PHYLOGENETIC RELATIONSHIPS WITHIN THE STYLONEMATALES (STYLONEMATOPHYCEAE,RHODOPHYTA): BIOGEOGRAPHIC PATTERNS DO NOT APPLY TO STYLONEMA ALSIDII1

The Stylonematales is the sole order of the Stylonematophyceae. The order consists of a mixture of filamentous or unicellular taxa that are small, grow on various surfaces, and are described from many floras, indicating that they may be cosmopolitan. Such ubiquity has been proposed to be due to properties of microorganisms, such as large population sizes, rather than human‐derived phenomena. While their small nature makes most records fortuitous, we targeted these red algae to get a better understanding of their global distribution, genetic variation, and phylogeographic relationships. Our results indicated that the genera are mostly well supported, except for the position of Stylonema cornu‐cervi with Goniotrichopsis reniformis, while intergeneric relationships are mostly unsupported. The most commonly isolated species was Stylonema alsidii. Within this species, several well‐supported clades were present. The phylogeographic relationships in S. alsidii showed no obvious biogeographic pattern, with supported clades containing samples from disparate locations, and multiple samples from the same area not grouping together. Some clades showed little genetic variation and wide distributions, possibly indicating human‐derived dispersal. Other clades, also with wide distribution, showed more genetic structure and could be candidates for groups formed by natural long‐distance dispersal. While all issues on ubiquity cannot be answered with this data set, it would appear that at least S. alsidii is a true ubiquitous taxon. The sister relationship of Rufusia pilicola to the remaining Stylonematophyceae, the presence of the carbohydrate floridoside, and this species’ unusual habitat indicate that it belongs to a new order, Rufusiales.     

MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES1

Glutamine synthetase (GS) is encoded by three distinct gene families (GSI, GSII, and GSIII) that are broadly distributed among the three domains of life. Previous studies established that GSII and GSIII isoenzymes were expressed in diatoms; however, less is known about the distribution and evolution of the gene families in other chromalveolate lineages. Thus, GSII cDNA sequences were isolated from three cryptophytes (Guillardia theta D. R. A. Hill et Wetherbee, Cryptomonas phaseolus Skuja, and Pyrenomonas helgolandii Santore), and GSIII was sequenced from G. theta. Red algal GSII sequences were obtained from Bangia atropurpurea (Mertens ex Roth) C. Agardh; Compsopogon caeruleus (Balbis ex C. Agardh) Mont.; Flintiella sanguinaria F. D. Ott and Porphyridium aerugineum Geitler; Rhodella violacea (Kornmann) Wehrmeyer and Dixoniella grisea (Geitler) J. L. Scott, S. T. Broadwater, B. D. Saunders, J. P. Thomas et P. W. Gabrielson; and Stylonema alsidii (Zanardini) K. M. Drew. In Bayesian inference and maximum‐likelihood (ML) phylogenetic analyses, chromalveolate GSII sequences formed a weakly supported clade that nested among sequences from glaucophytes, red algae, green algae, and plants. Red algal GSII sequences formed two distinct clades. The largest clade contained representatives from the Cyanidiophytina and Rhodophytina and grouped with plants and green algae. The smaller clade (C. caeruleus, Porphyra yezoensis, and S. alsidii) nested within the chromalveolates, although its placement was unresolved. Chromalveolate GSIII sequences formed a well‐supported clade in Bayesian and ML phylogenies, and mitochondrial transit peptides were identified in many of the sequences. There was strong support for a stramenopile‐haptophyte‐cryptophyte GSIII clade in which the cryptophyte sequence diverged from the deepest node. Overall, the evolutionary history of the GS gene families within the algae is complex with evidence for the presence of orthologous and paralogous sequences, ancient and recent gene duplications, gene losses and replacements, and the potential for both endosymbiotic and lateral gene transfers.     

Genetic diversity and differentiation among Lagopus lagopus populations in Scandinavia and Scotland: evolutionary significant units confirmed by SNP markers

Single Nucleotide Polymorphism in four Scandinavian populations of willow grouse (Lagopus lagopus) and two Scottish populations of red grouse (Lagopus lagopus scoticus) were assessed at 13 protein‐coding loci. We found high levels of diversity, with one substitution every 55 bp as an average and a total of 76 unlinked parsimony informative SNPs. Different estimators of genetic diversity such as: number of synonymous and non‐synonymous sites, average number of alleles, number and percentage of polymorphic loci, mean nucleotide diversity (π_s, π_a) and gene diversity at synonymous and non‐synonymous sites showed higher diversity in the northern populations compared to southern ones. Strong levels of purifying selection found in all the populations together with neutrality tests conforming to neutral expectations agree with large effective population sizes. Assignment tests reported a clear distinction between Scandinavian and Scottish grouse suggesting the existence of two different evolutionary significant units. The divergence time between willow and red grouse ranging between 12 500 and 125 000 years, in conjunction with the presence of ‘specific’ markers for each subspecies prompt a reassessment of the taxonomical status of the Scottish red grouse.     

DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA)1

Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well‐supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1–3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter‐clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera).     

A phylogeographic study of the cosmopolitan genus Phragmites (Poaceae) based on AFLPs

Within the genus Phragmites (Poaceae), the species P. australis (the common reed) is virtually cosmopolitan, and shows considerable variation in ploidy level and morphology. Genetic variation in Phragmites was studied using AFLPs, and analysed with parsimony and distance methods. Groups of P. australis strongly supported in the analyses include one that comprises all South American clones, a distinct group from the US Gulf Coast, and a group of E. Asian and Australian octoploids. Among the other species, the paleotropical P. vallatoria is supported as monophyletic and most closely related to the paraphyletic P. mauritianus and to the Gulf Coast and S. American groups. The E. Asian species P. japonicus is closely related to a group of P. australis clones mostly from central North America. Tetraploidy predominates in the genus, and optimisation of chromosome numbers onto the phylogeny shows that higher ploidy levels have evolved many times.     

Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby,Pomatoschistus minutus

An excellent model to elucidate the mechanisms and importance of evolution in the marine environment is the spectral tuning mechanism of the visual pigment in vertebrates. In the sand goby Pomatoschistus minutus (Teleostei; Gobiidae), a distribution‐wide study showed that spatial variation at the rhodopsin gene (RH1) matches the characteristics of specific light environments. This match suggests that populations are locally adapted to selective light regimes targeting the RH1 gene. If so, then the direction of selection should depend on the regional spatial and temporal stability of the light conditions. We tested this prediction by comparing goby populations from two regions: the Baltic Sea, characterized by divergent, but temporally stable light conditions, and the North Sea, characterized by locally heterogeneous and temporally variable light conditions. RH1 sequences of 491 Pomatoschistus minutus individuals from 15 locations were analysed. We found that variation at the RH1 gene in the Baltic populations showed signatures of diversifying selection, whereas the RH1 gene in the North Sea showed signatures of stabilizing selection. These different modes of selection are consistent with the regional light conditions and hence support our predictions, but may also be influenced by migration between the open sea and more turbid estuarine environments. An interesting observation is that within one gene, synonymous and non‐synonymous SNPs show a totally different pattern between populations. Population differentiation based on non‐synonymous SNPs of the RH1 gene correlated with spectral variation of the local environment of the sand goby populations. In contrast, the differentiation based on synonymous SNPs of RH1 reflects more the neutral historical pattern of the species.     

Introgression and phylogeography of Betula nana (diploid), B. pubescens (tetraploid) and their triploid hybrids in Iceland inferred from cpDNA haplotype variation

Aim The objective was to find direct genetic evidence supporting introgressive hybridization between tetraploid tree birch (Betula pubescens) and diploid dwarf birch (B. nana), via triploid hybrids, and to investigate an association between the introgression and phylogeographical distribution of Icelandic birch. Location Samples were collected from 463 trees in 12 woodlands in Iceland and eight locations in Norway, Sweden, Scotland and Greenland. Methods Ploidy status of individual trees was determined by chromosome counting. Variation in the chloroplast genome was assessed using polymerase chain reaction‐restriction fragment length polymorphism. The geographical distribution of the haplotypes was mapped. The haplotype variation and introgression ratios (IG) were analysed statistically. Results Thirteen haplotypes were identified among Icelandic samples. The most common haplotype (T, 49% occurrence) was present in all ploidy groups and in all woodlands. All common haplotypes were shared between the triploid group and the parental species, indicating introgressive hybridization. This was supported by the statistical analysis of IG indices and the variation components. Considerable differences existed among samples, shaped by isolation by distance and local introgression. An east–west phylogeographical distribution in Iceland was observed. Main conclusions Despite extensive introgression across species and ploidy levels, a biogeographical pattern has been observed, and this may indicate different population histories or multiple origins of Icelandic birch. The chloroplast haplotype diversity found in Iceland resembles that found in birch populations from northern Scandinavia.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.     

