substructuring in O. viverrini over a small spatial scale which is similar to that found at a larger scale. This provides the basis for the investigation of the role of parasite genetic diversity and differentiation in transmission dynamics and control of O. viverrini.