Related Articles

The present study reveals significant genetically determined differences in a range of growth and ecophysiological traits between different Phragmites australis genotypes, and provides evidence that the differences are neither related to ploidy level per se nor to the phylogeographic relationships of the genotypes.

Background and aims

Phragmites australis is a wetland grass with high genetic variability, augmented by its cosmopolitan distribution, clonal growth form and large variation in chromosome numbers. Different ploidy levels and ecotypes differ in morphology and ecophysiological traits, and may possess different levels of phenotypic variation. The aim of this study was to quantify the natural variation in ecophysiological characteristics of P. australis, and to explore whether differences in ecophysiological traits can be related to ploidy levels or to the geographic origin of the clones.

Methodology

Fifteen clones of P. australis from Europe and Asia/Australia, representing five ploidy levels (4x, 6x, 8x, 10x and 12x), were grown in a common garden design for 119 days. Plant growth and light-saturated rate of photosynthesis (Pmax), stomatal conductance (gs), water use efficiency (WUE) and concentrations of photosynthetic pigments and mineral ions in the leaves were measured.

Principal results

The growth of the plants and most ecophysiological parameters differed significantly between clones. The mean maximum shoot height varied from 0.9 to 1.86 m, Pmax from 9.7 to 27 µmol m−2 s−1, gs from 0.22 to 1.41 mol m−2 s−1 and WUE from 13 to 47 µmol mol−1. The concentrations of chlorophylls did not vary significantly between clones, but the chlorophyll a/b ratio and the concentrations of total carotenoids did. The observed differences were not explained either by the ploidy level per se or by the geographic origin or phylogenetic relationships of the clones.

Conclusions

Phylogeographic relationships in P. australis on a global scale do not mirror the environment where the adaptations have evolved, and high phenotypic variation among and within clones complicates comparative studies. Future studies aimed at explaining differences in plant behaviour between P. australis populations should be careful in the selection of target genotypes and/or populations, and should avoid generalizing their findings beyond the genotypes and/or populations studied.

Hybridization of Phragmites has occurred in the Gulf Coast and likely is occurring elsewhere in North America. However, detection failure may be due to limited genetic tools. Additionally, nomenclature confusion necessitates a revision of the current classification system.

Background and aims

We review evidence for hybridization of Phragmites australis in North America and the implications for the persistence of native P. australis ssp. americanus populations in North America. We also highlight the need for an updated classification system, which takes P. australis intraspecific variation and hybridization into account.

Methodology

We reviewed available published, in press and in preparation literature to assess the likelihood of hybridization and interbreeding in genotypes of P. australis present in North America.

Principal results

Experimental results demonstrate that hybridization among introduced and native haplotypes is possible within the genus Phragmites, yet evidence that hybridization has occurred naturally is only starting to emerge. The lag in identifying hybridization in Phragmites in North America may be related to under-sampling in some parts of North America and to a lack of molecular tools that provide the capability to recognize hybrids.

Conclusions

Our understanding of the gene flow within and between species in the genus Phragmites is moving at a fast pace, especially on the east and Gulf coasts of North America. More attention should also be focused on the Great Lakes region, the southwestern and the west coast of the USA, where sympatry has created opportunities for hybridization. Where hybridizations have been detected, there are currently no published data on how hybridization affects plant vigour, morphology, invasiveness or conservation of the genetic integrity of the North American native subspecies. We conclude that the detection of more hybridization is highly likely and that there is a need to develop new markers for the different Phragmites species and lineages to fill current knowledge gaps. Finally, we suggest that the classification system for P. australis should be updated and published to help clarify the nomenclature.

Determination of spatial genetic structure (SGS) in natural populations is important for both theoretical aspects of evolutionary genetics and their application in species conservation and ecological restoration. In this study, we examined genetic diversity within and among the natural populations of a cosmopolitan grass Phragmites australis (common reed) in the Yellow River Delta (YRD), China, where a mosaic of habitat patches varying in soil salinity was detected. We demonstrated that, despite their close geographic proximity, the common reed populations in the YRD significantly diverged at six microsatellite loci, exhibiting a strong association of genetic variation with habitat heterogeneity. Genetic distances among populations were best explained as a function of environmental difference, rather than geographical distance. Although the level of genetic divergence among populations was relatively low (F’ST = 0.073), weak but significant genetic differentiation, as well as the concordance between ecological and genetic landscapes, suggests spatial structuring of genotypes in relation to patchy habitats. These findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.