GENETICAL POPULATION STRUCTURE IN PLANTS: GENE FLOW BETWEEN DIPLOID SEXUAL AND TRIPLOID ASEXUAL DANDELIONS (TARAXACUM SECTION RUDERALIA)

Levels and distribution of genetic variation were studied in central and western European populations of Taraxacum section Ruderalia containing differing mixtures of sexual diploid and asexual triploid plants. All sexual populations were panmictic with their variation partitioned mainly among populations. Genotypic diversity in triploid samples was very high with few clones widespread and many clones restricted to one or a few populations. Extensive amounts of gene (pollen) flow between the diploid and triploid components of a population were inferred from the following data: (1) the two ploidy levels share all major allozyme polymorphisms; (2) the intrapopulational homogeneity in genic variation between diploids and triploids contrasts strongly with the geographic differentiation at each ploidy level separately; (3) population-unique alleles simultaneously occur at the two ploidy levels; (4) not only sexuals but also asexuals generally simulate Hardy-Weinberg expectations. Most likely, intrapopulational gene exchange occurs bidirectionally by mechanisms such as reductional pollen meiosis in apomictic plants, facultative apomixis, and formation of unreduced gametes in sexuals. Thus, diploid and triploid Taraxacum section Ruderalia are less genetically isolated than has previously been supposed and probably form a cohesive evolutionary unit with the level at which gene pools are shared differing by population.     

Diversity of the Luciferin Binding Protein Gene in Bioluminescent Dinoflagellates – Insights from a New Gene in Noctiluca scintillans and Sequences from Gonyaulacoid Genera

Dinoflagellate bioluminescence systems operate with or without a luciferin binding protein, representing two distinct modes of light production. However, the distribution, diversity, and evolution of the luciferin binding protein gene within bioluminescent dinoflagellates are not well known. We used PCR to detect and partially sequence this gene from the heterotrophic dinoflagellate Noctiluca scintillans and a group of ecologically important gonyaulacoid species. We report an additional luciferin binding protein gene in N. scintillans which is not attached to luciferase, further to its typical combined bioluminescence gene. This supports the hypothesis that a profound re‐organization of the bioluminescence system has taken place in this organism. We also show that the luciferin binding protein gene is present in the genera Ceratocorys, Gonyaulax, and Protoceratium, and is prevalent in bioluminescent species of Alexandrium. Therefore, this gene is an integral component of the standard molecular bioluminescence machinery in dinoflagellates. Nucleotide sequences showed high within‐strain variation among gene copies, revealing a highly diverse gene family comprising multiple gene types in some organisms. Phylogenetic analyses showed that, in some species, the evolution of the luciferin binding protein gene was different from the organism's general phylogenies, highlighting the complex evolutionary history of dinoflagellate bioluminescence systems.     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.     

Variation in chicken populations may affect the enzymatic activity of lysozyme

The chicken lysozyme gene encodes a hydrolase that has a key role in defence, especially in ovo. This gene was resequenced in global chicken populations [red, grey, Ceylon and green jungle fowl (JF)] and related bird species. Networks, summary statistics and tests of neutrality indicate that although there is extensive variation at the gene, little is present at coding sites, with the exception of one non‐synonymous site. This segregating site and a further fixed non‐synonymous change between red JF and domestic chicken populations are spatially close to the catalytic sites of the enzyme and so might affect its activity.     

Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): higher classification and biogeography

The systematic relationships of the butterfly family Pieridae are poorly understood. Much of our current understanding is based primarily on detailed morphological observations made 50–70 years ago. However, the family and its putative four subfamilies and two tribes, have rarely been subjected to rigorous phylogenetic analysis. Here we present results based on an analysis of molecular characters used to reconstruct the phylogeny of the Pieridae in order to infer higher‐level classification above the generic level and patterns of historical biogeography. Our sample contained 90 taxa representing 74 genera and six subgenera, or 89% of all genera recognized in the family. Three complementary approaches were employed: (1) a combined analysis of a 30 taxon subset for sequences from four gene regions, including elongation factor‐1 alpha (EF‐1α), wingless, cytochrome oxidase subunit I (COI), and 28S (3675 bp, 1031 parsimony‐informative characters), mainly to establish higher‐level relationships, (2) a single‐gene analysis of the 90 taxon data set for sequences from EF‐1α (1066 bp, 364 parsimony‐informative characters), mainly to establish lower‐level relationships, and (3) an all available data analysis of the entire data set for sequences from the four genes, to recover both deep and shallow nodes. Analyses using maximum parsimony, maximum likelihood and Bayesian inference provided similar results. All supported monophyly for the four subfamilies but not for the two tribes, with the Anthocharidini polyphyletic and the Pierini paraphyletic. The combined and all available data analyses support the following relationships among the subfamilies: ((Pseudopontiinae + Dismorphiinae) + (Coliadinae + Pierinae)), corroborating Ehrlich’s 1958 phenetic hypothesis. On the basis of these analyses, and additional morphological and life history evidence, we propose a reclassification of the subfamily Pierinae into two tribes (Anthocharidini s.s., Pierini s.s.) and two informal groups (Colotis group, Leptosia), with the tribe Pierini s.s. subdivided into three subtribes (Appiadina, Pierina, Aporiina) and three genera (Elodina, Dixeia, Belenois) of uncertain status (incertae sedis). The combined and all available data analyses support the following relationships among the Pierinae: (Colotis group + Anthocharidini s.s. + Leptosia + (Elodina + ((Dixeia + Belenois) + Appiadina + Pierina + Aporiina))). Application of a molecular clock calibrated using fossil evidence and semiparametric rate smoothing suggests that divergence between the Pierina and Aporiina occurred no later than the Palaeocene (> 60 Myr). The minimum estimate for the age of the crown‐group of the Pieridae was 112–82 Myr, with a mean of 95 Myr. A historical biogeographical hypothesis is proposed to explain the present‐day distribution of the clade Pseudopontiinae + Dismorphiinae, which argues for an origin of the two subfamilies in western Gondwana (Africa + South America) during the Late Cretaceous. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 147 , 239–275.     