Plants are naturally colonized by many fungal species that produce effects ranging from beneficial to pathogenic. However, how many of these fungi are linked with a single host plant has not been determined. Furthermore, the composition of plant-associated fungal communities has not been rigorously determined. We investigated these essential issues by employing the perennial wetland reed Phragmites australis as a model. DNA extracted from roots, rhizomes, stems, and leaves was used for amplification and cloning of internal transcribed spacer rRNA gene fragments originating from reed-associated fungi. A total of 1,991 clones from 15 clone libraries were differentiated by restriction fragment length polymorphism analyses into 345 operational taxonomical units (OTUs). Nonparametric estimators for total richness (Chao1 and ACE) and also a parametric log normal model predicted a total of about 750 OTUs if the libraries were infinite. Sixty-two percent of the OTUs sequenced were novel at a threshold of 3%. Several of these OTUs represented undocumented fungal species, which also included higher taxonomic levels. In spite of the high diversity of the OTUs, the mycofloras of vegetative organs were dominated by just a few typical fungi, which suggested that competition and niche differentiation influence the composition of plant-associated fungal communities. This suggestion was independently supported by the results of nested PCR assays specifically monitoring two OTUs over 3 years, which revealed significant preferences for host habitat and host organ.

Novel species of microfungi described in the present study include the following from Australia: Diaporthe ceratozamiae on Ceratozamia robusta, Seiridium banksiae on Banksia marginata, Phyllosticta hymenocallidicola on Hymenocallis littoralis, Phlogicylindrium uniforme on Eucalyptus cypellocarpa, Exosporium livistonae on Livistona benthamii and Coleophoma eucalyptorum on Eucalyptus piperita. Several species are also described from South Africa, namely: Phoma proteae, Pyrenochaeta protearum and Leptosphaeria proteicola on Protea spp., Phaeomoniella niveniae on Nivenia stokoei, Toxicocladosporium leucadendri on Leucadendron sp. and Scorias leucadendri on Leucadendron muirii. Other species include Myrmecridium phragmitis on Phragmites australis (Netherlands) and Camarographium carpini on Carpinus betulus (Russia). Furthermore, Pseudoidriella syzygii on Syzygium sp. represents a novel genus of hyphomycetes collected in Australia. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

In this study, we compared ecological characteristics of wetland vegetation in a series of restoration projects that were carried out in the wetlands of Yellow River Delta. The investigated characteristics include plant composition structure, species diversity and community similarity in three kinds of Phragmites australis wetlands, i.e. restored P. australis wetlands (R1, R2, R3 and R4: restored in 2002, 2005, 2007 and 2009, respectively), natural P. australis wetland (N) and degraded P. australis wetland (D) to assess the process of wetlands restoration. The coverage of the R1 was 99%, which was similar to natural wetland. Among all studied wetlands, the highest and lowest stem density was observed in R1 and R2, respectively, Plant height and stem diameter show the same trend as N > R2 > R1 > R3 > D > R4. Species diversity of restored P. australis wetlands became closed to natural wetland. Both species richness and Shannon–Wiener index had similar tendency: increased first and then decreased with restored time. The highest species richness and species diversity were observed in R2, while the lowest values of those parameters were found in natural P. australis wetland. Similarity indexes between restored wetlands and natural wetland increased with the restoration time, but they were still less than 50%. The results indicate that the vegetation of P. australis wetlands has experienced a great improvement after several years’ restoration, and it is feasible to restored degraded P. australis wetlands by pouring fresh water into those wetlands in the Yellow River Delta. However, it is notable that costal degraded P. australis wetland in this region may take years to decades to reach the status of natural wetland.

Background

Nonnative Phragmites australis (common reed) is one of the most intensively researched and managed invasive plant species in the United States, yet as with many invasive species, our ability to predict, control or understand the consequences of invasions is limited. Rapid spread of dense Phragmites monocultures has prompted efforts to limit its expansion and remove existing stands. Motivation for large-scale Phragmites eradication programs includes purported negative impacts on native wildlife, a view based primarily on observational results. We took an experimental approach to test this assumption, estimating the effects of nonnative Phragmites australis on a native amphibian.

Methodology/Principal Findings

Concurrent common garden and reciprocal transplant field experiments revealed consistently strong positive influences of Phragmites on Rana catesbeiana (North American bullfrog) larval performance. Decomposing Phragmites litter appears to contribute to the effect.

Conclusions/Significance

Positive effects of Phragmites merit further research, particularly in regions where both Phragmites and R. catesbeiana are invasive. More broadly, the findings of this study reinforce the importance of experimental evaluations of the effects of biological invasion to make informed conservation and restoration decisions.

Roads, bridges, and dikes constructed across salt marshes can restrict tidal flow, degrade habitat quality for nekton, and facilitate invasion by non-native plants including Phragmites australis. Introduced P. australis contributes to marsh accretion and eliminates marsh surface pools thereby adversely affecting fish by reducing access to intertidal habitats essential for feeding, reproduction, and refuge. Our study assessed the condition of resident fish populations (Fundulus heteroclitus) at four tidally restricted and four tidally restored marshes in New England invaded by P. australis relative to adjacent reference salt marshes. We used physiological and morphological indicators of fish condition, including proximate body composition (% lipid, % lean dry, % water), recent daily growth rate, age class distributions, parasite prevalence, female gravidity status, length-weight regressions, and a common morphological indicator (Fulton’s K) to assess impacts to fish health. We detected a significant increase in the quantity of parasites infecting fish in tidally restricted marshes but not in those where tidal flow was restored to reduce P. australis cover. Using fish length as a covariate, we found that unparasitized, non-gravid F. heteroclitus in tidally restricted marshes had significantly reduced lipid reserves and increased lean dry (structural) mass relative to fish residing in reference marshes. Fish in tidally restored marshes were equivalent across all metrics relative to those in reference marshes indicating that habitat quality was restored via increased tidal flushing. Reference marshes adjacent to tidally restored sites contained the highest abundance of young fish (ages 0–1) while tidally restricted marshes contained the lowest. Results indicate that F. heteroclitus residing in physically and hydrologically altered marshes are at a disadvantage relative to fish in reference marshes but the effects can be reversed through ecological restoration.

Global change is predicted to promote plant invasions world-wide, reducing biodiversity and ecosystem function. Phenotypic plasticity may influence the ability of introduced plant species to invade and dominate extant communities. However, interpreting differences in plasticity can be confounded by phylogenetic differences in morphology and physiology. Here we present a novel case investigating the role of fitness trait values and phenotypic plasticity to global change factors between conspecific lineages of Phragmites australis. We hypothesized that due to observed differences in the competitive success of North American-native and Eurasian-introduced P. australis genotypes, Eurasian-introduced P. australis would exhibit greater fitness in response to global change factors. Plasticity and plant performance to ambient and predicted levels of carbon dioxide and nitrogen pollution were investigated to understand how invasion pressure may change in North America under a realistic global change scenario. We found that the introduced Eurasian genotype expressed greater mean trait values in nearly every ecophysiological trait measured – aboveground and belowground – to elevated CO2 and nitrogen, outperforming the native North American conspecific by a factor of two to three under every global change scenario. This response is consistent with “jack and master” phenotypic plasticity. We suggest that differences in plant nitrogen productivity, specific leaf area, belowground biomass allocation, and inherently higher relative growth rate are the plant traits that may enhance invasion of Eurasian Phragmites in North America. Given the high degree of genotypic variability within this species, and our limited number of genotypes, our results must be interpreted cautiously. Our study is the first to demonstrate the potential importance of jack-and-master phenotypic plasticity in plant invasions when facing imminent global change conditions. We suggest that jack-and-master invasive genotypes and/or species similar to introduced P. australis will have an increased ecological fitness, facilitating their invasion in both stressful and resource rich environments.

Background

Present day distributions of Palearctic taxa in northern latitudes mainly result from populations having survived in local patches during the Late Pleistocene and/or from recolonizing populations from southern temperate refugia. If well-studied Mediterranean and eastern European refugia are widely accepted, some recent biogeographical assumptions still remain unclear, such as the occurrence of multiple glacial refugia in Iberia and cryptic refugia in northern Europe during the last glaciations. The Lusitanian snail Elona quimperiana has a remarkably disjunct distribution, limited to northwestern France (Brittany), northwestern Spain and the Basque Country. By describing the phylogeographical structure of this species across its entire range, the present study attempts to identify refugia and subsequent recolonization routes.

Results

Results based on 16S and COI gene sequences showed that the low genetic diversity observed in the Brittany populations should be associated with a recent demographic expansion. By contrast, populations from Spain exhibit several differentiated lineages and are characterized by demographic equilibrium, while the Basque populations are the only ones harboring typical distinct haplotypes. The center of the star-like networks of both gene sequences is occupied by a common ancestral-like haplotype found in Brittany and Spain, which might have originated from the middle of Northern Spain (i.e. Asturias, eastern Lugo and western Cantabria). Estimates of the divergence time between the Spain-Brittany and Basque lineages strongly suggest that E. quimperiana survived the Pleistocene glaciations in distinct refugia on the Iberian Peninsula, one of which is situated in Picos de Europa, and the other in the Basque Country. The occurrence of a northern refugium in France cannot be rejected as of yet.

Conclusion

Present results confirm the Iberian origin of the land snail E. quimperiana and strongly support the emerging phylogeographic hypothesis of multiple refugia in Iberia during the last glaciations. The scenario of a spatial expansion of E. quimperiana from an Iberian refuge located in Asturias to northern areas provides the most probable explanation for the present distribution of this land snail. By harboring distinct haplotypes, the Basque Country populations appear to be of great importance in terms of potential adaptation, long term persistence and hence, the conservation of E. quimperiana.

The invasive species Spartina alterniora Loisel was introduced to the eastern coast of China in the 1970s and 1980s for the purposes of land reclamation and the prevention of soil erosion. The resulting interspecific competition had an important influence on the distribution of native vegetation, which makes studying the patterns and mechanisms of the interactions between Spartina alterniora Loisel and the native species Phragmites australis (Cav.) Trin ex Steud in this region very important. There have been some researches on the interspecific interactions between P. australis and S. alterniora in the Dongtan wetland of Chongming, east China, most of which has focused on the comparison of their physiological characteristics. In this paper, we conducted a neighbor removal experiment along a tidal gradient to evaluate the relative competitive abilities of the two species by calculating their relative neighbor effect (RNE) index. We also looked at the influence of environmental stress and disturbance on the competitive abilities of the two species by comparing interaction strength (I) among different tidal zones both for P. australis and S. alterniora. Finally, we measured physiological characteristics of the two species to assess the physiological mechanisms behind their different competitive abilities. Both negative and positive interactions were found between P. australis and S. alterniora along the environmental gradient. When the direction of the competitive intensity index for P. australis and S. alterniora was consistent, the competitive or facilitative effect of S. alterniora on P. australis was stronger than that of P. australis on S. alterniora. The interspecific interactions of P. australis and S. alterniora varied with environmental conditions, as well as with the method used, to measure interspecific interactions.

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.

Background

Fungal endophyte communities are often comprised of many species colonizing the same host. However, little is known about the causes of this diversity. On the one hand, the apparent coexistence of closely related species may be explained by the traditional niche differentiation hypothesis, which suggests that abiotic and/or biotic factors mediate partitioning. For endophytes, such factors are difficult to identify, and are therefore in most cases unknown. On the other hand, there is the neutral hypothesis, which suggests that stochastic factors may explain high species diversity. There is a need to investigate to what extent each of these hypotheses may apply to endophytes.

Results

The niche partitioning of two closely related fungal endophytes, Microdochium bolleyi and M. phragmitis, colonizing Phragmites australis, was investigated. The occurrences of each species were assessed using specific nested-PCR assays for 251 field samples of common reed from Lake Constance, Germany. These analyses revealed niche preferences for both fungi. From three niche factors assessed, i.e. host habitat, host organ and season, host habitat significantly differentiated the two species. M. bolleyi preferred dry habitats, whereas M. phragmitis prevailed in flooded habitats. In contrast, both species exhibited a significant preference for the same host organ, i.e. roots. Likewise the third factor, season, did not significantly distinguish the two species. Differences in carbon utilization and growth temperature could not conclusively explain the niches. The inclusion of three unrelated species of Ascomycota, which also colonize P. australis at the same locations, indicated spatio-temporal niche partitioning between all fungi. None of the species exhibited the same preferences for all three factors, i.e. host habitat, host organ, and time of the season.

Conclusions

The fungal species colonizing common reed investigated in this study seem to exploit niche differences leading to a separation in space and time, which may allow for their coexistence on the same host. A purely neutral model is unlikely to explain the coexistence of closely related endophytes on common reed.

The Etruscan culture developed in Central Italy (Etruria) in the first millennium BC and for centuries dominated part of the Italian Peninsula, including Rome. The history of the Etruscans is at the roots of Mediterranean culture and civilization, but their origin is still debated: local or Eastern provenance? To shed light on this mystery, bovine and human mitochondrial DNAs (mtDNAs) have been investigated, based on the well-recognized strict legacy which links human and livestock populations.

In the region corresponding to ancient Etruria (Tuscany, Central Italy), several Bos taurus breeds have been reared since historical times. These breeds have a strikingly high level of mtDNA variation, which is found neither in the rest of Italy nor in Europe. The Tuscan bovines are genetically closer to Near Eastern than to European gene pools and this Eastern genetic signature is paralleled in modern human populations from Tuscany, which are genetically close to Anatolian and Middle Eastern ones.

The evidence collected corroborates the hypothesis of a common past migration: both humans and cattle reached Etruria from the Eastern Mediterranean area by sea. Hence, the Eastern origin of Etruscans, first claimed by the classic historians Herodotus and Thucydides, receives strong independent support. As the Latin philosopher Seneca wrote: Asia Etruscos sibi vindicat (Asia claims the Etruscans back).

A high-affinity K+ transporter PutHKT2;1 cDNA was isolated from the salt-tolerant plant Puccinellia tenuiflora. Expression of PutHKT2;1 was induced by both 300 mM NaCl and K+-starvation stress in roots, but only slightly regulated by those stresses in shoots. PutHKT2;1 transcript levels in 300 mM NaCl were doubled by the depletion of potassium. Yeast transformed with PutHKT2;1, like those transformed with PhaHKT2;1 from salt-tolerant reed plants (Phragmites australis), (i) were able to take up K+ in low K+ concentration medium or in the presence of NaCl, and (ii) were permeable to Na+. This suggests that PutHKT2;1 has a high affinity K+-Na+ symport function in yeast. Arabidopsis over-expressing PutHKT2;1 showed increased sensitivities to Na+, K+, and Li+, while Arabidopsis over-expressing OsHKT2;1 from rice (Oryza sativa) showed increased sensitivity only to Na+. In contrast to OsHKT2;1, which functions in Na+-uptake at low external K+ concentrations, PutHKT2;1 functions in Na+-uptake at higher external K+ concentrations. These results show that the modes of action of PutHKT2;1 in transgenic yeast and Arabidopsis differ from the mode of action of the closely related OsHKT2;1 transporter.

Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity.

The tiger beetle fauna of the Balkan Peninsula is one of the richest in Europe and includes 19 species or 41% of the European tiger beetle fauna. Assembled by their biogeographical origins, the Balkan tiger beetle species fall into 14 different groups that include, Mediterranean, Middle Oriental, Central Asiatic, Euro-Siberian, South and East European, Pannonian-Sarmatian, West Palaearctic, Turano-European and Afrotropico Indo-Mediterranean species. The Mediterranean Sclerophyl and the Pontian Steppe are the Balkan biogeographical provinces with the highest species richness, while the Balkan Highlands has the lowest Cicindelidae diversity. Most species are restricted to single habitat types in lowland areas of the Balkan Peninsula and only Calomera aulica aulica and Calomera littoralis nemoralis occur in respectively 3 and 4 different types of habitat. About 60% of all Balkan Cicindelidae species are found in habitats potentially endangered by human activity.

The interactions among Spartina patens and sediment microbial populations and the interactions among Phragmites australis and sediment microbial populations were studied at monotypic sites in Piermont Marsh, a salt marsh of the Hudson River north of New York, N.Y., at key times during the growing season. Arbuscular mycorrhizal fungi (AMF) effectively colonized S. patens but not P. australis, and there were seasonal increases and decreases that coincided with plant growth and senescence (17 and 6% of the S. patens root length were colonized, respectively). In sediment samples from the Spartina site, the microbial community and specific bacterial populations were at least twice as large in terms of number and biomass as the microbial community and specific bacterial populations in sediment samples from the Phragmites site, and peak values occurred during reproduction. Members of the domain Bacteria, especially members of the α-, γ-, and δ-subdivisions of the Proteobacteria, were the most abundant organisms at both sites throughout the growing season. The populations were generally more dynamic in samples from the Spartina site than in samples from the Phragmites site. No differences between the two sites and no differences during the growing season were observed when restriction fragment length polymorphism analyses of nifH amplicons were performed in an attempt to detect shifts in the diversity of nitrogen-fixing bacteria. Differences were observed only in the patterns generated by PCR or reverse transcription-PCR for samples from the Spartina site, suggesting that there were differences in the overall and active populations of nitrogen-fixing bacteria. Regression analyses indicated that there was a positive interaction between members of the δ-subdivision of the Proteobacteria and root biomass but not between members of the δ-subdivision of the Proteobacteria and macroorganic matter at both sites. In samples from the Spartina site, there were indications that there were bacterium-fungus interactions since populations of members of the α-subdivision of the Proteobacteria were negatively associated with AMF colonization and populations of members of the γ-subdivision of the Proteobacteria were positively associated with AMF colonization.

• Background and Aims The free-floating aquatic bladderwort Utricularia australis f. australis is a sterile F1 hybrid of U. australis f. tenuicaulis and U. macrorhiza. However, co-existence of the hybrids and parental species has not been observed. In the present study, the following questions are addressed. (a) Does the capacity of the two parental species to reproduce sexually contribute to higher genotypic diversity than that of sterile F1 hybrid? (b) Are there any populations where two parental species and their hybrid co-exist? (c) If not, where and how do hybrids originate?

• Methods The presence and absence of Utricularia was thoroughly investigated in two regions in Japan. An amplified fragment length polymorphism (AFLP) analysis was conducted for 397 individuals collected from all populations (33 in total) where Utricularia was observed.

• Key Results The mean number of genotypes per population (G) and genotypic diversity (D) were extremely low irrespective of the capacity to reproduce sexually: G was 1·1–1·2 and D was 0·02–0·04. The hybrid rarely co-existed with either parental species, and the co-existence of two parental species was not observed. Several AFLP bands observed in the hybrid are absent in both parental genotypes, and parent and hybrid genotypes in the same region do not show greater genetic similarity than those in distant regions.

• Conclusions The capacity to reproduce sexually in parental species plays no role in increasing genotypic diversity within populations. The observed genotypes of the hybrid could not have originated from hybridization between the extant parental genotypes within the study regions. Considering the distribution ranges of three investigated taxa, it is clear that the hybrid originated in the past, and hybrid populations have been maintained exclusively by clonal propagation, which may be ensured by both hybrid vigor and long-distance dispersal of clonal offspring.

Objectives

To identify the genes responsible for tetracycline resistance in a strain of Streptococcus australis isolated from pooled saliva from healthy volunteers in France. S. australis is a viridans Streptococcus, originally isolated from the oral cavity of children in Australia, and subsequently reported in the lungs of cystic fibrosis patients and as a cause of invasive disease in an elderly patient.

Methods

Agar containing 2 mg/L tetracycline was used for the isolation of tetracycline-resistant organisms. A genomic library in Escherichia coli was used to isolate the tetracycline resistance determinant. In-frame deletions and chromosomal repair were used to confirm function. Antibiotic susceptibility was determined by agar dilution and disc diffusion assay.

Results

The tetracycline resistance determinant from S. australis FRStet12 was isolated from a genomic library in E. coli and DNA sequencing showed two open reading frames predicted to encode proteins with similarity to multidrug resistance-type ABC transporters. Both genes were required for tetracycline resistance (to both the naturally occurring and semi-synthetic tetracyclines) and they were designated tetAB(46).

Conclusions

This is the first report of a predicted ABC transporter conferring tetracycline resistance in a member of the oral microbiota.

Mitochondrial DNA (mtDNA) diversity in European and Asian pigs was assessed using 1536 samples representing 45 European and 21 Chinese breeds. Diagnostic nucleotide differences in the cytochrome b (Cytb) gene between the European and Asian mtDNA variants were determined by pyrosequencing as a rapid screening method. Subsequently, 637 bp of the hypervariable control region was sequenced to further characterize mtDNA diversity. All sequences belonged to the D1 and D2 clusters of pig mtDNA originating from ancestral wild boar populations in Europe and Asia, respectively. The average frequency of Asian mtDNA haplotypes was 29% across European breeds, but varied from 0 to 100% within individual breeds. A neighbour-joining (NJ) tree of control region sequences showed that European and Asian haplotypes form distinct clusters consistent with the independent domestication of pigs in Asia and Europe. The Asian haplotypes found in the European pigs were identical or closely related to those found in domestic pigs from Southeast China. The star-like pattern detected by network analysis for both the European and Asian haplotypes was consistent with a previous demographic expansion. Mismatch analysis supported this notion and suggested that the expansion was initiated before domestication.

Chemical communication and perception strategies between plants are highly sophisticated but are only partly understood. Among the different interactions, the suppressive interaction of a class of chemicals released by one plant through root exudates against the neighbouring plants (allelopathy) have been implicated in the invasiveness of many exotic weedy species. Phragmites australis (common reed) is one of the dominant colonizers of the North American wetland marshes and exhibits invasive behavior by virtually replacing the entire native vegetation in its niche. Recently, by adopting a systematic bioassay driven approach we elucidated the role of root derived allelopathy as one of the important mechanisms by which P. australis exerts its invasive behavior. Additionally, our recent preliminary data indicates the involvement of rhizobacterial signaling in the invasive success of P. australis. A better understanding of biochemical weaponry used by P. australis will aid scientists and technologists in addressing the impact of root secretions in invasiveness of weedy species and thus promote a more informed environmental stewardship.

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.

Author Summary

The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.

Sequences of the first hypervariable segment of the mitochondrial DNA (mtDNA) control region were obtained from 353 individuals representing nine groups and four major linguistic families (Indo-European, Altaic and North and South Caucasian) of the Caucasus region. The diversity within and between Caucasus populations exceeded the diversity within Europe, but was less than that in the Near East. Caucasus populations occupy an intermediate position between European and Near Eastern populations in tree and principal coordinate analyses, suggesting that they are either ancestral to European populations or derived via admixture from European and Near Eastern populations. The genetic relationships among Caucasus populations reflect geographical rather than linguistic relationships. In particular, the Indo-European-speaking Armenians and Altaic-speaking Azerbaijanians are most closely related to their nearest geographical neighbours in the Caucasus, not their linguistic neighbours (i.e. other Indo-European or Altaic populations). The mtDNA evidence thus suggests that the Armenian and Azerbaijanian languages represent instances of language replacement that had little impact on the mtDNA gene pool.

Background

Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin.

Results

According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification.

Conclusions

A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.