Hybridization,polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)

In plant species, variation in levels of clonality, ploidy and interspecific hybridization can interact to influence geographic patterns of genetic diversity. These factors commonly vary in plants that specialize on saline habitats (halophytes) and may play a role in how they adapt to salinity variation across their range. One such halophyte is the turfgrass and emerging genomic model system seashore paspalum (Paspalum vaginatum Swartz). To investigate how clonal propagation, ploidy variation, and interspecific hybridization vary across ecotypes and local salinity levels in wild P. vaginatum, we employed genotyping‐by‐sequencing, cpDNA sequencing and flow cytometry in 218 accessions representing > 170 wild collections from throughout the coastal southern United States plus USDA germplasm. We found that the two morphologically distinct ecotypes of P. vaginatum differ in their adaptive strategies. The fine‐textured ecotype is diploid and appears to reproduce in the wild both sexually and by clonal propagation; in contrast, the coarse‐textured ecotype consists largely of clonally‐propagating triploid and diploid genotypes. The coarse‐textured ecotype appears to be derived from hybridization between fine‐textured P. vaginatum and an unidentified Paspalum species. These clonally propagating hybrid genotypes are more broadly distributed than clonal fine‐textured genotypes and may represent a transition to a more generalist adaptive strategy. Additionally, the triploid genotypes vary in whether they carry one or two copies of the P. vaginatum subgenome, indicating multiple evolutionary origins. This variation in subgenome composition shows associations with local ocean salinity levels across the sampled populations and may play a role in local adaptation.     

Development of chloroplast genomic resources for Cynara

In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high‐throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole‐genome sequencing project, while the others were obtained by means of long‐range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference‐based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes (‘Brindisino’ artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty‐nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short ‘variable’ cp regions. The evaluation of the molecular resources obtained from this study led us to support the ‘super‐barcode’ theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.     

Cyanobacterial multi-copy chromosomes and their replication

ABSTRACT

While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts.     

A pair of receptor‐like kinases is responsible for natural variation in shoot growth response to mannitol treatment in Arabidopsis thaliana

Growth is a complex trait that adapts to the prevailing conditions by integrating many internal and external signals. Understanding the molecular origin of this variation remains a challenging issue. In this study, natural variation of shoot growth under mannitol‐induced stress was analyzed by standard quantitative trait locus mapping methods in a recombinant inbred line population derived from a cross between the Col‐0 and Cvi‐0 Arabidopsis thaliana accessions. Cloning of a major QTL specific to mannitol‐induced stress condition led to identification of EGM1 and EGM2, a pair of tandem‐duplicated genes encoding receptor‐like kinases that are potentially involved in signaling of mannitol‐associated stress responses. Using various genetic approaches, we identified two non‐synonymous mutations in the EGM2[Cvi] allele that are shared by at least ten accessions from various origins and are probably responsible for a specific tolerance to mannitol. We have shown that the enhanced shoot growth phenotype contributed by the Cvi allele is not linked to generic osmotic properties but instead to a specific chemical property of mannitol itself. This result raises the question of the function of such a gene in A. thaliana, a species that does not synthesize mannitol. Our findings suggest that the receptor‐like kinases encoded by EGM genes may be activated by mannitol produced by pathogens such as fungi, and may contribute to plant defense responses whenever mannitol is present.     

Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assay

Aim: To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources. Methods and Results: Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571‐bp product was detected in 76% of poultry‐associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 10⁷–10⁹ gene copies per gram in soiled litter, up to 10⁵ gene copies per gram in spread‐site soils, and 10⁷ gene copies per litre in field run‐off water. Results were corroborated by a blinded study conducted by a second laboratory. Conclusion: The poultry‐specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land‐applied poultry litter. Significance and Impact of the Study: This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination.